BIOL Molecular Basis of Life Slides

Reference Material
What is Science? (& Why do it?) Introduction, The nature of biology and
science; Knox, Ladiges, Evans and
Prof. Jim Mitchell Saint, Biology: an Australian Focus,
Biology room 110 4th Edition, McGraw Hill, Australia
OR just email me (jim.mitchell@flinders.edu.au) OR
Happy to discus science
Remember I know nothing about how the topic runs Chapter 1, Themes in the study of life;
Campbell, Reece and Meyers, Biology
Eighth Edition, Pearson Education
Australia
Research Project in China

Complete BIOL3700, BIOL2704 and BIOL0000 &
0010 in China and you may be eligible for up to
$22,000 in funding* to cover expenses.
Let us know what youre interested in studying and
we will aim to find you a suitable supervisor in China
Some of our locations

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Contact Jim Mitchell for further *$7,000 cash,

information the remaining from
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1
Is this science?
2
Is this science? Is this science?
HOW DO WE KNOW SOMETHING?

Q: What is Science?
Description of the physical, real world For example
What makes the modern world work
Something that has principles
That insects have 6 legs
That which survives testing
Genetic information is coded in
An area with doubt
DNA
A process investigating the unknown
That smoking causes cancer
All of this
What impacts on the quality of Wide variety of sources of

(scientific) Knowledge? scientific information
1. The quality of the scientific Journal Articles (Peer Reviewed)
enquiry. (more on this later) Subject Specific Scientific Books
Wikipedia
2. The quality of scientific reporting Text books
How do you know when to believe
Web sites
something ?
Public lectures
Television Programs
3
Q: Which of the following is the best
Peer Review Process ensures quality source of information to cite in your
research project?
Peer reviewed journal articles are
scrutinised by experts in the field 1. Wikipedia
The experts ensure that a suitable 2. The text book Biology
experimental design has been used and
that the data have been appropriately
3. An article in the journal Blood
analysed. 4. An article in the journal New
Generally all other information sources Scientist
repeat or interpret these peer reviewed
5. A professor conducting research
articles. Therefore, peer-reviewed journal
articles are often referred to as Primary in the area
Literature.
Discovery Science: Inductive

The Process of Scientific Enquiry Reasoning
In Biology two main processes to Is the process of making a several
scientific enquiry observations and then
extrapolating that the pattern
Discovery Science observed holds for all.
Describing nature Example, observe that the sun
rises in the east every morning for
a week. Leads to the sun always
Hypothesis-based Science rises in the east.
Explaining nature
Limitations of inductive reasoning Hypothesis Based Science

Regardless of how many observations, Is used to seek the cause of the
there is always an uncertainty. Unless observations and inductions
you can falsify the proposition.
Example An hypothesis is a tentative
Observe: 100 000 crows All black answer to a well framed question-
Conclusion: All crows are black (not an explanation on trial
certain) An hypothesis must be testable
Observe one albino crow
An hypothesis must be falsifiable
Conclusion: Not all crows are black
(certain)
4
Everyday example of hypothesis based enquiry
Does this prove that the bulb was
Observations burnt out?
Questions
1. Yes
Hypothesis # 1: Hypothesis # 2:
2. No
Dead batteries Burnt-out bulb
Prediction: Prediction:
Replacing batteries Replacing bulb
will fix problem will fix problem
Test prediction Test prediction
Campbell, Figure 1.25 Test falsifies hypothesis Test does not falsify hypothesis
An hypothesis can not be proven Controlled Experiments

In the flashlight example a loose Many experimental designs to test
bulb may have given the same hypotheses, require comparing an
experimental group with a control
result.
group.
To gain credibility a hypothesis Ideally two groups differ by only 1 factor
must survive various attempts to Example: smoking leads to higher risk
disprove it. of cancer
This requires testing of alternative Control group = non smokers
hypotheses Experimental group = smokers
Scientific Theories Biology as a Science

A scientific theory is much Interdisciplinary science
broader than a single hypotheses. Chemistry
A scientific theory is general Physics
enough to generate many specific Mathematics
hypotheses
Contrary to the everyday use Eleven themes that unify the
of theory a scientific theory science
is NOT a mere speculation
5
Learning Objectives
1. Understand what the peer-review
process is
2. Know how to judge the credibility
of a scientific report (identify
primary literature)
3. Be able to construct a hypothesis
4. Know what a control is in a
scientific experiment
Campbell Table 1.1
What is a scientist? What does a scientist do?

Someone that Works in lab, field, or ocean
Tests hypotheses Writes grants to get money
Finds information new to the world Writes scientific papers
Creates information pathways for
others to use Trains young scientists
Teaches sometimes
Today, well this year anyway
6
100 years ago, the age of metal
7
Reference Material
Cell Structure Chapter 4, Functioning Cells; Knox,

Ladiges, Evans and Saint, Biology:
an Australian Focus, 4th Edition,
Prof Jim Mitchell McGraw Hill, Australia
Biology room 110
Jim.mitchell@flinders.edu.au
Chapter 6, A tour of the cell;Campbell,
Reece and Meyers, Biology Eighth Edition,
Pearson Education Australia
All cells have several basic

Cells features in common
All organisms are composed of cells They are bounded by a plasma
REVISION
membrane
REVISION
They contain a semifluid substance called
the cytosol
They contain chromosomes
They all have ribosomes
2 types of cell organisation Cell Sizes
Typical Prokaryotes- ~ 1-10m

Organisms can be classified as
REVISION
1.Prokaryotic Typical Plant and animal cells- ~10-
2.Eukaryotic 100m
Based on the structure of the cell
karyon refers to kernal
pro = before
Nerve cells- ~ 0.1 -1m
eu = true
1
Prokaryotic Cells The First Prokaryotes
Do not contain a nucleus Prokaryotes were Earths sole inhabitants

Have their DNA located in a
REVISION
From 3.5 to about 2 billion years ago
region called Most prokaryotes are microscopic
the nucleoid But what they lack in size they more than
make up for in numbers
Do not have membrane Prokaryotes reproduce quickly by binary fission
bound organelles Some species can divide every 20 minutes
7 8
Fig 4.1: Prokaryotic cells

Prokaryotes
Most prokaryotes are

unicellular
Although some species
membrane
enclosing the cytoplasm
form colonies
Nucleoid: region where the cells DNA is Prokaryotic cells have
a variety of shapes
located (not enclosed by a membrane)
Locomotion apparatus
of some bacteria
The three most
attachment structures on common of which are
spheres (cocci), rods
the surface of some
prokaryotes
jelly-like outer coating (bacilli), and spirals

of many prokaryotes
membrane
enclosing the cytoplasm
organelles that
synthesize Fig 34.2 a)Salmonella (rod shaped),
proteins
b) dividing coccus, e) a spiral bacterium
Copyright 2010 McGraw-Hill Australia Pty Ltd
4-9 10
More on prokaryotes Cell-Surface Structures

The cell wall of many prokaryotes
One of the most important features of nearly all
Is covered by a capsule, a sticky layer of
prokaryotic cells
polysaccharide or protein
Is their cell wall, which maintains cell shape, provides
REVISION
physical protection, and prevents the cell from
Most motile bacteria propel themselves by
flagella bursting in a hypotonic environment
Which are structurally and functionally Using a technique called the Gram stain
different from eukaryotic flagella Many bacterial species can be classified into two
groups based on cell wall composition, Gram-positive
and Gram-negative
H. Berg
Prokaryotic cells
Usually lack complex compartmentalization
11 12
2
Bacterial Cell Walls Eukaryotic cells
Lipopolysaccharide
Contain a true nucleus,

Outer
membrane
Peptidoglycan
Cell wall Cell wall
layer Peptidoglycan
bounded by a membranous
layer
REVISION
Plasma membrane Plasma membrane
Protein Protein nuclear envelope

Gram-
positive
bacteria
Gram-
negative
bacteria
Are generally quite a bit
20 m
bigger than prokaryotic cells
Contain membrane bound
(a) (b)
Gram-positive. Gram-positive bacteria have Gram-negative. Gram-negative bacteria have less
a cell wall with a large amount of peptidoglycan peptidoglycan, and it is located in a layer between the
that traps the violet dye in the cytoplasm. The plasma membrane and an outer membrane. The
alcohol rinse does not remove the violet dye,
which masks the added red dye.
violet dye is easily rinsed from the cytoplasm, and the
cell appears pink or red after the red dye is added. organelles
Figure 27.3a, b
13 14
An animal cell The plasma membrane
Functions as a selective
REVISION
barrier
Allows sufficient
passage of nutrients
and waste
Prokaryote
size
Fig 4.2 16
The plasma membrane Plant and animal cells what

are the differences
most have the same
organelles
What are the exceptions?
17 18
Fig 4.6
3
A plant cell The Cytoskeleton
The cytoskeleton is a network of fibers

that organizes structures and activities
in the cell
REVISION
Is a network of fibers extending throughout
the cytoplasm
Gives mechanical support to the cell
Is involved in cell motility, which
utilizes motor proteins
20
Cytoskeleton The nucleus

There are three main types of fibers that
make up the cytoskeleton Contains the cells
1. microtubules genetic material the
REVISION25nm dia made of tubulin
2. microfilaments
7nm dia made of actin
chromosomes are
housed here
REVISION
3. intermediate filaments
8-12nm dia, proteins including keratin
Functions: Support, Adhesion,
Movement, Regulation
21 22
The nucleus and its envelope

Ribosomes
Are particles made of

ribosomal RNA and
protein
Carry out protein
synthesis
Fig 4.7
23
REVISION 24
4
Ribosomes Endoplasmic reticulum (ER)
ER
Ribosomes Cytosol Is continuous with the nuclear envelope
Endoplasmic reticulum (ER)
There are two distinct regions of ER
Free ribosomes
Smooth ER, which lacks ribosomes
REVISION
Rough ER, which contains ribosomes
Bound ribosomes
Large
The smooth ER contains enzymes
subunit which can:
Synthesizes lipids
Small
0.5 m subunit Metabolizes carbohydrates
TEM showing ER and ribosomes Diagram of a ribosome Stores calcium
Detoxifies poison
25 26
Rough ER Lysosome
Has bound ribosomes
Produces proteins and membranes, which Is a membranous sac of hydrolytic
are distributed by transport vesicles enzymes
Can digest all kinds of macromolecules
REVISION REVISION
27 28
Golgi Apparatus Mitochondria
Mitochondria
Receives many of the transport vesicles Are the sites of cellular respiration
produced in the rough ER Are found in nearly all eukaryotic cells
REVISION
Consists of flattened membranous sacs - Are enclosed by two membranes
called cisternae
A smooth outer membrane
Functions of the Golgi apparatus An inner membrane folded into cristae
include:
Modification of the products of the rough
REVISION
ER
Manufacture of certain macromolecules
29 30
5
Mitochondrion
Chloroplast
The chloroplast
Is a specialized member of a family of
closely related plant organelles called
plastids
Contains chlorophyll
Are found in leaves and other green organs
of plants and in algae
Fig 4.15 31
REVISION 32
Choroplast Cilia and flagella

Contain specialized arrangements of
microtubules
Are locomotor appendages of some cells
33
REVISION 34
Cell Wall Learning Objectives
The cell wall 1. Know the names and function of the

Is an extracellular structure of plant cells various structures/organelles in a cell.
that distinguishes them from animal cells 2. Know the differences that characterise
Are made of cellulose fibers embedded in eukaryotic and prokaryotic cells
other polysaccharides and protein
May have multiple layers
REVISION 35
6
Reference Material
Plasma Membranes (PMs), Fluid
Moasic Model and Osmosis
Chapter 2 Biological Molecules; Chapter 4
Functioning Cells; Chapter 35 The Protists;
Knox, Ladiges, Evans and Saint, Biology:
Dr. Jim Mitchell an Australian Focus, 4th Edition, McGraw
Hill, Australia
Biology room 140
Chapter 5, The structure and Function of
Macromolecules & Chapter 7, Membrane structure
and function; Campbell, Reece and Meyers, Biology
Seventh Edition, Pearson Education Australia
Learning Objectives Life at the Edge

1. be able to list the constituents of a plasma PM is
living and non-living
membrane boundary Lingwood and Simons Sci. 2010
2. Understand how changes to the chemistry of lipids selective permeability
and other constituents in the plasma membrane some substances
influence its fluid properties cross more easily
than others
3. Explain the fluid mosaic model of plasma
membranes
4. Understand the various functional roles that
membrane proteins have
Figure 4.6
Cellular membranes Lipids and Fats

PM are fluid mosaics of Lipids
lipids and proteins hydrophobic.
components free to Fats, phospholipids
move & steroids
NCBI
mosaic = embedded
proteins
Fats
2 types of molecules
Phospholipids a single glycerol
most abundant usually 3 fatty acids
Amphipathic:
hydrophobic & Wikipedia
hydrophilic regions
5 6
1
Fatty Acids & Fats Phospholipids
Phospholipids
only two fatty acids
Saturated fatty phosphate group
acids instead of a third
Max # H atoms fatty acid
Phospholipid structure
= no double bonds
hydrophilic head
and hydrophobic
Unsaturated fatty tails
acids The structure of
one or more phospholipids
double bonds Results in a bilayer
arrangement found
in cell membranes
7 8
The Fluidity of Membranes Fluidity

Phospholipids in the plasma membrane The type of hydrocarbon tails in phospholipids
Can move within the bilayer Affects the fluidity of the plasma membrane
Fluid Viscous
Lateral movement Flip-flop Unsaturated hydrocarbon Saturated hydro-

(~107 times per second) (~ once per month) tails with kinks Carbon tails
(b) Membrane fluidity
(a) Movement of phospholipids
Campbell Figure 7.5
Campbell Figure 7.5 A
BMG LABTECH Polarstar

9 wikibooks
Stryer, NCBI
Membrane Proteins and Their

Steroids Functions
The steroid cholesterol Integral proteins
Penetrate the
Has different effects on membrane fluidity at
hydrophobic core of the
different temperatures lipid bilayer
Are often
transmembrane
proteins, completely
spanning the
membrane
Peripheral proteins
Are appendages loosely
bound to the surface of
Cholesterol
the membrane
11 12
Campbell Figure 7.5 (c) Cholesterol within the animal cell membrane
2
An overview of six major functions (d) Cell-cell recognition. Some glyco-proteins serve as
identification tags that are specifically recognized
of membrane proteins by other cells.
Glyco-
(a) Transport. (left) A protein that spans the membrane protein
may provide a hydrophilic channel across the
membrane that is selective for a particular solute.
(right) Other transport proteins shuttle a substance (e) Intercellular joining. Membrane proteins of adjacent cells
from one side to the other by changing shape. Some may hook together in various kinds of junctions, such as
of these proteins hydrolyze ATP as an energy ssource gap junctions or tight junctions (see Figure 6.31).
to actively pump substances across the membrane.
ATP
(b) Enzymatic activity. A protein built into the membrane Enzymes

may be an enzyme with its active site exposed to
substances in the adjacent solution. In some cases,
several enzymes in a membrane are organized as
a team that carries out sequential steps of a (f) Attachment to the cytoskeleton and extracellular matrix
metabolic pathway. (ECM). Microfilaments or other elements of the
cytoskeleton may be bonded to membrane proteins,
a function that helps maintain cell shape and stabilizes
(c) Signal transduction. A membrane protein may have
the location of certain membrane proteins. Proteins that
a binding site with a specific shape that fits the shape Signal
adhere to the ECM can coordinate extracellular and
of a chemical messenger, such as a hormone. The intracellular changes (see Figure 6.29).
external messenger (signal) may cause a
conformational change in the protein (receptor) that
relays the message to the inside of the cell.
Campbell Figure 7.9
13 14
Campbell Figure 7.9 Receptor
The Role of Membrane Carbohydrates Synthesis and Sidedness of

(Glycoproteins) Membranes
Membranes have
distinct inside and
outside faces
This affects the
Cell-cell recognition movement of
Is a cells ability to distinguish one type of proteins synthesized
in the
neighboring cell from another endomembrane
Membrane carbohydrates system
Membrane proteins
Interact with the surface molecules of other and lipids
cells, facilitating cell-cell recognition Are synthesized in
the ER and Golgi
apparatus
15 Figure 4.12 16
What kinds of molecules pass

through a cell membrane most Learning Objectives
easily?
1. be able to list the constituents of a plasma
1. large and membrane
2. Understand how changes to the chemistry of lipids
hydrophobic and other constituents in the plasma
2. small and membranbrane influence its fluid properties
3. Explain the fluid mosaic model of plasma
hydrophobic membranes
3. large polar 4. Understand the various functional roles that
membrane proteins have
4. ionic
5. monosaccharides
such as glucose
17
3
The Permeability of the Lipid
Diffusion
Bilayer
tendency
Explains why cells
Membrane structure results for
in selective permeability are small
molecules
A cell must exchange to spread
materials with its The time to move x
surroundings, a process
out length by diffusion
controlled by the plasma evenly is
membrane i.e. move t = x2/D
Hydrophobic molecules down
Are lipid soluble and can their where D is diffusion
pass through the constant 10-5 cm2/s
membrane rapidly
concentra
(expanding balloon units,
Polar molecules
tion Surface area increase with
Do not cross the
gradient time)
membrane rapidly
1 ms to go 1 um
Figure 5.2 1 day to go 1 cm
Figure 5.3 19 20
Effects of Osmosis on Water Water Balance of Cells Without

