General Biology

General Biology
Wikibooks.org
March 15, 2013
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Contents
1
Getting Started
Biology - The Life Science

2.1 Characteristics of life . .
2.2 Nature of science . . . .
2.3 Scientific method . . . .
2.4 Charles Darwin . . . . .
2.5 After Darwin . . . . . .
2.6 Challenges to Darwin . .
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5
5
6
6
9
9
10
The
3.1
3.2
3.3
3.4
3.5
3.6
3.7
Nature of Molecules
Matter . . . . . . . . .
The atom . . . . . . .
Mass and isotopes . .
Electrons . . . . . . .
Chemical bonds . . . .
Chemical reactions . .
Water . . . . . . . . .
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11
11
11
12
12
13
13
13
The
4.1
4.2
4.3
4.4
4.5
4.6
Chemical Building Blocks of Life

Carbon . . . . . . . . . . . . . . . . .
Carbohydrates . . . . . . . . . . . .
Stereoisomers . . . . . . . . . . . . .
Lipids . . . . . . . . . . . . . . . . .
Proteins . . . . . . . . . . . . . . . .
Hereditary (Genetic) information . .
Life:
5.1
5.2
5.3
5.4
5.5
5.6
5.7
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History and Origin

Properties of life . . . . . . . .
Origin of life: 3 hypotheses . .
The early earth . . . . . . . . .
Origin of cells . . . . . . . . . .
The RNA world? . . . . . . . .
The earliest cells . . . . . . . .
Major steps in evolution of life
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15
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16
16
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18
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19
19
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21
21
21
22
Cells
23
Cell structure
7.1 What is a cell? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.2 History of cell knowledge . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
25
29
III
Contents
7.3
7.4
8
Microscopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cell size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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31
31
32
32
34
34
34
35
Membranes
9.1
Biological membranes . . . . .
9.2
Phospholipid . . . . . . . . . .
9.3
Fluid mosaic model . . . . . . .
9.4
Membrane proteins . . . . . . .
9.5
Receptor-mediated endocytosis
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37
37
38
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40
10 Cell-cell interactions
10.1 Cell signaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10.2 Communicating junctions . . . . . . . . . . . . . . . . . . . . . . . . . . .
41
41
42
11 Energy and Metabolism

11.1 Energy . . . . . . . . .
11.2 OxidationReduction .
11.3 NAD+ . . . . . . . . .
11.4 Free energy . . . . . .
11.5 Enzymes . . . . . . . .
11.6 ATP . . . . . . . . . .
11.7 Biochemical pathways
Structure of Eukaryotic cells

8.1
Structure of the nucleus .
8.2
Chromatin . . . . . . . . .
8.3
Endoplasmic reticulum . .
8.4
The Golgi apparatus . . .
8.5
Ribosomes . . . . . . . . .
8.6
DNA-containing organelles
8.7
Cytoskeleton . . . . . . .
30
30
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43
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46
46
12 Respiration: harvesting of energy

12.1 Energy . . . . . . . . . . . . . . .
12.2 Respiration . . . . . . . . . . . .
12.3 Respiration of glucose . . . . . .
12.4 Alternative anaerobic respiration
12.5 Glycolysis overview . . . . . . . .
12.6 Regeneration of NAD+ . . . . . .
12.7 Alcohol fermentation . . . . . . .
12.8 Lactate formation . . . . . . . . .
12.9 Krebs cycle: overview . . . . . .
12.10 ATP production . . . . . . . . . .
12.11 Evolution of aerobic respiration .
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47
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49
13 Photosynthesis
13.1 Light Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13.2 Dark reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
13.3 Prokaryote cell division . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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53
53
IV
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Contents
13.4
13.5
13.6
13.7
13.8
13.9
13.10
13.11
13.12
13.13
13.14
13.15
13.16
13.17
Bacterial DNA replication . . . . . . . . . . . . . .

Chromosome number . . . . . . . . . . . . . . . . .
Eukaryotic chromosomes . . . . . . . . . . . . . . .
Chromosome organization . . . . . . . . . . . . . .
Human karyotype stained by chromosome painting
Chromosomes . . . . . . . . . . . . . . . . . . . . .
Human chromosomes . . . . . . . . . . . . . . . . .
Mitotic cell cycle . . . . . . . . . . . . . . . . . . .
Replicated human chromosomes . . . . . . . . . . .
Mitosis . . . . . . . . . . . . . . . . . . . . . . . . .
Plant mitosis . . . . . . . . . . . . . . . . . . . . .
Controlling the cell cycle . . . . . . . . . . . . . . .
Cancer . . . . . . . . . . . . . . . . . . . . . . . . .
Mutations and cancer . . . . . . . . . . . . . . . .
14 Sexual reproduction
14.1 Sexual . . . . . . . . . . . . .
14.2 Sexual life cycle . . . . . . . .
14.3 Meiosis . . . . . . . . . . . . .
14.4 Prophase I: synapsis . . . . .
14.5 Crossing over . . . . . . . . .
14.6 Microtubules and anaphase I
14.7 Meiosis II . . . . . . . . . . .
14.8 Evolution of sex . . . . . . . .
14.9 Consequences of sex . . . . .
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59
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15 Genetics
63
16 Gregor Mendel and biological inheritance

16.1 Mendel . . . . . . . . . . . . . . . . . . . .
16.2 Mendels experiments . . . . . . . . . . . .
16.3 Mendels seven pairs of traits . . . . . . .
16.4 Locus . . . . . . . . . . . . . . . . . . . .
16.5 Modern Y chromosome . . . . . . . . . . .
16.6 Chromosome phenomena . . . . . . . . . .
16.7 X-chromosome inactivation . . . . . . . .
16.8 Barr body . . . . . . . . . . . . . . . . . .
16.9 Human genetic disorders . . . . . . . . . .
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67
17 DNA: The Genetic Material

17.1 DNA . . . . . . . . . . . . .
17.2 Historical perspective . . . .
17.3 Hershey-Chase Experiment
17.4 DNA/RNA components . .
17.5 Chemical structure of DNA
17.6 3D structure of DNA . . . .
17.7 Franklin . . . . . . . . . . .
17.8 DNA replication . . . . . .
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Contents
17.9
17.10
17.11
17.12
17.13
17.14
17.15
17.16
DNA replication . . . . .
DNA polymerases . . . . .
DNA replication complex
DNA replication . . . . .
DNA replication fork . . .
Replication units . . . . .
Replicon . . . . . . . . . .
What is gene? . . . . . . .
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18 Gene expression
18.1 Central Dogma . . . . .
18.2 The Genetic Code . . . .
18.3 Transcription . . . . . . .
18.4 Transcription bubble . . .
18.5 Eukaryote mRNA . . . . .
18.6 Translation . . . . . . . .
18.7 Translation in bacteria . .
18.8 Aminoacyl tRNA synthase
18.9 Ribosome structure . . . .
18.10 Large ribosome subunit .
18.11 Translation . . . . . . . .
18.12 Initiation complex . . . .
18.13 Elongation, translocation .
18.14 Introns/exons . . . . . . .
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19 Gene regulation
19.1 Transcriptional control
19.2 DNA grooves . . . . .
19.3 Regulatory proteins . .
19.4 Lac operon of E. coli .
19.5 Alternative splicing . .
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20 Mutation
20.1 Point Mutations . . . . . . . . . .
20.2 Substitution . . . . . . . . . . . .
20.3 Larger mutations . . . . . . . . .
20.4 Chromosomal mutations . . . . .
20.5 Causes of mutations . . . . . . .
20.6 Effects of mutations . . . . . . .
20.7 Further reading . . . . . . . . . .
20.8 Original notes . . . . . . . . . . .
20.9 Point mutation . . . . . . . . . .
20.10 Acquisition of genetic variability
20.11 Eukaryote genome . . . . . . . .
20.12 Barbara McClintock . . . . . . .
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21 Recombinant DNA technology

21.1 Recombinant DNA technology . . . . . . . . . . . . . . . . . . . . . . . . .
87
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VI
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Contents
21.2
21.3
21.4
21.5
21.6
21.7
21.8
21.9
21.10
21.11
21.12
21.13
Restriction endonucleases . . . .
Restriction endonucleases . . . .
Uses of cloned gene . . . . . . . .
Other molecular procedures . . .
RFLP(restriction fragment length
Sanger DNA sequencing . . . . .
Automated sequencing . . . . . .
Genome projects . . . . . . . . .
Biochips . . . . . . . . . . . . . .
DNA chip controversies . . . . .
Gene patenting . . . . . . . . . .
Stem cells . . . . . . . . . . . . .
22 Classification of Living Things

22.1 Introduction . . . . . . . . . . .
22.2 Viral Replication . . . . . . . .
22.3 Viral Genome . . . . . . . . . .
22.4 Viruses Practice Questions . . .
22.5 Archaea . . . . . . . . . . . . .
22.6 Prokaryote evolution . . . . . .
22.7 Domains of life: characteristics
22.8 Introduction . . . . . . . . . . .
22.9 Classification of Protists . . . .
22.10 Protozoa . . . . . . . . . . . . .
22.11 Algae . . . . . . . . . . . . . . .
22.12 Slime molds & Water molds . .
22.13 Protists Practice Questions . .
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polymorphism)
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analysis
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93
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103
104
23 Multicellular Photosynthetic Autotrophs

23.1 Plants . . . . . . . . . . . . . . . . . . .
23.2 Plant phyla . . . . . . . . . . . . . . . .
23.3 Plant evolution . . . . . . . . . . . . . .
23.4 Plant phylogeny . . . . . . . . . . . . . .
23.5 Plant life cycles . . . . . . . . . . . . . .
23.6 Moss life cycle . . . . . . . . . . . . . . .
23.7 Vascular plants . . . . . . . . . . . . . .
23.8 Vascular plant life cycles . . . . . . . . .
23.9 Pterophyta (ferns) . . . . . . . . . . . .
23.10 Non-seed plants, continued . . . . . . . .
23.11 Seed plants . . . . . . . . . . . . . . . .
23.12 Sporophyte/gametophyte . . . . . . . .
23.13 Megasporangium (nucellus) . . . . . . .
23.14 Pollen . . . . . . . . . . . . . . . . . . .
23.15 Gymnosperms . . . . . . . . . . . . . . .
23.16 Pine life cycle . . . . . . . . . . . . . . .
23.17 Other Coniferophyta . . . . . . . . . . .
23.18 Other gymnosperms . . . . . . . . . . .
23.19 Angiosperms . . . . . . . . . . . . . . .
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107
107
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111
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VII
Contents
23.20
23.21
23.22
23.23
23.24
23.25
23.26
23.27
23.28
23.29
23.30
23.31
23.32
23.33
23.34
23.35
23.36
23.37
23.38
23.39
23.40
Earliest angiosperm . . . . . .
Angiosperm flower . . . . . .
Angiosperm life cycle . . . . .
Introduction . . . . . . . . . .
Nutrition . . . . . . . . . . .
Fungal Reproduction . . . . .
Types of Fungi . . . . . . . .
Key Terms . . . . . . . . . . .
Introduction . . . . . . . . . .
Characteristics of an Animal .
Introduction to animal phyla
Phylum Porifera . . . . . . .
Phylum Cnidaria . . . . . . .
Phylum Platyhelminthes . . .
Phylum Rotifera . . . . . . .
Phylum Nematoda . . . . . .
Phylum Annelida . . . . . . .
Phylum Arthropoda . . . . .
Phylum Mollusca . . . . . . .
Phylum Echinodermata . . .
Phylum Chordata . . . . . . .
24 Chordates
24.1 Characteristics . . . . . . . .
24.2 Subphylum Urochordata . . .
24.3 Subphylum Cephalochordata
24.4 Subphylum Vertebrata . . . .
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111
111
111
111
112
112
113
114
114
114
116
117
118
120
121
121
122
123
124
124
125
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127
127
127
128
128
25 Tissues and Systems
135
26 Epithelial tissue
137
27 Connective tissue
139
28 Muscle tissue
143
29 Vertebrate digestive system
147
30 Circulatory system
151
31 Respiratory system
31.1 Neuron structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
31.2 Central nervous system . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
31.3 Peripheral nervous system . . . . . . . . . . . . . . . . . . . . . . . . . . .
155
156
157
157
32 Sensory systems
159
32.1 Taste and smell (chemoreception) . . . . . . . . . . . . . . . . . . . . . . . 159
32.2 Response to gravity and movement . . . . . . . . . . . . . . . . . . . . . . 159
32.3 Vision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
VIII
Contents
32.4
32.5
Homeostasis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Osmotic environments and regulations . . . . . . . . . . . . . . . . . . . . 161
33 Additional material
165
33.1 External Links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
34 Glossary
167
34.1 Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
35 Contributors
169
List of Figures
175
36 Licenses
179
36.1 GNU GENERAL PUBLIC LICENSE . . . . . . . . . . . . . . . . . . . . 179
36.2 GNU Free Documentation License . . . . . . . . . . . . . . . . . . . . . . 180
36.3 GNU Lesser General Public License . . . . . . . . . . . . . . . . . . . . . . 181
1 Getting Started
2 Biology - The Life Science

The word biology means, "the science of life", from the Greek bios, life, and logos, word
or knowledge. Therefore, Biology is the science of Living Things. That is why Biology is
sometimes known as Life Science.
The science has been divided into many subdisciplines, such as botany1 , bacteriology,
anatomy2 , zoology, histology, mycology, embryology, parasitology, genetics3 , molecular biology4 , systematics, immunology, microbiology5 , physiology, cell biology6 , cytology, ecology7 ,
and virology. Other branches of science include or are comprised in part of biology studies,
including paleontology8 , taxonomy, evolution, phycology, helimentology, protozoology, entomology, biochemistry, biophysics, biomathematics, bio engineering, bio climatology and
anthropology.
2.1 Characteristics of life

Not all scientists agree on the definition of just what makes up life. Various characteristics
describe most living things. However, with most of the characteristics listed below we can
think of one or more examples that would seem to break the rule, with something nonliving
being classified as living or something living classified as nonliving. Therefore we are careful
not to be too dogmatic in our attempt to explain which things are living or nonliving.
Living things are composed of matter structured in an orderly way where simple
molecules are ordered together into much larger macromolecules.
An easy way to remember this is GRIMNERD C All organisms; - Grow, Respire, Interact,
Move, Need Nutrients, Excrete (Waste), Reproduce,Death, Cells (Made of)
Living things are sensitive, meaning they are able to respond to stimuli.
Living things are able to grow, develop, and reproduce.
Living things are able to adapt over time by the process of natural selection.
All known living things use the hereditary molecule, DNA9 .
1
2
3
4
5
6
7
8
9
http://en.wikibooks.org/wiki/botany
http://en.wikibooks.org/wiki/anatomy
http://en.wikibooks.org/wiki/genetics
http://en.wikibooks.org/wiki/Molecular%20Biology
http://en.wikibooks.org/wiki/microbiology
http://en.wikibooks.org/wiki/Cell%20Biology
http://en.wikibooks.org/wiki/ecology
http://en.wikibooks.org/wiki/paleontology
http://en.wikipedia.org/wiki/DNA

Internal functions are coordinated and regulated so that the internal environment of a
living thing is relatively constant, referred to as homeostasis10 .
Living things are organized in the microscopic level from atoms up to cells11 . Atoms are
arranged into molecules, then into macromolecules12 , which make up organelles13 , which
work together to form cells. Beyond this, cells are organized in higher levels to form entire
multicellular organisms. Cells together form tissues14 , which make up organs, which are
part of organ systems, which work together to form an entire organism. Of course, beyond
this, organisms form populations which make up parts of an ecosystem. All of the Earth's
ecosystems together form the diverse environment that is the earth.
Example:sub atoms, atoms, molecules, cells, tissues, organs, organ systems, organisms, population,
community, eco systems
2.2 Nature of science

Science is a methodology for learning about the world. It involves the application
of knowledge.
The scientific method deals with systematic investigation, reproducible results, the
formation and testing of hypotheses, and reasoning.
Reasoning can be broken down into two categories, induction (specific data is used to
develop a generalized observation or conclusion) and deduction (general information leads
to specific conclusion). Most reasoning in science is done through induction.
Science as we now know it arose as a discipline in the 17th century.
2.3 Scientific method

The scientific method is not a step by step, linear process. It is an intuitive process, a
methodology for learning about the world through the application of knowledge. Scientists
must be able to have an "imaginative preconception" of what the truth is. Scientists will
often observe and then hypothesize the reason why a phenomenon occurred. They use all
of their knowledge and a bit of imagination, all in an attempt to uncover something that
might be true. A typical scientific investigation might go like so:
You observe that a room appears dark, and you ponder why the room is dark. In an attempt
to find explanations to this curiosity, your mind unravels several different hypotheses. One
hypothesis might state that the lights are turned off. Another hunch might be that the
room's lightbulb has burnt out. Worst yet, you could be going blind. To discover the truth,
10
11
12
13
14
http://en.wikipedia.org/wiki/homeostasis
http://en.wikipedia.org/wiki/cell
http://en.wikipedia.org/wiki/macromolecule
http://en.wikipedia.org/wiki/organelle
http://en.wikibooks.org/wiki/General%20Biology%2FTissues
Scientific method
you experiment. You feel your way around the room and find a light switch and turn it on.
No light. You repeat the experiment, flicking the switch back and forth. Still nothing. That
means your initial hypothesis, the room is dark because the lights are off, has been rejected.
You devise more experiments to test your hypotheses, utilizing a flashlight to prove that
you are indeed not blind. In order to accept your last remaining hypothesis as the truth,
you could predict that changing the light bulb will fix the problem. If all your predictions
succeed, the original hypothesis is valid and is accepted. In some cases, however, your
predictions will not occur, in which you'll have to start over. Perhaps the power is off.
Figure 1
How Science is Done
A diagram that illustrates scientific investigation
Scientists first make observations that raise a particular question. In order to explain the
observed phenomenon, they develop a number of possible explanations, or hypotheses. This
is the inductive part of science, observing and constructing plausible arguments for why

an event occurred. Experiments are then used to eliminate one of more of the possible
hypotheses until one hypothesis remains. Using deduction, scientists use the principles of
their hypothesis to make predictions, and then test to make sure that their predictions are
confirmed. After many trials (repeatability) and all predictions have been confirmed, the
hypothesis then may become a theory.
Quick Definitions
Observation - Quantitative and qualitative measurements of the world.
Inference - Deriving new knowledge based upon old knowledge.
Hypotheses - A suggested explanation.
Rejected Hypothesis - An explanation that has been ruled out through experimentation.
Accepted Hypothesis - An explanation that has not been ruled out through excessive
experimentation and makes verifiable predictions that are true.
Experiment - A test that is used to rule out a hypothesis or validate something already
known.
Scientific Method - The process of scientific investigation.
Theory - A widely accepted hypothesis that stands the test of time. Often tested, and
usually never rejected.
The scientific method is based primarily on the testing of hypotheses by experimentation.
This involves a control, or subject that does not undergo the process in question. A scientist
will also seek to limit variables to one or another very small number, single or minimum
number of variables. The procedure is to form a hypothesis or prediction about what you
believe or expect to see and then do everything you can to violate that, or falsify the
hypotheses. Although this may seem unintuitive, the process serves to establish more firmly
what is and what is not true.
A founding principle in science is a lack of absolute truth: the accepted explanation is the
most likely and is the basis for further hypotheses as well as for falsification. All knowledge
has its relative uncertainty.
Theories are hypotheses which have withstood repeated attempts at falsification. Common
theories include evolution by natural selection and the idea that all organisms consist of
cells. The scientific community asserts that much more evidence supports these two ideas
than contradicts them.
Charles Darwin
2.4 Charles Darwin
Figure 2
Charles Darwin is most remembered today for his contribution of the theory of evolution
through natural selection.
The seeds of this theory were planted in Darwin's mind through observations made on a
five-year voyage through the New World on a ship called the Beagle. There, he studied
fossils and the geological record, geographic distribution of organisms, the uniqueness and
relatedness of island life forms, and the affinity of island forms to mainland forms.
Upon his return to England, Darwin pondered over his observations and concluded that
evolution must occur through natural selection. He declined, however, to publish his work
because of its controversial nature. However, when another scientist, Wallace, reached similar
conclusions, Darwin was convinced to publish his observations in 1859. His hypothesis
revolutionized biology and has yet to be falsified by empirical data collected by mainstream
scientists.
2.5 After Darwin

Since Darwin's day, scientists have amassed a more complete fossil record, including
microorganisms and chemical fossils. These fossils have supported and added subtleties
to Darwin's theories. However, the age of the Earth is now held to be much older than
Darwin thought. Researchers have also uncovered some of the preliminary mysteries of
the mechanism of heredity as carried out through genetics and DNA, areas unknown to
Darwin. Another growing area is comparative anatomy including homology and analogy.
Today we can see a bit of evolutionary history in the development of embryos, as certain
(although not all) aspects of development recapitulate evolutionary history.

The molecular biology15 study of slowly mutating genes reveal considerable evolutionary
history consistent with fossil and anatomical record.
2.6 Challenges to Darwin
Figure 3
Darwin and his theories have been challenged many times in the last 150 years. The
challenges have been primarily religious based on a perceived conflict with the preconceived
notion of creationism. Many of those who challenge Darwin have been adherents to the
young earth hypothesis that says that the Earth is only some 6000 years old and that all
species were individually created by a god. Some of the proponents of these theories have
suggested that chemical and physical laws that exist today were different or nonexistent in
earlier ages. However, for the most part, these theories are either not scientifically testable
and fall outside the area of attention of the field of biology, or have been disproved by one
or more fields of science.
This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of Cleveland
State University.
15
10
http://en.wikibooks.org/wiki/molecular%20biology
3 The Nature of Molecules

3.1 Matter
Matter is defined as anything that has mass1 (an amount of matter in an object) and
occupies space2 (which is measured as volume3 ).
Particles, from smallest to largest
1. Subatomic particles
Electrons4
Protons5
Neutrons6
2. Atoms
3. Molecules
4. Macromolecules
Origin of matter
1. Big Bang7 , about 13.7 billion years ago
2. Hydrogen8 , helium9
3. Heavier elements formed in suns, super nova
Earth's matter predates formation of sun, 4.5 billion years ago
All matter consists of atoms, which are composed of : electrons, protons, neutrons
3.2 The atom

Example: Hydrogen
The simplest element
One proton (+)
One electron in orbit (-)
Built by adding one proton (and one electron) at a time
Number of protons determines atomic number and number of electrons
Neutrons
Neutral charge
1
2
3
4
5
6
7
8
9
http://en.wikipedia.org/wiki/mass
http://en.wikipedia.org/wiki/space%23Physics
http://en.wikipedia.org/wiki/volume
http://en.wikipedia.org/wiki/Electrons
http://en.wikipedia.org/wiki/Protons
http://en.wikipedia.org/wiki/Neutrons
http://en.wikipedia.org/wiki/Big%20Bang
http://en.wikipedia.org/wiki/Hydrogen
http://en.wikipedia.org/wiki/Helium
11
The Nature of Molecules

Contribute mass
May decay
Oxygen10
8 protons (mass)
8 electrons
8 neutrons (mass)
3.3 Mass and isotopes

Atomic mass
Sum of masses of protons and neutrons
Measured in daltons or AMU (Atomic Mass Unit)
An AMU is 1/12 the mass of Carbon-12
proton 1 AMU or dalton
6.024 x 1023 daltons/gram
Atoms with same atomic number belong to same element
Isotopes
Same atomic number but different atomic mass
Some are radioactive
Uses of isotopes
Radioactive: 3H, 14C, 32P, 35S
Tracers in biochemical reactions
Detection of molecules in recombinant DNA technology (genetic engineering)
Half-life: dating of rocks, fossils
Non-radioactive (N, C, O)
Diet of organisms (including fossils)
Biochemical tracers
3.4 Electrons
Negative charge
Held in orbit about nucleus by attraction to positively charged nucleus
Atom may gain or lose electron, altering charge
Cation: loses electron, positive charge
Na+
Anion: gains electron, negative charge
Cl Determine chemical properties of atoms
Number
Energy level
10
12
http://en.wikipedia.org/wiki/Oxygen
Chemical bonds
3.5 Chemical bonds
Form molecules
Enzymes: make, break, rearrange chemical bonds in living systems
Ionic
Covalent
Sharing of one or more pairs of electrons
Called single, double, or triple
No net charge (as in ionic bonds)
No free electrons
Give rise to discrete molecules
Hydrogen
3.6 Chemical reactions
Formation and breaking of chemical bonds

Shifting arrangement of atoms
Reactants -> products
Reactions are influenced by:
Temperature
Concentration of reactants, products
Presence of catalysts (enzymes)
Oxidation:reduction
3.7 Water
Essential for life

75% earth's surface is water
Life evolved in water
Solvent for many types of solutes
High specific heat
High polarity
Creates a slightly negative Oxygen and a Slightly positive hydrogen
allows formation of Hydrogen Bonds
3.7.1 Hydrogen bonding

A type of polar interaction
Critical for:
Protein structure
Enzymatic reactions
Movement of water in plant stems
Weak and transient
Powerful cumulative effect
13
The Nature of Molecules

Solubility of many compounds
Cohesion (capillary action)
Lower density of ice
Formed between molecules other than water
Protein structure
DNA11 , RNA12 structure
Water organizes nonpolar molecules
Nonpolar molecules: no polarity (+/-) charges
Hydrophobic: exclude water because they don't form hydrogen bonds with it
Consequences:
Membranes
Protein structure
Hydrophilic: polar substances associate with water
Ionization of water: H2 O -> H+ + OH Forms a Hydrogen ion (H+ ), hydroxide ion (OH- )
Due to spontaneous breakage of covalent bond
At 25C, 1 liter of water contains 10-7 moles of H+ ions: 10-7 moles/liter
pH
A convenient way of indicating H+ concentration

pH13 = -log[H+ ]
For water, pH = -log[10-7] = 7
Since for each H+ in pure water, there is one OH- , pH of 7 indicates neutrality
Logarithmic scale
Buffer
Reservoir for H+
Maintains relatively constant pH over buffering range
This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the
Cleveland State University.
11
12
13
14
http://en.wikipedia.org/wiki/RNA
http://en.wikipedia.org/wiki/pH
4 The Chemical Building Blocks of Life