Balance Walls
Osmosis (water and salt specific diffusion) Tonicity
Is the Ability of a solution to cause a cell to gain or lose water

movement of Big impact on cells without walls
water across a Isotonic solution
semipermeable solute concentration is equal on both sides of PM
membrane
no net water movement
Is affected by
Hypertonic solution
the
concentration Solute concentration is greater outside than inside PM
gradient of The cell loses water
dissolved Hypotonic solution
substances Solute concentration is less outside the cell than it is
inside the cell
Fig 5.9 21 22
The cell gains water
Water balance
Figure 5.10
23
4
Facilitated Diffusion: Passive
Transport Proteins Transport Aided by Proteins
Passive transport is diffusion of a substance across a In facilitated diffusion
membrane with no energy investment
Channel proteins
Transport proteins provide corridors Fig 5.5
that allow a specific
Allow passage of hydrophilic substances across the molecule or ion to
membrane cross the
membrane
3 types of transport proteins
Uniport- carrier a single solute across the Carrier proteins
membrane undergo a subtle
change in shape
Symport- translocates 2 different solutes that translocates
simultaneously in the same direction. Eg: sodium the solute-binding
and glucose symport in animal cells site across the Fig 5.6
membrane
Antiport- exchanges 2 solutes, one into the cell and
one out of the cell. Eg: sodium in and calcium out
25 26
The Need for Energy in Active Maintenance of Membrane

Transport Potential by Ion Pumps
Membrane potential
Active transport Is the voltage
Moves substances against their concentration difference across a
gradient membrane
Requires energy, usually in the form of ATP An electrochemical
Can be primary or secondary (co-transport) gradient
Is caused by the
concentration
gradient of ions
across a membrane
An electrogenic pump
Is a transport protein
that generates the
voltage across a
membrane
Fig 5.7 27 28
5
Reference Material
Membranes, Proteins and
Enzymes Chapter 2 Biological Molecules; Chapter 3 The
Chemistry of Life; Chapter 5, Movement across
membranes; Functioning Cells; Knox, Ladiges,
Evans and Saint, Biology: an Australian Focus, 4th
Edition, McGraw Hill, Australia
Jim Mitchell
Biology room 140
Chapter 5, The structure and Function of
Macromolecules; Chapter 7, Membrane structure
and function;Campbell, Reece and Meyers, Biology
Seventh Edition, Pearson Education Australia
The Permeability of the Lipid

Diffusion
Bilayer
The tendency for
Membrane structure results molecules of any
in selective permeability substance to
A cell must exchange spread out
materials with its
surroundings, a process
evenly into the
controlled by the plasma available space
membrane Substances
Hydrophobic molecules diffuse down
Are lipid soluble and can their
pass through the
membrane rapidly
concentration
Polar molecules
gradient, the
Do not cross the
difference in
membrane rapidly concentration of
a substance from
one area to Figure 5.2
another
Figure 5.3 3 4
Effects of Osmosis on Water

Balance Water balance
Osmosis
Is the
movement of
water across a
semipermeable
membrane
Is affected by
the
concentration
gradient of
dissolved
substances Figure 5.10
Fig 5.9 5 6
1
Learning objectives Learning Objectives
1. Understand what types of molecule are permeable 7. Be aware of the different functions
to biological membranes
2. Know the 3 types of transport proteins of proteins in the cell
3. Understand the difference between active and 8. Understand how proteins are made
passive transport process
4. Understand how a voltage is generated across a
up of individual amino acids
biological membrane 9. Understand what an enzyme is
5. Understand the process of osmosis and the
consequences for a cell placed in a variety of 10. Understand the 4 different levels of
different environments protein structure
6. Understand the processes of Phagocytosis
Pinocytosis and Receptor-mediated endocytosis
Facilitated Diffusion: Passive

Transport Proteins Transport Aided by Proteins
Passive transport is diffusion of a substance across a In facilitated diffusion
membrane with no energy investment
Channel proteins
Transport proteins provide corridors Fig 5.5
that allow a specific
Allow passage of hydrophilic substances across the molecule or ion to
membrane cross the
membrane
3 types of transport proteins
Uniport- carrier a single solute across the Carrier proteins
membrane undergo a subtle
change in shape
Symport- translocates 2 different solutes that translocates
simultaneously in the same direction. Eg: sodium the solute-binding
and glucose symport in animal cells site across the Fig 5.6
membrane
Antiport- exchanges 2 solutes, one into the cell and
one out of the cell. Eg: sodium in and calcium out
9 10
The Need for Energy in Active Maintenance of Membrane

Transport Potential by Ion Pumps
Membrane potential
Active transport Is the voltage
Moves substances against their concentration difference across a
gradient membrane
Requires energy, usually in the form of ATP An electrochemical
Can be primary or secondary (co-transport) gradient
Is caused by the
concentration
gradient of ions
across a membrane
An electrogenic pump
Is a transport protein
that generates the
voltage across a
membrane
Fig 5.7 11 12
2
Large Proteins and Bulk Transport
3 Methods
Large proteins cross the membrane a) Phagocytosis
by different mechanisms
In exocytosis
Transport vesicles migrate to the
plasma membrane, fuse with it, and b) Pinocytosis
release their contents
In endocytosis
The cell takes in macromolecules by
c) Receptor-
forming new vesicles from the plasma
membrane mediated
endocytosis
13 14
You are working on a team that is designing a new drug. In

order for this drug to work, it must enter the cytoplasm of
specific target cells. Which of the following would not be a
factor that determines whether the molecule enters the An overview of protein functions
cell?
1. size of the drug molecule Proteins have many structures, resulting in a
2. polarity of the drug molecule wide range of functions
3. charge on the drug molecule Have many roles inside the cell
4. similarity of the drug See Table 2.4
molecule to other molecules
transported by the target
cells
5. lipid composition of the
target cells' plasma
membrane
15 16
Enzyme activity
Enzymes
Are a type of
protein that
acts as a
catalyst,
speeding up
chemical
reactions
18
3
Polypeptides Amino Acid Monomers
Polypeptides
Amino acids
Are polymers of amino acids
Are organic molecules possessing both
A protein carboxyl and amino groups
Consists of one or more polypeptides Differ in their properties due to differing side
chains, called R groups
19 20
Amino acids
Amino Acid Polymers
OH
20 different Amino acids

amino acids Are linked by
make up peptide bonds
proteins
21 22
Upon chemical analysis, a particular protein was

found to contain 556 amino acids. How many Protein Conformation and Function
peptide bonds are present in this protein?
A proteins
specific
conformation
Determines
1. 139 how it
2. 554 functions
Two models
3. 555 of protein
4. 556 conformation
5. 558
23 24
4
Four Levels of
Protein Structure Secondary structure
Primary structure
Is the unique sequence of amino acids in
a polypeptide
Secondary structure
Is the folding or coiling of the
N-terminus polypeptide into a repeating
configuration
Includes the helix and the
pleated sheet
C-terminus
Fig 2.21
25 26
Tertiary
structure Quaternary structure
Tertiary structure
Is the overall three-
dimensional shape of
a polypeptide
Or the way the Quaternary structure
secondary structure
elements are Is the overall protein
arranged relative to structure that results
one another from the aggregation
Results from of two or more
interactions between
polypeptide subunits
amino acids and R
groups
27 Fig 2.24 28
Fig 2.23
The globular protein transthyretin results from the

aggregation of four polypeptide subunits. Each of
the subunits is a polypeptide chain with an helix
region. Which structure(s) must the transthyretin Learning objectives
protein have?
1. Understand what types of molecule are permeable
1. primary structure
to biological membranes
2. primary and secondary 2. Know the 3 types of transport proteins
structure 3. Understand the difference between active and
3. primary, secondary, and passive transport process
tertiary structure 4. Understand how a voltage is generated across a
biological membrane
4. primary, secondary,
5. Understand the process of osmosis and the
tertiary, and quaternary consequences for a cell placed in a variety of
structure different environments
5. primary, secondary, 6. Understand the processes of Phagocytosis
tertiary, quaternary, and Pinocytosis and Receptor-mediated endocytosis
alpha structure
29
5
Learning Objectives
7. Be aware of the different functions

of proteins in the cell
8. Understand how proteins are made
up of individual amino acids
9. Understand what an enzyme is
10. Understand the 4 different levels of

protein structure
6
17/03/2015
What are bacteria?

Bacteria are microscopic and cannot be
Prokaryotes
seen with the naked eye.
organisation, diversity and roles They are so small that the sizes of
in the biosphere bacteria are measured in micrometers
including as pathogens
(1,000 micrometers = 1 millimeter).
Jim Mitchell
jim.mitchell@flinders.edu.au
Bacteria; their organisation Bacterial ribosomes

All bacterial cells share certain basic Ribosomesthe cell's protein-
structures in common, such as cytoplasm, synthesizing factoriesare particulate
a cytoplasmic membrane, ribosomes and structures composed of RNA (ribonucleic
a cell wall. acid) and various proteins suspended in
Bacterial cells have a simpler internal the cytoplasm.
structure than eukaryotic cells, lacking It takes a ribosome to make a ribosome
membrane-enclosed organelles no ribosome, what happens?
1
17/03/2015
Nuceloid
Atomic Force Microscopy
The nucleoid, in contrast, is the
aggregated mass of DNA that constitutes
the chromosome of Bacteria.
usually 1 circular strand
1 5 million base pairs usually
compare humans at 3.4 billion base pairs
Wiley 2004
Bacteria
Tree of Life Archaea
3 domains
RNA based
Quantitative
Comprehensive
Focus today Visible
life
Simplest
Most important
Bacteria
Eukarya
NSF, Lydia-Marie Joubert
FACTOIDS These like it 50 90 C

Most prokaryotes are beneficial; we couldnt live
without them. They:
- fix nitrogen gas into ammonia
- reduced CO2 from 98% to 0.025%
- recycle organic matter, all of it
- they digest our food
- produce most of our vitamin K
..
A very few cause illness (<<0.00000000000000000000001%)

bubonic plague, diphtheria, salmonella
Smithsonian
2
17/03/2015
Most prokaryotes secrete sticky substances that form

a protective layer and enable them to adhere to
substrates.
The sticky protective layer secreted by prokaryotes is
called the capsule.
How do they stay Some prokaryotes adhere to substrates using pili.

where they are?
Some pili are specialized for DNA transfer. This
process is called conjugation; note for later in class.
Smithsonian
Movement
Many prokaryotes are motile
- > 100 body lengths per second
Modes of movement 3 types:

Flagellum: driven by rotary motor
Twitching: driven by pili contraction

Gliding: driven by slime hydration
Move up or down chemical gradients,

called chemotaxis
U Maryland
3
17/03/2015
Bacterial
Bacterial reproduction
reproduction
Bacteria undergo a type of asexual reproduction
known as "binary fission."
This simply means they divide in two, and each
new bacterium is a clone of the original they
each contain a copy of the same DNA.
Bacteria can reproduce very quickly. In fact, in
an ideal laboratory situation, an entire population
of bacteria can double in only twenty minutes.
Plasmids
Plasmids are circular
extrachromosomal genetic elements
(DNA), nonessential for growth, found in
prokaryotes.
Bacterial morphological diversity General metabolic diversity
ENVIRONMENTAL BIOTECHNOLOGY
Kunkel 2010
4
17/03/2015
Specialized membranes of prokaryotes
Chemoautotrophs
- Energy from oxidation of inorganic substances
(e.g. NH4, and S)
- CO2 is the carbon source
Example: Sulfolobus, Beggiatoa (shown on slide)
Bacteria can divide every few minutes

48 hours gives 2 solar masses
3 ways for gene transfer:
Transformation
gene uptake from the environment
Transduction
viruses transfer genes between prokaryotes
Conjugation
direct transfer of genes from one prokaryote to
another. Use the sex pilus to conjugate
5
17/03/2015
Prokaryotic
conjugation In summary
Most abundant organisms on Earth >1030
Bacteria occupy every habitat
Bacteria can use any compound which
occurs naturally.
And almost every person-made compound
6
11/03/2016
Virology Viruses
BIOL 1102 examples in people

what are they?
Peter Speck, room 328, ext 12765 what do they infect?
how do they get in?
Mon, Wed, (all day); Fri am. viral diseases: some examples
what does the infected host do?
peter.speck@flinders.edu.au what can we do about them?
examples of viruses: What have we learnt from this?
that you might: Quite a lot:
1. have been infected with There are lots of viruses that infect people
2. have been vaccinated against Some are endemic, others come in epidemics
3. hope to never, ever catch. Consequences of infection range from minor annoyance to death
There are strategies for management.
Some rules:
*its got to be a virus
*must be in the correct column
*no personal medical history
1
11/03/2016
What are viruses? Viral structure
obligate intracellular parasites

small
Viruses are composed of a nucleic acid genome
among the simplest biological systems
theyre not really alive, e.g:
surrounded by a symmetrical capsid made of
need another living organism repeating units of virus-encoded proteins called
dont have independent metabolism capsomeres.
some viruses have a lipid envelope surrounding
the capsid.
the whole thing the virus particle- is called a
virion
Viral genomes There are 2 systems of virus classification

consist of:
1. Baltimore system, based on what type of genome it has and how
single stranded DNA, or it replicates
double stranded DNA, or
single stranded RNA, or 2. International committee on taxonomy of viruses
double stranded RNA. ICTV database:
The smallest genomes are about 2000 bases and http://www.ncbi.nlm.nih.gov/ICTVdb/

encode 4 genes.
The largest are over a million bases and encode
hundred of genes.
2
11/03/2016
viruses are small

Virus
so they can pass thru filters that would stop bacteria
Bacterium
were referred to historically as filterable
Animal
cell Comparing the size
of a virus,
a bacterium, and an
animal cell
Animal cell nucleus

0.25 m
What do viruses look like?

Capsomere RNA
Capsomere
Membranous
Viruses.
of capsid
DNA envelope Head
Capsid Tail
DNA
RNA
sheath
key concept no. 1:
Tail
fiber
viruses are obligate intracellular parasites
Glycoprotein Glycoprotein
18 250 mm 7090 nm (diameter) 80200 nm (diameter) 80 225 nm
20 nm 50 nm 50 nm 50 nm
(a) Tobacco mosaic virus (b) Adenoviruses (c) Influenza viruses (d) Bacteriophage T4
3
11/03/2016
what do viruses infect?
All living things: people, mammals, birds, fish, invertebrates, bacteria,

plants, all get viruses.
A viruss sole purpose is to reproduce.
Even viruses get viruses.
The simplest possible viral host range

virus life cycle.
Each type of virus can infect and parasitize only a limited range of
host cells, called its host range.
This hypothetical virus has only Viruses identify host cells by a lock and key fit between proteins on
one gene, encoding a coat the outside of the virus and specific receptor molecules on the host
protein. cell surface (which evolved for functions that benefit the host).
This virus would totally depend on

the infected cell enzymes and
machinery for viral genome
replication, transcription,
translation.
No known virus is this simple.
4
11/03/2016
viral host range How are viruses transferred between people?
Some viruses have a broad enough host range to infect several

species
others infect only a single species.
West Nile virus infects mosquitoes, birds, horses, and humans.
Measles virus only infects humans.
How are viruses transferred between people? how do viruses get in to cells?
Sex Viruses attach to receptor molecules on the host cell surface;

Mosquitoes i.e. viruses use a door or portal that the cell intended to be for
Respiratory something else.
Saliva after attachment, viruses enter the cell by one of several means, e.g.
by membrane fusion or by endocytosis.
Blood products
IV drug use.
Faecal-oral route.
5
11/03/2016
How do viruses cause damage? How do viruses cause damage?
Entry of a virus into a cell could result in:

no effect
cell death: lysis or apoptosis
loss of control of cellular growth (?cancer: eg papilloma
virus causing cervical carcinoma)
Viral disease can be contributed to by the immune

system, e.g.
SARS (severe acute respiratory syndrome)
1918 influenza pandemic: 50 million deaths, mainly
affecting young, healthy people.
smallpox
Images of
killed >500 million people in the 20th century smallpox sufferers
haemorrhagic form
images courtesy Dr Rich Whitley, University of

Alabama.
6
11/03/2016
smallpox: a terrible disease smallpox vaccination
an ancient scourge;
Benjamin Jesty, a farmer from Dorset, England, in 1774 used fluid
in some cultures, infants were not named until they had caught the
from cowpox as a smallpox vaccine, having seen that dairymaids
disease and survived;
who caught cowpox from cows were spared smallpox.
cause of up to half of all blindness;
killed up to half of its victims;
the word vaccine is derived from the Latin word vacca meaning
no treatment was ever developed. cow.
Smallpox
Frank Fenner standing

by the grave of
Benjamin Jesty, at
Worth Matravers,
Dorset, UK
7
11/03/2016
Edward Jenner publicized this
Edward Jenner, FRS,

the inventor of vaccination
repeated the experiment,
publicised the results, and got
all the credit.
Smallpox eradication
Benjamin Jesty
The World Health Organisation in 1967 appointed Frank Fenner &
Don Henderson to head the smallpox eradication program.
in 1979 Frank announced that the virus was gone forever.
this is the only human infectious disease ever completely globally-
wiped out.
8
11/03/2016
Measles Measles: a mass killer

In 2000 killed about 0.5
million children/year Might be eradicable because:
WHO aimed to eradicate safe & effective vaccine

it by 2015, now revised to no animal reservoir
2020
lifelong immunity
can kill by encephalitis or

pneumonia
caused by measles virus, a

ssRNA virus
Herpes simplex virus: it can spread

Herpes simplex virus
in the absence of symptoms
In a lot of people, HSV
(1 or 2) gets in, lies dormant,
causes lifelong infection, lying dormant in the occasionally reactivating,
nervous system innervating either: infecting others,
WITHOUT causing lesions
the mouth (usually HSV-1), or
like this, and
the genitals (usually HSV-2). WITHOUT the patient
knowing!
About 75-95% of adults have HSV-1
About 20% of adults have HSV-2
Many people with genital herpes
DONT KNOW THEY HAVE IT!
9
11/03/2016
Some vaccines dont work some viruses dont cause illness
e.g., against: there are viruses that DONT cause disease

e.g. Torque Teno Virus in humans
HIV
Epstein-Barr virus. there might be lots of these how would we discover them?
Theres a lousy vaccine against HSV-2 Viruses tend to be discovered thru their association with illness.
Viruses: what does the infected host do?
key concept no. 2: there is a vigorous immune response, involving many & varied
components of the immune system:
some viruses but not all- are formidable pathogens.
antibodies, T cells, B cells, interferon
Innate and adaptive immunity
10
11/03/2016
what does the infected host do? what can we do about viruses?
the vigorous immune response is, in the case of many viruses, Lots:
entirely successful
public health measures
this is the basis of vaccination Can you think of examples?
vaccinations
antivirals
antivirals: there are many classes of antivirals
e.g: acyclovir (Zovirax): Mainly used against HIV:

entry blockers
replication blockers
a fabulous drug against HSV viral protease inhibitors
integration inhibitors
blocks replication of the viral DNA release blockers
has no effect on host cell DNA. cocktails are highly effective in controlling HIV.
11
11/03/2016
Antibiotics WWW resources
Eg penicillins, etc All the virology on the WWW, a very useful site: www.virology.net
and:
www.twiv.tv/
Dont work against viruses!
What have we learned today? two key concepts:
what are viruses? 1. viruses are obligate intracellular parasites

viral genomes and structure
what do they infect? 2. some viruses but not all- are formidable pathogens.
how do they get in?
diseases they cause
what can we do about it?
To learn more, enrol in BIOL2761 Virology
12
BIOL 1102 Molecular Basis of Life: Week 4
Tuesday and Wednesday
How more DNA is made:

Replication in prokaryotic and
eukaryotic cells
Week 4: Tuesday and Wednesday
Dr Masha Smallhorn
masha.smallhorn@flinders.edu.au
Consulting: Mon 10-11am, Wed 12-

1pm SILC room 3 2
Dr Masha Smallhorn 1
Relevant Material
Scitable by Nature Education:
Web address: http://www.nature.com/scitable
DNA Learning Centre:
Web address: https://www.dnalc.org/
DNA from the beginning:
Web address: http://www.dnaftb.org/
Textbook:
Knox, B., Ladiges, P., Evans, B. And Saint, R. (2014), Biology: An Australian
Focus, 5th edition, McGraw Hill Australia PTY LTD, North Ryde, New South
Wales.
Reece, J. B., Meyers, N., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky,
P. V., Jackson, R. B., Cooke, B. J., and Campbell, N. A (2014). Campbell 4
Biology. 10th Edition. Australian and New Zealand Version.
Over the next two weeks. . .