Building blocks of life
Carbon based: organic molecules

Carbohydrates: CHO
Lipids: CHO, water insoluble
Proteins: CHONS, structure/function in cells
Nucleic acids: CHONP, hereditary (genetic) information
4.1 Carbon
Can make 4 covalent bonds1
Chains
Straight
Branched
Ring
Hydrocarbons2 (C, H): store energy
Functional groups
Attach to carbon
Alter chemical properties
Form macromolecules
Sapoteton
4.2 Carbohydrates
Principally CHO (rare N, S and P)
1C:2H:1O ratio
Energy rich (many C-H bonds)
Monosaccharides (principal: glucose3 )
Simple sugars
Principle formula: C6 H12 O6
Form rings in water solution
Disaccharides (sucrose, lactose)
Polysaccharides (starch, glycogen, cellulose, chitin)
1
2
3
http://en.wikipedia.org/wiki/covalent%20bonds
http://en.wikipedia.org/wiki/Hydrocarbons
http://en.wikipedia.org/wiki/glucose
15
The Chemical Building Blocks of Life
4.3 Stereoisomers
Bond angles of carbon point to corners of a tetrahedron
When 4 different groups are attached to a carbon, it is asymmetric, leading to various
types of isomerism
Stereoisomers: (D, L)
Same chemical properties
Different biological properties
D sugars, L amino acids
4.4 Lipids
C-H bonds (nonpolar) instead of C-OH bonds as in carbohydrates
High energy
Hydrophobic (insoluble in water)
Categories
Fats: glycerol and three fatty acids
Phospholipids: primary component of membranes
Prostaglandins: chemical messengers (hormones)
Steroids: membrane component; hormones
Terpenes: pigments; structure
4.4.1 Fatty acids

Hydrocarbon chain
Even number of C, 14->20
Terminates in carboxyl group
Saturated: contain maximum number of hydrogens (all single bonds); maximum energy
Unsaturated: one or more double bonds
Usually higher melting point
Many common oils are polyunsaturated
4.5 Proteins
Polymer of amino acids
21 different amino acids found in proteins
Sequence of amino acids determined by gene
Amino acid sequence determines shape of molecule
Linked by peptide bond (covalent)
Functions
regulate chemical reactions and cell processes [enzymes]
form bone and muscle; various other tissues
facilitate transport across cell membrane [carrier proteins]
16
Proteins
fight disease [antibodies]
Motifs: folding patterns of secondary structure
Domains: structural, functional part of protein often independent of another part; often
encoded by different exons
Shape determines protein's function
4.5.1 Amino acids

21 commonly found in proteins
21st is selenocysteine, not mentioned in text
Common structure
Amino group: NH2
Carboxyl group: COOH
R group- 4 different kinds of R groups
acidic
basic
hydrophilic (polar)
hydrophobic (nonpolar)
Confer individual properties on amino acids
List of amino acids4
4.5.2 Structure
Primary structure: the amino acid sequence
Determines higher orders of structure
Critical for structure and function of protein
Secondary: stabilized by intramolecular hydrogen bonding
helix
sheet
Tertiary: folding, stabilized by ionic bonds (between R groups), hydrogen bonding, van
der Waal's forces, hydrophobic interactions
Quaternary: _2 polypeptides
4.5.3 Function
Requires proper folding, cofactors, pH, temperature, etc.
Proteins are often modified after synthesis
Chemical modification
Addition of heme groups (hemoglobin, cytochrome)
Denatured proteins can not function properly
Proteins are degraded by proteosome as part of constant turnover of cell components
http://en.wikipedia.org/wiki/Amino%20acid%23List%20of%20amino%20acids
17
The Chemical Building Blocks of Life
4.6 Hereditary (Genetic) information

Nucleic acids
DNA: deoxyribonucleic acid
Hereditary information of all cells
Hereditary information for many viruses
RNA: ribonucleic acid
Hereditary information of certain viruses (HIV5 )
Intermediate in gene expression
Composed of nucleotides
Ribonucleotides
Deoxyribonucleotides
4.6.1 RNA DNA origin

Which came first?
Paradox: DNA encodes protein necessary for its own replication
Discovery of catalytic RNA by Cech and Altman suggested that RNA might have been
first self-replicating molecule
DNA evolved as more stable type of storage molecule
Proteins: Their building block is amino acids. The bond connecting 2 of the amino acids
together are called peptide bonds. One of these bonds makes a monopeptide, two a dipeptide,
and any more than that makes a polypeptide.
18
http://en.wikipedia.org/wiki/HIV
5 Life: History and Origin

5.1 Properties of life
1. Organization: Being structurally composed of one or more cells, which are the basic
units of life.
prokaryote: no nucleus
eukaryote: membrane bound nucleus.
2. Sensitivity: respond to stimuli.
3. Energy Processing
4. Growth and Development
5. Reproduction
hereditary mechanisms to make more of self; DNA based.
6. Regulation, including homeostasis.
7. Evolution.
5.2 Origin of life: 3 hypotheses

Extraterrestrial origin (panspermia): meteor, comet borne from elsewhere in universe
evidence of amino acids and other organic material in space (but often both D & L
forms)
questionable bacterial fossils in Martian rock
-However, this would imply that some other origin of life was likely because it would have
had to happen elsewhere before it could be transported here, and the only difference would
be that life did not originate on Earth.
Spontaneous origin on earth: primitive self-replicating macromolecules acted upon by
natural selection ((macro)Evolution is one example of this)
-This is often attacked for the seeming impossibility for life to have been produced by a
chemical reaction triggered by lightning and the ability of any produced DNA to actually be
in a sequence that could produce a working model of life if replicated. It is also attacked
for religious reasons, as it bypasses things like the idea of a supreme being directly creating
humans. It also seems unlikely to some that such huge changes are possible in evolution
19
Life: History and Origin

without evidence of an "in-between stage" that is credible. Many of the stages of man are
disputed due to their somewhat shakey grounds. For example, bones from other animals
have been taken accidentally in some cases to be part of a humanoid, and complete skeletons
have been sketched out from a limited number of bones.
Special creation: religious explanations (Intelligent Design is one popular example of
this.) These explanations contend that life was created by God (or perhaps some other
Intelligent Designer).
Proponents of Intelligent design suggest that the vast complexity of life could only
have been intentionally designed while other creationists cite biblical support.
-This is often attacked for many of the same reasons that religion is attacked, and is often
regarded as superstitious and/or unscientific.
It is debated as to whether schools should teach one hypothesis or the other when talking
about the origin of life. However, since they are all currently known major hypotheses
(and sometimes hypotheses proven wrong are shown for educational purposes), this
wikibook includes what it can without discriminating unfairly against one hypothesis or
the other.
5.3 The early earth

It is believed that the Earth was formed about 4.5 billion years ago.
Heavy bombardment by rubble ceased about 3.8 billion years ago.
Reducing atmosphere: much free H
also H2 O, NH3 , CH4
little, if any, free O2
with numerous H electrons, require little energy to form organic compounds with C
Warm oceans, estimated at 49-88C
Lack of O2 and consequent ozone (O3 ) meant considerable UV energy
Chemical reactions on early earth
UV and other energy sources would promote chemical reactions and formation of organic
molecules
Testable hypothesis: Miller-Urey experiment
simulated early atmospheric conditions
found amino acids, sugars, etc., building blocks of life
won Nobel prize for work
experiment showed prebiotic synthesis of biological molecules was possible
Issues
Miller later conceded that the conditions in his experiments were not representative of
what is currently thought to be those of early earth
He also conceded that science has no answer for how amino acids could self-organize into
replicating molecules and cells
In the 50 years since Miller-Urey, significant issues and problems for biogenesis have been
identified. This is a weak hypothesis at this time.
20
Origin of cells
Conclusion: Life exists, we don't know why.
5.4 Origin of cells

Cells are very small and decompose quickly after death. As such, fossils of the earliest cells
do not exist. Scientists have had to form a variety of theories on how cells (and hence life)
was created on Earth.
Bubble hypothesis
A. Oparin, J.B.S. Haldane, 1930s
Primary abiogenesis: life as consequence of geochemical processes
Protobionts: isolated collections of organic material enclosed in hydrophobic bubbles
Numerous variants: microspheres, protocells, protobionts, micelles, liposomes, coacervates
Other surfaces for evolution of life
deep sea thermal vents
ice crystals
clay surfaces
tidal pools
5.5 The RNA world?

DNA RNA polypeptide (protein)
Catalytic RNA: ribozyme
discovered independently by Tom Cech and Sid Altman (Nobel prize)
catalytic properties: hydrolysis, polymerization, peptide bond formation, etc.
Self-replicating RNA molecule may have given rise to life
consistent with numerous roles for RNA in cells as well as roles for ribonucleotides
(ATP)
relationship to bubble-like structures is uncertain
5.6 The earliest cells

Microfossils
3.5 by
resemble bacteria: prokaryotes
biochemical residues
stromatolites
Archaebacteria (more properly Archaea)
extremophiles: salt, acid, alkali, heat, methanogens
may not represent most ancient life
Eubacteria
cyanobacteria: photosynthesis
atmospheric O2 ; limestone deposits
21
Life: History and Origin

chloroplasts of eukaryotes
Cyanobacteria
5.7 Major steps in evolution of life

Prebiotic synthesis of macromolecules
Self replication
RNA? (primitive metabolism)
DNA as hereditary material
1st cells
Photosynthesis
Aerobic respiration
Multicellularity (more than once)
22
6 Cells
23
7 Cell structure
7.1 What is a cell?
The word cell comes from the Latin word "cella", meaning "small room", and it was first
coined by a microscopist observing the structure of cork. The cell is the basic unit of all
living things, and all organisms are composed of one or more cells. Cells are so basic and
critical to the study of life, in fact, that they are often referred to as "the building blocks of
life". Organisms - bacteria, amoebae and yeasts, for example - may consist of as few as one
cell, while a typical human body contains about a trillion cells.
According to Cell Theory, first proposed by Schleiden and Schwann in 1839, all life consists
of cells. The theory also states that all cells come from previously living cells, all vital
functions (chemical reactions) of organisms are carried out inside of cells, and that cells
contain necessary hereditary information to carry out necessary functions and replicate
themselves.
All cells contain:
Lipid bilayer boundary (plasma membrane1 )

Cytoplasm2
DNA3 (hereditary information)
Ribosomes4 for protein synthesis
Eukaryotic cells also contain:

At least one nucleus5
Mitochondria6 for cell respiration and energy
Cells may also contain:
1
2
3
4
5
6
7
8
9
10
Lysosomes7
Peroxisomes8
Vacuoles9
Cell walls10
http://en.wikipedia.org/wiki/plasma%20membrane
http://en.wikipedia.org/wiki/Cytoplasm
http://en.wikipedia.org/wiki/Ribosome
http://en.wikipedia.org/wiki/Cell%20Nucleus
http://en.wikipedia.org/wiki/Mitochondrion
http://en.wikipedia.org/wiki/Lysosome
http://en.wikipedia.org/wiki/Peroxisome
http://en.wikipedia.org/wiki/Vacuole
http://en.wikipedia.org/wiki/Cell%20Wall
25
Cell structure
7.1.1 Concepts
Plasma Membrane
Phospholipid bilayer, which contains great amount of proteins, the most important functions
are the following:
1. It selectively isolates the content of the cell of the external atmosphere.
2. It regulates the interchange of substances between the cytoplasm and the environment.
3. Communicates with other cells.
Model of the fluid mosaic
Describes the structure of the plasma membrane, this model was developed in 1972 by
cellular biologists J. Singer and L. Nicholson.
Phospholipid bilayer
Is in the plasma membrane and produces the fluid part of membranes.
Proteins
Long chains of amino acids.
Glucose proteins
Proteins together with carbohydrates in the plasma membrane, mostly in the outer parts
of the cell.
Functions of proteins
Transport oxygen, they are components of hair and nails, and allow the cell interact with
its environment.
Transport Proteins
Regulate the movement of soluble water molecules, through the plasma membrane. Some
transport proteins called channel proteins form pores or channels in the membrane so
that water soluble molecules pass.
Carrying proteins
Have union sites that can hold specific molecules.
Reception proteins
They activate cellular responses when specific molecules join.
Proteins of recognition
They work as identifiers and as place of union to the cellular surface.
Fluid
It is any substance that can move or change of form.
Concentration
Number of molecules in a determined unit of volume.
26
What is a cell?
Gradient
Physical difference between two regions of space, in such a way that the molecules tend to
move in response to the gradients.
Diffusion
Movement of the molecules in a fluid, from the regions of high concentration to those of
low concentration.
Passive transport
Movement of substances in a membrane that doesnt need to use energy.
Simple diffusion
Diffusion of water, gases or molecules across the membrane.
Facilitated diffusion
Diffusion of molecules across the membranes with the participation of proteins.
Osmosis
Diffusion of the water across a membrane with differential permeability.
Transport that needs energy
Movement of substances across a membrane generally in opposition to a gradient of
concentration with the requirement of energy.
Active transport
Movement of small molecules using energy (ATP).
Endocytosis
Movement of big particles towards the interior of the cell using energy. The cells enclose
particles or liquids.
Pinocytosis
(Literally cell drinking) Form in which the cell introduces liquids.
Phagocytosis
Way of eating of the cells. It feeds in this case of big particles or entire microorganisms.
Pseudopods
False feet (the amoeba).
Exocitosis
Movement of materials out of the cell with the use of energy. It throws waste material.
Isotonic
The cytoplasm fluid of the interior of the cells is the same that the outer.
Hypertonic solution
27
Cell structure
The solutions that have a higher concentration of dissolved particles than the cellular
cytoplasm and that therefore water of the cells goes out with osmosis.
Hypotonic
The solutions with a concentration of dissolved particles lower than the cytoplasm of a cell
and that therefore do that water enters the cell with osmosis.
Swelling
Pressure of the water inside the vacuole.
Endoplasmic Reticulum
It is the place of the synthesis of the cellular membrane.
7.1.2 Structure and function of the cell

Rudolf Virchow
Zoologist, who proposed the postulates of the cellular theory, observes that the living cells
could grow and be in two places at the same time, he proposed that all the cells come from
other equal cells and proposed 3 postulates:
1. Every living organism is formed from one or more cells
2. The smallest organisms are unicellular and these in turn are the functional units of
the multicellular organisms.
3. All the cells come from preexisting cells.
7.1.3 Common characteristics of all the cells

Molecular components
Proteins, amino acids, lipids, sweeten, DNA, RNA.
Structural components
Plasmatic membrane, citoplasm, ribosomes.
Robert Hooke
He postuled for the first time the term cell
Prokaryotes
Their genetic material is not enclosed in a membrane ex. Bacterias
Eukaryotes
Their genetic material is contained inside a nucleus closed by a membrane
28
History of cell knowledge
7.2 History of cell knowledge

The optical microscope was first invented in 17th century. Shortly thereafter scientists began
to examine living and dead biological tissues in order to better understand the science of
life. Some of the most relevant discovery milestones of the time period include:
The invention of the microscope11 , which allowed scientists for the first time to see
biological cells
Robert Hooke12 in 1665 looked at cork under a microscope and described what he called
cork "cells"
Anton van Leeuwenhoek13 called the single-celled organisms that he saw under the
microscope "animalcules"
Matthias Jakob Schleiden14 , a botanist, in 1838 determined that all plants consist of
cells
Theodor Schwann15 , a zoologist, in 1839 determined that all animals consist of cells
Rudolf Virchow16 proposed the theory that all cells arise from previously existing cells
In 1838, the botanist Matthias Jakob Schleiden and the physiologist Theodor Schwann
discovered that both plant cells and animal cells had nuclei. Based on their observations,
the two scientists conceived of the hypothesis that all living things were composed of cells.
In 1839, Schwann published 'Microscopic Investigations on the Accordance in the Structure
and Growth of Plants and Animals', which contained the first statement of their joint cell
theory.
7.2.1 Cell Theory

Schleiden and Schwann proposed spontaneous generation as the method for cell origination,
but spontaneous generation (also called abiogenesis17 ) was later disproven. Rudolf Virchow
famously stated "Omnis cellula e cellula"... "All cells only arise from pre-existing cells." The
parts of the theory that did not have to do with the origin of cells, however, held up to
scientific scrutiny and are widely agreed upon by the scientific community today.
The generally accepted portions of the modern Cell Theory are as follows: (1) The cell is the
fundamental unit of structure and function in living things. (2) All organisms are made up
of one or more cells. (3) Cells arise from other cells through cellular division. (4) Cells carry
genetic material passed to daughter cells during cellular division. (5) All cells are essentially
the same in chemical composition. (6) Energy flow (metabolism and biochemistry) occurs
within cells.
11
12
13
14
15
16
17
http://en.wikipedia.org/wiki/microscope
http://en.wikipedia.org/wiki/Robert%20Hooke
http://en.wikipedia.org/wiki/Anton%20van%20Leeuwenhoek
http://en.wikipedia.org/wiki/Matthias%20Jakob%20Schleiden
http://en.wikipedia.org/wiki/Theodor%20Schwann
http://en.wikipedia.org/wiki/Rudolf%20Virchow
http://en.wikipedia.org/wiki/Abiogenesis
29
Cell structure
7.3 Microscopes
Allow greater resolution, can see finer detail

Eye: resolution of 100 m
Light microscope18 : resolution of 200 nm
Limited to cells are larger organelles within cells
Confocal microscopy19 : 2 dimension view
Electron microscope20 : resolution of 0.2 nm
Laser tweezers: move cell contents
7.4 Cell size

One may wonder why all cells are so small. If being able to store nutrients is beneficial
to the cell, how come there are no animals existing in nature with huge cells? Physical
limitations prevent this from occurring. A cell must be able to diffuse gases and nutrients in
and out of the cell. A cell's surface area does not increase as quickly as its volume, and as a
result a large cell may require more input of a substance or output of a substance than it
is reasonably able to perform. Worse, the distance between two points within the cell can
be large enough that regions of the cell would have trouble communicating, and it takes a
relatively long time for substances to travel across the cell.
That is not to say large cells don't exist. They are, once again, less efficient at exchanging
materials within themselves and with their environment, but they are still functional. These
cells typically have more than one copy of their genetic information, so they can manufacture
proteins locally within different parts of the cell.
Key concepts: Cell size:
Is limited by need for regions of cell to communicate
Diffuse oxygen and other gases
Transport of mRNA21 and protein22 s
Surface area to volume ratio limited
Larger cells typically:
Have extra copies of genetic information
Have slower communication between parts of cell
18
19
20
21
22
30
http://en.wikipedia.org/wiki/Light%20microscope
http://en.wikipedia.org/wiki/microscopy
http://en.wikipedia.org/wiki/Electron%20microscope
http://en.wikipedia.org/wiki/RNA
http://en.wikipedia.org/wiki/protein
8 Structure of Eukaryotic cells

Eukaryotic1 cells feature membrane delimited nucleii containing two or more linear chromosome2 s; numerous membrane-bound cytoplasmic organelles: mitochondria, RER3 , SER4 ,
lysosomes, vacuole5 s, chloroplast6 s; ribosomes and a cytoskeleton7 . Also, plants, fungi, and
some protists have a cell wall.
8.1 Structure of the nucleus

The nucleus is the round object in the cell that holds the genetic information (DNA) of the
cell. It is surrounded by a nuclear envelope and has a nucleolus inside.
8.1.1 Nuclear envelope

The nuclear envelope is a double-layered plasma membrane8 like the cell membrane, although
without membrane proteins. To allow some chemicals to enter the nucleus, the nuclear
envelope has structures called Nuclear pore9 s. The nuclear envelope is continuous with the
endoplasmic reticulum.
8.1.2 Nucleolus
The nucleolus appears in a microscope as a small dark area within the nucleus. The nucleolus
is the area where there is a high amount of DNA transcription10 taking place.
1
2
3
4
5
6
7
8
9
10
http://en.wikipedia.org/wiki/Eukaryote
http://en.wikipedia.org/wiki/chromosome
http://en.wikipedia.org/wiki/RER
http://en.wikipedia.org/wiki/SER
http://en.wikipedia.org/wiki/vacuole
http://en.wikipedia.org/wiki/chloroplast
http://en.wikipedia.org/wiki/cytoskeleton
http://en.wikibooks.org/wiki/Plasma%20membrane
http://en.wikibooks.org/wiki/Nuclear%20pore
http://en.wikibooks.org/wiki/DNA%20transcription
31
8.2 Chromatin
Chromosomes consist of chromatin11 . This is made up of strings of DNA, which typically
measure centimeters in length if stretched out. This DNA is wound around a histone12 core
and organized into nucleosome13 s.
The chromatin14 must be uncoiled for gene expression15 and replication16 . Chromosome
micrograph
8.3 Endoplasmic reticulum

The endoplasmic reticulum17 is a cellular organelle18 made up of a series of extended folded
intracellular membranes. It is continuous with the nuclear membane.
There are two main types of endoplasmic reticulum:
RER: rough endoplasmic reticulum (site of protein synthesis19 ) associated with ribosomes
SER: smooth endoplasmic reticulum (site of lipid synthesis20 )
8.3.1 Rough Endoplasmic Reticulum

Proteins are directed to the RER by a signal sequence of a growing polypeptide21 s on
the ribosome. This is recognised by a signal recognition particle which brings the ribosome/polypeptide complex to a channel on the RER called a translocon. At the translocon,
the signal sequence and ribosome/polypeptide complex interact with the translocon to open
it. The signal sequence becomes attached to the translocon. The ribosome can continue to
translate the polypeptide into the lumen of the RER. As synthesis continues, 2 processes
can happen.
1. If the protein is destined to become a membrane bound protein then the protein
synthesis will continue until termination. The ribosome can then dissociate, allowing
protein folding within the RER lumen to occur and continuation to the golgi apparatus
for processing of the polypeptide.
2. If the protein is destined for storage for later secretion after stimulation or for continuous
secretion then a protease-enzyme which cuts proteins at the peptide bond-can cut the
signal sequence from the growing polypeptide. Continuation to the golgi etc. can then
occur.
11
12
13
14
15
16
17
18
19
20
21
32
http://en.wikipedia.org/wiki/chromatin
http://en.wikipedia.org/wiki/histone
http://en.wikipedia.org/wiki/nucleosome
http://en.wikipedia.org/wiki/chromatin
http://en.wikipedia.org/wiki/gene%20expression
http://en.wikipedia.org/wiki/replication
http://en.wikipedia.org/wiki/endoplasmic%20reticulum
http://en.wikipedia.org/wiki/organelle
http://en.wikipedia.org/wiki/protein%20synthesis
http://en.wikipedia.org/wiki/lipid%20synthesis
http://en.wikipedia.org/wiki/polypeptide
Endoplasmic reticulum
When produced, proteins are then exported to one of several locations. The proteins are
either modified for extracellular membrane insertion or secretion. Note, this is in contrast
with ribosomes which do not associate with the RER and produce proteins which will become
cytosolic enzymes for example.
8.3.2 Smooth Endoplasmic Reticulum

Smooth endoplasmic reticulum produces enzyme22 s for lipid and carbohydrate biosynthesis
and detoxification RER
8.3.3 Sarcoplasmic Reticulum

This is a specialised form of endoplasmic reticulum found in some muscle cell typesparticularly striated, skeletal muscle. Its main function is different from the other 2 types in
that is mainly acts as a storage of calcium. This reticulum has voltage gated channels which
respond to signals from 'motor neurones' to open and release calcium into the cytoplasm.
This can then bring about the next part in muscle contraction.
Figure 1 :Image of nucleus23 , endoplasmic reticulum and Golgi apparatus.
Figure 4
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Nucleus.
Nuclear pore.
Rough endoplasmic reticulum (RER).
Smooth endoplasmic reticulum (SER).
Ribosome on the rough ER.
Proteins that are transported.
Transport vesicle.
Golgi apparatus.
Cis face of the Golgi apparatus.
Trans face of the Golgi apparatus.
Cisternae of the Golgi apparatus.
1.
22
23
http://en.wikipedia.org/wiki/enzyme
http://en.wikipedia.org/wiki/cell%20nucleus
33
8.4 The Golgi apparatus

The golgi apparatus24 is made up of multiple stacks of bilipid membranes.
Proteins made on the RER are modified and then sorted
Formation of secretory vesicles
Formation of lysosomes (intracellular digestion)
Other membrane-bound cytoplasmic organelles include:
Microbodies25 (generic term)
Glyoxysome (transforms fat into carbohydrate in plants)
Peroxisome26 (uses oxidative metabolism to form hydrogen peroxide and is destroyed by
catalase27 )
8.5 Ribosomes
Ribosomes are the site of protein synthesis. Ribosomes themselves are synthesized in the
cell nucleoli28 and are structured as two subunits, the large and the small. These parts are
composed of RNA and protein.
Prokaryotic and eukaryotic ribosomes are different, the eukaryotic ones being larger and
more complicated.
8.6 DNA-containing organelles

Mitochondria
Double membrane
Aerobic metabolism, internal membrane
DNA, ribosomes
Give rise to new mitochondria
Chloroplast29
Double membrane
Photosynthesis, internal membrane
DNA, ribosomes
Give rise to new chloroplasts
Centriole30 s
24
25
26
27
28
29
30
34
http://en.wikipedia.org/wiki/Golgi%20apparatus
http://en.wikipedia.org/wiki/Microbody
http://en.wikipedia.org/wiki/Peroxisome
http://en.wikipedia.org/wiki/catalase
http://en.wikipedia.org/wiki/nucleoli
http://en.wikipedia.org/wiki/Chloroplast
http://en.wikipedia.org/wiki/Centriole
Cytoskeleton
Microtubule organizing centers
Animal cells and many protists
Pair constitutes the centrosome
Give rise to flagellum during spermatogenesis
Consist of 9 triplet microtubules
Mitosis31 , meiosis32
8.7 Cytoskeleton
Cytoskeleton is a collective term for different filaments of proteins that can give physical
shape within the cell and are responsible for the 'roads' which organelles can be carried
along.
Gives the cell shape
Anchors other organelles
Vital to intracellular transport of large molecules
The cytoskeleton is composed of 3 main types of filaments:
Actin33 filaments (7 nm)
Microtubule34 s: (25 nm) polymer of tubulin; 13/ring.
Intermediate Filament35 s
Both actin and microtubules can have associated motor proteins.
8.7.1 Intermediate Filaments

These are rope like filaments, 8-10nm in diameter and tend to give the structural stability to
cells. Examples inculude Vimentin, neurofilaments and keratin. It is keratin which priniciply
makes up hair, nails and horns.
8.7.2 Actin Filaments

Growth
These filaments are 2-stranded and composed of dimeric subunits called G-Actin. They
contain a GTP molecule in order to bind (polymerise). As GTP is hydrolysed then the
structure becomes unstable and depolymerisation occurs. The growth of actin filaments is
concentration dependant-that is, the higher the concentration of free G-actin, the greater
the polymerisation. The are also polar, having a + and a - end (not related to charge) and
polymerisation tends to happen faster at the + end.
31
32
33
34
35
http://en.wikipedia.org/wiki/mitosis
http://en.wikipedia.org/wiki/meiosis
http://en.wikipedia.org/wiki/Actin
http://en.wikipedia.org/wiki/Microtubule
http://en.wikipedia.org/wiki/Intermediate%20Filament
35

Cilia and flagella are threads of microtubules that extend from the exterior of cells and used
to move single celled organisms as well as move substances away from the surface of the cell.
motor proteins-move, wave motion
36
9 Membranes
9.1 Biological membranes
Figure 5
Plasma membrane bilayer
37
Membranes
Biological membranes surround cells and serve to keep the insides separated from the outsides.
They are formed of phospholipid bilayer1 s, which by definition are a double layer of fatty
acid2 molecules (mostly phospholipid3 s, lipids containing lots of phosphorus).
Proteins4 serve very important functions in cellular membranes. They are active transports
in and out of the cell, acting as gatekeepers. They relay signals in and out of the cell.
Proteins are the site of many enzymatic reactions in the cell, and play a role in
regulation of cellular processes.
9.2 Phospholipid
basis of biological membranes and cellular organisms
contains a charged, hydrophilic (attracted to water) head and two hydrophobic (repelled
by water) hydrocarbon tails
In presence of water, phospholipids form bilayer
maximize hydrogen bonds between water
creates barrier to passage of materials
fluid mosaic model shows horizontal (common) and "flip-flop" (rare) movement of
phospholipids
9.3 Fluid mosaic model

Current model of membrane
Phospholipids
Move freely in lipid layer, but rarely switch layers
Different phospholipids in each layer in different organelles
Glycolipids
Sterols (cholesterol in animals)
Transmembrane proteins "float" in fluid lipid bilayer
also called intrinsic, integral proteins
Exterior (extrinsic, peripheral) proteins
9.4 Membrane proteins

Transport channels
Enzymes
Cell surface receptors
1
2
3
4
38
http://en.wikibooks.org/wiki/lipid%20bilayer
http://en.wikibooks.org/wiki/Fatty%20acid
http://en.wikibooks.org/wiki/phospholipid
http://en.wikibooks.org/wiki/Proteins
Membrane proteins
Cell surface identity markers
Cell adhesion proteins
Attachments to cytoskeleton
Integral membrane proteins
Anchoring to membrane
Protein has attached phosphatidylinositol (GPI) linkage, anchors protein in outer
layer (no picture)
Protein has one or more hydrophobic transmembrane domains
-helix
-sheet
Channel protein Transport across membranes * Diffusion
From higher concentration to lower concentration
Membranes are selectively permeable
Ions diffuse through membrane channels
Selective
Movement determined by diffusion and voltage differences
Facilitated diffusion
Carrier protein, physically binds transported molecule
Osmosis
Diffusion of water down concentration gradient
In cell: various solutes (amino acids, ions, sugars, etc.)
interact with water, e.g., hydration shells
Water moves through aquaporin channels into cell
Depends upon the concentration of all solutes in solution
Hyperosmotic solution: higher concentration of solutes
Hypoosmotic solution: lower concentration of solutes
Isoosmotic solution: solute concentrations equal
Water moves from hypoosmotic solution to hyperosmotic solution
Osmotic pressure Bulk transport
Endocytosis: energy requiring
Phagocytosis
Solid material, typically food
Pinocytosis
Primarily liquid
** Receptor-mediated endocytosis
Pits on cell surface coated with clathrin and receptors
Bind specific proteins
Exocytosis
Discharge of materials from vesicle at cell surface
39
Membranes
9.5 Receptor-mediated endocytosis

Active transport
Energy required (usually ATP)

Highly selective
Works against concentration gradient
Many examples, e.g., Na+ /K+ pump
Cotransport (coupled transport)

Does not use ATP directly
Molecule is transported in connection with another molecule that is moving down a
concentration gradient
Example: Na+ gradient is established by a Na+ pump, with higher concentration on
outside of cell. Cotransport channel carries Na+ and another molecule (e.g. glucose)
into cell
May involve proton (H+ ) pumps (chemiosmosis - ATP production)
40
10 Cell-cell interactions
with the environment with each other
10.1 Cell signaling

Signaling requires
Signal
Cell receptor (usually on surface)
Signaling is important in:
Response to environmental stimuli
Sex
Development
Major area of research in biology today
10.1.1 Types of signaling
Direct contact (e.g., gap junctions between cells)

Paracrine: Diffusion of signal molecules in extracellular fluid; highly local
Endocrine: Signal (hormone) molecule travels through circulatory system
Synaptic: neurotransmitters
Types of signal molecules

Hormones: chemically diverse
Steroid
Polypeptide
Vitamin/amino acid derived
Cell surface proteins/glycoproteins
Ca2+ , NO
Neurotransmitter
Several hundred types
Some are also hormones e.g. Estrogen, progesterone
Receptor molecules
Intracellular
Protein that binds signal molecule in cytoplasm
41
Cell-cell interactions
Bound receptor may act as:
Gene regulator
Enzyme
Cell surface
Gated ion channels (neurotransmitter receptor)
Enzymic receptors
G protein-linked receptors
Cell surface protein
Tissue identity
glycolipids
MHC proteins
Immune systems
distinguish self from not-self
Intercellular adhesion
permanent contact
help form sheets of cells, tissues
may permit signaling
Example: G proteins
Transmembrane surface receptor binds signal molecule

Conformational change allows binding of G protein on cytoplasmic side
G protein binds GTP, becomes activated
G protein activates intracellular signal cascade
Change in gene expression
Secrection
Many other possible consequences
10.2 Communicating junctions

Gap junctions
animals
small molecules and ions may pass
Plasmodesmata
plants
lined with plasma membrane
permit passage of water, sugars, etc.
10.2.1 Gap junctions

42
11 Energy and Metabolism

11.1 Energy
The capacity to do work.
Kinetic energy: energy of motion (ex. jogging).
Potential energy: stored energy (ex. a lion that is about to leap on its prey).
Many forms of energy: e.g.,
Heat
Sound
Electric current
Light
All convertible to heat
Most energy for biological world is from sun
Heat (energy of random molecular motion, thermal energy)
Convenient in biology
All other energy forms can be converted to heat
Thermodynamics: study of thermal energy
Heat typically measured in kilocalories
Kcal: 1000 calories
1 calorie: amount of heat required to raise the temperature of one gram of water one
degree Celsius (C)
Heat plays major role in biological systems
Ecological importance
Biochemical reactions
11.2 OxidationReduction
Energy flows into biological world from sun
Light energy is captured by photosynthesis
Light energy raises electrons to higher energy levels
Stored as potential energy in covalent C-H bonds of sugars
Strength of covalent bond is measured by amount of energy required to break it
98.8 kcal/mole of C-H bonds
In chemical reaction, energy stored in covalent bonds may transfer to new bonds. When
this involves transfer of electrons, it is oxidationreduction reaction
Always take place together
Electron lost by atom or molecule through oxidation is gained by another atom or
molecule through reduction
Potential energy is transferred from one molecule to another (but never 100%)
43
Energy and Metabolism

Often called redox reactions
Photosynthesis
Cellular Respiration
Chemiosynthesis
Autotrophs
Heterotrophs
11.3 NAD+
Common electron acceptor/donor in redox reactions
Energetic electrons often paired with H+
11.4 Free energy

Energy required to break and subsequently form other chemical bonds
Chemical bonds: sharing of electrons, tend to hold atoms of molecule together
Heat, by increasing atomic motion, makes it easier to break bonds (entropy)
Energy available to do work in a system
In cells, G = H - TS
G = Gibbs free energy
H = H (enthalpy) energy in molecules chemical bonds
TS (T, temperature in K; S, entropy)
Chemical reactions break and make bonds, producing changes in energy
Under constant conditions of temperature, pressure and volume, G = H - TS
G, change in free energy
If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction,
does not proceed spontaneously; require input of energy (e.g., heat)
If negative (), H is lower, S is higher. Product has less free energy; exergonic;
spontaneous
===Activation energy = ==
Reactions with G often require activation energy
e.g., burning of glucose
Must break existing bonds to get reaction started
Catalysts lower activation energy
11.5 Enzymes
Biological catalysts
Protein
RNA (ribozyme)
Stabilizes temporary association between reactants (substrates) to facilitate reaction
Correct orientation
Stressing bonds of substrate
44
Enzymes
Lower activation energy
Not consumed (destroyed) in reaction
11.5.1 Carbonic anhydrase

Important enzyme of red blood cells
CO2 + H2 O H2 CO3 -> HCO3 + H+
Carbonic anhydrase catalyzes 1st reaction
Converts water to hydroxyl
Orients the hydroxyl and CO2
11.5.2 Enzyme mechanism

One or more active sites which bind substrates (reactants)
Highly specific
Binding may alter enzyme conformation, inducing better fit
11.5.3 Factors affecting enzyme activity
Substrate concentration
Product concentration
Cofactor concentration
Temperature
pH
Inhibitors
Competitive: bind to active site
Noncompetitive: bind to 2nd site, called allosteric site; changes enzyme conformation
Activators
Bind to allosteric sites, increase enzyme activity
Cofactors
Required by some enzymes
Positively charged metal ions
e.g., ions of Zn1 , Mo, Mg, Mn
Draw electrons away from substrate (stress chemical bonds)
Non-protein organic molecules (coenzymes)
E.g., NAD+ , NADP+ , etc.
Major role in oxidation/reduction reactions by donating or accepting electrons
http://en.wikibooks.org/wiki/Zinc
45
Energy and Metabolism
11.6 ATP
Adenosine triphosphate
Major energy currency of cells, power endergonic reactions
Stores energy in phosphate bonds
Highly negative charges, repel each other
Makes these covalent bonds unstable
Low activation energy
When bonds break, energy is transferred
ATP ADP + Pi + 7.3 kcal/mole
11.7 Biochemical pathways

Metabolism: sum of chemical reactions in cell/organism
Many anabolic and catabolic reactions occur in sequences (biochemical pathways)
Often highly regulated
Evolution of biochemical pathways
Protobionts or 1st cells likely used energy rich substrates from environment
Upon depletion of a substrate, selection would favor catalyst which converts another
molecule into the depleted molecule
By iteration, pathway evolved backward
This text is based on notes very generously donated by Paul Doerder, Ph.D., of the Cleveland
State University.
46
12 Respiration: harvesting of energy

Glucose + O2 CO2 + H2 O + ATP
12.1 Energy
Energy is primarily in C-H bonds (C-O too)
Chemical energy drives metabolism
Autotrophs: harvest energy through photosynthesis or related process (plants, algae,
some bacteria)
Heterotrophs: live on energy produced by autotrophs (most bacteria and protists,
fungi, animals)
Digestion: enzymatic breakdown of polymers into monomers
Catabolism: enzymatic harvesting of energy
Respiration: harvesting of high energy electrons from glucose
12.2 Respiration
Transfer of energy from high energy electrons of glucose to ATP
Energy depleted electron (with associated H+ ) is donated to acceptor molecule
Aerobic respiration: oxygen accepts electrons, forms water
Anaerobic respiration: inorganic molecule accepts hydrogen/electron
Fermentation: organic molecule accepts hydrogen/electron
12.3 Respiration of glucose
C6 H12 O6 + 6 O2 6 CO2 + 6 H2 O + energy

G = -720 kcal/mole under cellular conditions
Largely from the 6 C-H bonds
Same energy whether burned or catabolized
In cells, some energy produces heat, most is transferred to ATP
12.4 Alternative anaerobic respiration

Methanogens (Archaebacteria).
CO2 is electron acceptor, forming CH4
47
Respiration: harvesting of energy

Sulfur bacteria
SO4 reduced to H2 S
Formation of H2 S set stage for evolution of photosynthesis (H2 S as electron donor
before H2 O)
About 2.7 by, based on ratio of 32S/34S, where only biological processes produce 32S
enrichment
12.5 Glycolysis overview

Glycolysis accounting
Oxidation
Two electrons (one proton) are transferred from each G3P to NAD+ forming NADH
2NADH
Substrate level phosphorylation
G3P to pyruvate forms 2 ATP molecules
4 ATP (from 2 G3P)
2 ATP (priming)
2 ATP (net gain)
Summary: The net input of glycolysis is 2 ATP molecules which are used to split one glucose
molecule. The net yield of this step is 2 ATP and 2 pyruvate.
12.6 Regeneration of NAD+

Reduction of NAD+ to NADH can deplete NAD+ supply; it must be regenerated
Two pathways, coupled to fate of pyruvate
With oxygen: enter electron transport chain, forming water (and ATP)
Without oxygen: fermentation
lactate
ethanol
12.7 Alcohol fermentation

12.8 Lactate formation
Either lactic acid1 or alcohol can be formed as a result of anaerobic respiration in cells.
1
48
http://en.wikipedia.org/wiki/Lactate
Krebs cycle: overview
12.9 Krebs cycle: overview

Matrix of mitochondrion
Priming steps
Joining of acetyl-CoA to oxaloacetate
Isomerization reactions
Energy extraction steps in Krebs cycle
Per glucose
6 NADH
2 FADH2
2 ATP (from GTP)
4 CO2
12.10 ATP production

Chemiosmosis (Mitchell)
H+ (from NADH and FADH2 ) is pumped against a gradient into the intermembranal
space of the mitochondrion (creates voltage potential)
Diffusion back into matrix through ATP synthase channels drives synthesis of ATP (ADP
+ Pi ATP)
ATP exits mitochondrion by facilitated transport
12.11 Evolution of aerobic respiration

Preceded by evolution of photosynthesis (O2 needed; also, prior evolution of electron
transport and chemiosmosis)
High efficiency of ATP production compared to glycolysis
Fostered evolution of heterotrophs
Fostered evolution of mitochondria by endosymbiosis in eukaryotes
49
13 Photosynthesis
6 CO2 + 6 H2 O C6 H12 O6 + 6 O2
One of most important reactions in history of life:
source of atmospheric O2
ultimately led to aerobic respiration and eukaryotes
Responsible for bulk of glucose production
Early experiments showed that mass of plant must be derived from substances in the air,
not the soil
Experiments with isotopes showed that liberated oxygen comes from water
Experiments also showed that light is essential but that some reactions (e.g., reduction of
CO2 ) continue in the dark
Plants do two big, important things during photosynthesis: gain energy (absorb light)
and build sugar (glucose).
Photosynthesis can be divided into two series of chemical reactions: the light (lightdependent) reactions and the dark (light-independent) reactions. In light reactions, light
is absorbed; in dark reactions, sugar is built.
Occurs when plants, algae, and autotrophic bacteria absorb light energy and build glucose.
13.1 Light Reactions
Part of the electromagnetic spectrum

Consists of units of energy called photons
Photons at UV end of spectrum have more energy than those at the red end
Occur on the surface of thylakoid disks
Chlorophyll and other plant pigments differentially absorb photons
Chlorophyll a: light to chemical energy
Chlorophyll b: accessory chlorophyll
Chlorophylls absorb primarily blue and red (green reflected back, hence the green
color of plants)
13.1.1 Accessory pigments

Chlorophyll is a major light gathering pigment
Absorbs light with considerable efficiency (i.e., retaining energy)
Accessory pigments
Chlorophyll b
Carotenoinds
capture light of wavelengths not captured by chlorophylls
51
Photosynthesis
Confer other colors to plant leaves (autumn colors too)
Photosynthetic steps
Primary photoevent: light photon captured by photosystem and energy transferred to
electron donated by water
Electron transport: excited electron is shuttled along imbedded series of electron carriers
to proton pump and electron is transferred to acceptor
Chemiosmosis: transport of protons back into chloroplast drives synthesis of ATP
13.1.2 The Even More Detailed Light Reactions

What the Light Reactions Do:
The light reactions of photosynthesis occur in chloroplasts in and on the thylakoid disks.
During the light reactions, light energy charges up ATP molecules. More specifically, light
turns the chloroplast into an acid battery, and this battery charges up ATP.
How the "Chloroplast-Battery" Charges ATP:
The stroma is the fluid inside of the chloroplasts, and it carries a negative charge. This
means that it contains about a "gazillion" extra electrons. The solvent of stroma is water.
The fluid inside the thylakoid disks is positively charged because it contains a lot of hydrogen
(H+) ions. The pH here is low, making the fluid very acidic. The solvent of thylakoid disk
fluid is water.
A chloroplast acts like a battery, because it has separated a strong positive charge and a
strong negative charge in two different compartments. Energy is released when H+ ions
(free protons) flow from the inside of a thylakoid disk to the stroma. This is electrical energy,
since it is a flow of charged particles.
The protons pass through special channels (made of protein) in the thylakoid membrane;
this reaction is 'exothermic.' The energy that is given off is used to fuel this reaction (Pi is
the phosphate ion):
ADP + Pi --> ATP
The proton can go to the negative stroma, but only if it uses its energy to charge up ATP.
Since one reaction wants to go, and the other one doesn't, and since the first reaction releases
energy and the second one absorbs energy, the two reactions are known to be 'coupled'
together so that the first fuels the second. Of course, a special enzyme must be involved for
this to happen.
Chlorophyll Molecules on a Thylakoid Disk:
Hundreds of chlorophyll molecules cover the surface of a thylakoid disk, making the disk
green. The nonpolar "tails" of the chlorophyll molecule are embedded in the membrane of
the thylakoid.
52
Dark reactions
13.2 Dark reactions
ATP drives endergonic reactions

NADPH provides hydrogens for reduction of CO2 to carbohydrate (C-H bonds)
Occur in the stroma
First step in carbon fixation
13.2.1 The Detailed Dark Reactions

What the Dark Reactions Do:
The dark reactions build sugar from carbon dioxide gas (CO2), water (H2O), and energy
from ATP molecules that were charged up during the light reactions. The dark reactions
occur in the stroma of a chloroplast. Dark reactions usually occur in the light, but they
don't have to. They'll occur in the dark until the chloroplast's supply of ATP runs out
(usually about 30 seconds).
The Calvin Cycle:
The Calvin Cycle is the fancy name for the metabolic pathway that builds sugar. This
means that it involves a whole lot of chemical reactions, and it uses a lot of different enzymes
to catalyze the reactions.
Carbon dioxide gas is stable, therefore the bonds that hold the carbon and oxygen atoms
are strong. Therefore it takes a lot of energy to break the bonds and separate the carbon
atoms from the oxygen atoms. The energy needed to do this comes from ATP molecules.
When inorganic carbon (like from CO2) is being added to an organic molecule (such as
sugar), this is called carbon fixation.
It takes 2 complete turns of the Calvin Cycle to make a glucose molecule.
Some portions of this text is based on notes very generously donated by Paul Doerder, Ph.D.,
of the Cleveland State University. The detailed portions are not provided by Dr. Doerder.
How cells divide
13.3 Prokaryote cell division

Binary fission
Doubling of cell contents, including DNA
Fission to divide contents
Segregation of replicated genomes by growth of membrane between attachment points
Partitioning of cytoplasmic components
Escherichia coli
Capable of cell division every 20 minutes under optimal conditions (DNA in continuous
state of replication)
Model organism of bacterial cell division
53
Photosynthesis
13.4 Bacterial DNA replication

Replication follows rules of base pairing, with each polynucleotide chain serving as
template for synthesis of its complement.
Genetic evidence showed that the bacterial chromosome is circular long before there was
corroborating physical evidence.
Eukaryotic chromosomes
Discovered by Walther Fleming in 1882 in dividing cells of salamander larvae, following
improvements in microscopes and staining technology
He called division mitosis (mitos = thread)
Chromosome number is constant in a species
Ranges from 2 to >500 (46 in human somatic cells)
Homologous pairs, one contributed by each parent
Change in number is cause and consequence of speciation
Chromosome constancy and their precise division in mitosis and meiosis led biologists to
postulate that they were carriers of hereditary information
13.5 Chromosome number
1N = number of chromosomes in gamete

1N = haploid chromosome number
2N = number of chromosomes in somatic cells (cells that are not egg or sperm)
2N = diploid
Deviations from N or 2N are usually lethal in animals
Chromosome numbers
13.6 Eukaryotic chromosomes

Consist of chromatin
DNA and associated proteins, mainly histones
Nucleosomal organization
Euchromatin: unwound chromatin, in basic nucleosomal configuration; genes available
for expression
Heterochromatin: highly condensed except during replication
Karyotype: array of chromosomes an individual possesses
Clinical importance (Down syndrome; cancer)
Evolutionary importance (speciation)
54
Chromosome organization
13.7 Chromosome organization

13.8 Human karyotype stained by chromosome painting
13.9 Chromosomes
Homologous pairs
Inherited one from each parent
Identical in length and position of centromere
Contain identical or similar genes
Homologous pair = homologs
Morphology
After replication, consist of two sister chromatids attached to a centromere
13.10 Human chromosomes

Diploid number = 2n = 46 = 23 pairs of homologs
Haploid number = 23 (gametes)
Each replicated chromosome contains 2 sister chromatids = 92 chromatids
Cell cycle
Growth and division cycle of cells
Precisely controlled by biochemical and gene activity, except in cancer
Phases
G1: primary growth phase
S: DNA replication; chromosome replication
G2: second growth phase; preparation for mitosis
M: mitosis; nuclear division
C: cytoplasmic division
13.11 Mitotic cell cycle

Cells exiting the cell cycle are said to be in G0
Cell cycle time varies with stages of life cycle and development, with G1 the most variable
DNA replication occurs during S phase of the cell cycle following G1.
- at this point the chromosomes are composed of two sister
chromotids connected by a common centromere.
55
Photosynthesis
13.12 Replicated human chromosomes

13.13 Mitosis
Nuclear division
equational division of replicated chromosomes
chromatids move to opposite poles
Continuous process
prophase
metaphase
anaphase
telophase
Driven by motors and microtubules
No change in chromosome number
N N by mitosis
2N 2N by mitosis
May be accompanied by cytokinesis
Kinetochore Microtubules attach to kinetochores. Metaphase
Momentary alignment of chromosomes in center of cell
Anaphase
13.14 Plant mitosis

Similar to animal mitosis
New cell wall formed between cells from membrane partition
Cell cycle control
Cell cycle events are regulated by protein complexes and checkpoints
Discovered by microinjection of proteins in to eggs, by mutational analysis and by
techniques of molecular biology
Molecular control of cell cycle: Cdk and cyclin
Cyclin dependent protein kinase (Cdk)
Phosphorylate serine/threonine of target regulatory proteins
Function only when bound to cyclin
Cyclin: short-lived proteins that bind to cdks
13.15 Controlling the cell cycle

External signals initiate cell division in multicellular organisms
Growth factors: extracellular regulatory signals
Usually soluble; bind to cell surface receptor
56
Cancer
Sometimes membrane bound, requiring cell-cell contact with receptor
E.g., upon wound, platelets release PDGF which stimulates fibroblasts to enter cell
cycle (exit G0), to heal wound
13.16 Cancer
Unregulated cell proliferation
Cancer cells have numerous abnormalities
>46 chromosomes
Mutations in proto-oncogenes
Encode proteins stimulating the cell cycle
May be regulated by phosphorylation
Often over expressed in cancer cells
Mutations in tumor-suppressor genes
Encode proteins inhibiting the cell cycle
Often bind to products of proto-oncogenes
May be regulated by phosphorylation
13.17 Mutations and cancer

State University.
57
14 Sexual reproduction
14.1 Sexual
Exclusively eukaryotes
Fusion of two haploid genomes
Fertilization (= syngamy)
Forms new individuals in multicellular organisms as result of fusion of egg and sperm
Plants
Animals
Meiosis yields haploid genomes at some point in life cycle
14.2 Sexual life cycle

Typical animal life cycle
Meiosis occurs in germ line cells in gonads producing haploid gametes

All other cells are somatic cells
Alternation of generations
Sexual intercourse
14.3 Meiosis
Gives rise to genetic variation

Reduction division: 2n to n
Preceded by one round of DNA (chromosome) replication
Two rounds of nuclear (& usually cell) division
Meiosis I
Synapsis of homologs
Segregation of homologs
Reduction division, 2n to n
Meiosis II
No chromosome replication
Segregation of sister chromatids
Formation of 4 haploid (n) cells
Two nuclear divisions, usually 2 cell divisions, only one round of replication
Meiosis I
Prophase: synapsis and crossing over
Metaphase
59
Sexual reproduction
Anaphase: chromosome segregation
Telophase
Meiosis II (mitosis-like)
Prophase
Metaphase
Anaphase: sister chromosome segregation
Telophase
14.4 Prophase I: synapsis
Complete alignment of replicated homologs

Synapsis occurs throughout the entire length of a pair of homologs
Key to chromosome segregation
Synapsis, crossing over
Subdivided into 5 continuous stages
14.5 Crossing over

Reciprocal, physical exchange between nonsister chromatids
Type of recombination; mixes maternal and paternal genes
Visual evidence: chiasmata
14.6 Microtubules and anaphase I

During prophase microtubules attach to kinetochores on one side of centromere
The metaphase checkpoint insures proper attachment
A phosphorylation event initiates motor activity and anaphase
14.7 Meiosis II
Cytologically similar to mitosis
No preceding DNA replication
Chromatids segregate and move to opposite poles as chromosomes
4 haploid cells produced
In animals, these cells differentiate into gametes
In plants and many other organisms, these cells divide by mitosis, followed some time
later by gamete formation
14.8 Evolution of sex

Asexual reproduction: all offspring genetically identical to parent
60
Consequences of sex
Sex: recombination destroys advantageous combinations
So why sex?
Many hypotheses
Effect repair of genetic damage?
Much pachytene repair as well as gene conversion
Some protists form diploid cells in response to stress
Recombination breaks up combinations of genes favoring parasites, thus reducing
parasitism?
14.9 Consequences of sex