Discover DNA and how more is made
Replication (week 4)
Understand the central dogma of gene
expression
Transcription and translation (week 5)
Learn how content discussed in lectures
can be applied to real world problems
Problem solve
5
Questions
What is genetic material? (PART 1)
How is more genetic material made?
(PART 2)
Learning Objectives
To understand DNA properties and
organisation in prokaryotic and eukaryotic
cells
To understand how DNA is replicated 6
Francis
Crick
James
Watson
Awarded Nobel Prize in 1962

Watson, JD and Crick FHC (1953) Molecular structure of nucleic acid: 7
a structure of deoxyribose nucleic acid, Nature 171(4356): 737-8.
Double Helix
Structure of DNA
Proposed by
Watson and Crick
(1953)
Knox et al. (2014) Figure 2.2

8
DNA is a double helix

Watson and Crick (1953) based their model
on earlier work:
1. Knowledge of basic building blocks of
DNA (Deoxyribose Nucleic Acids)
Phosphate + sugar + base (nucleotide)
2. Chargaffs rules of base composition
A + G = T + C (total amount purine = total
amount pyrimidine)
3. X-ray diffraction analysis of DNA
9
Two strands, parallel, helical
A nucleotide consists of three

parts
Nitrogen
containing
The other monosaccharide base
is deoxyribose
Monosaccharide
Phosphate
10
Knox et al. (2014) Figure 2.1a
There are two types of

nitrogenous bases
Pyrimidines Purines
Base with single ring of Base with two ring
carbon and nitrogen structure of
atoms carbon and nitrogen
atoms
Cytosine (C)
Thymine (T) Guanine (G)
Uracil (U) Adenine (A) 11
There are two types of

nitrogenous bases
Pyrimidines Purines
Base has single Base has two
ring of carbon + ring structure of
nitrogen atoms carbon + nitrogen
Thymine atoms
Cytosine Adenine
Uracil Guanine
12
Knox et al. (2014) Figure 2.1b
Nucleotides are the building

units of nucleic acids
Nucleic acids consist of long chains of nucleotides

joined through phosphodiester linkages between their
5 and 3 carbon atoms on the monosaccharide
13
Knox et al. (2014) Figure 2.1c
There are two types of nucleic

acids
Deoxyribose Nucleic Acids Ribose Nucleic Acids

(DNA) (RNA)
Bases are A, T, G, C Bases are A, U, G, C

Double stranded Single stranded
* RNA is made from DNA by a process called transcription
14
Multiple choice question

The number of adenine bases in a DNA molecule
always equals the number of thymine bases
because:
1. DNA contains equal numbers of all four bases
2. Adenine on one strand bonds to thymine on the
other strand
3. DNA is made of alternating adenine and thymine
bases
4. Thymine always follows adenine on each DNA
strand
Go to: respond.cc session key: 2175 15
If there are only 4 nucleotides,

how can DNA store all the
information that is needed for
life?
https://www.dnalc.org/resources/3d/08-how-
dna-is-packaged-advanced.html
16
The information is packaged

Human chromosome 1
247 million base pairs
About 3,000 genes
How?
DNA wound around
proteins called
histones
Form structure called
nucleosomes
Source: http://ghr.nlm.nih.gov/chromosome/1 Figure 4.8a, Knox et al. (2014) 17
The DNA molecule is supercoiled

which allows it to be packaged into the
cell
E. coli
4.6 million base pairs
About 4,000 genes
How?
Multiple proteins act
together to fold and
condense prokaryotic
DNA
One of the enzymes
involved in supercoiling is
called DNA gyrase
Griswald, A, (2008) Genome packaging in http://www.nature.com/scitable/topicpage/
prokaryotes: The circular chromosome of E. coli 18
genome-packaging-in-prokaryotes-the-circular-
Nature Education 1(1) chromosome-9113
Two structural types of cells are

recognised
Prokaryotes Eukaryotes
(pro = before karyon = nucleus) (eu = proper karyon = nucleus)
Simple internal structure Complex internal structure
No membrane-enclosed Membrane-enclosed
organelles Organelles
Nucleoid (DNA) Nucleus (contains DNA)

19
Prokaryotic cells have a nucleoid
Region containing
DNA
Semi-rigid
cell wall
cytoplasm
Knox et al. (2014) Figure 4.1a-b
Nucleoid is aggregated mass of DNA that constitutes

chromosome of cells of bacteria
20
Usually single circular chromosome
Eukaryotic cells have a nucleus

Nucleus: membrane-
bound structure
Contains DNA
DNA arranged in cells
to form chromosomes
Multiple linear
chromosomes
http://www.oncoursesystems.com/school/webpa
ge.aspx?id=10845583&xpage=788307
21
Is DNA only found in the

nucleus in eukaryotes?
22
Mitochondria and chloroplasts of

eukaryotes contain their own genomes
Circular
chromosome
http://www.oncoursesystems.com/school/webpa 23
ge.aspx?id=10845583&xpage=788307
The three domains of cellular

life
Prokaryotes Phylogenetic tree

Based on a
comparison
Oldest fossils of nucleic acid
3.5 billion years ago
sequence
Mitochondria Eukaryotes
and chloroplasts Oldest fossils
prokaryotic in 1.4 billion years ago
origin
24

In the average human cell there is around 2 meters of
DNA. This DNA is packaged into the nucleus which is 10
m in diameter. Which of the following best explains how
this occurs.
1. DNA is chopped up into smaller pieces by DNA gyrase
2. DNA is tightly packaged by ribosomes into
nucelosomes
3. DNA is packaged by proteins into smaller subunits
called amino acids
4. DNA wraps around histones forming loops of DNA and
protein called nucelosomes

on earlier work:
amount pyrimidine)
26
Double Helix
Structure of DNA
Proposed by
Watson and Crick
(1953)

27
5 end
hydrogen
bonds
The two
strands are
anti-parallel
The base pairing

of DNA is
complementary
Sugar phosphate Knox et al. (2014)

28
3 end backbone Figure 10.7
5 end
What does 5 and 3
mean?
Why is this
Each end of DNA is
important?
DNA
distinguished from other end
polymerase by terminal chemical entity:
works in the 5 5 end
to 3 direction 5 carbon has phosphate
adding new group attached to it
nucleotides to 3 end
the 3 end
3 carbon has hydroxyl
group attached to it
Sugar phosphate Knox et al. (2014)
29
3 end backbone Figure 10.7
Base pairing of DNA is

complementary
A T Hydrogen
bonds
C G
30
James Watson explains DNA

base pairing
http://www.youtube.com/watch?v=
PDeaLxoL75M&feature=plcp&con
text=C4567fa5VDvjVQa1PpcFMp
8m_wfy428vgD3WhsTP2ol9ucEF
xYz2U%3D 31
Chargaffs rules of base

composition
Organism Tissue Adenine Thymine Guanine Cytosine A + T
G+C
E.Coli - 26.0 23.9 24.9 25.2 1.00

(K12)
Yeast - 31.3 32.9 18.7 17.1 1.79
Human Liver 30.3 30.3 19.5 19.9 1.53
Rat Bone 28.6 28.4 21.4 21.5 1.33

Marrow
Adapted from table 7.1 Griffiths et al. (2008) Introduction to Genetic Analysis,
9th Edition, WH Freeman and Company: USA.
Vischer, E and Chargaff, E. (1948)The separation and quantitative estimation of
32
Purines and pyrimidines in minute amounts. J. Biol. Chem. 176: 703-714.

composition
HvJlnujmYcg&feature=plcp&conte
xt=C4c32e00VDvjVQa1PpcFMp8
m_wfy428iwNNjaPzXKRYhxuzFX
U5UE%3D
33

composition
Chargaffs work established empirical
rules about the amount of each type of
nucleotide found in DNA.
1. The amount of T equals the amount of A
and the amount of C equals the amount
of G
2. The total amount of pyrimidine
nucleotides (T+C) always equals the total
amount of purine nucleotides (A+G)
34

composition: summary
A=T
Purine Pyrimidine
G=C
A+G=T+C
Purine = Pyrimidine
35

If there is 29% of guanine in a section of
DNA, then there is __ thymine?
1. 21%
2. 29%
3. 42%
4. 58%

on earlier work:
amount pyrimidine)
37
The dark lady of DNA (Brenda Maddox)
Rosalind Franklin X-ray diffraction pattern 38

of DNA
Genetic information summary
Chromosome
Found?
Structure containing single DNA molecule
Gene Found?
Unit of inheritance
Genome
Cells complement of genes

Knox et al. (2014) Figure 10.4 39
Questions
What is genetic material? (PART 1)
How is more genetic material made?
(PART 2)
Learning Objectives
To understand DNA properties and
organisation in prokaryotic and eukaryotic
cells
To understand how DNA is replicated 40
Application: Recombinant DNA

technology
GloFish
Pray, L. (2008) Recombinant DNA technology and transgenic animals.
Nature Education 1(1):51
Image from: https://classconnection.s3.amazonaws.com/38/flashcards/
2463038/jpg/bio1001imageprokaryote1357159190223.jpg
Video: https://www.glofish.com/meet-glofish/glofish-videos/ 41
Why is DNA replicated?
fUpc93T12bk
42
Double Helix
Structure of DNA
Proposed by
Watson and Crick
(1953)

43
Watson and Cricks double helix

model of DNA
Didnt gain wide acceptance
Davis 2004, Meselson and Stahl: The art of DNA
replication, PNAS, 101(52): 17895-17896
Model suggests:
DNA replication could occur by synthesis of
new nucleotide stands opposite the original
strands using complementary base pairs to
create two new molecules that are exactly the
same as original
44
Meselson-Stahl experiment (1958)
Parental bacterial
DNA molecule
grown in 15N
Bacterial DNA
allowed to
replicate in 14N
45
Figure B10.2., Knox et al. (2014)
What would you expect after one round of replication if

conservative replication was true?
Pierce, Benjamin. (2005) Genetics: A Conceptual Approach, 2nd ed. (New York: W. H. Freeman 46
and Company), 322
Problem
The following sequence represents 10 bases
of one strand of a DNA double helix molecule
5 ATCGACTAGG 3
What would the complementary strand be?
47
How is more DNA made?
DNA replication
http://www.dnalc.org/resources/3d/03-
mechanism-of-replication-basic.html
48
DNA replication:
an overview
1. Two strands of helix
separate
2. Each strand used as
template to synthesise
complementary strand
3. Result: two identical
double helicases for
distribution to progeny
cells during mitosis
49
Figure 10.8 Knox et al. (2014)
Is DNA replication different in

prokaryotes and eukaryotes?
Basic processes are the same,
but simpler in prokaryotes
50
Bacterial chromosomes have a

single origin of replication
DNA gyrase This is where

cuts one strand
replication
starts
Where the
double
helix unwinds
51
Figure 10.10, Knox et al. (2014)
Bacterial chromosomes have a

single replication bubble
52
http://celliwood.blogspot.com.au/2008/03/replication.html
Leading strand Replication fork
DNA polymerase
Helicase
Primase
DNA polymerase can only work
Lagging strand in 5-3 direction-synthesises new strand
53
Bell, S. D (2006). Molecular biology: Prime-time progress. Nature 439, 542-543.
1.Cuts the
Strand
Keeps DNA 3. Keep strands
strand from apart
being twisted
2.Unwinds
DNA double
helix
54
DNA polymerase III
4. Catalyses addition of nucleotides

to growing strand in 5 to 3 direction
Also proof reads new DNA strand-
Removes incorrect bases
55
Problem: DNA synthesis

occurs only in the 5 to 3
direction
Both new strands are synthesised
at the same time
56
5. Grows towards
replication fork
only need single primer
6. Grows away from fork

synthesised in series of
short fragments- need
multiple primers
57
7. Synthesises
RNA primer
58
The enzyme primase is required

for DNA replication
DNA polymerase can only start
attaching nucleotides to a free
3OH group at the end of the
existing strand
Primer is removed by an editing

5 to 3 exonuclease
(RNase H)
59
8. Fills in gaps after removal of RNA-

replaces with DNA
9. Joins adjacent DNA

fragments
60

Which statement about the elongation of the
lagging strand during DNA replication is
correct?
1. It is synthesized in a 3' --> 5' direction
2. It grows toward the replication fork
3. It requires a short RNA primer to proceed
4. It is synthesized continuously

You are a scientist in a lab researching DNA replication.
You expose an organism undergoing replication to
radioactively labelled nucleotides. Following centrifugation,
the DNA separates into two classes. One class of labelled
DNA includes short stretches of DNA while the other class
includes very large molecules (thousands or even millions
of nucleotides long). These two classes of DNA probably
represent:
1. RNA primers and leading strands
2. Okazaki fragments and RNA primers
3. Okazaki fragments and leading strands
4. Okazaki fragments and lagging strands
62
How is replication more

complicated in eukaryotes?
63
There are differences in DNA replication

in prokaryotes and eukaryotes
In Eukaryotes
DNA molecule is bigger
Smaller Okazaki fragments
Replication fork moves slower than
prokaryotes
Chromosomes have many origins of
replication (many replication bubbles)
Different DNA polymerases are involved
64
What concepts have we

explored this week?
What is genetic material?
DNA: structure, composition and
packaging
Differences in DNA in prokaryotes and
eukaryotes
How is more DNA made?
DNA replication: why it is necessary
Mechanism of DNA replication
Main proteins involved 65
66
BIOL1102: Molecular Basis of Life: Week 5
How is the message made

and de-coded: Transcription
and Translation
Week 5: Tuesday and Wednesday
Dr Masha Smallhorn
masha.smallhorn@flinders.edu.au
Consulting: Mon 10-11am, Wed 12-1pm
SILC room 3 2
Relevant Material
Scitable by Nature Education:
Web address: http://www.nature.com/scitable
DNA Learning Centre:
Web address: https://www.dnalc.org/
Textbook:
Knox, B., Ladiges, P., Evans, B. And Saint, R. (2014), Biology:
An Australian Focus, 5th edition, McGraw Hill Australia PTY
LTD, North Ryde, New South Wales, chapter 11.
Reece, J. B., Meyers, N., Urry, L. A., Cain, M. L., Wasserman, S.
A., Minorsky, P. V., Jackson, R. B., Cooke, B. J., and Campbell,
N. A (2014). Campbell Biology. 10th Edition. Australian and New
Zealand Version.
3
Over the next two weeks. . .

Discover DNA and how more is made
Replication (week 4)
expression
Transcription and translation (week 5)
Learn how content discussed in lectures
can be applied to real world problems
Problem solve
4
Questions this week

MAIN : How does the information in the
genetic code produce a protein?
How is RNA synthesised from DNA?