Recombination: generates genetic diversity
Crossing over
Independent assortment
Random fertilization
Qualities of gamete usually do NOT reflect qualities of genes enclosed in gamete
State University.
61
15 Genetics
63
16 Gregor Mendel and biological

inheritance
Charles Darwin1 , for all he contributed to the science of biology, never knew about the
mechanism by which living things inherit traits from previous generations, or how new traits
arise.
As any schoolchild can tell you, this mechanism of interitance has since been found to be
DNA2 , or deoxyribonucleic acid. DNA allows for stable inheritance of traits: the code in
each strand of DNA is replicated precisely through the pairing of basic units along each
strand. The error rate in this replication is amazingly low; not even one base pair in a
million matches out of sequence.
However, when even one base pair is added to a new strain of DNA in an order differently
than in the parent chain, it can be the basis of a mutation. These changes in DNA sequences
are the microscopic origin of changes in traits of all studied living things. Even the smallest
difference in a strand of DNA can result in a change in traits that can cost the life of the
organism. Mutations can produce proteins with a new or altered function. In humans, the
example of Sickle cell anemia3 is commonly given as its origin is a difference of only one
base pair in a section of DNA that encodes red blood cells.
Individual sequences of DNA that encode for specific proteins are called genes and are the
units of heredity. Each one has a set nucleotide4 , and together all of the genes (and some
sequence of DNA that apparently do not code for any biologically important functions)
together make up the entire chromosome5
16.1 Mendel
Discovered principle of genetic segregation via numerous experiments utilizing pea plants
Inferred the existence of genes through segregation of phenotypes
Used quantitative methods: counted; ratios
Work is model of scientific method
In particular, observed the F2 progeny, which lead to the discovery of dominant and
recessive traits
Published work in 1866, went unnoticed
In 1900 his scientific paper was rediscovered
1
2
3
4
5
http://en.wikibooks.org/wiki/Charles%20Darwin
http://en.wikipedia.org/wiki/Sickle%20cell%20anaemia
http://en.wikipedia.org/wiki/nucleotide
http://en.wikipedia.org/wiki/chromosome
65
Gregor Mendel and biological inheritance

Mendel is acknowledged as founder of Genetics
still used alphabet letters to designate genes
still refer to dominant and recessive genes
still refer to segregation of alleles in meiosis
principle of segregation applies to all sexually reproducing organisms; Mendels results
were immediately applied to humans in 1900
16.2 Mendels experiments
1856, began experiments with the garden pea, Pisum sativum

1865, presented results to the Bruno natural history society, which he helped found
1866, published his results in proceedings of the society
Naegeli encouraged Mendel to reproduce results in another species, which failed because
the species did not undergo true fertilization
discrete traits in Pisum sativum
pure-breeding lines
dominant/recessive alleles
alleles are two alternate versions of a gene
gametes contain hybridized chromosomes that are formed during meiosis
homozygous has two of the same allele
heterozygous has two different alleles
reciprocal F1 crosses (all exhibiting dominant phenotypes); F2; F3
counted offspring, noted ratios
inferred genotypes from phenotypes
tested hypotheses with testcrosses
attempted to repeat with another species
16.3 Mendels seven pairs of traits

1.
2.
3.
4.
5.
6.
7.
Seed form (round or wrinkled)

Cotyledon color (green or yellow)
Seed coat color (white or colored)
Pod form (inflated or constricted)
Pod color (green or yellow)
Flower position (axial or terminal)
Plant heights (tall or short)
16.4 Locus
The location of a specific gene within a chromosome
66
Modern Y chromosome
16.5 Modern Y chromosome

Y-chromosome is the most evolved chromosome. Generally it is thought that if Y- chromosome is present in an individual then he will be male. But if mutation occurs at sex
determining region or zinc factor then it will not code for testis determining factor, and
results in normal female. This type of female's frequency is 1/250000.
16.6 Chromosome phenomena

X-chromosome inactivation
Barr bodies
Nondisjunction: failure of chromosome segregation at meiosis or mitosis
Results in 2N 1 chromosome number
Trisomy 2N + 1
Usually lethal. Trisomy 21 (Down) exception
Monosomy 2N ** 1
Lethal except XO
Usually maternal origin in humans
16.7 X-chromosome inactivation

In females, one X-chromosone is randomly switched off forming a Barr body.
16.8 Barr body

Dense region in the nucleus formed by the inactive X-chromosome.
16.9 Human genetic disorders

Down's Syndrome(Mongolism)
Down's Syndrome is usually produced by the nondisjunction of chromosome 21 during
oogenesis and sometimes during spermatogenesis. The individual suffering from this type of
syndrome has 47 chromosomes instead of the normal 46. The extra chromosome is not a sex
chromosome but an autosome.
Most cases of mongolism were found to occur in children born by women in their forties.
The affected children, called mongoloids, show mental retardation and have a shorter life
expectancy. Their most prominent feature is the Mongolian folds in their eyes; hence, the
term mongolism.
Klinefelter's Syndrome
67
Gregor Mendel and biological inheritance

When an XY-bearing sperm unites with an X-bearing egg, the resulting condition is called
Klinefelter's Syndrome, or sexually undeveloped male. Individuals having the syndrome
show the following characteristics:
testes are small

sperms are never produced
breasts are enlarged
body hair is sparse
individuals are mentally defective
The same abnormal meiotic division may occur in females. They produce eggs with XX or
no sex chromosomes. Such egg, when fertilized by a Y-bearing sperm, will not develop (YO).
This is because YO is lethal--it wil cause death to the offspring.
68
17 DNA: The Genetic Material

17.1 DNA
DNA stands for Deoxyribose Nucleic Acid. That is, a nucleic acid with two sugars. DNA is
the hereditary material of cells and is considered the blueprint of life. DNA is found in all
kingdoms of life. Even most viruses have DNA. A molecule of DNA is chemically stable (it
does not have a 2-prime alcohol group.)
When someone says DNA, they may be referring to one's genetic material on multiple levels:
They may be speaking about a single deoxyribose nucleic acid molecule, a section of a double
helix, a section of a chromosome, or one's entire hereditary composition.
antiparallel
Double helix
Semiconservative replication
Sequence of nucleotides encodes functional RNA or polypeptide
17.2 Historical perspective

Mitosis and meiosis
Regular distribution of chromosomes suggested that they contain hereditary information
Bridges/Morgan, using Drosophila melanogaster showed that genes are on chromosomes
(1910s)
Hammerling: nucleus contains hereditary information (1930s)
Griffith: transformation of bacteria (1928)
Avery, MacLeod, McCarty: transforming substance is DNA (1944)
Hershey, Chase: DNA is hereditary material of viruses (1952)
Rosalind Franklin
Watson and Crick: structure of DNA (1953)
17.3 Hershey-Chase Experiment

The Hershey and Chase experiment was one of the leading suggestions that DNA was a
genetic material. Hershey and Chase used phages, or viruses, to implant their own DNA
into a bacterium. They did two experiments marking either the DNA in the phage with
a radioactive phophorus or the protein of the phage with radioactive sulfur. With the
bacteria that was infected by the phages with radioactive DNA the DNA in the bacteria
69
DNA: The Genetic Material

was radioactive. In the bacteria that was infected with the radioactive protein the bacteria
was radioactive, not the DNA. This proves that DNA is a genetic material and it is passed
on in viruses.
17.4 DNA/RNA components

Miescher: discovered DNA, 1869
17.4.1 Structure of DNA

DNA is in a double helix structure made up of nucleotides. The "backbone" of the double
helix is composed of phosphates connected to a five carbon sugar called deoxyribose, . The
"rungs" are composed of nitrogenous bases, Purines and Pyrimidines. Purines contain
Adenine(A) and Guanine(G) and have two rings in their structures. Pyrimidines contain
Cytosine(C) and Thymine (T) and have one ring in their structures.
17.5 Chemical structure of DNA

Polynucleotide
Phosphodiester bonds between nucleotides
5-pGpTpCpGpTpApApTp-OH 3
Chargaffs rules, in DNA: equimolar amounts
A=T
G=C
17.6 3D structure of DNA

James Watson1 and Francis Crick2 ( 19533 )
Nucleotide
Keto and amino forms of bases
Chargaffs rules
X-ray crystallographic data ( Rosalind Franklin4 )
17.7 Franklin
X-ray diffraction of DNA crystals
revealed regular pattern explained by antiparallel double helix
1
2
3
4
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http://en.wikipedia.org/wiki/James_D._Watson
http://en.wikipedia.org/wiki/Francis_Crick
http://en.wikipedia.org/wiki/1953
http://en.wikipedia.org/wiki/Rosalind_Franklin
DNA replication
DNA model
Double helix of polynucleotides
antiparallel
3-5 phosphodiester bonds
Base pairs held by hydrogen bonds
AT
GC
There are about 10 base pairs per turn of helix
model has predictive power
mode of DNA replication
encoding of genetic information
17.8 DNA replication

Conservative model
One double helix of both old strands
One double helix of two new strands
Dispersed
Each strand mixture of old new
Semiconservative
Meselson-Stahl experiment confirmed its viability over the previous two
grew E. coli bacterium in a culture containing 15N (a heavy isotope of nitrogen)
bacterium assimilated the 15N into their DNA
a similar process was then done using 14N, a lighter isotope
following centrifugation, the densities were observed to be that of combined in the
middle, and 14N on top, thereby confirming the semiconservative model

Semiconservative
New nucleotides added to 3 OH
Replication fork
Replication complex
DNA polymerase
Associated enzymes/proteins
Energy from phosphate bonds of triphosphate nucleotide substrates (dNTP)
17.10 DNA polymerases

Prokaryotes, E. coli
3 DNA polymerases
III is main enzyme for DNA replication
1000 nt/sec
71
DNA: The Genetic Material

Eukaryotes
6 DNA polymerases
Add nucleotide to 3 OH end
All require primer, i.e., free 3 OH
17.11 DNA replication complex
Helicase "unzips" the DNA double helix

Primase: synthesize RNA primer
Single-strand binding proteins
DNA gyrase (topoisomerase)
DNA polymerase III

DNA polymerase I (remove primer, fill gaps)

5 3 replication
Nucleotide addition at 3 OH
No exceptions
New strands are oriented in opposite direction due to 5 3 constraint
Leading strand: continuous replication
Lagging strand: discontinuous replication
contains multiple Okazaki fragments
Joined by DNA ligase
17.13 DNA replication fork

primer required by all DNA polymerases
17.14 Replication units

17.15 Replicon
A region of DNA that is replicated from a single origin.
17.16 What is gene?

Garrod
inborn errors of metabolism
Alkaptonuria: enzyme deficiency
72
What is gene?
Beadle and Tatum
One gene one enzyme
Genetic and biochemical analysis in Neurospora
Today: gene is sequence of nucleotides encoding functional RNA molecule or the amino
acid sequence of a polypeptide
State University.
73
18 Gene expression
Flow of genetic information
DNA mRNA polypeptide
Transcription: DNA mRNA
RNA polymerase
Nucleus in eukaryotes
Transcription also makes rRNA and tRNA
Translation: mRNA polypeptide
Ribosomes: protein and rRNA
Genetic code and tRNA
18.1 Central Dogma

18.2 The Genetic Code
Triplet codon
64 triplet codons (43)
Experimentally deciphered in 1961
Nearly universal
Implies common ancestor to all living things
Minor exceptions: certain ciliates, mitochondria, chloroplasts
Still evolving
18.3 Transcription
RNA polymerase
NTP substrates
Synthesizes single stranded RNA complementary to template strand of DNA
New nucleotides to 3 end
Begins at promoter site
no primer necessary
Ends at terminator site
Much posttranscriptional modification in eukaryotes
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Gene expression
18.4 Transcription bubble

Promoter site
Prokaryotes
-10 nt, TATA box
-35 nt, additional signal
Eukayotes
-25, TATAAA box
Additional signals upstream
Promoters may be strong or weak
In eukaryotes, access to promoter depends upon state of chromatin coiling
18.5 Eukaryote mRNA

Synthesized as pre-mRNA, processed in nucleus
5 end: GTP cap placed in inverted position
Essential for ribosome recognition
3 end: poly-A tail; non-templated addition of 50-250 A nucleotides; stability
Introns: intervening sequences removed
18.6 Translation
Requires:
mRNA
tRNA
ribosomes
translation factors (various proteins)
In prokaryotes, takes place on growing mRNA
In eukaryotes, in cytoplasm on free ribosomes and RER
AUG start codon to stop codon
18.7 Translation in bacteria

tRNA
Transfer RNA
Two important parts
Anticodon
Hydrogen bonds with mRNA codon
3 end
Accepts amino acid (using energy of ATP)
Aminoacyl-tRNA synthetase
76
Aminoacyl tRNA synthase
18.8 Aminoacyl tRNA synthase

Enzyme used to bind amino acid from the cytoplasm to tRNA, which then transfers that
amino acid to the ribosome for polypeptide formation
18.9 Ribosome structure

18.10 Large ribosome subunit
18.11 Translation
Initiation complex
Small ribosomal subunit
mRNA
fMet-tRNA (prokaryotes only; met-tRNA in eukaryotes)
Initiation factors
Elongation
Ribosome
mRNA
tRNAs
Elongation factors
18.12 Initiation complex

18.13 Elongation, translocation
incoming tRNA enters the A site
rRNA catalyzes peptide bond formation. Note that growing peptide is attached to what
was incoming tRNA at P site after translocation.
empty tRNA leaves via E site; recycled
A site ready for next charged tRNA
18.14 Introns/exons
In eukaryotes, coding regions of gene may be interrupted by introns, noncoding regions
of DNA (RNA)
Introns
22- >10,000 nt in length
5 GU . . . 3 AG removal sequence
Not essential to genes
May constitute >90% of gene
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Gene expression
removed from pre-mRNA to form mRNA
Exon: often codes for functional domain of protein
translatable mRNA
State University.
78
19 Gene regulation
Not all genes are expressed in a cell
Gene expression can be turned on and off
Multiple levels of regulation gene function
Transcription initiation
State of chromatin
Transcription factors
Post-transcriptional
mRNA processing
mRNA half-life
Translational
Post-translational
Protein modification
19.1 Transcriptional control

State of chromatin
Euchromatin: transcriptionally active
Heterochromatin: transcriptionally inactive
Chemical modification of histones
Methylation of bases
Transcription factors
Bind to DNA at promoter or other regulatory sites (enhancers)
Recognize base sequence through major and minor grooves
Recruit RNA polymerase
19.2 DNA grooves

Categories of transcription factors in eukaryotes
Helix-turn-helix
Two small "-helices
Fit into DNA groove
Homeodomain
Highly conserved helical domains
60 amino acids
Zinc finger motif
Zn atom bound
Leucine zipper
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Gene regulation
dimer
19.3 Regulatory proteins

Activity may depend upon allosteric binding of small molecules
cAMP
Co-repressors
Inhibitors
Binding to promoter region may bend DNA, making it accessible to other regulatory
proteins
19.4 Lac operon of E. coli
Single promoter region for cluster of genes

Regulated and transcribed as a single unit
Operons typical in prokaryotes
Repressor: turns OFF gene expression
lac repressor
Turns off transcription by blocking access by RNA polymerase
repressor in activated by allosteric binding of lactose
Regulation in eukaryotes
Both proximal (promoter) and distal (enhancer) to gene
Typically transcription unit encodes a single polypeptide
Promoter
TATA box
Other elements (regulatory sequences) may be present
Enhancers
Work upstream, downstream, close, far from gene
Bend DNA
19.5 Alternative splicing

Single transcript gives rise to 2 or more mature mRNAs
encode different polypeptides with shared domains
tissue and developmentally specific
State University.
(This Page was Last Edited December 2005)
80
20 Mutation
A mutation is a permanent change to an organism's genetic material (DNA1 or RNA).
Mutations are a rare but significant biological process, since they provide the variation on
which evolution2 acts and are also the source of cancer.
An organism's genetic material is made up of polymers (chains) of four different nucleotides3 ,
like a recipe book written in a language of only four letters. A mutation event is when the
order of the nucleotides in DNA change, usually when the DNA is being copied.
Mutations come in a number of forms:
20.1 Point Mutations

Point mutations are all mutations which involve a single nucleotide. These come in the form
of substitutions, insertions and deletions:
20.2 Substitution
Substitution Mutations: In substitution mutations, a nitrogenous base of a triplet codon of
DNA is replaced by another nitrogen base or some derivative of the nitrogen base, changing
the codon. The altered codon codes for a different amino acid substitution.The substitution
mutations are of two types:
1.Transitions: It is the replacement of one purine in a polynucleotide chain by another
purine(A by G or C by A) or one pyrimidine by another pyrimidine(T by C or C by T)
2.Transversions:A base pair substitution involving the substitution of a purine by pyrimidine
or pyrimidine by a purine is called transversion.
1
2
3
http://en.wikibooks.org/wiki/General%20Biology%2FEvolution
http://en.wikipedia.org/wiki/nucleotide
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Mutation
20.2.1 Insertion
20.2.2 Deletion
20.3 Larger mutations

Larger mutations which involve more than one nucleotide also include insertions and deletions,
but can also include inversions, rearrangement of nucleotides and duplication of entire genes:
20.3.1 Inversion
20.3.2 Rearrangement
20.3.3 Gene/Exon Duplications
Transposition
Retrotransposition
20.4 Chromosomal mutations

Chromosomal mutations involve changes to entire chromosomes. These mutations are
particularly rare:
20.4.1 Translocation
20.4.2 Fusion
20.4.3 Fission
20.4.4 Segmental Duplication
20.4.5 Chromosomal Duplication
20.4.6 Genome Duplication
20.5 Causes of mutations

20.6 Effects of mutations
Mutations can have a variety of different effects depending on the type of mutation, the
significance of the piece of genetic material affected and whether the cells affected are germ-
82
Further reading
line cells. Only mutations in germ-line cells can be passed on to children, while mutations
elsewhere can cause cell-death or cancer.
Mutations can be classified by their effects:
20.6.1 Silent Mutation

Silent Mutations are DNA mutations that do not result in a change to the amino acid
sequence or a protein. They may occur in a non-coding region (outside of a gene or within
an intron), or they may occur within an exon in a manner that does not alter the final
amino acid chain.
20.6.2 Frameshift
20.6.3 Missense Mutation
Missense mutations are types of point mutations where a single nucleotide is changed to
cause substitution of a different amino acid. This in turn can render the resulting protein
nonfunctional. Such mutations are responsible for diseases such as Epidermolysis bullosa.
20.6.4 Nonsense Mutation
20.7 Further reading

20.7.1 Books
Jones, S. 1993. The Language of the Genes. Harper Collins ISBN 0006552439.
20.7.2 Websites
Wikipedia: Mutation4
http://www.evowiki.org/Mutation
20.8 Original notes

Rare change in nucleotide sequence
Somatic vs germline
only those in germline are heritable
Point mutation
Single nucleotide change
Change in gene position
http://en.wikipedia.org/wiki/Mutation
83
Mutation
Transposition
Chromosomal rearrangement
Mutagenic agents
Raw material for evolutionary change
20.9 Point mutation

Ionizing radiation
UV light induces thymine dimers
Reparable
Error during DNA synthesis
Movement of transposons
McClintock
Chemical mutagens
May alter
Properties of promoter, enhancer
Amino acid sequence of polypeptide
20.10 Acquisition of genetic variability

Mutation
Sex (fusion of genomes)
Recombination
Crossing over
Reciprocal (may result in gene conversion)
Unequal (gives rise to gene families)
Independent segregation
Transposition by transposons
Conjugation in bacteria
One way transfer from donor to recipient
20.11 Eukaryote genome

Thousands of transposons
Millions of transposon derived elements
LINES, SINES
Above may constitute largest portion of genome
Pseudogenes
Tandem clusters (rRNA genes; nucleolus)
Multigene families
Single-copy genes (one copy per 1n)
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Barbara McClintock
20.12 Barbara McClintock

Discovered transposons in perhaps greatest and ultimately most important intellectual
endeavors in genetics
Maize
Worked alone
Transposons: likely responsible for considerable evolution in eukaryotic genomes
Likely origin of viruses
State University.
85
21 Recombinant DNA technology

Revolutionized modern biology
Ability to manipulate genes in vitro
Hybrid genes, including combining genes of different species
Detailed study of gene function
Determine nucleotide sequences of genes and their regulators (deduce amino acid
sequences of proteins)
Genome projects: complete nucleotide sequence of >40 genomes, including human
Made possible by convergence of:
discovery of restriction enzymes
genetics of bacteria and their plasmids
21.1 Recombinant DNA technology

Uses
Detailed study of gene function
Homeostasis, response to stress
Development (birth defects)
Evolution of genes informs on evolution of life
Human betterment
Medicine
Identification, treatment of genetic disorders
Molecular medicine: from deduced amino acid sequences, design better drugs
Foods
Improve crop yield, resistance to disease
Improve nutritional value
Forensics
DNA fingerprinting: guilt or innocence
21.2 Restriction endonucleases

Originally found in bacteria to prevent invasion of viral DNA, cuts double stranded DNA
that is unmethylated, will not cut newly synthesized DNA since hemi-methylated, a product
of semi-conservative replication of DNA
sever phosphodiester bonds of both polynucleotide strands in order to combine foreign
DNA
create restriction fragments (restriction digestion)
5 phosphate and 3 OH at ends
87
Recombinant DNA technology

usually nucleotide specific target sequence
4-6 bp most common, the more bases, then the more specific for recombination
cuts in or near sequence
ends
sticky=overhanging ends, 5 or 3
blunt ends - straight cut, will anneal with any other blunt end in the presence of high
ligase
Hundreds of know restriction endonucleases, usually named after the bacteria that it was
found in
e.g. EcoR1, Alu1, BAM, HIND3
21.3 Restriction endonucleases

Gene cloning
Cloning:
Restriction digestion of DNA
insertion of restriction fragment into cloning vector
Bacterial plasmid
Bacterial virus
Yeast artificial chromosomes
Transformation of bacteria with recombinant plasmid, virus
Screening for clone of interest by using reporter genes or resistance upon exposure to
anti-biotic
21.4 Uses of cloned gene

Determine nucleotide sequence and deduce amino acid sequence from genetic code
Submit to GenBank (available on WWW)
Manipulate gene to study function
In vitro
In vivo
Transgenic (recombinant) organisms
Knockout organisms
Medical and commercial uses
21.5 Other molecular procedures

Polymerase chain reaction (Mullis)
Amplifies target DNA without cloning
Target amount can be single molecule
Amplified DNA can be sequenced, cloned, etc.
Southern blotting
Used to identify restriction fragments carrying particular gene
88
RFLP(restriction fragment length polymorphism) analysis

Also used for DNA fingerprinting and RFLP analysis
cDNA construction
Reverse transcription from mRNA template
21.6 RFLP(restriction fragment length polymorphism)

analysis
Basis of DNA fingerprinting using SNP - single nucleotide polymorphisms and repeats of
DNA sequence
Many uses
Criminal cases using multiple probes
Parentage
Species identification
Gene evolution
Species evolution
21.7 Sanger DNA sequencing

Uses dideoxynucleotides (ddNTP), a template strand, DNA polymerase 1 (Also known
as Kornberg enzymes) and dNTPs
Missing 3-OH for nulceopjilic attack for elongation
DNA synthesis stops after one is incorporated into DNA fragment
ratio of ddNTP to dNTP determines likelihood of termination
Manual method with 32P-labeled ddATP and 4 test tubes - ddATP, ddCTP, ddGTP,
ddTTP
Automated method using ddNTPs labeled with fluorescent dyes in capillary tube
Often done commercially
21.8 Automated sequencing

Typical machine
2 hour sequencing run
600-1000 bases per sample
multiple samples
Up to 500,000 bases per day (12 hr)
Data processed by computer
In big labs, sequencing reactions also are automated
21.9 Genome projects

Determine entire nucleotide sequence of genome
89
Recombinant DNA technology

>40 genomes sequenced
Helicobacter pylori
Escherichia coli
Saccharomyces cerevisiae
Caenorhabditis elegans
Drosophila melanogaster
Homo sapiens (first rough draft)
Computer identifies all genes, based on properties of genes (e.g., start/stop codons,
introns, etc.).
21.10 Biochips
Microarray of DNA fragments, size of postage stamp; can be expensive, but has decreased
in cost
Microarray chips contain wells of DNA that code for specific genes that uses the concept of
hybridization with the gene of interest to see if a gene is expressed or is present.
Designed to detect:
mutated genes (SNPs)
expressed genes
Instant DNA profile (GATTACA)
21.11 DNA chip controversies

Medicine
Risks and informed consent for gene replacement therapy
Alteration of human gene pool
Parental choice
Privacy
Genetically modified foods
Safety
Labeling
Forensics
Mandatory tests
Reliability standards
21.12 Gene patenting

Techniques to study and manipulate genes are patented (e.g., cloning and PCR)
Should genes be patented?
Are they the intellectual property of the discoverer?
Dont they belong to all of us?
Should indigenous peoples be compensated for useful genes extracted from their local
plants and fungi?
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Stem cells
21.13 Stem cells

Totipotent cells from early embryo
grow into any tissue or cell type
Recombinant genes can be introduced
Considerable use in analyzing gene expression in mice
Possible therapeutic use in humans
Very controversial
State University.
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22 Classification of Living Things

22.0.1 Classification of Living Things & Naming
With so many flora and fauna on planet Earth, there must be a method to classify each
organism to distinguish it from others so it can be correctly identified. Classification does
not only apply to biology. For example, supermarkets and grocery stores organise their
products by classifying them. Beverages may occupy one aisle, while cleaning supplies may
occupy another. In science, the practice of classifying organisms is called taxonomy (Taxis
means arrangement and nomos means law). The modern taxonomic system was developed
by the Swedish botanist Carolus (Carl) Linneaeus (1707-1788). He used simple physical
characteristics of organisms to identify and differentiate between different species.
Linneaeus developed a hierarchy of groups for taxonomy. To distinguish different levels of
similarity, each classifying group, called taxon (pl. taxa) is subdivided into other groups.
To remember the order, it is helpful to use a mnemonic device. The taxa in hierarchical
order:
Domain - Archea, Eubacteria, Eukaryote

Kingdom - Plants, Animals, Fungi, Protists, Eubacteria (Monera), Archaebacteria
Phylum
Class
Order
Family
Genus
Species
The domain is the broadest category, while species is the most specific category available.
The taxon Domain was only introduced in 1990 by Carl Woese, as scientists reorganise
things based on new discoveries and information. For example, the European Hare would
be classified as follows:
Eukaryote --> Animal --> Chordata --> Mammalia --> Lagomorpha --> Leporidae -->
Lepus --> Lepus europaeus.
Binomial nomenclature is used to name an organism, where the first word beginning
with a capital is the genus of the organism and the second word beginning with lower-case
letter is the species of the organism. The name must be in italics and in Latin, which was
the major language of arts and sciences in the 18th century. The scientific name can be also
abbreviated, where the genus is shortened to only its first letter followed by a period. In our
example, Lepus europaeus would become L. europaeus'.
Taxonomy and binomial nomenclature are both specific methods of classifying an organism.
They help to eliminate problems, such as mistaken identity and false assumptions, caused
by common names. An example of the former is the fact that a North American robin is
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Classification of Living Things

quite different from the English robin. An example of the latter is the comparison between
crayfish and catfish, where one might believe that they both are fish when in fact, they are
quite different.
Nomenclature is concerned with the assignment of names to taxonomic groups in agreement
with published rules.
22.0.2 Eukaryotes & Prokaryotes