(PART 1: Transcription)
How does the sequence of nucleotides in

the RNA determine the synthesis of a
polypeptide? (PART 2: Translation) 5
Learning Objectives (PART 1)

expression: DNA to RNA to Protein
Understand the differences between
prokaryotic and eukaryotic transcription
Understand and describe the 3 phases of
transcription; initiation, elongation
termination
Learning Objectives (PART 1)

Understand what a transcriptional unit and
an operon are
Understand and describe the processing
of pre-mRNA to mature mRNA in
eukaryotes
If DNA is a book,
how is it read?
Instructions stored
within DNA are read
and processed by
cell in two steps
8
Image from: http://en.bioinformatyk.eu/wp-content/uploads/2011/09/DNA_book.jpg
Transcription
Synthesis of RNA
from a DNA template
Translation
Synthesis of proteins
using messenger RNA
as a template
9
Transcription: terminology to
remember
DNA
Three major types of RNA
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
RNA polymerase
Promoter
10
Where does transcription

and translation occur in the
cell?
Differs for prokaryotes and
eukaryotes
11
In prokaryotes transcription and

translation are coupled
Occurs in the
cytoplasm
Knox et al. (2014) Figure 11.2a 12
In eukaryotes RNA transcripts

are modified before becoming
true mRNA
Transcription and
RNA processing
occurs in nucleus
Translation occurs
in cytosol
13
What do we know about the

genetic code?
How many bases does DNA have?
How many bases does RNA have?
What is a protein made of?
What is a codon?
14
Transcription: an overview
http://www.dnalc.org/resources/3d
/12-transcription-basic.html
15
RNA is copied from one strand

of a segment of DNA
RNA polymerase
Coding DNA strand
5 3
3 RNA 5
Template DNA Strand
16
Problem
The following sequence is the coding
strand of a DNA molecule. Following
transcription, what would the mRNA
sequence be?
5 ATGGCTCCA 3
mRNA
17
How does transcription begin?
When the enzyme RNA

polymerase attaches to template
DNA and begins to catalyse
production of complementary RNA
18
What do we know about RNA

polymerase?
Function
Synthesizes RNA from DNA
Growth of synthesized RNA strand occurs in 5-
3 direction
Adds bases onto the 3' ends of growing chains
Doesnt need a primer to begin synthesis
Recognizes a specific start site on the DNA
called promoter
In eukaryotes, three different RNA polymerases
(I, II, III) RNA polymerase II transcribes mRNA 19
Transcription: a three step

process
Initiation
Elongation
Termination
20
Initiated when RNA polymerase binds to DNA template

at promoter sequence
DNA double helix unwinds, RNA polymerase reads the template DNA and
adds nucleotides to the 3 end of a growing RNA transcript 21
Figure 2, Clancy, S. (2008) DNA transcription. Nature Education 1(1):41
How does transcription

terminate?
22
RNA polymerase reaches termination sequence on DNA template strand
mRNA transcript and RNA polymerase released from complex
23
Figure 2, Clancy, S. (2008) DNA transcription. Nature Education 1(1):41

Which of the following statements is true
about RNA polymerase?
1. It synthesises DNA from RNA
2. It binds to the promoter sequence to
initiate transcription
3. It requires a primer to start transcribing
4. It synthesises an RNA strand that grows
in the 3 to 5 direction
What happens next?
Depends if transcription occurring

in prokaryotes or eukaryotes
25
In prokaryotes transcription and

translation are coupled
Occur in the
cytoplasm
Knox et al. (2014) Figure 11.2a 26
In eukaryotes RNA transcripts

are modified before becoming
true mRNA
Transcription and
RNA processing
occurs in nucleus
Translation occurs
in cytosol
27
RNA processing occurs in

eukaryotes
Post-transcriptional processing of mRNA
transcripts
Occurs before the genetic messages are
dispatched to the cytoplasm
28
Alteration of mRNA Ends

Each end of a eukaryotic pre-mRNA
molecule is modified in a particular way
The 5 end receives a modified nucleotide cap
The 3 end gets a poly-A tail
A modified guanine nucleotide 50 to 250 adenine nucleotides
added to the 5 end added to the 3 end
Protein-coding segment Polyadenylation signal

5 3
G P P P AAUAAA AAAAAA
Start codon Stop codon
5 Cap 5 UTR 3 UTR Poly-A tail
29
Campbell, Figure 17.9
So, is that all the RNA

processing that occurs in
eukaryotes?
http://www.dnalc.org/resources/3d
/rna-splicing.html
30
RNA processing in eukaryotes:

a summary
Primary transcript
5 end: modified nucleotide cap
3 end: poly-A-tail
Non-coding
regions of DNA
Splicing of primary transcript
Introns spliced out of primary transcript
Exons joined together to become mature
mRNA
Coding regions of DNA
31
Transcription Unit
dsDNA region
UTR = untranslated regions

5 cap Poly-A-tail
Introns spliced out
Mature mRNA
32
Who does the splicing?

Spliceosome
Protein complex
Composed of protein and small
RNA molecules known as

snRNP (small nuclear
ribonucleoprotein particles)
Function
Recognises the 5 and 3 splice
sites, excises intron and ligates
flanking exons together
33
How is transcription
regulated?
34
TRANSCRIPTION
RNA PROCESSING
DNA
Pre-mRNA
1 Eukaryotic promoters
Transcription factors
mRNA
Proteins
TRANSLATION Ribosome
Polypeptide
Promoter
5 T A T A A A A 3
A T A T T T T
3 5
TATA box Start point
Template
DNA strand
Bind to promoter help
2 Several transcription
factors
form transcription
initiation complex
Campbell et al. (2014) Figure 17.8

Transcription
factors
5 3
3 5
3 Additional transcription
factors
Help RNA polymerase
recognise promoter
sequences
RNA polymerase II
Transcription factors
5 3
Control which genes
are turned on and off
3 5 5
RNA transcript
35
Transcription initiation complex
Does a transcription unit

encode more than one
protein?
36
Prokaryotic transcription units can

encode for more than one polypeptide
Prokaryotes
Many mRNA transcripts are polycistronic
Contain information for more than one
polypeptide
Eukaryotes
mRNA transcripts usually monocistronic
Code for a single polypeptide
37
In prokaryotes, several genes can be

present in the same mRNA transcript
Genes that are transcribed together from
a single promoter constitute an operon
DEFINITION:
Region of chromosome that contains
transcription unit, regulatory genes and
sequences required for regulated transcription
of unit
38

Consider what you have learnt about RNA
processing. Which of the following
statements is incorrect?
1. Nucleotides may be added at both ends of the
RNA
2. RNA splicing is catalyzed by spliceosomes
3. Exons are cut out before mRNA leaves the
nucleus
4. It only occurs in eukaryotes
How is transcription different

in prokaryotes and
eukaryotes?
40
Transcription: prokaryotes vs
eukaryotes
PROKARYOTES EUKARYOTES
41
Questions this week

MAIN: How does the information in the
genetic code produce a protein?
How is RNA synthesised from DNA?

(PART 1: Transcription)
How does the sequence of nucleotides in

the RNA determine the synthesis of a
polypeptide? (PART 2: Translation) 42
Learning objectives (PART 2)

Understand the structure and function of
tRNAs
Understand the structure and function of
ribosomes
Understand what a codon is and be able
to use the universal genetic code to
determine the resulting protein sequence
from a DNA or RNA sequence
43
Learning objectives (PART 2)

Describe the process of translation and
each of its 3 phases; initiation, elongation
and termination
Understand the differences between
prokaryotic and eukaryotic translation
Understand and describe how proteins are
targeted to different cellular locations
44
If DNA is a book,
how is it read?
Instructions stored
within DNA are read
and processed by
cell in two steps
45
Transcription
synthesis of RNA
from a DNA template
Translation
synthesis of proteins
using messenger RNA
as a template
46
Translation: an overview
http://www.dnalc.org/view/15501-
Translation-RNA-to-protein-3D-
animation-with-basic-
narration.html
47
Translation: an overview
DEFINITION: Translation is the RNA-
directed synthesis of a polypeptide
A cell translates an mRNA message into a

protein
The ribosome is the molecular machine that
carries out this process
With the help of transfer RNA (tRNA)
Ribosome reads mRNA according to genetic
code 48
Gene 2
DNA dsDNA Molecule
molecule
Gene 1
Gene 3
Template strand
DNA strand 3 5
(template) A C C A A A C C G A G T
TRANSCRIPTION Genetic message read in triplets
U G G U U U G G C U C A
mRNA 5 3
Codon
Each codon specifies an amino acid
TRANSLATION
Protein Trp Phe Gly Ser

49
Genetic code
Start codon
AUG
Stop codons
UAA
UAG
UGA
*codon either translated
into amino acid or serves
as translation stop signal
50

Use the genetic code table to determine
what amino acid sequence will be
generated, based on the following mRNA
sequence?
5' AUG-AAU-UUA-UCC 3'
1. met-ile-phe-ser
2. met-asn-leu-ser Go to: respond.cc
3. met-asn-phe-tyr session key: 91569
4. met-ile-leu-tyr 51
Is the starting point of

translation important?
52
The open reading frame is the

region of the mRNA that is read
during synthesis of a protein

53
54
Translation: the main players

Ribosome
Cytoplasmic organelle where protein
synthesis occurs
Transfer RNA (tRNA)

Carries amino acid to ribosome and
transfers it to growing polypeptide chain
55

TRANSCRIPTION DNA
mRNA
Ribosome
TRANSLATION
Polypeptide
Campbell et al. (2011) Biology Figure 17.14
Amino
Polypeptide acids
tRNA with
amino acid
attached
Ribosome
Gly
tRNA
Ribosome E P A tRNA
Anticodon
A A A
U G G U U U G G C
5 Codons 3 56
mRNA
Ribosomes consist of a large

and small subunit
Constructed of proteins and RNA
molecules called ribosomal RNA (rRNA)
A site
Binds incoming
aminoacyl-tRNA
P site
Binds peptidyl-tRNA
57
Ribosomes consist of a large

and small subunit
Bacterial large subunit

structure
2 rRNA molecules (grey)

34 proteins (gold)
58
*based on X-ray crystallography
S = Svedberg Unit (measure of how fast molecules move through centrifuge
59

Ribosome
Cytoplasmic organelle where protein
synthesis occurs
Transfer RNA (tRNA)

Carries amino acid to ribosome and
transfers it to growing polypeptide chain
60
Transfer RNAs are adaptor

molecules
tRNA molecule
One end reads triplet
amino acid code in mRNA through
attaches here
complementary base
pairing
Other end attaches to
specific amino acid
Consists of a single
RNA strand that is
anticodon only about 75
nucleotides long
61
Transfer RNAs are adaptor

molecules
One or more transfer RNAs exist for each
of the 20 amino acids found in proteins
Each can carry a specific amino acid on one
end
Each has an anticodon on the other end
Wobble rules: tRNA with single amino acid
can recognise all codons for that amino acid
Enzymes called aminoacyl-tRNA
synthetases attach an amino acid to a
tRNA 62
Translation can be divided into

3 stages
Initiation Elongation Termination
63
Initiation stage of translation
Initiator tRNA
AUG =
Start codon
Brings together mRNA, tRNA bearing the first amino acid

of the polypeptide, and two subunits of a ribosome
64
Elongation stage of translation
Amino acids added one by one to the preceding amino

acid
Peptide bond forms between carboxyl group of first
amino acid and amino group of second amino acid
65
Termination of translation
Releases
polypeptide
No tRNA that
recognises
stop codons
Ribosome reaches stop codon (termination codon)

Aminoacyl bond between polypeptide and peptidyl-tRNA
is hydrolysed
Ribosomal subunits dissociate
66
Knox et al. (2014) Figure 11.16c

A particular triplet of bases in the template
sequence of DNA is TTT. The anticodon on
the tRNA that binds the mRNA codon is:
1. UUA
2. UUU
3. TTT
4. AAA
So. . . . .is a single mRNA

translated by one ribosome at
a time?
68
Polyribosomes are clusters of

several ribosomes
mRNA molecules are normally translated simultaneously

by several ribosomes in clusters called polyribosomes
Why?
Can make many copies of polypeptide at a time
69
Campbell et al. (2011). Biology, Figure 17.21
What happens once the

protein is made?
1. Protein needs to be folded
properly to function
2. Protein needs to be transported
from where made to site of
action 70
To function correctly proteins

must be properly folded
Protein folding:
May occur spontaneously
Or involve other proteins called chaperone
proteins (chaperonins)
Some proteins require post-translational

modifications, such as glycosylation, to
be functional
71
Protein targeting
Two populations of ribosomes
72
Protein targeting in eukaryotic cells
Main pathway 1
Involves free
ribosomes
73
Protein targeting in eukaryotic cells
Main pathway 2
Involves
ribosomes
bound to ER
74
How do the polypeptides know

where to go?
Signal sequence
75
Signal peptides are like an

address label
Signal peptides
Short amino acid sequences in protein
Used to target protein to the correct
location
May be excised from the protein during
targeting
76
What are the main differences

between translation in
prokaryotes and eukaryotes?
77
Prokaryotic cells lack a nuclear

envelope
RNA polymerase
DNA
mRNA
Polyribosome
Direction of 0.25 m
RNA
transcription
polymerase
DNA
Polyribosome
Polypeptide
(amino end)
Ribosome
mRNA (5 end)
Thus, translation begins while transcription is still in

progress 78
Translation and human

disease
79
Translation matters!
Human inherited diseases can be caused
by protein synthesis defects
Mutations that effect essential components of
translational machinery
Examples?
Inherited diseases include: Hereditary
spastic paraplegia, mitochondrial
myopathy, mental retardation, deafness
Scheper et al. (2007) Translation matters: protein synthesis defects in inherited diseases
Nature Reviews Genetics, 8:711-723 80
Summary
5 ATCGACCAG 3 Coding strand
3 TAGCTGGTC 5 Template strand
transcription
5 AUCGACCAG 3 Messenger RNA

(mRNA)
translation
Ile Asp Gln Polypeptide
Amino acids 81
Reference Material
Energy, Enzymes & Life Chapter 3 The chemistry of life

Knox, Ladiges, Evans and Saint, Biology: an
Australian Focus, 5th Edition, McGraw Hill,
Australia
Associate Professor Ian Menz
Biology room 205 (via school office)
Chapter 8 An introduction to Metabolism
ian.menz@flinders.edu.au
Reece, J. B., Meyers, N., Urry, L. A., Cain, M.
L., Wasserman, S. A., Minorsky, P. V.,
Jackson, R. B., Cooke, B. J., and Campbell,
N. A (2014). Campbell Biology. 10th
Edition. Australian and New Zealand
Version
Why do we eat? Metabolism
a) Because we like the taste. Is the complement of all chemical

b) Because we require energy and the reactions in a cell or organism.
food provides energy.
c) Because the chemical reactions in These chemical reactions are fuelled
the body require building blocks in terms of both energy and
which come from food substrates from the food we eat.
d) 2 and 3 above
e) All of the above
https://respond.cc session key
1
Organisation of the Chemistry of Life into There are two types of metabolic
Metabolic Pathways pathways
A metabolic pathway has many Catabolic pathways

steps Break down complex molecules into
That begin with a specific molecule and simpler compounds
end with a product Release energy
Each catalyzed by a specific enzyme
Anabolic pathways
Enzyme 1 Enzyme 2 Enzyme 3
Build complicated molecules from
A B C D simpler ones
Reaction 1 Reaction 2 Reaction 3
Starting Product Consume energy
molecule
Biological Order and Disorder Free Energy G

Entropy is the measure of disorder The free-energy change of a reaction
Living systems use energy to maintain tells us whether the reaction occurs
order spontaneously
50m
The change in free energy, G during

a biological process
Is related directly to the enthalpy change
(H) and the change in entropy (S)
G = H - T S
Campbell Figure 8.4
2
Exergonic and Endergonic
Reactions in Metabolism
An exergonic reaction An endergonic reaction

Proceeds with a net release of free energy and is Is one that absorbs free energy from its
spontaneous surroundings and is non-spontaneous
Free
Free
Knox Figure 3.4
Knox Figure 3.4
The Structure and Hydrolysis of

ATP the energy currency of the cell ATP
ATP powers cellular work by coupling ATP (adenosine triphosphate)
exergonic reactions to endergonic reactions
Is the cells energy shuttle
Provides energy for cellular functions
A cell does three main kinds of work
Mechanical
Transport
Chemical
Energy coupling
Is a key feature in the way cells manage their
energy resources to do this work
Knox Figure 3.15
3
ATP hydrolysis
Energy is released from ATP Can be coupled to other reactions
When the terminal phosphate bond is broken Endergonic reaction: G is positive, reaction
is not spontaneous
P P P NH2
+ NH3 G = +3.4 kcal/mol

Glu Glu
Adenosine triphosphate (ATP) Glutamic Ammonia Glutamine
acid
H 2O Exergonic reaction: G is negative, reaction

is spontaneous
ATP + H2O ADP + P G = - 7.3 kcal/mol

P i
+ P P Energy
Campbell Coupled reactions: Overall G is negative;

Figure 8.10 together, reactions are spontaneous G = 3.9 kcal/mol
Campbell Figure 8.9 Inorganic phosphate Adenosine diphosphate (ADP)
Which of the following reactions could only occur in

a cell if it were coupled to the hydrolysis of ATP
(ATP + H2O ADP + Pi (G = -7.3 kcal/mol)? Three types of cellular work
P i
P
1. A + Pi AP (G = +10 kcal/mol) Motor protein Protein moved
B + Pi BP (G = +8 kcal/mol)
(a) Mechanical work: ATP phosphorylates motor proteins
2.
Membrane
CP C + Pi (G = -4 kcal/mol)
protein
ADP
3. ATP +
P i
4. DP D + Pi (G = -10 kcal/mol) Solute

P
Solute transported
P i
E + Pi EP (G = +5 kcal/mol)
(b) Transport work: ATP phosphorylates transport proteins
5.
P
NH2
Glu + NH3 + P i
Glu
https://respond.cc session key Reactants: Glutamic acid Product (glutamine)
and ammonia made
Campbell Figure 8.11 (c) Chemical work: ATP phosphorylates key reactants
4
Approximately how much ATP do I
hydrolyse every day? The Regeneration of ATP
1. 65 mg Catabolic pathways
Drive the regeneration of ATP from ADP and
2. 6.5 g phosphate
3. 650 g ATP synthesis from ATP hydrolysis to
6.5 kg
ADP + P i requires energy ADP + P i yields energy
4.
5. 65 kg ATP

Energy from catabolism Energy for cellular work
(exergonic, energy yielding (endergonic, energy-
processes) consuming processes)
ADP + P i
Campbell Figure 8.12
ENZYMES The activation barrier

Enzymes speed up metabolic The hydrolysis of sucrose
reactions by lowering energy Is an example of a an exogernic
barriers chemical reaction
A catalyst
Is a chemical agent that speeds up a CH2OH CH2OH CH2OH CH2OH
reaction without being consumed by H H
O
H O H Sucrase H
H
O H O H
the reaction OH O H HO
CH2OH
+ H2O
HO
OH H OH HO H HO
CH2OH
An enzyme H OH OH H H OH OH H
Is a catalytic protein Sucrose Glucose Fructose

C12H22O11 C6H12O6 C6H12O6
Campbell Figure Concept 8.4
5
The energy profile for an exergonic
The activation energy, EA reaction
Is the initial amount of energy needed to