Recall that there are two basic types of cells: eukaryotes and prokaryotes.
Eukaryotes are more complex in structure, with nuclei and membrane-bound organelles.
Some characteristics of eukaryotes are:
Large (100 - 1000 m)

DNA in nucleus, bounded by membrane
Genome consists of several chromosomes.
Sexual reproduction common, by mitosis and meiosis
Mitochondria and other organelles present
Most forms are multicellular
Aerobic
Prokaryotes refer to the smallest and simplest type of cells, without a true nucleus and no
membrane-bound organelles. Bacteria fall under this category. Some characteristics:
Small (1-10 m)
DNA circular, unbounded
Genome consists of single chromosome.
Asexual reproduction common, not by mitosis or meiosis.
No general organelles
Most forms are singular
Anaerobic
22.0.3 The Three Domains

The three domains are organised based on the difference between eukaryotes and prokaryotes.
Today's living prokaryotes are extremely diverse and different from eukaryotes. This fact has
been proven by molecular biological studies (e.g. of RNA structure) with modern technology.
The three domains are as follows:
Archea (Archeabacteria) consists of archeabacteria, bacteria which live in extreme
environments. The kingdom Archaea belongs to this domain.
Eubacteria consists of more typical bacteria found in everyday life. The kingdom Eubacteria
belongs to this domain.
Eukaryote encompasses most of the world's visible living things. The kingdoms Protista,
Fungi, Plantae, and Animalia fall under this category.
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Stem cells
22.0.4 The Six Kingdoms

Under the three domains are six kingdoms in taxonomy. The first two, Plants and Animals,
are commonly understood and will not be expounded here.
Protista, the third kingdom, was introduced by the German biologist Ernst Haeckel in
1866 to classify micro-organisms which are neither animals nor plants. Since protists are
quite irregular, this kingdom is the least understood and the genetic similarities between
organisms in this kingdom are largely unknown. For example, some protists can exhibit
properties of both animals and plants.
Fungi are organisms which obtain food by absorbing materials in their bodies. Mushrooms
and moulds belong in this kingdom. Originally, they were part of the plant kingdom but
were recategorised when they were discovered not to photosynthesise.
Eubacteria are bacteria, made up of small cells, which differ in appearance from the
organisms in the above kingdoms. They lack a nucleus and cell organelles. They have cell
walls made of peptidoglycan.
Archae (or Archaebacteria) are bacteria which live in extreme environments, such as
salt lakes or hot, acidic springs. These bacteria are in their own category as detailed studies
have shown that they have unique properties and features (ex. unusual lipids that are not
found in any other organism)which differ them from other bacteria and which allow them to
live where they live. Their cell walls lack peptidoglycan.
22.0.5 Origins of Diversity

The diversity in our planet is attributed to diversity within a species. As the world changed
in climate and in geography as time passed, the characteristics of species diverged so much
that new species were formed. This process, by which new species evolve, was first described
by British naturalist Charles Darwin as natural selection.
For an organism to change, genetic mutations must occur. At times, genetic mutations are
accidental, as in the case of prokaryotes when they undergo asexual reproduction. For most
eukaryotes, genetic mutations occur through sexual reproduction, where meiosis produces
haploid gametes from the original parent cells. The fusion of these haploid gametes into
a diploid zygote results in genetic variation in each generation. Over time, with enough
arrangement of genes and traits, new species are produced. Sexual reproduction creates an
immense potential of genetic variety.
One goal of taxonomy is to determine the evolutionary history of organisms. This can be
achieved by comparing species living today with species in the past. The comparison in
anatomy and structure is based on data from development, physical anatomy, biochemistry,
DNA, behaviour, and ecological preferences. The following are examples of how such data is
used:
Anatomy:
Although a horse and a human may look different, there is evidence that their arm structures
are quite similar. Their arms' sizes and proportions may be different, but the anatomical
structures are quite similar. Such evidence reveals that animals in different taxa may not
95

be that different. Biological features from a common evolutionary origin are known as
homologous.
Development
Biochemistry:
Biochemical analysis of animals similar in appearance have yielded surprising results. For
example, although guinea pigs were once considered to be rodents, like mice, biochemistry
led them to be in their taxon of their own.
22.0.6 Phylogeny, Cladistics & Cladogram

Modern taxonomy is based on many hypotheses' of the evolutionary history of organisms,
known as phylogeny. As with the Scientific Method, scientists develop a hypothesis on the
history of an animal and utilise modern science and technology to prove the phylogeny.
Cladistics is a classification system which is based on phylogeny. Expanding on phylogeny,
cladistics is based on the assumption that each group of related species has one common
ancestor and would therefore retain some ancestral characteristics. Moreover, as these
related species evolve and diverge from their common ancestor, they would develop unique
characteristics. Such characteristics are known as derived characteristics
The principles of phylogeny and cladistics can be expressed visually as a cladogram,
a branching diagram which acts as a family (phylogenetic) tree for similar species. A
cladogram can also be used to test alternative hypotheses for an animal's phylogeny. In
order to determine the most likely cladogram, the derived characteristics of similar species
are matched and analysed.
22.0.7 Classification of Living Things Practice Questions

1. If taxonomists had to select an existing kingdom to reclassify, which of the six would
most likely be chosen? Why?
2. Complete the following without consulting external sources:
a) The species caudatum is in the family Paramecidae. What would be the binomial name
of this organism?
b) Give the abbreviation of the binomial name.
3.
a) Irish moss belongs to the genus Chondrus. The name for this species is crispus. Give the
binomial name.
b) Give the abbreviation of the binomial name.
4. Humans and chimpanzees are alike. Which of the following data would most accurately
prove this correct?
a) biochemistry
96
Introduction
b) DNA
c) appearance
d) development
e) A, B, C
5. Which of the following is out of order?
a) Kingdom --> Phyllum --> Class
b) Class --> Family --> Order
c) Family --> Order --> Genus
d) Genus --> Species
e) A, C
f) A, B, D
g) B, C
6. A taxonomist discovers Organism A and Organism B and wishes to classify them. Which
of the following choices is the most informative?
a) Both organisms are brown.
b) Both organisms have a tail.
c) Both organisms have ears.
d) Both organisms are nocturnal.
7. DNA analysis is usually done using DNA found in a cell's mitochondria, and not in a
cell's nucleus. From your knowledge of mitosis, explain why this is so.
1. Arachbacteria 3.a) Chondrus crispus b) C. cripus 4. B 5. G 6. B
22.1 Introduction
Viruses are the smallest biological particle (the tiniest are only 20 nm in diameter). However,
they are not biological organisms so they are not classified in any kingdom of living things.
They do not have any organelles and cannot respire or perform metabolic functions. Viruses
are merely strands of DNA or RNA surrounded by a protective protein coat called a capsid.
Viruses only come to life when they have invaded a cell. Outside of a host cell, viruses are
completely inert.
Since first being identified in 1935, viruses have been classified into more than 160 major
groups. Viruses are classified based on their shape, replication properties, and the diseases
that they cause. Furthermore, the shape of a virus is determined by the type and arrangement
of proteins in its capsid. Viruses pathogenic to humans are currently classified into 21 groups.
Viruses can also attack bacteria and infect bacterial cells. Such viruses are called bacteriophages.
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22.2 Viral Replication

As previously stated, viruses are not a biological life form so they cannot reproduce by
themselves. They need to take over a functioning eukaryotic or prokaryotic cell to replicate
its DNA or RNA and to make protein coat for new virus particles.
In order to enter a cell, a virus must attach to a specific receptor site on the plasma membrane
of the host cell. The proteins on the surface of the virus act as keys which fit exactly into a
matching glycoprotein on the host cell membrane. In some viruses, the attachment protein
is not on the surface of the virus but is in the capsid or in the envelope.
There are two forms of viral replication: the lytic cycle and the lysogenic cycle.
22.2.1 Lytic Cycle

1. Attachment: The virus binds to specific receptors on the host cell.
2. Entry: There are two ways in which a virus can enter cells. Firstly, the virus can inject
its nucleic acid into the host cell. Secondly, if a virus is contained in an envelope, the
host cell can phagocytosise the entire virus particle into a vacuole. When the virus
breaks out of the vacuole, it then releases its nucleic acid into the cell.
3. Replication: The virus's nucleic acid instructs the host cell to replicate the virus's
DNA or RNA.
4. Assembly: New virus particles are assembled.
5. Lysis and Release: The virus directs the production of an enzyme which damages
the host cell wall, causing the host cell to swell and burst. The newly formed virus
particles are now released.
22.2.2 Lysogenic Cycle

1. Attachment: Similar to Lytic Cycle
2. Entry: Similar to Lytic Cycle
3. Incorporation: The viral nucleic acids is not replicated, but instead integrated by
genetic combination (crossing over) into the host cell's chromosome. When integrated
in a host cell this way, the viral nucleic acid as part of the host cell's chromosome is
known as a prophage.
4. Host Cell Reproduction: The host cell reproduces normally. Subsequent cell divisions,
daughter cells, contain original father cell's chromosome embedded with a prophage.
5. Cycle Induction: Certain factors now determine whether the daughter cell undergoes
the lytic or lysogenic cycle. At any time, a cell undergoing the lysogenic cycle can
switch to the lytic cycle.
The reproduction cycle of viruses with RNA and no DNA is slightly different. A notable
example of a RNA-based virus is HIV, a retrovirus.
98
Viral Genome
Retrovirus reproductive cycle
1. The retrovirus force RNA into cell, by either one of the two methods of entry (See
above).
2. In the retrovirus are reverse transcriptase enzymes, which catalyses the synthesis of a
DNA strand complementary to the viral RNA.
3. Reverse transcriptase catalyses a second DNA strand complementary to the first. With
these two strands, the double-stranded DNA can be created.
4. DNA is then incorporated into the host cell's chromosomes. Similar to the concept of
a prophage, this incorporated DNA is called a provirus. However, the provirus never
leaves the host cell, unlike a prophage.
5. The infected host cell undergoes the lytic or lysogenic cycle.
22.3 Viral Genome

The genome of a virus consists of DNA or RNA, whose size and configuration vary. The
entire genome can exist as a single nucleic acid molecule or several nucleic acid segments.
Also, the DNA or RNA may be single-stranded or double-stranded, and either linear or
circular.
Not all viruses can reproduce in a host cell by themselves. Since viruses are so small, the
size of their genome is limiting. For example, some viruses have coded instructions for only
making a few different proteins for the viruses' capsid. On the other hand, the human
genome codes for over 30,000 different proteins. Therefore, the lack of coded instructions
cause some viruses to need the presence of other viruses to help them reproduce themselves.
Such viruses are called replication defective.
Lastly, it is worthy to note that 70% of all viruses are RNA viruses. As the process of RNA
replication (with enzymes and other organelles of the host cell) is more prone to errors, RNA
viruses have much higher mutation rates than do DNA viruses.
22.4 Viruses Practice Questions

1. As the name implies, the Tomato Spotted Wilt Virus targets tomatoes. Would it be
possible for this virus to target other fruits as well? Explain.
2. If a DNA and a RNA virus both infected somatic cells, which virus would be more
difficult to detect?
3. Many people have had cold sores, which are caused by infection with the herpes
simplex virus. One characteristic of cold sores is that after a period of inactivity, they
will reappear many times during the course of a person's life. Which cycle would the
herpes simplex virus undergo?
4. Chicken pox is a common, non-fatal disease usually acquired in adolescence and caused
by the varicella zoster virus. In adulthood, many people suffer from shingles, an altered
form of the varicella zoster virus. Which cycle would the varicella zoster virus have
undergone?
5. Would an antibiotic work for a person suffering from a cold of flu? Explain.
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Answers to Viruses Practice Questions1
For Eubacteria, please visit General Biology/Classification of Living Things/Eubacteria2 .
22.5 Archaea
Proposed as separate group from (eu)bacteria by Carl Woese
based on structure and metabolic pathways
inhabit extreme environments
unique branched lipids in membrane
Share traits with both eukaryotes and eubacteria, e.g., RNA polymerase, introns
Biochemically diverse
Economically important
Taq polymerase used in PCR
22.5.1 Types
Methanogens
Halophiles
Thermophiles
Underground bacteria
Metabolism
built around inorganic energy sources
e.g., basalt reacts with H2 O to release hydrogen which is catalytically combined with
CO2 to form carbohydrate (akin to photosynthesis)
may result in deposit of minerals
Unresolved problems
Did bacteria move downward from surface or did they first evolve there, protected
from harsh surface conditions?
Could bacteria be ejected into space in rocks?
22.6 Prokaryote evolution

Tentative, subject to change
Derived largely from molecular systematics (rRNA sequences)
Note: most bacteria cant be cultured, thus hard to study! (Studied by PCR of water/soil
samples)
1
2
100
http://en.wikibooks.org/wiki/%2FAnswers
http://en.wikibooks.org/wiki/General%20Biology%2FClassification%20of%20Living%
20Things%2FEubacteria
Domains of life: characteristics
22.7 Domains of life: characteristics

State University.
22.8 Introduction
Out of the six kingdoms, Protista is the most diverse. This is the kingdom of organisms
with strange, atypical characteristics. In essence, this kingdom is designated for organisms
which do not belong in any other kingdom. The majority of protists are microscopic.
22.9 Classification of Protists

There are three phyla of protists, based on their type of nutrition.
1. Protozoa (animal-like protists) are heterotrophs that ingest or absorb their food.
2. Algae (plant-like protists) are autotrophs they get nutrition from photosythesis.
3. Slime moulds and water moulds (fungus-like protists) are also heterotrophs, like
protozoa.
22.10 Protozoa
As heterotrophs, protozoa scavenge materials from their surroundings. Others are predators
which actively hunt or ambush small organisms such as bacteria and other protozoa for a
source of nutrition. Protozoa can be parasitic as well; they may live inside larger organisms,
like humans. Most protozoa live as single cells, although a few form colonies.
Protozoa are generally difficult to identify due to their varied shape. They may appear as
jelly-like blobs, spherical sunbursts, or a flattened leaf. Tiny blood parasites may be only 2
m long. On the other hand, shell-covered marine may be 5 cm or more in diameter.
Furthermore, different protozoans have their own complex life cycles. The complexity has
led certain organisms to be mistakenly classified for other species.
Nevertheless, protozoa can move, and so, they are classified based on their methods of
locomotion.
Characteristics of Protozoa :
About 30,000 species known
About 10,000 species are pathogenic, including some of the worst human diseases
heterotrophic
highly variable in form and life cycle
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mostly unicellular
range in size from 0.005 mm to 50 mm
lack cell walls
they love environment and each other..............
22.11 Algae
Algae are much simpler than protozoa. They are aquatic and contain chlorophyll. Algae can
exist as a single cell or as giant seaweeds 60 m in length. Formerly, algae were classified as
plants but this was incorrect as algae lack parts of true plants: leaves, stems, roots, xylem,
and phloem. Since algae belong in the kingdom Protista, algae is a broad term used to
denote all aquatic eukaryotes which photosynthesise; algae can differ in size and shape as
well.
There are six phyla of algae:chlorophytes (green algae), phaeophytes (brown algae),
rhodophytes (red algae), chrysophytes (diatoms), pyrrophytes (dinoflagellates),
and euglenophytes (euglenoids).
22.11.1 Chlorophytes
Chlorophytes resemble plants the most. Like plants, their cell walls contain cellulose and
they store food in reserve as starch. Chlorophytes can be unicellular or multicellular. Most
chlorophytes use flagellae for some locomotion.
22.11.2 Phaeophytes
Phaeophytes are nearly all multicellular marine organisms, which are known to us as seaweeds.
They have cell walls composed of cellulose and alginic acid (a substance similar to pectin).
The cellulose and alignic acid help to retain water and prevent seawood from drying out
when exposed to air at low tide.
Since phaeophytes live in a tidal environment, they have large, flat fronds (a large leaf)
which can withstand pounding by waves. Their bases strongly anchor the algae to the rocky
seabed and prevent them from being washed out to sea. Phaeophytes are usually found in
areas of cold water.
22.11.3 Rhodophytes
Rhodophytes are typically found in warmer seawater, and are more delicate and smaller
than brown algae (phaeophytes). Rhodophytes are also able to grow at deeper depths in
the ocean, since red algae absorb green, violet, and blue light, the wavelengths of which
penetrate the deepest below the water surface. They also have mucilaginous material to
resist drying.
102
Slime molds & Water molds
22.11.4 Chryosophytes
Chryosophytes are the most abundant unicellular algae in the oceans. They are also one
of the biggest components of plankton, a free-floating collection of microorganisms, eggs,
and larvae. As photosynthetic organisms, they produce a significant amount of atmospheric
oxygen.
The reproduction cycle of chryosophytes is particularly interesting. Note that diatoms
reproduce both asexually and sexually. Since diatoms have a rigid cell wall with an outer
layer of silica (found in sand and glass), the daughter cells produced by mitosis must fit
inside the original cell wall. Therefore, each generation of diatoms is smaller than the one
before. The reduction in size continues until the diatoms produce sexually, producing a
zygote which eventually grows to the original size as it matures.
22.11.5 Pyrrophytes
Pyrrophytes are unicellular, photosynthetic, and mostly aquatic. They have protective coats
composed of stiff cellulose. They are more easily identifiable, due to the presence of two
flagellae. The longer flagellae propels the dinoflagellate, while the second shorter, flatter
flagellae functions as a rudder.
Some species of pyrrophytes are zooxanthellae. Since they lack cellulose plates, they make
their home in coral reefs and animals, such as sea anemones, and molluscs. In returning
the favour of sheltering them, dinoflagellates provide carbohydrates to their host through
photosynthesis. This is why there are nutrient-rich coral reefs in malnutritions water.
A negative aspect of pyrrophytes is that under certain conditions, species of dinoflagellates
reproduce rapidly to form a harmful algal bloom (HAB), known as a red tide if dinoflagellates are the cause. Such pyrrophytes can produce toxins which may injure or kill wildlife,
and additionally any consumers of contaminated wildlife.
22.11.6 Euglenophytes
Like pyrrophytes, euglenophytes are small unicellular freshwater organisms with two flagella.
They are mainly autotrophic or heterotrophic, depending if they have a red, light-sensitive
structure called an eyespot.
22.12 Slime molds & Water molds

There are two phyla of slime moulds and one phylum of water moulds.
22.12.1 Oomycotes (Water moulds)

Oomycotes are filamentous organisms which resemble fungi, in that they live as saprotrophs.
Oomycotes differ from other moulds with the presence of spores and their sexual life cycle.
103
22.12.2 Myxomycotes (Plasmodial slime moulds)

Myxomycoties are visible to the naked eye as tiny slug-like organisms which creep over decayed
and dead matter. This streaming blob containing many nuclei is called a plasmodium.
22.12.3 Acrasiomycotes (Cellular slime moulds) and its reproductive

cycle
Acrasiomycotes exist as individual amoeboid cells with one nucleus each. When in unfavourable conditions, each acrasiomycete cell gathers together to form a pseudoplasmodium.
Reproductive Cycle:
1. One acrasiomycete cell joins with others to form a pseudoplasmodium.
2. The pseudoplasmodium shrinks and forms a smaller plasmodium.
3. The plasmodium migrates to a suitable environment.
4. The plasmodium develops a sporangia, where original parental nuclei has divided by
meiosis into haploid spores to be germinated.
5. When favourable conditions arise, the spores germinate and are carried away by animals
or the wind.
6. Cycle repeats.
22.13 Protists Practice Questions

1. Which of the following adjectives describe the major food source of protozoa?
a) chemoautotrophic
b) photoheterotrophic
c) chemoheterotrophic
d) heterotrophic
e) A, C, D
f) C, D
2. The protozoan Giardia lamblia can inhabit a human body's intestinal tract and cause
gastroenteritis.
a) Give the abbreviated binomial name of this protozoan.
b) Would the relationship between this protozoan and human being be mutualistic, commensalistic, or parasitic?
104
Protists Practice Questions

3. Found in many products, such as Petri dishes, agar is made from mucilagnious material
in seaweed. Of the six phyla of algae, which phyllum/phyla would agar be made from?
4. Which of the following adjectives describe the major food source of Euglenophytes without
an eyespot?
a) photoautotrophic
b) photoheterotrophic
c) chemoautotrophic
d) chemoheterotrophic
e) B or C
f) C or D
5. Can coral reefs exist in nutrient-poor areas? Explain.
105
23 Multicellular Photosynthetic
Autotrophs
23.1 Plants
Multicellular
Cellulose cell walls
Chlorophylls a and b
Develop from embryophyte
Major food source for terrestrial life
Atmospheric O2 and CO2 balance
Coal deposits
Intimate association with mycorrhizal fungi
>250,000 species (500,000?)
Taxonomy
State of flux
DNA sequencing
Developmental studies
Division (old literature) = phylum (new literature)
12 phyla, 9 of which are vascular plants
23.2 Plant phyla

Phyla are 12 groupings
23.3 Plant evolution

Evolved from green algae, likely related to charophytes
Evidence
DNA sequences
homologous chloroplasts: chlorophyll b and beta-carotene; thylakoids in grana;
Cellulose in both groups; also peroxisomes
Mitosis and cytokinesis similar
Sperm ultrastructure
107
Multicellular Photosynthetic Autotrophs
23.3.1 Terrestrial adaptations

Stomata: pores in leaves for exchange of gases; prevent desiccation
Secondary metabolites:
cuticle: waxy coating to prevent H2O loss
lignin: hardens wood
sporopollenin: resistant polymer; coats pollen
predator defenses
Embryonic development
gametangia in early plants
spores; seeds
Mycorrhizae
Water/food conducting systems
23.4 Plant phylogeny

23.5 Plant life cycles
Sporophyte
diploid
produces spores in sporangia
Gametophyte
develops from spore
haploid
produces gametes in gametangia
Haplodiplontic life cycle
23.6 Moss life cycle

23.7 Vascular plants
Most have roots
Aerial shoot systems
Vascular tissue
xylem: water, mineral transport
phloem: food transport
Lignin
Branched sporophyte is dominant stage
amplified production of spores
evolution of complex plant bodies
Dominated Carboniferous (360 my)
108
Vascular plant life cycles
23.8 Vascular plant life cycles

Homosporous (single type of spore)
Heterosporous (two types of spore)
23.9 Pterophyta (ferns)
Non-seed plant
Sporophyte conspicuous (vascular tissue)
Rhizome: ground stem, roots
Fronds: leaves
Sori: clusters of sporangia
Motile sperm require external water for fertilization
Originated in Devonian, 350 my
Tree fern Fern life cycle
23.10 Non-seed plants, continued

Lycophyta: club mosses
E.g., Lycopodium (ground pine)
Many species became extinct 270 my, once dominant (coal formations)
Gametophyte non-photosynthetic, nourished by fungi
Arthrophyta: horsetails
Equisitum
Some fossil forms (300 my) were tree-size (coal)
Photosynthetic stems, no leaves
Silica deposits in epidermal cells
23.11 Seed plants

1st appeared in Devonian, 360 my
Seed develops from ovule, protects embryo
withstands drought
dispersal is enhanced
no immediate need for water for germination
Heterosporous
male gametophyte: arise from microspores
female gametophyte: arise from megaspores in ovule in ovary
Two groups
gymnosperms
angiosperms
109
plant
23.12 Sporophyte/gametophyte
23.13 Megasporangium (nucellus)
Key to seed development

Nucellus: solid, fleshy, surrounded by integuments derived from sporophyte (seed coat)
Entire structure called ovule
Flower may have many ovules
23.14 Pollen
Develop from microspores, become male gametophyte

Protected by sporopellenin
In most plants, sperm lack flagella (loss)
Many mechanisms to transport pollen
wind
insects, birds,
23.15 Gymnosperms
naked seed
ovule not fully enclosed by sporophyte at time of pollination
Conifers, cycads, gnetophytes, Ginkgo
Small, inconspicuous plants to giants like sequoia
Conifers: to carry cones fv
male cones, Female conesvv
evergreen
23.16 Pine life cycle

23.17 Other Coniferophyta
Cycadophyta: cycads
tropical, subtropical
flagellated sperm
Gnetophyta
e.g., Ephedra, Mormon Tea
Ginkgophyta: Ginkgo
110
Other gymnosperms
only one surviving species
diocious (separate % and &trees)
23.18 Other gymnosperms

23.19 Angiosperms
Flowering plants, Anthophyta
monocots- single seed leaf (grasses, lilies, etc.)
dicots- two seed leaves (roses, pulses, maples)
More specialized xylem (water transport)
vessel elements
fiber cells
Fossils date to 130 my
Animal (e.g., insect) coevolution
23.19.1 Monocots vs dicots
23.20 Earliest angiosperm

What is earliest angiosperm?
Recent analysis of nucleotide and amino acid sequences suggests that Amborella, a tropical
plant found only on the island of New Caledonia, is closest relative to flowering plants
23.21 Angiosperm flower

Insert non-formatted text hereInsert non-formatted text here
23.22 Angiosperm life cycle

State University.
23.23 Introduction
Although you may not recognise fungi, they are just as prevalent as plants and animals.
Their spores are in the air which we breathe, fungi allow us to make bread, and mushrooms
(a type of fungi) are eaten by us. A few types of fungi are unicellular. For example, yeasts live
as individual oval or cylindrical cells. However, the majority of fungi live are multicellular.
Their bodies are composed of hyphae, a network of fine filaments. In a mushroom, the
111

hyphae are densely packed so it is difficult to see the individual structures when a mushroom
is eaten. However, a mushroom is only a specialised reproductive part of the whole fungus.
The main part of the fungi is underground in a whole web of hyphae, called a mycelium.
In the mycelium, each fungal cell is separated from each other by a septum. Each fungal
cell may have one or more nuclei and remains connected to the mycelium because the septa
are porous, allowing cytoplasm to flow through the hyphae and fungal cell walls, made of a
hard material called chitin. Some fungi do not have septa, and they appear to be large,
branching, multinucleate cells.
23.24 Nutrition
Fungi are saprophytes. When they find a source of food (e.g. dead wood, orange peel) ,
they decompose it and digest it. The enzymes break down larger organic molecules in the
substrate into smaller molecules. These smaller molecules diffuse into the fungus, where
they are used to allow growth and repair.
Fungi which feed on living cells are parasitic. For example, athlete's foot grows on the
human foot. These kinds of fungi produce hyphae called haustoria, which can penetrate
host cells without immediately killing them.
However, they are friendlier species of fungi. Many fungi live symbiotically with plants or
animals. For example, most trees have fungi living in close contact with their roots. In this
relationship, known as a mycorrhiza, there are many benefits:
Growing around the plant roots and often entering plant cells, the hyphae absorb minerals
from the soil and release them in the roots. The fungi gets its source of food (organic
nutrients) while delivering food to the plant.
The mycelium here would increase the surface area, thus the absorptive surface, of the
plant roots.
The fungal cells help to maintain air and water flow in the soil around the roots.
The fungi may prevent other potentially pathogenic fungi to attack the tree.
23.25 Fungal Reproduction

Fungi can reproduce in two ways. Firstly, they make asexually produce through fragmentation. This occurs when pieces of hyphae are broken off, which then grow into new
mycelia.
The second method is by spores. Spores are lightweight structures and windblown designed
to be transported over long distances and by many mediums, such as on the bodies of insects
and birds. They are additionally light enough to be blown away for hundreds of kilometers.
Spores may be asexual and sexual. Their sexual properties can be analysed to classify the
four phylla of fungi.
112
Types of Fungi
23.26 Types of Fungi

23.26.1 Zygospore Fungi (Zygomycetes)
This phyllum includes bread moulds and other saprotrophs. Comparable to bacteria, this
phyllum prefers asexual reproduction over sexual reproduction.
1. Two haploid hyphae of opposite types, also known as mating strain + and mating
strain -, combine and fuse together.
2. Plasmogamy, the union of the two parent hyphae, occurs and results in the creation
of a heterokaryotic (n + n) zygosporangium or zygospore. Note that the zygospore is
NOT diploid yet; the haploid nuclei are simply clumped together.
3. Immediately, a thick wall develops around the zygospore to protect it from drying and
other hazards. The zygospore becomes dormant.
4. When conditions are favourable, the zygospore absorbs water and undergoes karyogamy
(n + n = 2n), where the haploid nuclei contributed by the two parents fuse to produce
diploid zygosporangia.
5. The now diploid zygosporangium then undergoes meiosis to form haploid sporangia.
6. Through asexual reproduction of fungi (See above for more information), the spores from
the sporangia germinate and grow into new mycelia.
7. Back to step #1.
23.26.2 Club Fungi (Basidiomycetes)

This phyllum increases mushrooms and shelf fungi. In many ways, the reproduction stages
of this phyllum is similar to that of zygomycetes.
1. Two haploid hyphae of opposite types, also known as mating strain + and mating
strain -, combine and fuse together.
2. Plasmogamy takes place, and a dikaryotic mycelium forms. The dikaryotic mycelium
grows faster then the haploid parental mycelia.
3. Environmental factors cause the dikaryotic mycelium to form compact masses which develop into basidiocarps, short-lived reproductive structures. An example is the mushroom.
4. The basidiocarp gills are lined with terminal dikaryotic cells called basidia, which then
undergo karyogamy.
5. The basidia are now diploid. They undergo meiosis to develop haploid basidiospores, a
term referring to a basidiomycete's spores.
6. Still remaining on the basidiocarp, the haploid basidiospores eject, fall from the basidiocarp,
and are dispersed by the wind when mature.
7. In a favourable environment, the basidiospores germinate and grow into short-lived
haploid mycelia.
113

8. Back to Step #1.
23.27 Key Terms

synapomorphy
23.28 Introduction
What makes an animal an animal?
If animals are a monophyletic taxon, then animals should be able to be defined by synapomorphies, (shared, derived characteristics). Ideally, we would NOT define this or any taxon using
symplesiomorphies (shared ancestral or primitive characteristics) or homoplastic characters
(the independent evolution of similarity, or "convergent evolution"). See pages 654 - 656 and
Fig. 32.6 in your text to review these concepts. As you consider the characteristics listed
below, ask yourself whether or not each is a synapomorphy.
23.29 Characteristics of an Animal

There is no one universally accepted definition of an animal. The following treatment
follows your text, beginning on page 876.
Animals:
Are multicellular, heterotrophic eukaryotes . . .
Lack the distinctive cell walls of plants & fungi
Share unique characteristics . . .
Share certain reproductive characteristics . . .
Other commonly used definitions . . .
Animals are multicellular heterotrophic eukaryotes
Unfortunately, none of these traits is exclusive to animals:
Plants, fungi, and some algae are multicellular.
Many bacteria, protists, and all fungi are heterotrophic.
Everything other than bacteria and archaea are eukaryotic.
Moreover, all three of these characteristics also apply to fungi.
However, there is a difference here between animals and fungi. Animals generally
take in their food through ingestion, or eating and swallowing something. Fungi are
absorptive heterotrophs; they secrete their digestive enzymes onto their food, and then
absorb the resulting nutrients.
Animals share unique characteristics
Only animals have muscle tissue and nervous tissue.
Only animals have collagen, a structural protein
Only animals have the following types of intercellular junctions: (See pages 135 - 139,
Figure 7.15 in your text for more information on these junctions.)
114
Characteristics of an Animal
Tight junctions (sealing function)
Desmosomes (anchoring function)
Gap junctions (communication function)
Animals share certain reproductive characteristics
Most animals reproduce sexually, with the diploid stage dominating.
In most animals, a small, haploid, flagellated, motile sperm fertilizes a larger, haploid,
nonmotile egg to form a diploid zygote.
Mitotic division of the zygote yields a blastula stage, followed by a gastrula stage. A
synapomorphy? This feature could be another "unique characteristic" shared by animals.
Development may be direct to adult form, or there may be a sexually immature stage
(or stages) that are morphologically & ecologically distinct from the adult called a larva
(plural: larvae).
Other commonly used definitions or characterizations
It is surprisingly difficult to find two texts that agree on a precise definition of an animal.
Here are a few perspectives from some other texts.
Animals are multicellular eukaryotes; they are chemosynthetic heterotrophs that ingest
their food.
Animals are motile, though many are secondarily sessile. Gametes usually are produced
in multicellular sex organs, and the zygote passes through embryonic stages that include
a blastula.
Animals are organisms that are multicellular, with more than one type of cell. They
are heterotrophic. They reproduce sexually (at least sometimes), with a zygote formed
from two different haploid gametes. They go through a developmental stage called a
blastula.
Animals are not photosynthetic, have no cell wall, and no hyphae or mycelia. (What
would a cladist think of this definition of the taxon Animalia?)
What kinds of animals are there?
Kingdom Animalia generally is recognized to have approximately 30 phyla ...
There is relatively little dispute over the number of phyla recognized; however, the
phylogenetic relationships among the phyla are hotly debated.
Molecular techniques for assess similarity based on nucleotide sequences in nucleic
acids are providing valuable new perspectives on this question.
Remember that two animals in different phyla generally are considered to be more different
from each other than are animals within one phylum (e.g., nematodes are more different
from annelids than humans are from sharks).
This text is based on notes very generously donated by Ralph Gibson, Ph.D.1 of the Cleveland
State University2 .
1
2
http://bgesweb.artscipub.csuohio.edu/faculty/gibson.htm
http://www.csuohio.edu
115
23.30 Introduction to animal phyla

There currently are almost 40 recognized phyla.
Phylum Number of Species Common Name
Placozoa3 1
Monoblastozoa4 1
Rhombozoa5 50
Orthonectida6 50
Porifera7 9,000 sponges (figures)
Cnidaria8 9,000 corals (figures)
Ctenophora9 100 comb jellies
Platyhelminthes10 20,000 flatworms (figures)
Nemertea11 900 ribbon worms (figures)
Rotifera12 1,800 rotifers (figures)
Gastrotricha13 450 gastrotrichs
Kinorhyncha 150 kinorhynchids
Nematoda 12,000 roundworms (figures)
Nematomorpha 230 horsehair worms
Priapula 15
Acanthocephala 700 (figures)
Entoprocta 150
Gnathostomulida 80
Loricifera 35
Annelida 15,000 segmented worms (figures)
Sipuncula 250 peanut worms (figures)
Echiura 135
Pogonophora 145 beard worms
Vestimentifera 8 beard worms
Arthropoda 957,000 arthropods (figures)
Onychophora 80
Tardigrada 400 water bears
Pentastomida 95 tongue worms
Mollusca 100,000 molluscs (figures)
Phoronida 15
Ectoprocta 4,500 sessile zooids
Brachiopoda 335 lampshells
3
4
5
6
7
8
9
10
11
12
13
116
http://en.wikibooks.org/wiki/Placozoa
http://en.wikibooks.org/wiki/Monoblastozoa
http://en.wikibooks.org/wiki/Rhombozoa
http://en.wikibooks.org/wiki/Orthonectida
http://en.wikibooks.org/wiki/Porifera
http://en.wikibooks.org/wiki/Cnidaria
http://en.wikibooks.org/wiki/Ctenophora
http://en.wikibooks.org/wiki/Platyhelminthes
http://en.wikibooks.org/wiki/Nemertea
http://en.wikibooks.org/wiki/Rotifera
http://en.wikibooks.org/wiki/Gastrotricha
Phylum Porifera
Echinodermata 7000 echinoderms (figures)

Chaetognatha 100 arrow worms (figures)
Hemichordata 85 acorn worms
Chordata 50,000 chordates (figures)
23.31 Phylum Porifera
Figure 6
Sponges
Name means "pore-bearing".

This phylum consists of the sponges. The number of species is estimated to be between
5,000 and 10,000. All are aquatic and almost all are marine.
Animals in this phyla have no true tissues, which means, for example, that they have no
nervous system or sense organs. Although sponges are multicellular, they are described as
being essentially at a cellular level of organization. They are sessile as adults, but have a
free swimming larva.
Their bodies are porous. They are filter feeders; water flows in through many small openings,
and out through fewer, large openings. They have inner and outer cell layers, and a variable
middle layer. The middle layer often is gelatinous with spiny skeletal elements (called
spicules) of silica or calcium carbonate, and fibres made of spongin (a form of collagen).
117

Choanocytes are flagellated cells lining the inside of the body that generate a current, and
trap and phagocytize food particles.
Their cells remain totipotent, or developmentally flexible: they can become any type of
cell at any point in the sponge's development. This allows for the great regenerative power
sponges have.
Sponges are an ancient group, with fossils from the early Cambrian (ca. 540 mya) and
possibly from the Precambrian. Sponges often are abundant in reef ecosystems. They
somehow are protected from predators (spicules? bad taste?).
Many organisms are commensals of sponges, living inside them. Some sponges harbor
endosymbiotic cyanobacteria or algae (dinoflagellates, a.k.a. "zooxanthellae").
23.32 Phylum Cnidaria

See text pages 886 - 889.
Name comes from the Greek knide- meaning "nettle".
This phylum They have one opening, which serves as both mouth and anus. The body wall
has an outer ectoderm, an inner endoderm, and a variable undifferentiated middle layer
called mesoglea or mesenchyme that may be jelly-like. The mesoglea is NOT considered
to be true mesoderm and so the Cnidaria are described as diploblastic. Tentacles usually
extend from the body wall around the mouth/anus.
118
Phylum Cnidaria
Figure 7
Jellyfish Development
There are two basic body plans: the polyp14 and the medusa15 . The polyp is sessile and
attaches to substrate by the aboral end (i.e., the end away from the mouth). The medusa
("jellyfish") is a floating form, and looks like an upside-down version of the polyp. Some
cnidarians only have the polyp stage, some have only the medusa stage, and others have
both.
14
15
http://en.wikipedia.org/wiki/polyp
http://en.wikipedia.org/wiki/Medusa%20%28biology%29
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The typical life cycle of a cnidarian involves what is called "alternation of generations": an
alternation between an asexual polyp stage and a sexual medusa stage.
The tentacles are armed with cnidae (or nematocysts), small intracellular "harpoons" that
function in defense and prey capture. When fired, the cnidae deliver a powerful toxin that
in some cases is dangerous to humans. The phylum is named after the cnidae.
Cnidarians have no head, no centralized nervous system, and no specialized organs for gas
exchange, excretion, or circulation. They do have a "nerve net."
Many cnidarians have intracellular algae living within them in a mutualistic symbiotic
relationship (Dinoflagellates = zooxanthellae). This combination is responsible for much of
the primary productivity of coral reefs.
There are three main classes in the phylum
Class Hydrozoa16 (hydras and Portugese man-of-war are well-known but atypical examples
of this Class)
Class Scyphozoa17 (jellyfish)
The medusa stage is dominant and the polyp stage often is reduced.
Class Anthozoa18 (sea anemones, most corals)
No medusa (jellyfish) stage, so sexual reproduction occurs in the polyp stage in this
group. The polyps also can reproduce asexually, which is how individual "corals" grow.
23.33 Phylum Platyhelminthes

Name means "flat worm"
Most members of this phylum are parasitic (flukes and tapeworms), but some are free living
(e.g., planaria). There are about 20,000 species.
They are dorsoventrally compressed (i.e., "flat").
Animals in this phylum are acoelomate, triploblastic, bilaterally symmetrical, and unsegmented. Platyhelminths have a simple anterior "brain" and a simple ladder-like nervous
system. Their gut has only one opening. Flatworms have NO circulatory or gas exchange
systems. They do have simple excretory/osmoregulatory structures (protonephridia or "flame
cells").
Platyhelminths are hermaphroditic, and the parasitic species often have VERY complex
reproductive (life) cycles.
There are four main classes of platyhelminths:
Class Turbellaria19 (mostly free living flatworms, e.g., planaria)
16
17
18
19
120
http://en.wikipedia.org/wiki/Hydrozoa
http://en.wikipedia.org/wiki/Scyphozoa
http://en.wikipedia.org/wiki/Anthozoa
http://en.wikipedia.org/wiki/Turbellaria
Phylum Rotifera
Class Monogenea20 (parasitic flukes)
Class Trematoda21 (parasitic flukes, e.g., liver fluke and the human blood fluke, Schistosoma)
Class Cestoda22 (tapeworms)
Cestodes are endoparasitic in the gut of vertebrates. They do not have a mouth or
digestive system.
23.34 Phylum Rotifera

See text page 900
The Rotifers. The name means "wheel bearing," a reference to the corona, a feeding structure
(see below).
They are triploblastic, bilaterally symmetrical, and unsegmented. They are considered
pseudocoelomates.
Most less than 2 mm, some as large as 2 - 3 mm.
Rotifers have a three part body: head, trunk foot. The head has a ciliary organ called the
corona that, when beating, looks like wheels turning, hence the name of the phylum. The
corona is a feeding structure that surrounds the animal's jaws. The gut is complete (i.e.,
mouth & anus), and regionally specialized. They have protonephridia but no specialized
circulatory or gas-exchange structures.
Most live in fresh water, a very few are marine or live in damp terrestrial habitats. They
typically are very abundant. There are about 2,000 species.
Parthenogenesis, where females produce more females from unfertilized but diploid eggs, is
common. Males may be absent (as in bdelloid rotifers) or reduced. When males are present,
sexual and asexual life cycles alternate. Males develop from unfertilized haploid eggs and
are haploid. Males produce sperm by mitosis which can fertilize haploid eggs, yielding a
diploid zygote that develops into a diploid female. Sexual reproduction occurs primarily
when living conditions are unfavorable.
Most structures in rotifers are syncytial ("a mulitnucleate mass of protoplasm not divided into
separate cells," or "a multinucleated cell") and show eutely (here, "constant or near-constant
number of nuclei").
23.35 Phylum Nematoda

Name from the Greek for "thread".
20
21
22
http://en.wikipedia.org/wiki/Monogenea
http://en.wikipedia.org/wiki/Trematoda
http://en.wikipedia.org/wiki/Cestoda
121

This phylum consists of the round worms. There are about 12,000 named species but the
true number probably is 10 - 100 times this!
These animals are triploblastic, bilaterally symmetrical, unsegmented pseudocoelomates.
They are vermiform, or wormlike.
In cross-section, they are round, and covered by a layered cuticle (remember this cuticle !!).
Probably due to this cuticle, juveniles in this phylum grow by molting. The gut is complete.
They have a unique excretory system but they lack special circulatory or gas-exchange
structures. The body has only longitudinal muscle fibers. The sexes are separate.
Nematodes can be incredibly common, widespread, and of great medical and economic
importance. They are parasites of humans and our crops. They can live pretty much
anywhere.
In one rotting apple, there can be up to 90,000 nematodes, and in one tablespoon of coastal
mud, there can be 236 species of nematodes!
Nematodes can be free living or important parasites of our crops, or of humans and other
animals. They have become very important in development studies, especially the species
Caenorhabditis elegans, presumably due to its small size and constancy of cell number
(eutely - 959 cells in C. elegans).
23.36 Phylum Annelida

Name means "ringed", from the Greek annulatus.
This phylum consists of earthworms, leeches, and various marine worms given many different
names (e.g., sand worms, tube worms). There are about 12,000 - 15,000 species.
Animals in this phylum are triploblastic, bilaterally symmetrical, segmented coelomates.
Development is typically protostomous. They have a complete circulatory system, and
a well-developed nervous system. Typically, each segment has paired epidermal "bristles"
(setae or chaetae).
Most are marine but they are successful occupants of almost anywhere sufficient water is
available. They can be free living, parasitic, mutualistic, or commensalistic.
Major advances of this phylum include the true coelom, segmentation, both longitundinal
and circular muscles, a closed circulatory system and, for most, a more advanced excretory
system (metanephridia).
There are three main classes of Annelids
Class Oligochaeta (earthworms)
Class Polychaeta (marine worms)
Class Hirudinea (leeches)
122
Phylum Arthropoda
23.37 Phylum Arthropoda
Figure 8
Arthropods
Name means "jointed feet".

This phylum consists of spiders, ticks, mites, insects, lobsters, crabs, and shrimp, and is the
largest of all the phyla. So far, over 1 million species have been named, and it is likely that
the true number out there is 10 - 100 times greater.
This phylum also includes the extinct trilobites, which were prevalent in the Paleozoic era.
Because of their exoskeletons, these animals fossilized well and over 4000 species have been
named.
These animals are triploblastic, bilaterally symmetrical, segmented, protostome coelomates.
The coelom is generally reduced to portions of the reproductive and excretory systems. They
have an open circulatory system.
The most notable advancement of this phylum is a rigid exoskeleton. It has major implications
in these organisms' locomotion, flexibility, circulatory systems, gas exchange systems, and
growth. It also was partially responsible for the ability of the arthropods to move on to land.
There are several major groupings of arthropods:
Major subgroups include:
The chelicerates (eurytperids, horseshoe crabs, scorpions, spiders, ticks) have clawlike
feeding appendages. They lack antennae and usually have simple eyes.
The Trilobites...they get their own grouping
123

The uniramians (centipedes, millipedes, insects) have one pair of antennae and unbranched (uniramous) appendages.
The crustaceans (crabs, shrimp, lobsters, barnacles and many others) have two pairs of
antennae and branched (biramous) appendages.
Major Classes Include
Class
Class
Class
Class
Class
Arachnida (mites, scorpions, spiders, ticks)

Diplopoda (millipedes)
Chilopoda (centipedes)
Insecta (insects)
Crustacea (crabs, crayfish, lobsters, shrimp)
23.38 Phylum Mollusca

Name means "soft".
This phylum consists of snails, slugs, bivalves, chitons, squids, octopus, and many others.
About 110,000 species
All molluscs have a similar body plan:
A muscular foot, usually used for movement.
A visceral mass, containing most of the internal organs.
A mantle, a fold of tissue that drapes over the visceral mass and secretes the shell, if
present.
Most have a radula, or a rasping organ to scrape food.
Molluscs are bilaterally symmetrical, or secondarily asymmetrical. They are coelomates, but
the coelom generally has been greatly reduced; the main body cavity is a hemocoel. Development is typically protostomous. The gut is complete with marked regional specialization.
Large, complex, metanephridia (excretion).
Many molluscan life cycles include a trochophore larva. This stage also is characteristic of
annelids.
There are several major classes of molluscs:
Class
Class
Class
Class
Polyplacophora (chitons)
Gastropoda (snails, slugs, nudibranchs)
Bivalvia (clams, mussels, scallops, oysters)
Cephalopoda (squids, octopuses, chambered nautiluses)
23.39 Phylum Echinodermata

Name means "spiny skin"
This phylum consists of sea stars, brittle stars, sea urchins, and sea cucumbers.
124
Phylum Chordata
Echinoderms are mostly sessile or very slow moving animals.
As adults, they are radially symmetrical, but in the larval stage, they are bilaterally
symmetrical. They are considered deuterostomes.
Echinoderms are unique in that they have a water vascular system composed of a system
of fluid-filled canals. These canals branch into the tube feet, which function in feeding,
locomotion, and gas exchange.
There are six major classes of echinoderms:
Class
Class
Class
Class
Class
Asteroidea (sea stars)

Ophiuroidea (brittle stars)
Echinoidea (sea urchins, sand dollars)
Crinoidea (sea lilies)
Holothuroidea (sea cucumbers)
23.40 Phylum Chordata

Name means "the chordates", i.e., these animals have a notochord at some stage in their
lifecycle.
This phylum consists of tunicates, lancelets, and the vertebrates.
There are four major features that characterize the phylum Chordata.
A notochord, or a longitudinal, flexible rod between the digestive tube and the nerve
cord. In most vertebrates, it is replaced developmentally by the vertebral column. This
is the structure for which the phylum is named.
A dorsal hollow nerve cord which develops from a plate of ectoderm that rolls into a tube
located dorsal to the notochord. Other animal phyla have solid nerve cords ventrally
located. A chordate nerve cord splits into the central nervous system: the brain and
spinal cord.
Pharyngeal slits, which allow water that enters through the mouth to exit without
continuing through the entire digestive tract. In many of the invertebrate chordates,
these function as suspension feeding devices; in vertebrates, they have been modified for
gas exchange, jaw support, hearing, and other functions.
A muscular, postanal tail which extends posterior to the anus. The digestive tract of
most nonchordates extends the length of the body. In chordates, the tail has skeletal
elements and musculature, and can provide most of the propulsion in aquatic species.
Chordates have a segmented body plan, at least in development. This segmentation evolved
independently from the segmentation of annelids.
Three subphyla make up the phylum Chordata:
Subphylum Urochordata (tunicates): the adults are enclosed in a tunic made of a carbohydrate much like cellulose. They squirt water out of an excurrent siphon. Urochordates
are characterized by errant (mobile and active) larvae and sessile adults. All are filter
feeders. The only "chordate" characteristics retained in adult life are the pharyngeal slits.
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Larval urochordates look more like adult cephlochordates & adult vertebrates than adult
urochordates.
Subphylum Cephalochordata: Cephalochordates are known as lancelets because of their
blade-like shape; they are also known as amphioxus. They are marine animals and usually
live on the bottom, but can swim.
Subphylum Vertebrata (vertebrates) ...
Formally, the phyla Urochordata and Cephalochordata are considered invertebrates.
23.40.1 Subphylum Vertebrata

Vertebrata refers to the presence of vertebrae and a vertebral column.
This subphylum includes most of the animals with which most people are familiar.
Vertebrates show extreme cephalization.
The notochord generally is replaced by the cranium & vertebral column in adults.
Neural Crest Cells
Later in development, these give rise to many cells of the body, including some cartilage
cells, pigment cells, neurons & glial cells of the peripheral nervous systems, much of the
cranium, and some of the cells of the endocrine system.
Some scientists would like to classify the neural crest as the fourth germ layer.
Neural crest cells come from the dorsal edge of the neural plate, thus ectoderm.
126
24 Chordates
The phylum Chordata includes three subphyla. These include vertebrates and invertebrate
chordates.
24.1 Characteristics
Notochord: the rod-shaped supporting axis found in the dorsal part of the embryos of all
chordates, including vertebrates
Flexible, non-collapsible rod dorsal to the gut/coelom and below the nervous system,
hydrostatic, fluid wrapped in tough connective tissue. As bone does not compact, muscles
tensed on one side result in movement instead of shortening the animal. This allows much
better locomotion than do cilia for larger animals in water, a crucial victory for later success.
Pharyngeal slits: Slits in the pharynx originally used to gather food, water enters the mouth,
passes through pharynx and out gill-like slits, passing through a cavity called an antrium
and then outside. In humans, present only in embryo.
Dorsal nerve cord: A neural tube dorsal to the notochord
Postanal tail: Elongation of the body and notochord, nerve cord and muscles past anus into
tail, early locomotive function led to success.
Non-synapomorphic characteristics (not limited to chordates):
bisymmetrical (bilateral symmetry)
segmented muscles and bones
24.2 Subphylum Urochordata

The tunicates are located in this subphylum. Along with the subphylum Cephalochordata,
these two subphyla make up the invertebrate chordates. Only the tunicate larvae have
notochords, nerve cords, and postanal tails. Most adult tunicates are sessile, filter-feeders
which retain their pharyngeal slits. Adult tunicates also develop a sac, called a tunic,
which gives tunicates their name. Cilia beating within the turnicate cause water to enter
the incurrent siphon. The water enters the body, passes through the pharyngeal slits,
and leaves the body through the excurrent siphon. Undigested food is removed through
the anus. Tunicates are hemaphrodites and can reproduce asexually through budding.In
urochordates notochord is confined to larval tail.These lack cranium. These have an open
type of circulatory system.Excretion is by neural gland,nephrocytes.
127
Chordates
24.3 Subphylum Cephalochordata

The lancelets are located in this subphylum. Along with the subphylum Urochordata, these
two subphyla make up the invertebrate chordates. Lancelets receive their name from their
bladelike shape. They resemble fish but they are actually scaleless chordates only a few
centimeters long. They spend most of their time buried in the sand with their mouths
protruding. Fossils of lancelets have been found to be over 550 million years old.
Dropped out sessile stage, what was the larval stage is now sexually reproductive. Includes
Branchiostoma (amphioxus).
24.4 Subphylum Vertebrata

(Vertebra from Latin vertere, to turn). Characterized by separate bones or cartilage blocks
firmly joined as a backbone. The backbone supports and protects a dorsal nerve cord.
Vertebrates have tissues which are organized into organs which in turn are organized into
organ systems.
All vertebrates share the following characteristics: - segmentation - a true coelom - bilateral
symmetry - cephalization - a backbone - a bony skull - a closed circulatory system - chambered
heart - two pairs of jointed appendages - tissues organized into organs
Vertebrate Organ Systems: - Nervous System - Circulatory System - Digestive System Respiratory System - Reproductive System - Excretory System
Vertebral column: Not present in higher vertebrate adults. (In humans, the gel-like,
spongy core of the vertebral column is the only remainder. Ruptured or herniated disc is
an injury to this.)
Cranium: Composite structure of bone/cartilage. Two functions: 1. Supports sensory
organs of head and 2. Encloses or partially encloses the brain.
What evolutionary relationship could we imagine between sessile echinoderms and the higher
chordate animals?
Paedomorphic (child-form) hypothesis: basically, evolution of sexual reproduction in what
had previously been a larval life stage, or the retention of at least one juvenile characteristic
into the adult (adult = sexually reproducing) stage. Some scientists believe that this occurred
in a proto-chordate animal lineage. Maybe chordates (and vertebrates) arose from sessile
(attached) ancestors. Selection in these proto-chordates maybe began to favor more time in
the larval stage, as feeding was more successful or mortality lower in this stage. As larvae
got bigger physics shows that the cilia become less efficient for locomotion, favoring the
undulating motion allowed by a notochord.
Is this hypothesis crazy? A similar example of this today is Epemeroptera, the mayfly, which
has almost abandoned its adult stage. Its one-year lifespan is mostly larval with just a brief
day of reproduce-and-die as an adult, which doesnt even have usable mouthparts.
Tunicate (sea squirt) larva has all four chordate characteristics, although adult sessile
(attached).
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Subphylum Vertebrata
24.4.1 Class Agnatha

"jawless fish"
Ostracoderms: extinct Agnathans which had primitive fins and massive plates of bony
tissue on their body.
Cyclostomes: "circle mouth" - a group of Agnathans which is still alive in the form of
lampreys and hagfish.
Appeared approximately 500 million years ago and dominated the oceans for about 100
million years. The first group of fish to appear. They had neither jaws, paired fins, nor
scales, but they were the first organisms with a backbone.
Class Acanthodia
"spiny fish" Appeared about 430 million years ago. An extinct class of fish that developed
jaws with bony edges. They had internal skeletons made of cartilage and some bone.
Class Placodermi
Appeared about 410 million years ago, dominated the sea for about 50 million years. An
extinct class of fish with massive heads.
24.4.2 Class Chondrichthyes

"cartilaginous fish" Appeared about 400 million years ago with bony fish. Includes sharks,
skates and rays, and chimaeras. Their skeletons are made of cartilage strengthened by the
mineral calcium carbonate.
The main characteristics and distinguishing features of this class: - gills - single-loop blood
circulation - vertebral column - presence of placoid scales on their bodies - internal skeleton
of cartilage - paired, fleshy pectoral and pelvic fins - asymmetrical tail fin prevents sinking fatty liver provides neutral buoyancy - visceral clefts present as separate and distinct gills no external ear - oviparous - internal fertilization - ectoderms - cold blooded
24.4.3 Class Osteichthyes

"bony fish" Appeared about 400 million years ago with cartilaginous fish. Includes about
95% of today's fish species.
Subclass Sarcopterygii
fleshy-finned fishes. Fins have bones and muscles, homologous to our limbs.
Order Dipnoi
lung fishes, two groups isolated when continents separated
129
Chordates
Order Crossopterygii
includes coelacanths and rhipodistians, gave rise to amphibians, had lungs which evolved
into a swim bladder in bony fishes, and labyrinthodont teeth, characterized by complex
folding of enamel.
Skeleton made of bone, jaws, fins, most with scales, two-chambered heart.
24.4.4 Class Amphibia

means both lives, aquatic larvae, terrestrial adult Amphibians: - Legs - Lungs - DoubleLoop Circulation - Partially Divided Heart - Cutaneous Respiration (Breathes through
Skin)
Order Salientia
frogs (jumping) (aka Anura)
Order Urodela
salamanders (tailed)
Labyrinthodont amphibians: oldest known amphibians, inherited characteristic teeth from
crossopterygii ancestor, had stocky, aquatic larvae.
Amphibians have limbs instead of fins. Girdles and vertebral column now more substantial
and connected, support body on legs.
Lisamphybia: no scales, smooth, eggs with no shell, laid in water (water-reliant).
Amphibians gave rise to cotylosaurs, from which arose dinosaurs, turtles, lizards, and
therapsids.
Class Reptilia
amniotic egg allowed freedom from water, shelled egg. (Amnion: protection). Reptiles have
four extra-embryonic membranes:
Amnion: supports aquatic environment inside egg in fluid sac.