A B
start a chemical reaction
C D
Transition state
Is often supplied in the form of heat
from the surroundings in a system A B EA
Free energy
C D
Reactants
A B
G < O
C D
Products
Progress of the reaction
See Knox Figure 3.6
Knox Fig 3.5
The energy profile of an enzyme

catalysed reaction The active site
Is the region on the enzyme where the
substrate binds
An enzyme catalyzes reactions by lowering the EA barrier Knox Figure 3.7

and therefore increasing the rate of reaction See Campbell Fig 8.15
Knox Fig 3.6
See Campbell 8.14
6
The catalytic cycle of an enzyme
Allosteric Regulation of Enzymes
Allosteric regulation
Is the term used to describe any case in which
a proteins function at one site is affected by
binding of a regulatory molecule at another
site
Many enzymes are allosterically regulated
Allosteric regulation can result in either

inhibition or activation of an enzyme
Active site (and R groups of
its amino acids) can lower EA
and speed up a reaction by
acting as a template for
substrate orientation,
stressing the substrates
and stabilizing the
transition state,
providing a favorable
microenvironment,
participating directly in the
Knox Figure 3.10 catalytic reaction.
Allosteric activation & inhibition Feedback Inhibition
In feedback inhibition
The end product of a metabolic
pathway shuts down the pathway
Knox Figure 3.14
7
Feedback inhibition Learning Objectives
Initial substrate
Active site
available
(threonine)
Threonine
1. Understand what a metabolic
in active site
pathway is.
Enzyme 1
Isoleucine
used up by
(threonine
deaminase) 2. Be able to distinguish the difference
cell
Intermediate A between anabolic and catabolic
pathways
Feedback Active site of
inhibition Enzyme 2
enzyme 1 no
longer binds
Be able to describe the concept of

threonine; Intermediate B
pathway is
switched off Enzyme 3
3.
Intermediate C
free energy.
Isoleucine
binds to
allosteric
Enzyme 4
4. Be able to determine if a reaction or
series of coupled reactions would be
site Intermediate D
Enzyme 5
spontaneous or not if given the G

Campbell Figure 8.21 End product
(isoleucine)
value
Learning objectives
5. Understand why ATP is the energy

currency of the cell and the concept
that it is continually regenerated.
6. Be able to describe what an enzyme
is and why it speeds up chemical
reactions.
7. Understand the concept of enzyme
regulation and be able to predict
how flux through a metabolic
pathway may change under
different conditions.
8
Reference Material
Chapter 3 The chemistry of life;
Introduction to respiration Chapter 6 Harvesting Energy;
Knox, Ladiges, Evans and Saint, Biology: an Australian
Focus, 5th Edition, McGraw Hill, Australia
Biology room 205 (via school office) Chapter 8 An introduction to Metabolism
ian.menz@flinders.edu.au Chapter 9 Cellular respiration and fermentation
Reece, J. B., Meyers, N., Urry, L. A., Cain, M. L.,
Wasserman, S. A., Minorsky, P. V., Jackson, R. B.,
Cooke, B. J., and Campbell, N. A (2014). Campbell
Biology. 10th Edition. Australian and New Zealand
Version
Introduction to respiration Respiration
Catabolic pathways yield energy by C6H12O6 + 6O2 6CO2 + 6H2O +

oxidizing organic fuels ~36ATP + HEAT
Consists of three key processes:

The organic fuels used by cells are: Glycolysis
Carbohydrate, Fat, and Protein Krebs Cycle (Citric acid cycle, TCA cycle)
Electron transport and oxidative
phosphorylation
The energy from the oxidation of
these fuels is used to synthesise
ATP, the energy currency of the cell
1
An overview of cellular respiration The catabolism of various molecules
from food
Proteins Carbohydrates Fats
Electrons Electrons carried
carried via NADH and
Amino Sugars Glycerol Fatty
via NADH FADH2 acids acids
Glycolysis
Oxidative Glucose
Citric phosphorylation:
Glycolsis
acid electron
Glucose Pyruvate cycle Glyceraldehyde-3-P
transport and
chemiosmosis NH3 Pyruvate
Cytosol
Mitochondrion Acetyl CoA
Citric
ATP ATP ATP acid
cycle
Substrate-level Oxidative
Substrate-level
Campbell phosphorylation phosphorylation
phosphorylation Campbell Figure 9.19
Figure 9.6 Oxidative
See Knox Figure 6.2 phosphorylation
Redox Reactions:
Oxidation and Reduction The Principle of Redox
Respiration yields energy due to the In oxidation

transfer of electrons. A substance loses electrons, or is
oxidized
Reactions that transfer electrons

from one molecule to another are In reduction
known as an oxidation/reduction A substance gains electrons, or is
reactions or Redox reactions reduced
2
Oxidation of Organic Fuel Molecules During Why do the oxidations occur in small
Cellular Respiration steps?
During cellular respiration

2H + 1/
2 O2
(from food via
NADH)
Glucose is oxidized and oxygen is Controlled
release of
reduced
H2 + 1/2 O2
2 H+ + 2 e energy for
synthesis
of
ATP
Free energy, G
ATP
becomes oxidized ATP
Free energy, G
C6H12O6 + 6O2 6CO2 + 6H2O + Energy Explosive ATP
release of
becomes reduced heat and light
energy
2 e
Cellular respiration 2 H+
1/
2 O2
Oxidizes glucose in a series of steps Campbell H2 O H2O

Figure 9.5 A
Campbell Figure 9.5 B
(a) Uncontrolled reaction See Knox Figure 3.18 (b) Cellular respiration
Electrons from organic compounds such as

sugars
Are usually first transferred to NAD+, a coenzyme The 3 stages of respiration
Glycolysis
Breaks down glucose into two molecules of
pyruvate
The citric acid cycle
Completes the breakdown of glucose to CO2
NAD+ NADH Oxidative phosphorylation
Generates ATP
Is driven by the electron transport chain which
2[H]= 2H+ + 2e
oxidizes electron carriers such as NADH
Knox Fig 3.19
3
An overview of cellular respiration
CYTOSOL Electron shuttles
2 NADH
MITOCHONDRION Both glycolysis and the citric acid
cycle
span membrane
or
2 FADH2
2 NADH 2 NADH 6 NADH 2 FADH2

Can generate ATP by substrate-level
Glycolysis Oxidative
phosphorylation
2 Citric phosphorylation:
2 Acetyl acid electron transport
Glucose Pyruvate CoA cycle and
chemiosmosis
Enzyme Enzyme
+ 2 ATP + 2 ATP + about 34 -36 ATP
by substrate-level by substrate-level by oxidative phosphorylation, depending
phosphorylation phosphorylation on which shuttle transports electrons
from NADH in cytosol ADP
About P
Maximum per glucose: 38 or 40 ATP Substrate
+ ATP
See Knox Figure 6.2

Campbell Figure 9.7 Product
Glycolysis
Means splitting of sugar Glycolysis consists
Glycolysis Citric Oxidative

acid
cycle phosphorylation
Glucose pyruvic acid (10 of two major ATP ATP ATP
enzymatic steps) phases Energy investment phase
Energy investment
Net of 2 ATP molecules generated
Glucose
phase
Glycolysis occurs in the cytoplasm
2 ADP + 2 P 2 ATP used
Energy payoff
phase Energy payoff phase
Glycolysis does not require O2

(anaerobic)
4 ADP + 4 P 4 ATP formed
Glycolysis also results in reduction

2 NAD+ + 4 e- + 4 H + 2 NADH + 2 H+

of 2 NAD+ to 2 NADH 2 Pyruvate + 2 H2O
Glucose 2 Pyruvate + 2 H2O

4 ATP formed 2 ATP used 2 ATP
Campbell Figure 9.8 2 NAD+ +4 e +4H 2 NADH + 2 H+
+
4
What is the purpose of glycolysis?
1. Provide all the cells ATP

requirements
2. Provide some substrates for other
phases of respiration
3. Provide some ATP in the absence
of oxygen
4. 2+3 above
5. All of the above
Knox Fig 6.3 https://respond.cc session key
What happens to the rate of glycolysis

if NADH can not be oxidised by the
cell? The Citric Acid Cycle
1. Nothing The citric acid cycle completes the energy-

2. It speeds up yielding oxidation of organic molecules
3. It slows down
4. It will stop altogether The citric acid cycle
Takes place in the matrix of the mitochondrion
Pyruvate from glycolysis is transported to the
mitochondrion and converted to Acetyl CoA
which is the carbon input to the citric acid
cycle
5
Learning Objectives
1. Be able to explain what redox reactions
are and how they are important in
respiration.
2. Be able to state the three processes that
constitute cellular respiration
3. Be able to state what the inputs/outputs
are for glycolysis.
6
6/04/2017
Glycolysis Glycolysis consists

Glycolysis Citric Oxidative

acid
of two major ATP ATP ATP
phases Energy investment phase
Energy investment Glucose
phase 2 ADP + 2 P 2 ATP used
Energy payoff
phase Energy payoff phase
4 ADP + 4 P 4 ATP formed
2 NAD+ + 4 e- + 4 H + 2 NADH + 2 H+
2 Pyruvate + 2 H2O
Glucose 2 Pyruvate + 2 H2O

4 ATP formed 2 ATP used 2 ATP
Campbell Figure 9.8 2 NAD+ + 4 e + 4 H 2 NADH + 2 H+
+
CH2OH
Citric
H H Oxidative
H Glycolysis acid
HO H cycle phosphorylation
HO OH
H OH
Glucose
Glycolysis ATP 1
Hexokinase
ADP
CH2OH P
Means splitting of sugar H O H

HO
H
OH H
Glucose pyruvic acid (10

H OH
Glucose-6-phosphate
2
enzymatic steps)
Phosphoglucoisomerase
CH2O P
O CH2OH
Net of 2 ATP molecules generated

H HO
H HO
HO H
Fructose-6-phosphate
Glycolysis occurs in the cytoplasm ATP

3
Phosphofructokinase
Glycolysis does not require O2

ADP
P O CH2 O CH2 O P
(anaerobic) H
HO
HO H
OH
Fructose-
Glycolysis also results in reduction

1, 6-bisphosphate
Aldolase
4
of 2 NAD+ to 2 NADH P O CH2 Isomerase

5 H
C O
C O
CHOH
CH2OH
CH2 O P
Campbell Figure 9.9 A Dihydroxyacetone Glyceraldehyde-
phosphate 3-phosphate
See Knox Figure 6.3
1
6/04/2017
6
2 NAD+
Triose phosphate
dehydrogenase
2 NADH 2 Pi
+ 2 H+
2
P O C O
CHOH
CH2 O P
1, 3-Bisphosphoglycerate
What is the purpose of glycolysis?
2 ADP
7
Phosphoglycerokinase
Provide all the cells ATP

2 ATP
2 O
a)
requirements
C
CHOH
CH2 O P
Provide some substrates for other

3-Phosphoglycerate
b)
8
Phosphoglyceromutase
phases of respiration
2 O
C O
H C O P
Provide some ATP in the absence

CH2OH
2-Phosphoglycerate
9 c)
of oxygen
2 H2O Enolase
2 O
C O
b+c above
C O P
CH2
Phosphoenolpyruvate d)
2 ADP
10
2 ATP
Pyruvate kinase
e) All of the above
2 O
C O
Campbell Figure 9.8 B

See Knox Figure 6.3
C
CH3
O
https://respond.cc session key 917002
Pyruvate
What happens to the rate of glycolysis

if NADH can not be oxidised by the
cell?
a) Nothing
b) It speeds up
c) It slows down
d) It will stop altogether
Fig 6.3
2
6/04/2017
Anaerobic Glycolysis Pyruvate is a key juncture in catabolism

Glucose
ATP can not be stored thus, must be
synthesised continuously to power CYTOSOL
metabolism Pyruvate
No O2 present O2 present
Anaerobic glycolysis enables some ATP to Fermentation Cellular respiration
be made when O2 supply is inadequate eg

stressed muscle or anaerobic yeast in a
beer bottle Ethanol
MITOCHONDRION
Acetyl CoA
or
NAD required for glycolysis is made by

lactate
Citric
converting pyruvate to either lactic acid

acid
cycle
or ethanol.
Figure 9.18
Anaerobic glycolysis
Help doc, it hurts!
Fig 6.8
3
6/04/2017
The catabolism of various molecules

Fat as a fuel from food
Proteins Carbohydrates Fats
Fatty acids are more energy dense than glucose
stores and there are very large stores of fat in Amino Sugars Fatty
adipose tissue.
Glycerol
acids acids
if all of the energy stored as fat was stored as

Glycolysis
Glucose
glycogen, body mass would increase by 50 kg.
Glyceraldehyde-3- P
Fatty acids are catabolized via -oxidation and then

enter the Krebs cycle. If it is fully oxidized a typical NH3 Pyruvate
fat molecule yields ~129 molecules of ATP.
Acetyl CoA
Given that stores of fat in the body are so vast, they

would allow exercise at a maximal intensity (i.e. Citric
sprinting) to continue for >1 h. acid
cycle

Oxidative
13 See Knox Figure 6.2 phosphorylation
Fat as a fuel Now for the pain

However, the rate of ATP resynthesis from fat is too
slow to be of great importance during high intensity
activity.
Therefore, although fat is the preferred substrate
and dominates the energy contribution to resting
metabolism, carbohydrate stores are available when
energy requirements increase, for example at the
onset of exercise.
As exercise continues, however, fat metabolism may
become more important, particularly if muscle
glucose stores become depleted.
14 16
4
6/04/2017
Mr Andrews visits his GP complaining of

muscle pain and fatigue after mild Whats wrong
exercise. He says: I can barely walk up
a flight of stairs any more without having
with
to stop because the pain in my legs is Mr Andrews?
so bad. But if I sit down and rest, I feel
fine or if I push through it the pain goes
away
17 19
Mr Andrews is 31 years old, The GP arranges for Mr Andrews to

married, the father of two have some exercise tests.
small children who are both
healthy and well. He is a He is able to exercise on a treadmill for
5 min before the muscle pain in his
computer programmer.
legs becomes unbearable.
18 20
5
6/04/2017
Blood Test Results
At the same time, a control subject Control

exercises to exhaustion at an intensity Before exercise: Glucose 4.6mM, Lactate 1.2mM
of exercise that is almost twice that After exercise: Glucose 4.3mM, Lactate 4.3mM
which Mr Andrews is able to sustain.
Mr Andrews
Before exercise: Glucose 4.3mM, Lactate 1.0 mM
After exercise: Glucose 4.1mM, Lactate 1.1 mM
21 23
Blood samples are taken from Mr

Andrews before and after the What else happens during
exercise and compared to blood sudden activity?
samples taken from the control
subject.
22 24
6
6/04/2017
Storing glucose as glycogen

Breakdown process
catalyzed by the enzyme:
A muscle biopsy reveals that the Glycogen phosphorylase
glycogen content of Mr Andrews

muscle is much, much greater than
the control subject although the
molecular structure of his glycogen
Glucose
is normal.
Glyceraldehyde-3-P Glycolysis
Pyruvate
25 27
Glycogen is a readily mobilized Glycogen degradation consists of three steps:
storage form of glucose. It is a very 1. the release of glucose 1-phosphate from

large, branched polymer of glucose glycogen,
residues that can be broken down 2. the remodelling of the glycogen substrate to
permit further degradation, and
to yield glucose molecules when
3. the conversion of glucose 1-phosphate into
energy is needed glucose 6-phosphate for further metabolism.
The glucose 6-phosphate derived from the

breakdown of glycogen is the initial substrate for
glycolysis.
26 28
7
6/04/2017
McArdles Disease
When adrenaline is added to a suspension Is one of the most common metabolic
of muscle cells from a normal individual the myopathies and is caused by genetic
glycogen content of the cells declines defects of the muscle-specific isozyme of
rapidly. glycogen phosphorylase, which blocks
adenosine triphosphate (ATP) formation
In contrast, adrenaline has no effect on the from glycogen in skeletal muscle
glycogen content of Mr Andrews muscle
cells. Typically, patients with McArdle disease
have exercise intolerance, with premature
muscle fatigue, exercise-induced muscle
However, levels of adrenaline are normal in pain in working muscles,
Mr Andrews under various conditions, and
it does accelerate his heart rate and important under conditions where O2
constrict his blood vessels in the skin and supply to the muscle tissues is insufficient
kidneys when present to meet the demand for ATP
29 31
What is wrong with

Mr Andrews?
a) Defective enzyme glycogen
phosphorylase cant breakdown
glycogen
b) His Adrenalin is defective
c) He is very unfit
d) He cant metabolize fat
e) Defective enzyme lactate
dehydrogenase cant convert pyruvate
to lactate

30
8
An overview of cellular respiration
Cellular Respiration Electrons

carried
Electrons carried
via NADH and
FADH2
via NADH
Oxidative
Citric
Associate Professor Ian Menz Glycolsis
acid
phosphorylation:
electron
Glucose Pyruvate
Biology room 205 (via school office) cycle transport and
chemiosmosis
Cytosol
Mitochondrion
ATP ATP ATP
Substrate-level Oxidative
Substrate-level
phosphorylation phosphorylation
phosphorylation
Campbell Figure 9.6
Reference Material The Citric Acid Cycle

Chapter 6 Harvesting Energy
The citric acid cycle completes the energy-
Focus, 5th Edition, McGraw Hill, Australia yielding oxidation of organic molecules
Chapter 9 Cellular respiration and fermentation

Reece, J. B., Meyers, N., Urry, L. A., Cain, M. L., The citric acid cycle
Wasserman, S. A., Minorsky, P. V., Jackson, R. B., Takes place in the matrix of the mitochondrion
Cooke, B. J., and Campbell, N. A (2014). Campbell
Biology. 10th Edition. Australian and New Zealand
Version
An overview of the citric acid cycle
Before the citric acid cycle can begin
2 carbon compound Acetyl Pyruvate
Pyruvate must first be converted to acetyl CoA by
Citric
CoA enters cycle by joining

(from glycolysis,
acid
pyruvate dehydrogenase, which links the cycle to with oxaloacetate (4C) 2 molecules per glucose)
glycolysis.
ATP ATP ATP
CO2
Cycle has 8 steps, each NAD+
CoA
catalysed by an enzyme NADH
located in the Acetyl CoA
mitochondrial matrix
CoA
CoA
2 C released as CO2
(reduced form enters as Citric
Acetyl CoA- oxidised form acid 2 CO2
leaves as CO2) cycle
FADH2 3 NAD+
FAD 3 NADH
+ 3 H+
ADP + P i
Knox Fig 6.5 ATP
The Citric Acid Cycle

Citric Acid Cycle
The Citric Acid Cycle occurs in the
mitochondria
Oxidative reactions generate CO2
Process transfers electrons to the carrier
molecules NAD+ and FAD generating NADH
and FADH2 which are subsequently used to
make ATP by oxidative phosporylation
Generates 2 ATP by substrate level
phosphorylation (per glucose entering
glycolysis)
Knox Fig 6.5

The electron transport chain and
Citric Oxidative
Glycolysis
acid
cycle
phosphorylation
chemiosmosis
S CoA
C O
Inner
Mitochondrial
Chemiosmosis and the electron
CH3

Oxidative
Acetyl CoA Glycolysis phosphorylation. membrane
electron transport
CoA SH and chemiosmosis
NADH
+ H+
O C COO
CH2 1 COO H2O ATP ATP ATP
transport chain
NAD+ COO CH2 COO H+
8 Oxaloacetate HO C COO CH2 H+
CH2
2
COO HC COO
HO CH Malate
COO HO CH H+
CH2
Citrate
Figure 9.12 COO H+
Isocitrate Cyt c
COO Protein complex
CO2 Intermembrane
Citric of electron
acid 3 space carners
7 NAD+
H2O cycle Q IV
COO
COO NADH
CH
Fumarate
+ H+ I III
CoA SH CH2
HC
CH2 -Ketoglutarate ATP
COO
C O Inner II synthase
4
6
COO CoA SH COO COO mitochondrial FADH2 H2O
CH2 5 CH2 membrane FAD+ 2 H+ + 1/2 O2
FADH2
CO2 NADH+
FAD
CH2 CH2
NAD+ NAD+ ADP + Pi ATP
COO C O
Succinate Pi S CoA NADH (Carrying electrons
GTP GDP Succinyl + H+ from, food) H+
CoA Mitochondrial Chemiosmosis
Electron transport chain
ADP matrix Electron transport and pumping of protons (H+), ATP synthesis powered by the flow
ATP which create an H+ gradient across the membrane Of H+ back across the membrane
Campbell Figure 9.12 Campbell Figure 9.15 Oxidative phosphorylation
See Knox Figure 6.6
Electron transport Electron Transport Chain (ETC)

During oxidative phosphorylation, chemiosmosis couples
electron transport to ATP synthesis
The Citric Acid Cycle generates NADH & FADH2 which 50

NADH
donate electrons to the electron transport chain.

FADH2
Multiprotein
Proteins embedded in inner mitochondrial membrane accept
Free energy (G) relative to O2 (kcl/mol)

40 I FAD
FMN
FeS FeS II
complexes
electrons and pass them on to the next protein in the chain O

III
and finally to oxygen, yielding water.
Cyt b
30 FeS
Cyt c1
Cyt c IV
Proteins ordered in sequence (by capacity to accept

Cyt a
20
Cyt a3
electrons)
Energy released as electrons passed from one carrier to

10

another used to form a H+ gradient across membrane. This
H+ gradient is used to make ATP (oxidative phoshorylation), 0 2 H + + 12 O2
remainder released as heat. Campbell Figure 9.13

H 2O
See Knox Figure 3.18
ETC animation ATP synthase
http://vcell.ndsu.nodak.edu/animations Three catalytic
/etc/ETCAdvanced.wmv
sites in the
stationary knob
join inorganic
Phosphate to ADP
to make ATP.
A rotor within the
membrane spins
clockwise when
H+ flows past
it down the H+
gradient. A stator anchored
in the membrane
holds the knob
stationary.
Knox Figure 6.7

See Campbell Figure 9.14
Chemiosomosis ATP synthase animation

Energy from electron transport chain used to http://vcell.ndsu.nodak.edu/animations
pump H+ across mitochondrial membrane.
/atpgradient/movie.htm
Causes proton gradient (proton motive force)
Protein complex (ATP synthase) located in
mitochondrial membrane has a channel
through which protons can move.
Protons flow down gradient energy to
produce ATP from ADP and Pi
Electron Transport Brown Adipose tissue
The two processes of electron transport

and oxidative phosphorylation are
separate and coupled.
Plants and animals can deliberately
uncouple.
ie burn fuels to produce heat
Eg hibernating animals
Plant Respiratory Chains An overview of cellular respiration

Electron shuttles MITOCHONDRION
CYTOSOL 2 NADH
span membrane
or
2 FADH2
2 NADH 2 NADH 6 NADH 2 FADH2
2 Citric phosphorylation:
2 Acetyl acid electron transport
Glucose Pyruvate CoA cycle and
chemiosmosis
+ 2 ATP + 2 ATP + about 34 -36 ATP

by substrate-level by substrate-level by oxidative phosphorylation, depending
phosphorylation phosphorylation on which shuttle transports electrons
from NADH in cytosol
About
Maximum per glucose: 38or 40 ATP
See Knox Figure 6.2

Pyruvate is a key juncture in catabolism Catabolism of Food molecules
Glucose
CYTOSOL
Pyruvate
No O2 present O2 present
Fermentation Cellular respiration
MITOCHONDRION
Ethanol Acetyl CoA
or
lactate
Citric
acid
cycle
Figure 9.18
Key Concept
Glucose
Glycolysis and the citric acid cycle The control of

AMP
Glycolysis
Fructose-6-phosphate Stimulates
connect to many other metabolic cellular respiration

Phosphofructokinase
+

pathways Inhibits
Fructose-1,6-bisphosphate
Inhibits
Pyruvate
ATP Citrate
Acetyl CoA
Citric
acid
cycle
Oxidative
Campbell Figure 9.20 phosphorylation
Learning Objectives
1. Be able to state the three processes that
constitute cellular respiration
2. Be able to state what the inputs/outputs for
each process are and the cellular location for
each pathway.
3. To understand the interplay and regulation
between the processes of respiration so that
you could predict the consequences of a
particular scenario on the metabolism of the
cell (eg gene defect, inhibitor etc)
Learning Objectives
4. Be able to describe the role of glycolysis under
anaerobic conditions and the different types of
fermentation that result.
5. Appreciate that chemical intermediates from glycolysis
and the TCA cycle can be used as building blocks for
anabolic processes in the cell.
6. Be able to describe the process of chemiosmosis, the
notion of coupling and predict the consequences of
uncoupling electron transport and oxidative
phosphorylation.
7. Understand the regulation of cellular respiration so that
you can predict the metabolic outcome of the cell under
different conditions.
Introduction
Plants and other autotrophs feed the biosphere.
Photosynthesis
Photoautotrophs use light energy to drive the synthesis of
organic molecules from carbon dioxide via the process of
photosynthesis.
Net equation
Biology room 205 (via school office) 6CO2 + 6H2O + Light Energy C6H12O6 + 6O2
Photosynthesis is a redox process
Water is oxidized, carbon dioxide is reduced
All organisms (autotrophs and heterotrophs) use cellular

respiration to generate ATP that can be used for anabolic
processes.
Reference Material Photosynthesis
Chapter 6 Harvesting Energy; Knox, Photosynthesis occurs in plants, algae, certain other
protists, and some prokaryotes
Ladiges, Evans and Saint, Biology: an
Australian Focus, 5th Edition, McGraw
These organisms use light energy to drive the
synthesis of organic molecules from carbon dioxide
and (in most cases) water. They feed not only
themselves, but the entire living world. (a) On
Hill, Australia land, plants are the predominant producers of

food. In aquatic environments, photosynthetic
organisms include (b) multicellular algae, such
as this kelp; (c) some unicellular protists, such
as Euglena; (d) the prokaryotes called
cyanobacteria; and (e) other photosynthetic
prokaryotes, such as these purple sulfur
bacteria, which produce sulfur (spherical (a) Plants
globules) (c, d, e: LMs).
(c) Unicellular protist 10 m
(e) Pruple sulfur 1.5 m

bacteria
(b) Multicellular algae (d) Cyanobacteria

Campbell Figure 10.2 40 m
Photosynthesis occurs in two stages
Plant Photosynthesis
We will consider plant photosynthesis, however all 1. The light reactions
photosynthetic eukaryotes contain chloroplasts, the Use energy of sunlight to transfer electrons and
cellular organelle responsible for photosynthesis. H+ from water to the electron acceptor NADP+
Uses H2O, Light, ADP+Pi
Leaf cross section Generates O2, NADPH, ATP
Vein
2. The Calvin cycle (dark reactions)

Mesophyll Fixes Carbon from CO2 to make carbohydrate
Uses CO2, ATP and NADPH
Generates [CH2O] (sugar)
CO2 O2
Stomata
See Knox figure 6.15
The structure of the chloroplast Summary of photosynthesis

Mesophyll
Typical mesophyll cells

contain 30-40 Chloroplast
chloroplasts H2 O CO2
Typical size is 2-4m by 5 m
4-7m Light
Contain thylakoids NADP
Contains all the Outer

membrane
ADP
machinery to both
+ P
Thylakoid Thylakoid Intermembrane LIGHT CALVIN
capture light energy and Stroma Granum space
Inner
space REACTIONS CYCLE
synthesize carbohydrate membrane

ATP
NADPH
1 m
Chloroplast
[CH2O]
Campbell Figure 10.5 O2
See Knox Figure 6.15 See Knox Figure 6.10
(sugar)
Which wavelengths of Light are most
Photosynthetic pigments effective at driving photosynthesis?
EXPERIMENT Three different experiments helped reveal which wavelengths of light are photosynthetically important.
Are compounds The results are shown below.
which absorb light RESULTS

energy Light Chlorophyll a
The main Reflected
Light
Absorption of light by
Chlorophyll b
chloroplast pigments
photosynthetic Chloroplast
pigment is Carotenoids
Chlorophyll, which
absorbs violet blue
and red light and
reflect or transmit Absorbe
Wavelength of light (nm)
green light d Granum
light
(a) Absorption spectra. The three curves show the wavelengths of light best absorbed by
Transmitted three types of chloroplast pigments.
light
Which wavelengths of Light are most

The structure of Chlorophyll effective at driving photosynthesis?
Two types:
CH3 in chlorophyll a
CHO in chlorophyll b
CH2
chlorophyll a CH H CH3
C C C
chlorophyll b H3 C C C C C CH2 CH3 Porphyrin ring:

Light-absorbing
(measured by O2 release)
C N N C
head of molecule
H C Mg C H
Rate of photosynthesis
note magnesium
H3 C C N N C
atom at center
C C C C CH3
Other pigments such H C C C

CH2 H
H
C C
as carotenoids also CH2 O O
C O O
harvest light energy O

CH2
CH3
for photosynthesis
Hydrocarbon tail:
interacts with hydrophobic
regions of proteins inside (b) Action spectrum. This graph plots the rate of photosynthesis versus wavelength.
thylakoid membranes of The resulting action spectrum resembles the absorption spectrum for chlorophyll
chloroplasts: H atoms not
shown a but does not match exactly (see part a). This is partly due to the absorption of light
by accessory pigments such as chlorophyll b and carotenoids.
What happens to a pigment when it What happens to a pigment in a
absorbs light energy? chloroplast.
In solution Energy from light is

When a photon is transferred from Thylakoid
absorbed it excites the e

Excited molecule to molecule.
state
chlorophyll by boosting The energy is finally Photon Photosystem
an electron to an orbital used to excite the Light-harvesting Reaction

STROMA
Primary election
with more potential complexes center acceptor
Heat electrons on the
energy
cholorphyll a molecules
This excited state is
Thylakoid membrane

at the heart of the
short lived and the e
energy is given off as Photon reaction center and

the electron falls to the
(fluorescence) these electrons are
ground state Ground captured by the primary
Photon Chlorophyll
molecule
state e- acceptor. Transfer
of energy
Special
chlorophyll a
Pigment
molecules
molecules
THYLAKOID SPACE
(INTERIOR OF THYLAKOID)
Campbell Figure 10.11 A Campbell Figure 10.12
Photosystems The two types of photosystem

In the thylakoid membranes of the chloroplasts, the There are two types of photosystem found in the
photosynthetic pigments, other small organic thylakoid membrane which form part of the
molecules and proteins are organised into specialised photosynthetic electron transport chain.
structures called photosytems.
These are termed photosystem I and photosystem II,
The photosystem is composed of light harvesting they have different reaction-centres with different
complexes and a reaction centre. types of primary electron acceptor. The PS II reaction
centre is best at absorbing light of 680 nm whilst that
The reaction centre is where light energy harvested by of PS I is best at absorbing 700 nm light and are
the pigments is used to transfer the excited electrons therefore termed P680 and P700 respectively.
from chlorophyll a molecules to the primary electron
acceptor, this is the first step of the light reactions.
Photosynthetic Electron Transport Non-Cyclic Electron flow Summary
Like respiration, the electron transport chain of the
thylakoid membrane involves protein complexes and smaller Produces O2

mobile electron carriers.
Reduces NADP+ to NADPH
Energy transport of electrons through the chain results in
Generates ATP by chemisomosis
electrons that have been excited to a higher energy level

(by light) falling to a lower energy state, the liberated
energy is then used to pump protons from the stroma to the
thylakoid space generating a H+ gradient that can be used
to drive an ATP synthase complex and generate ATP.
There are two different ways the electrons can flow through
the electron transport chain, non-cyclic electron flow and
cyclic electron flow.
Non-cyclic Electron Flow Cyclic Electron Flow
Knox Figure 6.18 Knox Figure 6.19

Comparison of chemiosmosis in the
Cyclic Electron Flow Summary mitochondrion and chloroplast.
Produces ATP by chemiosmosis.

Key
Does NOT produce O2 Higher [H+]

Lower [H+]
Does NOT reduce NADP+ to NADPH Mitochondrion Chloroplast
Allows generation of ATP without

Production of NADPH. The Calvin cycle MITOCHONDRION CHLOROPLAST
requires more ATP than NADPH

STRUCTURE STRUCTURE
H+ Diffusion
Intermembrance Thylakoid
space Electron space
Membrance transport
chain
ATP
Synthase Stroma
Matrix
ADP+ P
ATP
H+
ATP and NADPH are used by the Calvin

Chemiosmosis in the chloroplast cycle to fix CO2 into sugar
H2O CO2
LIGHT
NADP+
ADP
CALVIN
LIGHT
CYCLE
REACTOR
ATP
NADPH
H2 O CO2
STROMA O2 [CH2O] (sugar)

(Low H+ concentration) Cytochrome
Photosystem II complex Photosystem I Light
Light NADP+
2 H+ reductase
3
Fd NADP+ + 2H+ NADP
NADPH + H+
Pq
ADP
Pc + P
2
H2 O 1 LIGHT CALVIN
THYLAKOID SPACE 2 O2
1 2 H+ REACTIONS CYCLE
Or LUMEN +2 H+
(High H+ concentration)
To
ATP
Calvin
cycle
NADPH
ATP
Thylakoid synthase
STROMA membrane ADP
(Low H+ concentration) ATP Chloroplast
P
Campbell Figure 10.17 H+
[CH2O]
See Knox Figure 6.18 Campbell Figure 10.5 O2
(sugar)
The Calvin Cycle Summary of Photosynthesis
Light reaction Calvin cycle
The first step of the cycle adds CO2 to a 5 carbon H2O CO2
molecule called Ribulose bisphosphate (RuBP). This Light

step is catalysed by RuBP carboxylase (rubisco), the NADP+
ADP
most abundant protein in chloroplasts. + Pi
RuBP 3-Phosphoglycerate
Photosystem II
The cycle has 3 phases Electron transport chain
Photosystem I
Carbon fixation ATP G3P
Reduction NADPH Starch
(storage)
Regeneration of CO2 acceptor RuBP Amino acids
Fatty acids
Chloroplast
O2 Sucrose (export)
The sugar that is produced is Glyceraldehyde-3-
phosphate (G3P)
Light reactions: Calvin cycle reactions:
Are carried out by molecules in the Take place in the stroma
thylakoid membranes Use ATP and NADPH to convert
Convert light energy to the chemical CO2 to the sugar G3P
energy of ATP and NADPH Return ADP, inorganic phosphate, and
Campbell Figure 10.21 Split H2O and release O2 to the NADP+ to the light reactions
See Knox Figure 6.10 atmosphere
The Calvin Cycle Photorespiration

H 2O CO2
Light Input
NADP+ 3 (Entering one
ADP
CALVIN
CO2 at a time)
Exchange of O2 and CO2
LIGHT
CYCLE

REACTION
ATP
Phase 1: Carbon Fixation
between the leaf and

NADPH
Rubisco
O2
the atmosphere occurs

[CH2O] (sugar)
3 P P
Leaf cross section
Short-lived
3 P
Ribulose bisphosphate
P
intermediate 6 P
3-Phosphoglycerate
via the stomata. Vein
6 ATP
In hot environments
(RuBP)
6 ADP
3 ADP CALVIN
CYCLE
opening of stomata Mesophyll
increases water loss

6 P P
3 ATP
1,3-Bisphoglycerate
6 NADPH
Phase 3:
Regeneration of
6 NADP+
6 P
Results in compromise
between Gas exchange
the CO2 acceptor
5 P
(G3P)
and water loss.