Allantois: allows gas exchange and elimination of wastes.
Chorion: gas exchange
Yolk sac: only one of the four left over from amphibian ancestor
Reptiles cold-blooded, or ectothermic, meaning that their heat come from their environment.
Sometimes defined as all amniotes that are not birds or mammals.
Reptiles can be classified by skull structure into four groups:
Anapsid
Synapsid
Diapsid
Euryasid
130
Refers to number of holes in the skull. Cotylosaurs had Anapsid skull
Dermatocranium: from bony outer skull structure, precursor to human cranium.
Subclass Anapsidia
Subclass Testudinata
turtles1 , terrapins
Subclass Diapsida
dinosaurs2 , snakes3 , most stuff
Subclass Synapsida
Order Therapsids
Subclass Diapsida
includes Ichthyosaurs, marine reptiles convergent on dolphins; Plesiosaurs, ancient sea
monsters; Squamates, including lizards and snakes; and Thecodonts, which gave rise to
birds
dinosaurs
crocodilians
Dinosaurs: broken into two groups, based on hip structure
Saurischia: lizard hips (gave rise to birds [!]), ancestrally bipedal
Ornithischian: bird hips, ancestrally quadripedal
Crocodilians: come from archosaurs, the only extant (still living today) archosaur descendant.
Ancestrally bipedal, secondarily quadripedal.
Synapsids: refers to joined (Greek syn-, together with) parts of skull. Led eventually to
mammals. Synapsid pelycosaur >> therapsid >> mammals
Pelycosaur: Sail-backed dinosaur, legs not spread out like lizard but more pillar-like and
under body, allowing greater activity and competence in motion, pendulum like rather than
constant push-up. Teeth differentiated into different types, for pre-processing of food needed
by higher metabolism. Skull changes, bone histology, suggestions of warm-bloodedness.
1
2
3
http://en.wikibooks.org/wiki/turtle
http://en.wikibooks.org/wiki/dinsosaur
http://en.wikibooks.org/wiki/snake
131
Chordates
Class Aves
arose late Jurassic, early Cretaceous. Feathers, skeleton modified for flight. Feathers:
epidermal derivative, made of keratin (like fingernails). Carpometacarpis: bears primary
flight feathers, parallel to hand parts. Keeled sternum: breastbone, powerful one needed
to support flight muscles. Strong, light, occasionally hollow bones. All birds lay eggs (as
contrasted to reptiles, which have developed live birthing over 100 independent times.) Why
are there no live-bearing birds? Early birds had teeth, lost them. With mammals, only
exothermic animals.
Archaeopteryx: ancient wing, Jurassic bird-reptile, very dinosaur-like. Good fossils found
in Zolenhoffen, German sandstone mine with fine sand, shows feathers clearly, found shortly
after Darwins publication and used to support his hypothesis. Thick, heavy bones and no
sternum, bony tail, not a good flyer but did have primary flight feathers.
Archaeornithes: includes archaeopteryx.
Paleognathae: gave rise to Australian flightless birds.
Neognathae: remaining live birds.
Class Mammalia
Two unique characteristics, or synapomorphies:
Hair
Mammary glands
(dont fossilize well)
Three skeletal characteristics (fossilize)
Lower jaw only one bone, the dentary (several in reptiles)
Three bones in middle ear: malleus, incus, stapes (reptiles have one or two, never three)
Joint between upper and lower jaws between dentary and squamosal of skull (in reptiles
this joint is between other bones)
Mammals basically have a synapsid skull design inherited from ancestor
Non diagnostic characteristics (not unique to mammals):
Warm-blooded
Skin glands: sweat glands and oil-producing sebaceous glands
Large nasal cavities (because of high metabolism) Clean, warm and humidify air
Heterodonty (differentiated teeth)
Diphiodonty: two sets of teeth: baby and adult (deciduous teeth, drop out) (reptile
teeth are continually replaced)
Subclass Protheria
monotremes (Greek mon-, one; and trema, hole), or egg-laying mammals, have one opening
for excretion and urination.
132
Subclass Theria
Metatheria: Marsupials (opossum, kangaroo. . . ) Eutheria: Placental mammals (all common
mammals)
Marsupium: (from Greek marsypion, purse or pouch). Gestation period much shorter than
in Eutherian mammals, but after leaving the uterus the tiny offspring crawls into a pouch
where it completes development latched onto a teat.
Recent molecular (read: genetic) evidence suggests that two different mammal groups
may have developed live-bearing ability separately. Instead of being a rough draft for
placental-style live bearing, perhaps the marsupial pouch approach is another solution to
the same problem. Advantage: in tough times the parent can pitch out the offspring and
increase its own chance of survival.
133
25 Tissues and Systems
135
26 Epithelial tissue
Comes from various sources, ectodermal or endodermal material. Cell sheet lines a
surface or body cavity. One side, called freesurface or Apical, is exposed to
animal interior (forming the lumen) or
exterior of its body cavity.
The other side rests on the basal layer.
Epithelial tissue is not penetrated by blood vessels.
Two categories:
sheets
glands
Classified on two features:
simple, (a single layer of cells),
stratified, (more than one cell layer.)
Cell shape at free surface:
squamous (broad and flat)
cuboidal (spherish)
columnar (tall and thin)
Simple squamous epithelium
usually lines body cavities and vessels,alveoli, glomeruli of kidney; in blood and lymph
vessels called endothelium; in body cavities called mesothelium (serosae): parietal serous
membranes line body wall, visceral serous membranes cover organ
Simple cuboidal epithelium
in ducts like kidney and salivary glands.
Simple columnar epithelium
nonciliated type lines digestive tract, ciliated type lines some regions of uterine tubes and
lungs
Stratified squamous epithelium
(important) lines mouth, esophagus,and vagina. Cells sometimes dead, flat and keratinized,
making them resistant to abrasion. Stratified squamous epithelium changes to columnar
squamous epithelium progressively down esophagus to the stomach.
Epidermis
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Epithelial tissue
from epithelium. Below this is dermis, thicker and with blood vessels.
Two specialized epithelia:
pseudostratified
transitional
Pseudostratified epithelia
lines the trachea (where it is ciliated)and the male urethra (where it is non ciliated), looks
stratified but not.
Transitional epithelia
found only in bladder and urinary system. As it stretches it appears to go from 6 to 3 cell
layers deep.
Glandular epithelia
(gland: group of cells that excretes something.. mostly derived from epithelium. Glands
are classified into endocrine and exocrine by where they excrete.
Endocrine glands
secrete hormones into the blood without use of ducts.
Exocrine glands
secrete onto the body surface or into a cavity, thru a duct. Exocrine substances include
sweat, mucous, oil, and saliva. An exocrine gland is the liver, which secretes bile.
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27 Connective tissue
This is a grab bag category of diverse tissue types. Functions include binding and
supporting. Types include bone, cartilage, fibrous connective tissue, blood and
adipose (fat) tissue.
If you took away everything in the body except the connective tissue, youd still be able to
see the basic form of the body.
Form: distinctive cells surrounded by a cell matrix made of extra-cellular fiber grounded
in a ground substance (excluding blood)
Types:
1. connectile connective tissues (can be 1. loose or 2. dense)
2. special connective tissue (includes blood, bones and cartilage).
Fibroblasts form connective tissue proper;
chondoroblasts form cartilage;
osteoblasts form bone;
and blood is formed from various sources.
Ground substance: unstructured material that fills space between cells and contains
fibers. Made of
1. interstitial fluid (bathes cells)
2. proteoglycans (protein core with attached polysaccharides, glycoaminoglycans or GAGs
such as chondroitin sulfate, keratin sulfate, and hyalronic acid, whose consistency is syrupy
to gelatin-like)
3. cell-adhesion proteins (connect connective tissue cells to the fibers).
Fibers of connective tissue:
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Connective tissue
1. Collagen (flexible protein resistant to stretching, tensile strength, most abundant
protein in animals, white)
2. elastin (rubbery, resilient protein, in dermis, lungs, blood vessels, yellow when fresh)
3. andreticulin (like collagen).
Loose connective tissue: found beneath skin, anchors muscles,nerves etc. Include fibroblasts, macrophages, mast cells,and adipose cells. Fibers include collagen and
elastic fibers. Ground substance is syrupy. Adipose included.
Dense connective tissue: largely densely packed fibers of collagen or elastin regularly
or irregularly arranged. Forms tendons and ligaments, coverings of muscles, capsules
around organs and joints, and dermis of skin.
Cartilage vs. bone
Feature
cell type
ground substance
vascularization
micro architecture
units called
fibrous sheath
Bone
osteocytes
calcium phosphate
vascular
highly ordered
osteons
peristeum
Cartilage
chondrocytes
chondroitin sulfate
avascular
less organized
perichondrium
Cartilage: There are three cartilage types:

1. hyaline cartilage
2. fibrocartilage (fibrous cartilage)
3. elastic cartilage
Hyaline cartilage: most widespread cartilage type, in adults forms articular surfaces of
long bones, rib tips, rings of trachea, and parts of skull. Mostly collagen, name refers to
glassy appearance. In embryo, bones form first as hyaline cartilage, later ossifies. Found
in tracheal rings. Few collagen fibers.
Fibrous cartilage: have lots of collagen fibers. Found in intervertebral discs, pubic
symphesis. Grades into dense tendon and ligament tissue.
Elastic cartilage: springy and elastic. Found in internal support of external ear and in
epiglottis, yellow when fresh.
Chondrocites (cartilage cells) rely on diffusion for nutrients, as cartilage has no direct
blood supply, and no enervation (nerves). Can be loaded with calcium salts.
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Bone: Specialized connective tissue, calcium phosphate arranged in highly ordered unit
called osteon, or Hyvercian system. Concentric rings around central canal with blood
vessels and enervation (nerves). Bone varied, not all vertebrate bone is even cellular. Our
concern: simple pattern for mammals.
Lacuna (spaces in which osteocytes found); canaliculi (little canals) bigger diagonal cells,
layers of bone called lamellae.
Three types of bone cells, ending in
-blast, (mend bone)
-cyte (fortify bone)
-clast (tear down bone)
Classified by
1. appearance (spongy vs. hard)
2. where found (outside or inside)
3. how it is formed (endochondral cartilage model forms first and then is ossified, and
entramembranous, bone forms directly without cartilage precursor)
Example of endochondral bone formation: long bone begins to ossify from center shaft,
calcified region expands and cuts off diffusion of nutrients as bone replaces cartilage. In
young mammals, secondary ossification centers then form at bone ends, growth has stopped
by sexual maturity as all primary bone is ossified. In other animals, bones continue growing
throughout their lifetime.
Three types of intramembrous bone:
1. dermal bone
2. sessamoid bone
3. perichondral bone.
Dermal bone forms skull, shoulder/pectoral girdle, and integument, descended from dermal
armor of ancestor. Comes from mesoderm, in dermis of skin.
Sessamoid bones: form directly in tendons. Example: kneecap, also in wrist. Deals with
stress.
Perichondral bone means around cartilage, forms around cartilage or bone. Functions in bone repair and in ossification of endochondral bone.
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Connective tissue
Bone remodeling and repair: bone has mineral structure, and develops tiny fractures,
which, under stress, can lead to larger fractures. To combat this, bone is constantly replaced.
Osteoclasts channel through existing bone, tear down and leave behind osteoblasts
and lacuna, leaving osteocytes. Continually resets mineral structure of bone, and is
preventative maintenance.
When bone broken, callus forms in open ends, periosteum gives rise to new bone with
calcium and new bone matrix, leaves irregular mend. Later, osteoblasts continue fixing over
time and slowly removing imperfection.
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28 Muscle tissue
Mesodermal in origin, muscle has several functions: supply force for movement, restrain
movement, proper posture, act on viscera (internal organs) for peristalsis (moving food
down digestive tract), give body shape, form sphincters, (such as in esophagus, between
stomach and intestine, large and small intestine, in anus), in sheets of muscles, affect air
flow in and out of lungs, line blood vessels and play vital role in circulation.
Secondary roles: heat production (shivering a specialized heat production to supplement
metabolism).
Muscles co-opted to other non-original functions: sharks detect electrical field created by fish
muscles. Some fish formed electric organs, create current strong enough to repel predators
or stun prey. Other fish can use field as radar to see things and communicate with other
animals. (Evolved independently in different groups).
Different classifications: by color, (red or white) location, nature of nervous system
control (voluntary or involuntary), embryonic origin, or by general microscopic appearance (striated, smooth, and cardiac.)
Striated muscle (or skeletal muscle): under voluntary control. Individual cells called
fibers, grouped into fascicle. Myofibrils founding one cell made of even smaller myofilaments. Each striated cell very long and multi-nucleated. Fibers joined end to end to
form longer composite fibers. Sarcomeres: repeating units make up myofibrils. Two
kinds of myofilaments, thick kind made up of myosin and thin of actin. Striations visible
in light microscope, smaller part only with electron microscope.
Cardiac muscle: occurs only in heart. Light banding visible under light microscope.
Each band short, principally mononucleate (occasionally dinucleate) often branched, joined
together with intercollated discs. Involuntary. Waves of contraction spread through intercollated discs. Initiated by nerve stimulation or can originate in the heart itself (useful in heart
transplants.)
Smooth muscle: no striations visible with light microscope. Almost entirely visceral
function: digestion, sphincters, urogenital tracts, piloerectory muscles (make hairs stand up),
lungs. Non-voluntary control. Slow and sustained action. Each cell mononucleate, short,
fusiform (spindly) in shape, cells usually uniform in size.
Striated muscle contraction: Muscle broken into units called fascicles, in units of myofibrils.
Repeating units called sarcomeres, consisting of two kinds of myofilaments:
1. thick, myosin filament
2. thin, actin filament.
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Muscle tissue
Sarcomere: Thick and thin filaments interspersed in ordered grid.
Sliding filament theory: thick and thin filaments move past each other in opposite
direction, shortening length. Longer muscles contract more rapidly than short ones (see cell
bio for details).
Myosin molecule: two polypeptides twisted together with two globular heads at end.
Myosin filament: many slender myosin molecules together.
Actin filament: chain of actin single, tropomyosin strands with repeated globular
troponin, and with actin. All play role in muscle contraction. Myocin heads have sites
that bind to actin. Actin filaments have many regular sites that can bind to myosin.
Troponin has four sites:
1. one to bind myosin
2. one for actin
3. one for tropomyocin
4. one for calcium ions
Nerve signal reaches muscle, triggers release of chemical signal called neurotransmitter,
that diffuses across cell membrane (sarcolimic reticulum) and binds to receptors in it.
Receptor is acetylcholine, ACH. When there is enough nerve signal, the message travels
through t-line to sarcoplasmic reticulum to release calcium ions.
Lacking calcium, tropomyosin site blocked. In calcium, myosin binding sites exposed and
heads bind to actin molecules, delivering force to move fibers in relation to each other.
Myocin head then interacts with ATP to get recocked, if myosin still exposed then it
fires again and results in further muscle contration. If there is no further nerve signal,
sarcoplasmic reticulum sequesters Ca+ ions again and no recocking occurs.
Quirari (or curare): known from movies, used in South America, blocks acetylcholine
receptors in cell and causes skeletal paralysis. Victim dies of asphyxiation because he cant
breathe.
Duchenne's muscular dystrophy: degeneration of sarcolema, plasma membrane of
muscle cell unable to release signal and quickly atrophies.
Fast and slow twitch fibers: vertebrate muscle fiber. Terms relative within one group
of animals. Differences related to differences in enervation, type of myocin, and actin
activation.
Two parts of force generated by muscle: 1. active component 2. elastic component (energy
stored in muscle when stretched by gravity or another force. Stored in muscle elastic tissue
around tendons. Especially important in limb oscillation, like running, or trunk twisting,
like fish swimming. Up to 90% of stored elastic energy can be recovered.)
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How does a muscle match its power to its job? Two ways:
1. rate modulation, derived from frequency of nervous stimulation of muscle, force
increases as frequency of stimulation increases up to point of tetanus.
2. selective involvement of motor units, a given neuron enervates a fixed number of
muscle cells, (a motor unit), and force is increased by recruiting more motor units. Motor
units may be small, such as in eye, or larger, like in leg muscle.
How do muscles grow stronger?
1. add more myofilaments, increases cross sectional area by up to 50%, more little ratchets
working
2. proliferation in blood vessels and connective tissue around muscle
Muscle strength is relative to cross sectional area, not length. Not always feasible to add
more cross sectional area.
Pinnate fibers: oriented obliquely (Y-shaped) to minimize muscle mass, in certain circumstances, like calf muscle. Spreads muscle out.
Velocity of shortening greater in long muscle than short. Why? Contraction tied to relation
between fibers, and to total length of muscle. Both long and short muscles reach same
percentage of contraction in same unit time, but distance covered by the longer muscle is
greater.
Synergist muscles: muscles work together to produce motion in same general direction.
Bicep shares work with brachialis.
Antagonist muscles: muscles that oppose each other. Bicep pulls forearm in, triceps pulls
it back out.
Origin vs. insertion: origin is the end of the muscle that more fixed in its attachment to
the body. The more movable end called insertion.
Fixators: muscles that act to stabilize a joint or lever system. Like upper arm when you
clench your fist hard.
Flexors and extensors: applied mainly to limbs. Flexor bends one part relative to another
about limb, extensor straightens it.
Adductor and abductor: adductor draws a limb toward the ventral surface. Abductor
moves limb away from ventral surface. (Adduct: drawn toward; abduct: carry away).
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29 Vertebrate digestive system

Functions to break down food into molecules small enough to absorb, or pass across digestive
membrane.
Digestive tract: tube extending from lips of mouth to anus or cloacae in bird, reptile or
monotreme.
Lumanal glands: empty into inner body cavity (lumen: inner surface).
Tract divided into three main regions: 1. buccal cavity 2. pharynx 3. alimentary canal
Alimentary canal divided into four regions: 1. esophagus 2. stomach 3. small intestine 4.
large intestine
Accessory digestive glands, outside digestive tract proper, secrete into lumen of tract
through ducts. Includes the salivary glands, liver and pancreas.
Buccal cavity, which includes palate and tongue, develops from infolding of stomadeum,
or second opening of blastula, whereas the rest of the digestive tract develops from the
primitive gut.
Teeth: capture and hold prey. In mammals in particular further process and break down
food into small particles, increasing surface area available for enzymatic action.
Tooth anatomy: 1. crown projects above gum, 2. root below gum, 3. enamel is outer
coating of crown, hardest surface in body, of epideral origin 4. dentin, below enamel,
bone-like and forms bulk of tooth, is harder than bone and contains nerves and blood vessels.
(Remember that mammals are heterodontic, with different types of teeth).
Pharynx: air passage for adult, gill slits in embryo. Important in lower vertebrates, site of
gills. Features derived from pharyngeal region: first pharyngeal pouch gives rise to parts
of the ear, other pouches give rise to various other structures.
Alimentary canal: epithelium lines lumen, glands secrete into lumen, longitudinal and
circular muscles help digestive movements (peristalsis).
Esophagus: tube carries food from mouth to stomach. Expands to fit large bolus (lump
of chewed food). Secretes mucus for lubrication. Birds have crop for storage, enlargement
of esophagus.
Epiglottis: keeps food out of air tube, an evolutionary kludge, or fix.
Stomach. Absorbs water, alcohol, nutrients, uses gastric juice with enzymes, mucous, HCl,
released by chief and parietal cells (release protein enzymes) in gastric pits. Rugae: folds
of stomach, disappear when full. Sphincter at both ends of stomach, control food passage.
Chyme: semi-digested food released to small intestine.
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Vertebrate digestive system