6 P
Glyceraldehyde-3-phosphate Phase 2: CO2 O2
(G3P) Reduction Stomata
1 P
Cmpbell Figure 10.18 G3P Glucose and
(a sugar) other organic Campbell Figure 10.3
See Knox Figure 6.20 Output compounds
Photorespiration C4 plants physiology and Biochemistry
Mesophyll
If during daylight a plant closes its stomates to
Mesophyll cell
Photosynthetic cell
PEP carboxylase CO
CO 2 2
reduce water loss then the concentration of CO2 will cells of C4 plant
leaf
Bundle-
sheath
decrease whilst the concentration of O2 will increase. cell
Oxaloacetate (4 C) PEP (3 C)
Rubisco can bind both CO2 and O2. If O2 is added to

Vein ADP
(vascular tissue)
RuBP the resulting product splits generating a 2- Malate (4 C) ATP
carbon compound. This compound is the rearranged C4 leaf anatomy

in the peroxisome and mitochondria generating CO2. Bundle- Pyruate (3 C)
Sheath
cell CO2
This process is termed photorespiration because it Stoma
happens in the light and consumes O2 and generates CALVIN

CYCLE
CO2. However, it produces no ATP (actually consumes
ATP) and produces no sugar and therefore reduces Sugar
photosynthetic output
Vascular
tissue
See Knox Figure 6.23, 6.24 & 6.25
Evolutionary Adaptations that reduce Evolutionary Adaptations that reduce

photorespiration photorespiration
C4 plants CAM plants (crassulacean acid
Have an adaptation to the C3 Calvin Cycle where metabolism)
CO2 is first fixed to form a 4-carbon compound An adaptation to very arid environments, these
before entering the cycle. plants keep there stomata closed during the day
and open them at night.
The enzyme PEP carboxylase is responsible for this
initial CO2 fixation, this enzyme has a no affinity for At night when the stomates are open the mesophyll
O2 cells fix CO2 into 4 carbon organic acids which are
stored in the vacuole.
These plants have a unique physiology that
physically separates the initial fixation of CO2 by During the day, when the light reactions of
PEP carboxylase and the Calvin cycle. This results photosynthesis can supply ATP and NADPH, CO2 is
in a higher CO2 concentration in the bundle sheath released from the organic acids and incorporated
cells which contain the Calvin cycle enzymes and into sugar by the Calvin cycle
reduced photorespiration.
Comparison of C4 and CAM plants Learning Objectives
5. Be able to describe the inputs and outputs of
the Calvin (-Benson) cycle
6. Be able to describe the process of
photorespiration and describe the outcomes of
different scenarios (eg elevated CO2
Sugarcane Pineapple
See Knox Figure 6.25 & 6.27
7. Be able to describe C4 and CAM
C4
CO2
CAM
CO2 photosynthesis.
Mesophyll Cell
Organic acid 1 CO2 incorporated Organic acid

Night 8. Be able to contrast the similarities and
Bundle-
into four-carbon
organic acids differences between C4 and CAM plants
sheath cell (carbon fixation) Day
(a) Spatial separation of (b) Temporal separation of
9. Be able to understand the connection between
steps. In C4 plants,
carbon fixation and the
CALVIN
CYCLE
2 Organic acids
release CO2 to
CALVIN
CYCLE
steps. In CAM plants,
carbon fixation and the
photosynthesis and water loss
Calvin cycle occur in Calvin cycle Calvin cycle occur in the
different same cells
types of cells. Sugar Sugar
at different times.
Learning Objectives
1. Be able to describe the cellular structures in
which photosynthesis occurs.
2. Be able to describe how photosynthetic
pigments harvest light energy and how this
links to the photosynthetic electron transport.
3. Be able to describe both non-cyclic and cyclic
photosynthetic electron transport and contrast
the differences
4. Be able to describe the process of
chemiosmosis in relation to photosynthesis.
Early Evolution of Life on Earth
Evolution of Tissues and Organs,

and water homeostasis

Knox
Fig 33.5
Reference Material The Precambrian

Chapter 32 Evolving Life; Chapter 7 Cells, Tissues and o 545 million years Metazoan Animals
Signals; Chapter 22 Homeostasis of Water and Solutes
Knox, Ladiges, Evans and Saint, Biology: an Australian o 570-680 million years Evidence of
Focus, 5th Edition, McGraw Hill, Australia Multicellular organism
Chapter 40 Basic principles of animal form and function; o 2.1 billion years First Eukaryotes
Chapter 42 Circulation and Gas Exchange; Chapter 44 (single cell)
Osmoregulation and Excretion, Reece, J. B., Meyers, N.,
Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. o 3.5 billion years photosynthetic
V., Jackson, R. B., Cooke, B. J., and Campbell, N. A prokaryotes
(2014). Campbell Biology. 10th Edition. Australian and
New Zealand Version o 3.5 billion years Prokaryotes
Animal Tissues
Why did multicellular organisms
evolve?
Whats the advantage?

Increased Size
Diffusion limits size
Increased Complexity
Different cell types can be specialised for
different function - tissues and organs
Fig 7.10
Animal Tissues Epithelial tissues
Animals are constructed from 4 basic

tissue types:
1. Epithelial tissue
Internal and external covering layer
2. Connective tissue Can be simple (single layer)
Or stratified (multiple layers)
Provides structure and support
Form is related to function
3. Muscular tissue
Allows movement
4. Nervous tissue
Carries information
Connective Tissues Balance of water and solutes in animals
Large external Internal extracellular

Fluctuations environment
Multiple types
Form related to function Small internal

fluctuations
Control
systems
Intracellular
environment
Muscle tissue Solutes

o Include Ions such as Na+, K+, Cl-, Ca2+ Mg2+,
SO42- and PO43-
o Includes organic solutes such as glucose, fatty
Two basic types Striated
acids, lipids, amino acids, proteins and
and smooth.
nitrogenous wastes
Form related to function o Osmolarity (Osm) = total concentration of
osmotically active solutes
o Animals unlike plants must maintain similar
osmotic concentration between extracellular
and intracellular environments.
Osmoregulation Osmoregulation by marine boney fish
Osmoconform
Internal = external
Osmoregulate Body fluids are hypotonic to

Internal external sea water.
Active mechanisms for reducing

ion concentration
Knox
Fig 22.1
Fig 22.5 Knox
Water and solute exchange Nitrogenous Wastes

Metabolism of proteins requires excretion of Nitrogen
Protein amino acid keto acid + ammonia (NH3, toxic)
The form of Nitrogen excreted is different for different animals

and depends on availability of water.
Knox Fig 22.4 The Primary avenues for
water and solute exchange are
food/drink intake urine/faeces loss.
Aquatic animals have body surface

exchange of solutes and water.
Terrestrial animals have evaporative

water loss.
Knox Fig 22.10

Excretion of nitrogenous waste by different
animals Kidneys
o Terrestrial vertebrates rely primarily on

their kidneys for both ionoregulation
and osmoregulation.
o Each kidney contains thousands or
millions of nephrons which are the
function unit of the kidney.
o Nephrons have four main functions:
filtration, reabsorption, secretion and
water reabsorption (osmoconcentration).
Knox
Fig 22.11
Excretory Organs The nephron
Two types of specialised excretory

organs
Epithelial solute pumps

eg Chloride pumps in gills of bony fish.
Internal tubular excretory organs

That form, modify and expel liquid urine
eg Vertebrate Kidney
Knox
Fig 22.18
Filtration Osmoconcentration
o The glomerular capillaries have o Mammals have evolved to excrete

specialised structures with filtration urine that is more concentrated
slits. The high blood pressure drives (hyperosmotic) than blood.
filtration of the contents of the blood. o The mammalian Kidney is divided into
Large constituents (blood cells, large functionally and structurally different
proteins >60 kDa) are retained in the regions the renal cortex, and renal
capillaries. Water and small pass from medulla.
the Bowmans capsule to the renal o The renal medulla is responsible for the
tube. osmoconcentration
Reabsorption and Secretion Kidney Structure

o Reabsorption
Cortical nephrons
Once filtered important ions such as Na+ and Cl-, carry out filtration
and nutrients such as glucose, amino acids, and reabsorption &
vitamins are reabsorbed. These solutes and secretion functions
water are returned to the blood stream by
diffusion and osmosis via the bed of capillaries Juxtamedullary
nephrons due to their
that surround the nephron.
long loop of Henle that
extends into the
o Secretion medulla are also able
to osmoconcentrate
Ions such as H+ K+ and NH4+ and many organic
molecules are actively secreted by the nephron.
Knox
Fig 22.20
How the Loop of Henle and collecting duct
Osmoconcentrates urine Gas Exchange in Animals
The ascending loop is impermeable to All animals must obtain sufficient O2
water and actively transports Cl- and Na+ is
passively transported to balance charge. and remove CO2 to survive.
In contrast the descending loop does not

pump Cl- and is permeable to water. Hence
Various homeostatic control
H2O moves out of the descending loop. mechanisms have evolved which differ
Local countercurrent exchange between

the ascending and descending loop
depending on the size and and level of
generates an osmotic concentration activity of the animal and whether the
gradient in the renal medulla.
The water permeability of the collecting
external respiratory medium is air or
duct can be controlled by the hormone water.
ADH. Allowing water to leave the duct due
to the osmotic gradient.
Knox Fig 22.21
Maintenance of Water homeostasis Gas Exchange Surfaces
Osmoreceptors in the central nervous

system detect osmotic concentration
of body fluids, and regulate the levels of
antidiuretic hormone (ADH) which
in turn regulates kidney function.
ADH levels
decrease
Knox Fig 22.3 Knox Fig 23.1

Air versus Water Convection and Ventilation
Even when Air is in equilibrium with [O2]

O2
water the O2 concentration of Air is 20 Boundary layer
times greater than that of water.

The O2 concentration of water is
greatly effected by temperature and Diffusion across a membrane can deplete
The oxygen concentration at the surface of
solutes. the cell (boundary layer), slowing the rate of
diffusion.
CO2 is much more soluble in water and
diffuses much faster than O2 in water. Movement of the bulk fluid (convection) disturbs
the boundary layer effect and increases the rate of
diffusion.
Convection of the external medium generated by the

animal is known as ventilation. Knox Fig 23.3
Lungs: the gas exchange organ of air

Surface Area to Volume Ratio and Diffusion
breathers
o As a the size of an animal increases, the ratio A muscular pump is used to drive air
of surface area to volume decrease. into speacalised gas diffusion
structures (aveoli) in order to increase
o This results in the metabolic needs of the cells the rate of gas diffusion. These
(volume=number of cells) exceeding the
amount of oxygen that can diffuse. structures are designed to facilitate gas
exchange between air and the internal
o As a result Animals bigger than 2-3mm in size, body fluid (blood). In the human lung
require some mechanism to enhance the rate the aveoli are approx. 250m and the
of diffusion. diffussion distance between air and
blood is only 0.62 m.
Oxygen binding properties of
The mammalian lung Haemoglobin
At high oxygen partial pressure

(concentration) haemoglobin is a good
binder of O2 whilst at low partial pressure
it is a poor binder.
Fig 23.16
Hence in the lungs haemoglobin binds
O2 whilst in the tissues it releases O2.
Movement of the diaphragm creates a
Negative pressure in the pleural cavity
This draws air into the aveoli relaxation
Of the diaphragm results in the pleural cavity
Returning to atmospheric pressure and air is
expelled.
Knox Fig 23.18 Knox Fig 23.25
Oxygen Carrying Pigments Carbon dioxide transport

Tissues Lungs
As the O2 carrying capacity of fluids
(blood) is low specialised respiratory
pigments that bind O2 are used to
increase the amount of O2 that can be
Knox
carried. Fig 23.29
In mammals the respiratory pigment is
haemoglobin which is found in
erythrocytes (red blood cells).
CO2 is much more soluble than O2 as it can be hydrated to carbonic acid and
dissociated to bicarbonate ions.
Haemoglobin can also bind CO2 and carries approx. 10% of CO2 in blood.
The circulatory systems Learning Objectives
o The pumping of blood by the 1. Be able to describe the advantages of being
heart allows movement of multicellular.
oxygenated blood from the lungs
to the tissues and deoxygenated 2. Be aware that there are many different tissue
blood from the tissues back to the types in an animal and that they have
lungs. specialised form that relates to their function.
Different animals have different
o
3. Understand that the different tissue types are
patterns of blood circulation.
the result of different protein expression
o Oxygenated blood is pumped from
the lungs through the left side of 4. Be able to describe the need for animals to be
the hear to the body. able to control there internal extracellular
o Deoxygenated blood is pumped Knox Fig 24.4e environment.
back from the body through the mammal and bird
right side of the heart back to the circulatory system 5. Understand the types of mechanism by which
lungs organisms osmoregulate.
Regulation of Ventilation Learning Objectives

Specialised chemoreceptor cell 6. Have a basic understanding of how the
detect changes in O2 or CO2/pH mammalian kidney functions.
levels.
These receptors are found in tiny 7. Appreciate the need for and the various ways
organs called carotid bodies that animals excrete nitrogenous wastes.
sense changes in blood O2 or CO2/pH 8. Have a basic understanding of how water
levels, and release neurotransmitters
homeostasis is regulated
that activate nerve cells to send
signals to the central nervous 9. Be able to describe the various systems used
system. by animals to facilitate the diffusion of O2
A decrease in O2 or pH, or an from the environment to the tissues and CO2
increase in CO2 will result in an Knox Fig 23.31
from the tissues to the external environment
The Carotid Body
increase, in heart rate and
diaphragm contraction, increasing 10. Be able to describe how ventilation of an
ventilation. organism is controlled.
Evolution of Tissues and Organs,
and water homeostasis

Reference Material
Chapter 32 Evolving Life; Chapter 7 Cells, Tissues and
Signals; Chapter 22 Homeostasis of Water and Solutes
Focus, 5th Edition, McGraw Hill, Australia
Chapter 40 Basic principles of animal form and function;

Chapter 42 Circulation and Gas Exchange; Chapter 44
Osmoregulation and Excretion, Reece, J. B., Meyers, N.,
Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P.
V., Jackson, R. B., Cooke, B. J., and Campbell, N. A
(2014). Campbell Biology. 10th Edition. Australian and
New Zealand Version
Early Evolution of Life on Earth
Knox
Fig 33.5
The Precambrian
o 545 million years Metazoan Animals

o 570-680 million years Evidence of
Multicellular organism
o 2.1 billion years First Eukaryotes
(single cell)
o 3.5 billion years photosynthetic
prokaryotes
o 3.5 billion years Prokaryotes
Why did multicellular organisms
evolve?
Whats the advantage?

Increased Size
Diffusion limits size
Increased Complexity
Different cell types can be specialised for
different function - tissues and organs
Animal Tissues
Animals are constructed from 4 basic

tissue types:
1. Epithelial tissue
Internal and external covering layer
2. Connective tissue
Provides structure and support
3. Muscular tissue
Allows movement
4. Nervous tissue
Carries information
Animal Tissues
Fig 7.10
Epithelial tissues
Can be simple (single layer)

Or stratified (multiple layers)
Form is related to function

Connective Tissues
Multiple types
Form related to function

Muscle tissue
Two basic types Striated

and smooth.
Form related to function

Balance of water and solutes in animals
Large external Internal extracellular

Fluctuations environment
Small internal
fluctuations
Control
systems
Intracellular
environment
Solutes
o Include Ions such as Na+, K+, Cl-, Ca2+ Mg2+,
SO42- and PO43-
o Includes organic solutes such as glucose, fatty
acids, lipids, amino acids, proteins and
nitrogenous wastes
o Osmolarity (Osm) = total concentration of
osmotically active solutes
o Animals unlike plants must maintain similar
osmotic concentration between extracellular
and intracellular environments.
Osmoregulation
Osmoconform
Internal = external
Osmoregulate
Internal external
Knox
Fig 22.1
Water and solute exchange
Knox Fig 22.4 The Primary avenues for

water and solute exchange are
food/drink intake urine/faeces loss.
Aquatic animals have body surface

exchange of solutes and water.
Terrestrial animals have evaporative

water loss.
Osmoregulation by marine boney fish
Body fluids are hypotonic to

sea water.
Active mechanisms for reducing

ion concentration
Fig 22.5 Knox

Nitrogenous Wastes
Metabolism of proteins requires excretion of Nitrogen
Protein amino acid keto acid + ammonia (NH3, toxic)
The form of Nitrogen excreted is different for different animals

and depends on availability of water.
Knox Fig 22.10

Excretion of nitrogenous waste by different
animals
Knox
Fig 22.11
Excretory Organs
Two types of specialised excretory

organs
Epithelial solute pumps

eg Chloride pumps in gills of bony fish.
Internal tubular excretory organs

That form, modify and expel liquid urine
eg Vertebrate Kidney
Kidneys
o Terrestrial vertebrates rely primarily on

their kidneys for both ionoregulation
and osmoregulation.
o Each kidney contains thousands or
millions of nephrons which are the
function unit of the kidney.
o Nephrons have four main functions:
filtration, reabsorption, secretion and
water reabsorption (osmoconcentration).
The nephron
Knox
Fig 22.18
Filtration
o The glomerular capillaries have

specialised structures with filtration
slits. The high blood pressure drives
filtration of the contents of the blood.
Large constituents (blood cells, large
proteins >60 kDa) are retained in the
capillaries. Water and small pass from
the Bowmans capsule to the renal
tube.
Reabsorption and Secretion
o Reabsorption
Once filtered important ions such as Na+ and Cl-,
and nutrients such as glucose, amino acids, and
vitamins are reabsorbed. These solutes and
water are returned to the blood stream by
diffusion and osmosis via the bed of capillaries
that surround the nephron.
o Secretion
Ions such as H+ K+ and NH4+ and many organic
molecules are actively secreted by the nephron.
Osmoconcentration
o Mammals have evolved to excrete

urine that is more concentrated
(hyperosmotic) than blood.
o The mammalian Kidney is divided into
functionally and structurally different
regions the renal cortex, and renal
medulla.
o The renal medulla is responsible for the
osmoconcentration
Kidney Structure
Cortical nephrons
carry out filtration
reabsorption &
secretion functions
Juxtamedullary
nephrons due to their
long loop of Henle that
extends into the
medulla are also able
to osmoconcentrate
Knox
Fig 22.20
How the Loop of Henle and collecting duct
Osmoconcentrates urine
The ascending loop is impermeable to

water and actively transports Cl- and Na+ is
passively transported to balance charge.
In contrast the descending loop does not
pump Cl- and is permeable to water. Hence
H2O moves out of the descending loop.
Local countercurrent exchange between
the ascending and descending loop
generates an osmotic concentration
gradient in the renal medulla.
The water permeability of the collecting
duct can be controlled by the hormone
ADH. Allowing water to leave the duct due
to the osmotic gradient.
Knox Fig 22.21