Small intestine: three regions, duodenum, jejunum, and ileum.
Duodenum site of most intestinal digestion. Jejunum and ileum do most of intestinal
absorption. Ileum ends with another sphincter, ileocolic valve or ileosecal valve. Structure:
Circular folds covered with villi (singular is villus).
Villi: finger-like cellular projections, covered with microvilli, tiny projections which increase
surface area. Increases surface area by 900x, speeds digestion (break down) and absorption
(taking in nutrients).
Large intestine: larger diameter, shorter length than small intestine. No villi. In mammals,
forms large gentle loop, colon, empties into straight region, rectum, empties into outside
world through anal sphincter. Colon: absorbs water left over, also absorbs vitamins released
by bacteria which live there (vitamin K).
Food: made up of 1. proteins, 2. fats, 3. carbohydrates 4. fibrous material.
Digestive system breaks foods down. Proteins must be broken to amino acids to be
absorbed. Polysaccharides to monosaccharides, lipids to fatty acids and monoglycerides to absorb.
Salivary glands in mouth, saliva contains mucous, salt and a few enzymes (amalase, begins
starch breakdown). Snake venom from oral gland, mixture of toxins and digestive enzymes.
Breaks down blood vessels and disables nervous system.
Stomach enzymes: released in inactive form, zymogene, converts to active form in lumen
of gut. Transformation is triggered by another enzyme, or the stomachs low pH. Pepsin
secreted as pepsinogen (-ogen means primitive form). Stomach glands secrete up to two or
three liters a day of gastric juice, which is reabsorbed.
Chyme released to duodenum.
Small intestine has two major accessory glands: 1. pancreas 2. liver
Pancreas has endocrine and exocrine functions, releases large amounts of carbonate to
neutralize acidic chyme, as intestinal enzymes work in neutral pH, and stuff to break down
lipids and starch (zymogens, like tripsin)
Liver releases bile. Bile made from cholesterol, stored in gall bladder, released in
duodenum, emulsifies fats.
Emulsify: keeps fats in tiny drops, which are suspended, increasing surface area and action
of lipases. Protein and carbohydrates absorbed in intestine, taken to liver for processing.
Fatty acids go to lymphatic system
Appendix: vestigial remnant. Much variation in digestive systems within mammals:
herbivore, carnivore, insectivore, non-ruminant herbivore.
Rumen: four-chambered stomach of animals like cows (ruminant herbivores). Cellulose
resistant to digestion, rely on microorganisms to break down cellulose. Some bacteria,
protists and fungi can break down cellulose, almost no animals can. Bacteria break down
cellulose in rumen, to be taken back to the mouth to chew their cud (ruminate). Later cow
swallows to proceed with digestion. (Horses not like this).
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Coprophagy: rabbits and other animals eat their own feces for the nutritious products of
the cecum.
149
30 Circulatory system
Circulatory system functions
1. Transportation
a. Respiration: gas exchange (O2 and CO2), overcomes limited rate

of
diffusion
b. Nutrition: 
c. Excretory: (remove metabolic wastes) 
2. Regulation
a. Transport hormones 
b. Regulate body temperature 
c. Protection 
i. Blood clotting 
ii. Immune system (carries white blood cells)
Vasodilation: allows heat loss across epidermis, as seen in elephant ears, takes more blood
to surface of body, sweating may accompany
Countercurrent heat exchange: used by dolphins in fins to conserve heat in cold water.
Veins surround an artery, and blood returning to body absorbs heat from blood traveling
out from body to fin, minimizing heat loss. Used by dogs in feet, etc.
Blood made of 1. plasma and 2. formed cellular elements (red and white blood cells,
and platelets).
Plasma makes up 55% of blood volume. Cellular elements make up the other 45%.
Plasma makeup: 90% water, 7-8% soluble proteins (albumin maintains blood osmotic
integrity, others clot, etc.) 1% electrolytes 1% elements in transit
Red blood cell (erythrocyte): contains hemoglobin, functions in oxygen transport. In
mammals, red blood cells lose nuclei on maturation, and take on biconcave, dimpled, shape.
No self repair, live 120 days. About 1000x more red blood cells than white blood cells.
About 7-8 micrometers in diameter.
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Circulatory system
Hematocrit: proportion of blood volume that is occupied by cells, about 43% in humans
on average. 48% for men and 38% for women.
White blood cells (leukocytes): Nucleated, about 10-14 micrometers in diameter, commonly amoeboid, escape circulatory system in capillary beds. Include basophils, eosinophils,
neutrophils, monocytes, B- and T-cell lymphocytes.
Platelets (thrombocytes) Membrane bound cell fragments in mammals, no nucleus. In
non-mammals, platelet role replaced by nucleated cells. Accumulate at site of broken blood
vessels, form clots. Bud off special cells in bone marrow. 1-2 micrometers in diameter. 7-8
day life span, 1/10 or 1/20 as abundant as white blood cells.
Arteries: carry blood away from heart. Smallest tubes called arterioles, feed blood to
capillaries.
Veins: return blood to heart. Smallest veins called venules.
Structure of arteries and veins, listed from inside (lumen) out: 1. epithelium (endothelium),
2. elastic connective tissue fibers, 3. smooth muscle, 4. connective tissue. Arteries
have thicker elastic layer than do veins.
Capillaries, where exchange of materials occurs, are very thin and narrow, and red blood
cells pass through single file. Capillaries are tiny but numerous, and their total volume is
greater than that of supplying arteries.
Blood velocity drops in capillaries, picks back up in veins. Pressure highest in arteries, lower
in capillaries and arteries.
Osmotic pressure draws interstitial fluid from blood in arterioles, but replaces it in venules.
One-way valves mean that blood can flow only one way, works with residual blood pressure
and compression by skeletal muscles. Low pressure in thoracic cavity caused by breathing
also helps move blood.
Lymphatic system: part of the immune system, a one-way, or open, system. Takes up
interstitial fluid not taken up by venules.
Lymphatic structures:
1. lymphatic capillaries
2. lymphatic vesicles
3. lymph nodes
4. lymphatic organs (spleen and thymus)
Lymph: movement in mammals through one-way valves, similar to blood movement in
veins. (Some non-mammals have lymphatic hearts of unknown embryonic origin. Frogs and
salamanders have several.) Lymph rejoins cardiovascular system into a large vein near the
heart via single large thoracic duct.
152
As lymph passes through system, passes lymphocytes, second part of immune system.
Heart: pumps blood, design varies between animals. In adult mammal,four chambers form
two separate circulations
1. pulmonary circulation to and from lungs and
2. systemic circulation to and from tissues of body.
Everything in the heart comes in pairs: 2 atria, 2 ventricles (left and right).
Diagrams usually drawn as though animal were on its back.
Pattern of blood flow through heart: blood returning from major veins (vena cava)
enters right atrium, contraction there delivers blood to right ventricle through a tricuspid
valve, one of atrial ventricular valves (AV valve). Contraction of right ventricle drives blood
through semi lunar valve into pulmonary circuit and to lungs.Blood return to heart in
pulmonary veins, is oxygenated. Goes to left atrium, which contracts and delivers blood
to left ventricleby way of aortic semi-lunar valve, then goes to systemic circulation.
Both atria and ventricles contract in unison, left is more powerful than right (to all system
vs. just lungs).
Systole: heart contraction, diastole: heart relaxed
Timing of heart contraction: ventricles rebound to relaxed shape (diastole), and semilunar valves close. Both atria(singular: atrium) fill with blood coming from pulmonary
and systemic circulations.Pressure rises in the atria and blood begins to move into the
ventricles.The atria then contract, forcing more blood into the ventricles. There is a pause,
then ventricles contract. This raises ventricle pressure, atrio-ventricular(AV) valves
shut and semi-lunar valves open, forcing blood from the left ventricle into the major arteries
and from the right ventricle into the aorta.
Control for this action doesnt rely on nervous stimulation, has intrinsic rhythmicity, called
myogenic. This is the case in mammal as well as in mollusk hearts. Other animals have
neurogenic hearts that rely on nervous stimulation for heart action, originating in the
cardiac ganglion.
The rhythmicity of mammalian heart relies on the sino-atrial (SA)node, or pacemaker.
This is a phylogenic (based on evolutionary history) remnant of an early vertebrate heart
that had one more chamber than modern hearts.
How the heart contracts: waves of depolarization start in SA node and spread
through atria. Connectile tissue pauses the spread of depolarization at the atrial ventricular
node. Signal continued by bundle branches to lower ventricle, begins to stimulate
heart to contract. Contraction starts at bottom of heart at heart apex,then signals spread
through heart.
Medulla (in the brain) controls autonomic nervous system. (The medulla is part of
the brain, is continuous with the spinal cord, and controls involuntary actions of the
body). Sympathetic cardiac acceleratorconnects to spinal cord, uses norepinephrine
to signal. Parasympathetic cardio-inhibitory center reaches heart through Vagus
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Circulatory system
nerve, usesacetylcholine to signal. Hyperpolarizes membrane to inhibit heart contraction.
(Autonomic nervous system: two parts working in contra to control from both sides.)
Dominant effect here is inhibitory. If we cut Vagus nerve, heart rate promptly rises about
25 bpm.
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31 Respiratory system
In humans and other animals, for example, the anatomical features of the respiratory system
include airways, lungs, and the respiratory muscles.
Other animals, such as insects, have respiratory systems with very simple anatomical features,
and in amphibians even the skin plays a vital role in gas exchange.
Plants also have respiratory systems but the directionality of gas exchange can be opposite
to that in animals. The respiratory system in plants also includes anatomical features such
as holes on the undersides of leaves known as stomata.
In mammals, the diaphragm divides the body cavity into the
abdominal cavity: contains the viscera (e.g., stomach and intestines)
thoracic cavity: contains the heart and lungs.
Respiratory tree: terminates in alveolus, alveoli. Respiratory bronchioles branch into

alveolar ducts and into alveoli. Alveolus: microscopic air sacs, 300 million of these in human
lungs. Total surface area large. Gas diffuses micrometer, very tiny distance.
Nervous System
Composed of tissues designed to integrate sensory information and direct a coordinated
response to the environment.
Basic unit of the nervous system is the neuron1 , a highly specialized cell that uses both
electrical and chemical processes to communicate. Neurons "listen" to sensory organs or
other neurons, and can simultaneously "hear" from 1 to hundreds of inputs simultaneously.
Likewise, a neuron can "talk" to other neurons or cells that can create an action, like muscle
cells or glands.
Neurons are outnumbered in the nervous system by glia. Glia were once thought to only play
a supportive role in helping neurons survive; today we know that they also are important
participants in the communication process. Glial cells include astrocytes, ependymal cells,
and a cell that has a macrophage like function. There are also oligodendocytes and Schwann
cells that provide a myelin sheath.
http://en.wikipedia.org/wiki/Neuron
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Respiratory system
31.1 Neuron structure
Figure 9
Neuron
Dendrite will receive information from other axons

Stoma is the neuron body and contains typical cell parts including the mitochondria and
nucleus. This is where neurotransmitters are synthesized.
Axon hillock is where the cell body and the axon meet.
Axon is surrounded by myelin.
Contains nodes of Ranvier
Types of axons include unipolar, bipolar, pseudopolar.
Action potentials results from excitatory stimuli received from the dendrites that results
in a signal that travels down the axon. On the cellular level, there is a Na+ influx via
channels causing a depolarization of the cell. Once those channels close, the slower opening
K+ channels will open resulting in hyperpolarization by the cell.
Synapses
Neurotransmitters allow a chemical signal to be sent from one neuron to the other. Neurotransmitters must bypass a physical gap called the synapse. Examples of neurotransmitters
include acetylcholine, epinephrine, and glutamate.
Example : Neuromuscular synapses
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Central nervous system

Circuits / Nuclei / Ganglia
31.2 Central nervous system

Central nervous system includes the brain and the spinal cord.
Brain There are four lobes of the brain.
Frontal lobe - decision making

Parietal lobe
Temporal lobe
Occipital lobe - vision
The areas of the brain are also dedicated to different functions.

Precentral gyrus
Postcentral gyrus
Protection The CNS is protected by three layers - the pia mater, the arachnoid mater, and
the dura mater. Protection also comes from the circulation of cerebral spinal fluid (CSF).
CSF helps to float the brain and also provide nutrients to both the brain and the spinal
cord. CSF is synthesized from the choroid plexus of the lateral ventricles. In total, there are
four ventricles - 2 lateral ventricles, a 3rd, and 4th ventricle.
31.3 Peripheral nervous system

The peripheral nervous system is broken down into two sub-systems, the somatic nervous
system and the autonomic nervous system.
ANS - Autonomic Nervous System The ANS has two components - parasympathetic and
sympathetic.
The sympathetic nervous system is the "fight or flight" or fright response and results in an
increased heart rate, increased rate of breathing, and an elevated blood glucose level. There
is also decreased digestion. The second neurotransmitter is epinephrine. In this case, the
first neuron is short and the second neuron is long.
The parasympathetic nervous system is the rest and digest system.
Drugs must be able to pass the blood brain barrier to have an effect on the CNS. Drugs act
by affecting the neuron and how likely it is to fire an action potential.
Stroke occurs when there is a blood clot that goes to the brain and prevent blood flow.
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32 Sensory systems
Categorized by
1. nature of stimulus, such as mechanical, chemicalor light stimulus, and
2. where stimulus received, such as outside (exteroceptors,such as the eye and
skin temp receptors) or insidebody (interoceptors, such as blood body temperature receptors).
Transduction of sensory input into signal. Means to carry across,signal transduced, or
carried, from environment into nervous signal.
Three sensory processes we cover
1. taste and smell (chemoreception)
2. gravity and movement
3. light
32.1 Taste and smell (chemoreception)

Found in mammal nose and mouth, fly feet, fish bodies, moth antennae.
Papilla: bumps on tongue, contain taste buds down between. Sweet, sour, salty and bitter.
Some act directly by ion channels, others act indirectly. Other taste sensations really
smell.
Smell: received in nasopharynx. Airborne molecules go into solution on moist epithelial
surface of nasal passage. Approximately 1000 genescode for sensory neuron receptors. Fried
onions odor not one receptor but a mixture of many odors registered in our mind as one.
Very sensitive, habituates rapidly (dont notice a smell after a bit). Odor sensation has
relatively unfiltered root to higher brain centers.
Snakes more chemosensory focused than us.
32.2 Response to gravity and movement

Registered in inner ear. Three semicircular canals loop in three planes at right angles
to each other, responsible for transduction of movement messages. Method: hair cells
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Sensory systems
deformed by gelatinous membrane. Vestibular apparatus, gives us perception of gravity
and movement. Due to physical response, not chemical binding.
Cochlea: bony, coil shaped part of inner ear, where hearing occurs.
Sound enters through auditory canal, vibrates tympanic membrane,moving three bones
of middle ear (malleus, incus, and stapes)against oval window opening in front of cochlea.
Cochlea has three fluid filled ducts, one of these the organ of Corti. Sound waves in air
go to vibration in organ of Corti; fluid tickles hair cells, which register the movement
along basilar membrane in cochlea. Different sound frequencies move different portions
of basilar membrane. Hearing loss due to loss of hair cells.Humans normally smell more
than 300 odors in a day(Facts and Truth).
Transduction of sound accomplished throgh physical deformation,not chemical binding.
32.3 Vision
Light enters pupil, focused by lensonto retina.
Sclera: hardened part behind retina.
Optic nerves and neurons attached to retina. Blind spot where optic nerve attaches, has
no receptors.
Two types of photoreceptors
1. rods - black and white low-light vision, 100 million in each retina in humans.
2. cones - color vision, work best under better illumination. 3 million in each retina.
Fovia: region of most acute vision, has most of the cones, few rods.
Transduction process of light to signal a molecular change, to light absorbing molecule
called photopigment. Located in outer parts of rods and cones in pigment discs. The rod
photopigment is called rhodopsin,cone has three photopigments, called photopsins. This
molecular change initiates pathways to result in action potential in downstream neuron
leading to vision center in brain.Parul Godika
Each of the three photopsins has a different peak of sensitivity: blue,green or red, and
changes isometric form (from cisto trans) based on light from a particular wavelength
range. Color blindness:inherited lack of one or more types of these cones. Gene carried on X
chromosome, therefore more common in men than women.
32.4 Homeostasis
Is a very important part of everyone's and everything's lives. Defined as dynamic constancy of internal environment, maintenance of a relatively stable environment inside
an organism usually involving feedback regulation.
160
Osmotic environments and regulations

Homeostasis is maintained in face of
1. a varying external environment, or
2. a non-ideal, constant external environment (as with the penguin).
Deals with temperature, pH, chemical concentrations,pressure, oxygen levels.
Occurs through negative feedback loops.
Various forms: simple thermostat in house turns off heater when above a certain temperature
and on when below a certain temperature Involves stimulus, sensor,integrating center,
effector and response.
More efficient control has two sensors and two effectors. Can be antagonistic to each
other, such as, one cools, the other heats.
Precise control through proportional control, not all-or-none, furnace comes on a little
bit if the house a bit cold. Examples in humans: vasoconstriction, change in metabolic rate,
shivering. Physiological responses for high body temp: blood goes to body surface, sweating,
behavioral changes (get out of sun).
Positive feedback loop: effector increases deviation from set point. Amplifies reaction.
Like blood clotting process, uterine contraction during childbirth. Negative feedback must
exist at some point for control.
32.5 Osmotic environments and regulations

1. Marine invertebrates
a) fully marine invertebrates (not intertidal or estuarine) osmoconformers (set
internal environment same as environment, no net flow of ions) in a stenohaline
(narrow non-changing salt level) environment
b) Coastal, intertidal, estuarine (ion levels fluctuate) invertebrates.Partly osmoconfomers, partly osmoregulators in a euryhaline (wide salt level variation)
environment (ex: shore crab, regulates sometimes when salt levels in environment
get real low).
2. Freshwater animals. Here, environment has lower solute concentrations than do
living organisms so water tends to flow in and solutes out.
a) Freshwater fish (bony) dilute urine, and gills actively take up ions (NaCl)
b) Freshwater invertebrates: same situation as freshwater fish but with different
structures
c) Freshwater amphibians: active uptake of salts across their skin
3. Marine fishes: Here the environment has a higher solute concentration than does
the organism so water tends to flow out and ions in.
a) Bony fishes: actively secrete salts (NaCl) across gills, absorb water across gut
wall, their kidney (unlike mammalian kidney) is unable to generate concentrated
urine so glomerulus is reduced, active tubular secretion of MgSO4
b) cartilaginous fishes (and coelacanth): blood retains urea and trimethylamineoxide
to increase its osmolality to that of seawater
161
Sensory systems
4. Terrestrial animals: here problem is loss of water to a drier environment, and
regulation of salt levels.
a) water loss adaptations
b) concentrated exception of salts and nitrogenous wastes
Hypoosmotic: having less osmotic potential than nearby fluid
Hyperosmotic: having more osmotic potential than nearby fluid
Isoosmotic: having equal osmotic potential than nearby fluid
Glomerulus: reduces volume of kidney
Fish started in salt water, spread to fresh water, later reinvaded salt-water environment.
Terrestrial animal water sources:
1. drinking
2. moist foods
3. from breakdown of metabolic molecules like fats. (Desert kangaroo rats get 90% of their
water from metabolism.)
Secretion of nitrogenous wastes: from metabolism of amino acids, amino group has to be
removed in one of three basically interchangeable chemical forms:
1. ammonia (aquatic life)
2. urea (mammals)
3. uric acid (birds)
Ammonia very toxic, soluble, and cheap to produce. Easy to expel for bony fishes.
Urea: low toxicity, good solubility, more costly to lose as it contains other groups on it.
Must be released in solution, water cost.
Uric acid (white part of bird poo) low toxicity, insoluble, secreted with little water loss,
more costly side groups lost than the others.
Mammalian kidney: Structure: fist-sized organ in lower back. About 1/5 of blood from
aorta at any time is passing through kidneys. Blood passes through kidney many times a
day.
Nephron: structural and functional unit of kidney.
Bowmans capsule: funnel-like opening, contains primary filter, the glomerulus.
Proximal convoluted tubule: receives stuff from Bowmans capsule.
Loop of Henle: descends and ascends.
162
Osmotic environments and regulations

Vasa recta: capillaries that surround the Loop of Henle.
Glomerulus: main filter of the nephron, located within the Bowman's capsule
Kidney properties and processes important to its function
1. Active transport of solutes from one fluid to another against a concentration gradient,
Na+ actively transported out of filtrate by cells of the thick ascending loop of Henley into
the interstitial fluid
2. Passive movement of solutes and water from one fluid to another(down a concentration gradient), movement of water and NaCl out of descending loop of Henley into
interstitial fluid.
3. Differential permeability of cells in different regions of the nephron to movement
of water and solutes, ascending thick look is impermeable to water, descending portion is
permeable to water
4. Hormonal control of that permeability, antidiuretic hormone(ADH) increases
permeability of collecting due to water, resulting in reduced volume of filtrate and thus
more concentrated urine.
5. Increasing solute concentration in the interstitial fluid of the kidney, from the
cortex to the deepest medulla, maintained by a countercurrent multiplier mechanism
163
33 Additional material
Francis Crick1 chemist and molecular biologist, discovered structure of DNA molecule
Charles Darwin2 the father of the science of evolutionary biology
Richard Dawkins3 zoologist and biology populariser
Stephen Jay Gould4 paleontologist and science populariser
J.B.S. Haldane5 geneticist and evolutionary biologist, founded population genetics and the
modern synthesis
Bill Hamilton6 formulated theory of inclusive fitness and kin selection
Thomas Huxley7 "Darwin's Bulldog", early evolutionary biologist and science populariser
Lynn Margulis8 introduced the theory of eukaryotic cell origin through endosymbiosis
Barbara McClintock9 geneticist and molecular biologist, discovered transposons
Gregor Mendel10 discovered the basic rules of heredity
Ernst Mayr11 evolutionary biologist and science populariser
Mark Ridley12 science populariser
Fred Sanger13 founder of DNA and protein sequencing techniques
John Maynard Smith14 evolutionary biologist and science populariser
Alfred Russel Wallace15 evolutionary biologist
James Watson16 molecular biologist, discovered structure of DNA molecule
Edward Wilson17 founded "sociobiology"
This book is intended as a compilation of biographies describing the lives and work of
influential biologists.
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http://en.wikipedia.org/wiki/Francis%20Crick
http://en.wikibooks.org/wiki/General%20Biology%2FGallery%20of%20Biologists%2FCharles%
20Darwin
http://en.wikipedia.org/wiki/Richard%20Dawkins
http://en.wikipedia.org/wiki/Stephen%20Jay%20Gould
http://en.wikipedia.org/wiki/J.B.S.%20Haldane
http://en.wikipedia.org/wiki/William%20Hamilton
http://en.wikipedia.org/wiki/Thomas%20Huxley
http://en.wikipedia.org/wiki/Lynn%20Margulis
http://en.wikipedia.org/wiki/Barbara%20McClintock
http://en.wikipedia.org/wiki/Gregor%20Mendel
http://en.wikipedia.org/wiki/Ernst%20Mayr
http://en.wikipedia.org/wiki/Mark%20Ridley
http://en.wikipedia.org/wiki/Fred%20Sanger
http://en.wikipedia.org/wiki/John%20Maynard%20Smith
http://en.wikipedia.org/wiki/Alfred%20Russel%20Wallace
http://en.wikipedia.org/wiki/James%20Watson
http://en.wikipedia.org/wiki/Edward%20O.%20Wilson
165
Additional material
33.1 External Links

EvoWiki: List of Biologists18
18
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http://wiki.cotch.net/index.php/List_of_biologists
34 Glossary
Autotroph1 : an organism which can make its own energy
Cell2 : Fundamental structural unit of all living things
Ether3 :
Eukaryote4 : an organism5 with a nucleus
Exoenzyme6 : an enzyme used to break down organic molecules7 outside the body
Glycerol8 :
Heterotroph9 : an organism which can not make its own energy
Hydrocarbon10 : an organic compound that contains carbon11 and hydrogen12 only.
Lipid13 : fatty acid14 esters15 which form the basis of cell membranes
Nucleus16 : Membrane17 -bound organelle18 which contains the chromosomes19
Prokaryote20 : an organism with no nucleus
Seed:
Flower:
Tracheid:
Haploid: A cell with a single set of chromosomes (23 in humans), in humans this is
usually in gametes. This is commonly represented by n.
Diploid: A cell with two sets of chromosomes (46 in humans). This is commonly
represented by 2n.
Sporangium:
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http://en.wikibooks.org/wiki/Cell
http://en.wikibooks.org/wiki/Ether
http://en.wikibooks.org/wiki/Eukaryote
http://en.wikibooks.org/wiki/organism
http://en.wikibooks.org/wiki/Exoenzyme
http://en.wikibooks.org/wiki/organic%20molecule
http://en.wikibooks.org/wiki/Glycerol
http://en.wikibooks.org/wiki/Heterotroph
http://en.wikibooks.org/wiki/Hydrocarbon
http://en.wikibooks.org/wiki/Carbon
http://en.wikibooks.org/wiki/Hydrogen
http://en.wikibooks.org/wiki/Lipid
http://en.wikibooks.org/wiki/fatty%20acid
http://en.wikibooks.org/wiki/ester
http://en.wikibooks.org/wiki/Cell%20nucleus
http://en.wikibooks.org/wiki/Membrane
http://en.wikibooks.org/wiki/organelle
http://en.wikibooks.org/wiki/chromosome
http://en.wikibooks.org/wiki/Prokaryote
167
Glossary
The majority of the modules making up this book are based on notes very generously donated
by Paul Doerder, Ph.D.21 and Ralph Gibson, Ph.D.22 both currently of the Cleveland
State University23 .
The book was initiated by Karl Wick24 , who donated many of his own class notes for other
modules, and who is fleshing out the outline format of Dr. Doerder's notes into text.
34.1 Users
Alsocal25
Darren Hess26 MD/PhD recent grad, enjoys teaching, hopes to help work up the Nervous
System Tissue section.
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http://bgesweb.artscipub.csuohio.edu/faculty/doerder.htm
http://bgesweb.artscipub.csuohio.edu/faculty/gibson.htm
http://www.csuohio.edu/
http://en.wikibooks.org/wiki/User%3AKarl%20Wick
http://en.wikibooks.org/wiki/User%3AAlsocal
http://en.wikibooks.org/wiki/User%3Admhessmdphd
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Moadeeb61
Monk62
Naryathegreat63
Neoptolemus64
NipplesMeCool65
Nmontague66
Obscureownership67
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Perl69
Petemella70
QuiteUnusual71
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http://en.wikibooks.org/w/index.php?title=User:Lexor
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http://en.wikibooks.org/w/index.php?title=User:Ltellez
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Starwindfury84
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Taoster90
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User:102
Unknown, The Hornet is no longer in publication and it is
very likely for a 20-year-old artist in 1871 to have died before
1939
Uploader, CDC
LadyofHats103
GFDL
PD
PD
PD
GFDL
GFDL
PD
GFDL
PD
102 http://en.wikibooks.org/wiki/User%3A
103 http://en.wikibooks.org/wiki/User%3ALadyofHats
177
36 Licenses
36.1 GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright 2007 Free Software Foundation, Inc.
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If the disclaimer of warranty and limitation of liability provided above cannot be given local legal ef-
fect according to their terms, reviewing courts shall

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END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to
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To do so, attach the following notices to the program. It is safest to attach them to the start of
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<one line to give the programs name and a brief
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<name of author>
This program is free software: you can redistribute
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This program is distributed in the hope that
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You should have received a copy of the GNU General Public License along with this program. If not,
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Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it
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NO WARRANTY; for details type show w. This is
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The hypothetical commands show w and show c
should show the appropriate parts of the General
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You should also get your employer (if you work
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For more information on this, and
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<http://www.gnu.org/licenses/>.
The GNU General Public License does not permit
incorporating your program into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with the library. If this is
what you want to do, use the GNU Lesser General
Public License instead of this License. But first,
please read <http://www.gnu.org/philosophy/whynot-lgpl.html>.
36.2 GNU Free Documentation License

Version 1.3, 3 November 2008
Copyright 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc. <http://fsf.org/>
it is not allowed. 0. PREAMBLE
The purpose of this License is to make a manual,
textbook, or other functional and useful document
"free" in the sense of freedom: to assure everyone
the effective freedom to copy and redistribute it,
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General Biology

March 15, 2013

Biology - The Life Science

Chemical Building Blocks of Life

History and Origin

11 Energy and Metabolism

Structure of Eukaryotic cells

12 Respiration: harvesting of energy

Bacterial DNA replication . . . . . . . . . . . . . .

16 Gregor Mendel and biological inheritance

17 DNA: The Genetic Material

21 Recombinant DNA technology

22 Classification of Living Things

23 Multicellular Photosynthetic Autotrophs

25 Tissues and Systems

29 Vertebrate digestive system

2 Biology - The Life Science

2.1 Characteristics of life

Biology - The Life Science

2.2 Nature of science

2.3 Scientific method

How Science is Done

A diagram that illustrates scientific investigation

Biology - The Life Science

2.4 Charles Darwin

2.5 After Darwin

Biology - The Life Science

2.6 Challenges to Darwin

3 The Nature of Molecules

3.2 The atom

The Nature of Molecules

3.3 Mass and isotopes

3.5 Chemical bonds

3.6 Chemical reactions

Formation and breaking of chemical bonds

Essential for life

3.7.1 Hydrogen bonding

The Nature of Molecules

A convenient way of indicating H+ concentration

4 The Chemical Building Blocks of Life

Carbon based: organic molecules

The Chemical Building Blocks of Life

4.4.1 Fatty acids

4.5.1 Amino acids

The Chemical Building Blocks of Life

4.6 Hereditary (Genetic) information

4.6.1 RNA DNA origin

5 Life: History and Origin

5.2 Origin of life: 3 hypotheses

Life: History and Origin

5.3 The early earth

5.4 Origin of cells

5.5 The RNA world?

5.6 The earliest cells

Life: History and Origin

5.7 Major steps in evolution of life