Maintenance of Water homeostasis
Osmoreceptors in the central nervous

system detect osmotic concentration
of body fluids, and regulate the levels of
antidiuretic hormone (ADH) which
in turn regulates kidney function.
ADH levels
decrease
Knox Fig 22.3

Gas Exchange in Animals
All animals must obtain sufficient O2

and remove CO2 to survive.
Various homeostatic control
mechanisms have evolved which differ
depending on the size and and level of
activity of the animal and whether the
external respiratory medium is air or
water.
Gas Exchange Surfaces
Knox Fig 23.1

Air versus Water
Even when Air is in equilibrium with

water the O2 concentration of Air is 20
times greater than that of water.
The O2 concentration of water is
greatly effected by temperature and
solutes.
CO2 is much more soluble in water and
diffuses much faster than O2 in water.
Surface Area to Volume Ratio and Diffusion
o As a the size of an animal increases, the ratio

of surface area to volume decrease.
o This results in the metabolic needs of the cells

(volume=number of cells) exceeding the
amount of oxygen that can diffuse.
o As a result Animals bigger than 2-3mm in size,

require some mechanism to enhance the rate
of diffusion.
Convection and Ventilation
[O2]
O2
Boundary layer
Diffusion across a membrane can deplete

The oxygen concentration at the surface of
the cell (boundary layer), slowing the rate of
diffusion.
Movement of the bulk fluid (convection) disturbs

the boundary layer effect and increases the rate of
diffusion.
Convection of the external medium generated by the

animal is known as ventilation. Knox Fig 23.3
Lungs: the gas exchange organ of air
breathers
A muscular pump is used to drive air

into speacalised gas diffusion
structures (aveoli) in order to increase
the rate of gas diffusion. These
structures are designed to facilitate gas
exchange between air and the internal
body fluid (blood). In the human lung
the aveoli are approx. 250m and the
diffussion distance between air and
blood is only 0.62 m.
The mammalian lung
Fig 23.16
Movement of the diaphragm creates a

Negative pressure in the pleural cavity
This draws air into the aveoli relaxation
Of the diaphragm results in the pleural cavity
Returning to atmospheric pressure and air is
expelled.
Knox Fig 23.18
Oxygen Carrying Pigments
As the O2 carrying capacity of fluids

(blood) is low specialised respiratory
pigments that bind O2 are used to
increase the amount of O2 that can be
carried.
In mammals the respiratory pigment is
haemoglobin which is found in
erythrocytes (red blood cells).
Oxygen binding properties of
Haemoglobin
At high oxygen partial pressure

(concentration) haemoglobin is a good
binder of O2 whilst at low partial pressure
it is a poor binder.
Hence in the lungs haemoglobin binds

O2 whilst in the tissues it releases O2.
Knox Fig 23.25

Carbon dioxide transport
Tissues Lungs
Knox
Fig 23.29
CO2 is much more soluble than O2 as it can be hydrated to carbonic acid and
dissociated to bicarbonate ions.
Haemoglobin can also bind CO2 and carries approx. 10% of CO2 in blood.
The circulatory systems
o The pumping of blood by the
heart allows movement of
oxygenated blood from the lungs
to the tissues and deoxygenated
blood from the tissues back to the
lungs.
o Different animals have different
patterns of blood circulation.
o Oxygenated blood is pumped from
the lungs through the left side of
the hear to the body.
o Deoxygenated blood is pumped Knox Fig 24.4e
back from the body through the mammal and bird
right side of the heart back to the circulatory system
lungs
Regulation of Ventilation
Specialised chemoreceptor cell
detect changes in O2 or CO2/pH
levels.
These receptors are found in tiny
organs called carotid bodies that
sense changes in blood O2 or CO2/pH
levels, and release neurotransmitters
that activate nerve cells to send
signals to the central nervous
system.
A decrease in O2 or pH, or an
increase in CO2 will result in an Knox Fig 23.31
The Carotid Body
increase, in heart rate and
diaphragm contraction, increasing
ventilation.
Learning Objectives
1. Be able to describe the advantages of being
multicellular.
2. Be aware that there are many different tissue
types in an animal and that they have
specialised form that relates to their function.
3. Understand that the different tissue types are
the result of different protein expression
4. Be able to describe the need for animals to be
able to control there internal extracellular
environment.
5. Understand the types of mechanism by which
organisms osmoregulate.
Learning Objectives
6. Have a basic understanding of how the
mammalian kidney functions.
7. Appreciate the need for and the various ways
animals excrete nitrogenous wastes.
8. Have a basic understanding of how water
homeostasis is regulated
9. Be able to describe the various systems used
by animals to facilitate the diffusion of O2
from the environment to the tissues and CO2
from the tissues to the external environment
10. Be able to describe how ventilation of an
organism is controlled.
5/14/2017
Why is your brain different to your liver?

Cellular Control and
Communication The obvious answer is that they are
different cell types that have different
physiology
Associate Professor Ian Menz BUT how is that controlled?
They have a different complement of
proteins with different activities
How is the protein complement of a cell
controlled ?
Reference Material Levels of Control

Chapter 7 Cells tissues and signals; Chapter 28 Hormonal Protein Synthesis
Control in Animals; Knox, Ladiges, Evans and Saint,
Biology: an Australian Focus, 5th Edition, McGraw Hill, Transcriptional Control turn genes on/off
Australia eg bacterial operons
Chapter 11 Cell Communication; Chapter 45 Hormones

and the Endocrine System; Chapter 48 Neurons, Activity of pre-synthesised proteins
Synapses, and Signalling; Reece, J. B., Meyers, N., Urry,
L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., Post-translational Control turn protein
Jackson, R. B., Cooke, B. J., and Campbell, N. A (2014). activity on/off eg allosteric regulation of a
Campbell Biology. 10th Edition. Australian and New metabolic pathway
Zealand Version
5/14/2017
Cellular activities are often influenced by

detecting signals in the environment or
from other cells Cell Signalling
The bacterial Lac operon Signal transduction pathways
If lactose is encountered the enzymes that Convert signals on a cells surface into
metabolise lactose are swithched on. cellular responses
Mating in yeast Signalling can be either local or distant

Sacchromyces Cerevisiae has two mating Direct contact
types a and Local (diffusion)
Which signal to each other using chemical Distant
signal molecule
Mating in Yeast Local and distant signalling
1 Exchange of Animal and plant cells

factor
mating factors.
Each cell type
Receptor Have cell junctions that directly connect the cytoplasm
secretes a of adjacent cells
mating factor a
that binds to
Plasma membranes
receptors on
the other cell
type. Yeast cell, a factor Yeast cell,
mating type a mating type
2 Mating. Binding
of the factors to
receptors
induces changes a
in the cells that
lead to their
fusion.
3 New a/ cell.
The nucleus of
the fused cell Gap junctions Plasmodesmata
includes all the
a/ Campbell Figure 11.3 between animal cells between plant cells
genes from the See Knox
Campbell Figure 11.2 (a) Cell junctions. Both animals and plants have cell junctions that allow molecules
a and cells. Figure 7.9 &7.13 to pass readily between adjacent cells without crossing plasma membranes.
5/14/2017
Local and distant signalling Local and distant signalling

In local signaling, animal cells In long-distance signaling
May communicate via direct contact Both plants and animals use hormones
Long-distance signaling
Endocrine cell Blood

vessel
Hormone travels
in bloodstream
to target cells
Target
cell
(c) Hormonal signaling. Specialized

Campbell Figure 11.3 endocrine cells secrete hormones
(b) Cell-cell recognition. Two cells in an animal may communicate by interaction into body fluids, often the blood.
between molecules protruding from their surfaces. Hormones may reach virtually all
Campbell Figure 11.4 C body cells.
Local and distant signalling Remote Cell Signalling

In other cases, animal cells
Communicate using local regulators
3 Important stages
Local signaling
1. Signal Reception
Target cell Electrical signal
along nerve cell
triggers release of
G-protein-linked receptors
neurotransmitter
Tyrosine-kinase receptor
Neurotransmitter
Ion-channel receptor
Secretory diffuses across
vesicle synapse
2. Signal Transduction
Local regulator
diffuses through
extracellular fluid
Target cell
is stimulated 3. Cellular response
(a) Paracrine signaling. A secreting cell acts (b) Synaptic signaling. A nerve cell
on nearby target cells by discharging releases neurotransmitter molecules
molecules of a local regulator (a growth into a synapse, stimulating the
factor, for example) into the extracellular target cell.
Campbell Figure 11.4 A B fluid.
5/14/2017
Overview of cell Signalling

Intracellular signalling
EXTRACELLULAR CYTOPLASM
FLUID Plasma membrane
1 Reception 2 Transduction 3 Response
Receptor
Activation
of cellular
response
Relay molecules in a signal transduction pathway
Signal
molecule
Knox Figure 7.25
Signalling Receptors in the plasma membrane
Signal molecules bind to a receptor molecule There are three main types of membrane
changing the conformation of the protein and
allowing it to interact with other proteins to receptors
transduce the signal.
G-protein-linked
The receptor proteins are often found in the Tyrosine kinases
plasma membrane because the signal
molecule cant get across Ion channel
If the signal molecule can cross membranes

then the receptor protein can be intacellular
eg steroid hormones
5/14/2017
G-protein linked receptors

Signal-binding site
Signal Signal-binding sitea
molecule
Signal
G-protein-linked receptors Receptor tyrosine kinases

Helix in the molecule
Membrane
Segment that Tyr Tyr

interacts with Tyr Tyr Tyr Tyr
G proteins
Tyrosines Tyr Tyr
Tyr Tyr Tyr Tyr
Tyr Tyr
Tyr Tyr Tyr Tyr
Inctivate Receptor tyrosine

G-protein-linked Activated Signal molecule
Plasma Membrane enzyme CYTOPLASM kinase proteins Dimer
Receptor Receptor (inactive monomers)
GDP
G-protein Activated
GDP GTP
CYTOPLASM (inactive) Enzyme relay proteins
Cellular
Tyr Tyr P Tyr Tyr P P Tyr Tyr P
Activated
Tyr P
response 1
Tyr Tyr P Tyr Tyr P P Tyr
enzyme
Tyr Tyr P Tyr Tyr P P Tyr Tyr P Cellular
6 ATP 6 ADP
response 2
Activated tyrosine- Fully activated receptor
GTP Inactive
GDP kinase regions tyrosine-kinase
Pi (unphosphorylated (phosphorylated relay proteins
dimer) dimer)
Campbell Figure 11.7 Cellular response
See Knox Figure 7.27 Campbell Figure 11.7

Tyrosine Kinase Receptors Ligand gated ion channel receptors
eg for growth factors eg at synapses between nerve cells

Pores in membrane allowing transmission of
specific ions
Single alpha helix transmits signal
Open or close in response to signal

Autophosphorylates tyrosine residues on
parts of protein inside membrane
Change in ion concentration directly affects
target cell function(s)
P-tyrosine binds to and activates proteins
that trigger cell response
5/14/2017
Ion channel receptors

Signal
molecule
Gate
closed Ions A phosphorylation cascade
(ligand)
Signal molecule
1 A relay molecule
Ligand-gated Plasma activates protein kinase 1.
ion channel receptor Membrane
Receptor Activated relay
molecule
2 Active protein kinase 1
Gate open transfers a phosphate from ATP
Inactive to an inactive molecule of
protein kinase protein kinase 2, thus activating
1 Active
this second kinase.
protein
kinase
1
3 Active protein kinase 2
Inactive then catalyzes the phos-
protein kinase ATP phorylation (and activation) of
Cellular Active P
2 ADP protein kinase 3.
response protein
PP kinase
Pi 2
4 Finally, active protein
Inactive kinase 3 phosphorylates a
protein kinase ATP protein (pink) that brings
Gate close ADP Active P
3 about the cells response to
protein the signal.
5 Enzymes called protein kinase
phosphatases (PP) PP
Pi 3
catalyze the removal of
the phosphate groups Inactive
ATP
Campbell Figure 11.7 from the proteins, protein
ADP P
making them inactive
Campbell Figure 11.8 Active Cellular
and available for reuse.
protein response
PP
Pi
Signal transduction pathways Second messengers

Many G-proteins
Signal reception may lead to multiple Trigger the formation of cAMP, which then acts as a second
metabolic effects messenger in cellular pathways
Ca2+ can also act as a second messenger (see Fig 7.28)
Cells without receptors do not respond to First messenger
signal (signal molecule
such as epinephrine) Adenylyl
Signal transduction inside cells may involve G protein cyclase
many steps
GTP
Often involves protein phosphorylation
G-protein-linked
receptor
(mediated by protein kinases) ATP
cAMP
Allows amplification of the signal Protein

kinase A
Campbell Figure 11.10 Cellular responses

5/14/2017
The cellular response Hormones & Growth Factors

Rapid Effects
Involves regulation of Eg Glugagon which binds to receptors on liver cells
Altered enzyme activity
Release of glucose
Cytoplasmic activities Elevation of blood glucose level
OR Adrenalin from adrenal glands, boosts glucose supply

at times of stress (scary movie, exams, etc)
Transcription Cell has G protein linked receptor
Causes G protein inside cell to bind GTP and become
active
First step in signal transduction pathway that amplifies
signal
One molecule lots of glucose
Hormones & Growth Factors Glucose Homeostatis

Hormones and growth factors (chemical
signals) secreted into blood stream.
Bind to protein receptors on surface of target
cells
Causes metabolic change in the interior of
the cell
2 types of effects:
Rapid (seconds minutes)
Slow (hours)
Campbell Fig 45.12

5/14/2017
Cytoplasmic response to a signal

Reception Regulation of gene expression
Binding of epinephrine to G-protein-linked receptor (1 molecule)
Growth factor Reception

Transduction
Receptor
Inactive G protein
Active G protein (102 molecules)
Inactive adenylyl cyclase

Phosphorylation
Active adenylyl cyclase (102) cascade
Transduction
ATP
Cyclic AMP (104)
CYTOPLASM
Inactive protein kinase A
Active protein kinase A (104)
Inactive
Inactive phosphorylase kinase transcription Active
Active phosphorylase kinase (105) factor transcription
factor Response
P
Inactive glycogen phosphorylase DNA
Active glycogen phosphorylase (106)
Gene
Response
Glycogen
Campbell Figure 11.14 NUCLEUS mRNA
Glucose-1-phosphate
(108 molecules) See Knox Figure 7.25a
Campbell Figure 11.13 Knox Figure 7.29
Hormones & Growth Factors Cell Signalling

Slow effects Signal reception may lead to multiple metabolic effects
Growth factors are slow Same receptor and signal in different cells can lead to
Bind to receptors on plasma membrane a different response
of target cell
Cells without receptors do not respond to signal
Cascade of changes in cell interior
Alteration in gene expression Multiple signalling pathways allow a specific cell
response to be controlled by many signals
Altered synthesis of proteins
Proliferation of cells
5/14/2017
The specificity of cell signalling Learning Objectives
4. Describe how signalling can result in

gene expression.
5. Be able to predict a cellular response
when given a scenario relating
detailing the signalling molecule type,
receptors and signal cascade
pathways. (including an appreciation
that different cells may react in
different ways)
Campbell Fig 11.15
Learning Objectives
1. Describe the ways cells communicate

both in local and distant environments
(eg contact, paracrine, hormonal,
synaptic)
2. Describe the purpose of a signal
transduction pathway.
3. Explain the structure and function of
G-protein linked receptors, tyrosine
kinase receptors and ligand gated ion
channels
The effect of Caffeine and
other substances on synapses
The white, bitter-tasting,

crystalline substance was first
isolated from coffee in 1820.
Need to study for long periods
What can you do to stay awake?

How does caffeine affect the body
physiologically?
What organs or systems would be affected
by caffeine?
Absorption of caffeine how
long does it take?
Its take about 30 minutes to have an effect
Maximal central nervous system effects
take about 2 hours
It is metabolized almost completely, with
only 10% or less being excreted from the
body unchanged.
half-life of caffeine is?
About six hours
If you have consumed coffee in the
evening it can act to keep you from the
sleep you need. (If the last cup of coffee
was taken at 3 p.m., by 9 p.m., you will still
have 100 mg. in your body.) So the next
morning you feel worseand you need
caffeine to get you out of bed.
What are the effects of caffeine on
the brain?
Caffeine belongs to the xanthine chemical
group.
Adenosine is a naturally occurring
xanthine in the brain and acts as a
neurotransmitter at some synapses what
does this mean?
One effect of caffeine is to interfere (block)
adenosine at synapses in the brain
How does a synapse work?
1. At the end of the pre-synaptic neuron there are voltage-gated
calcium channels. When an action potential reaches the synapse
these channels open, causing calcium ions to flow into the cell.
2. These calcium ions cause the synaptic vesicles to fuse with the
cell membrane, releasing their contents (the neurotransmitter
chemicals) by exocytosis.
3. The neurotransmitters diffuse across the synaptic cleft.
4. The neurotransmitter binds to the neuroreceptors in the post-
synaptic membrane, causing the channels to open. In the example
shown these are sodium channels, so sodium ions flow in.
5. This causes a depolarisation of the post-synaptic cell membrane,
which may initiate an action potential, if the threshold is reached.
6. The neurotransmitter is typically broken down by a specific
enzymes in the synaptic cleft; for example the enzyme
acetylcholinesterase breaks down the neurotransmitter
acetylcholine. The breakdown products are absorbed by the pre-
synaptic neuron by endocytosis and used to re-synthesise more
neurotransmitter, using energy from the mitochondria. This stops
the synapse being permanently on.
As your body becomes fatigued, adenosine is
made in the brain, and binds to adenosine
receptors (G-protein linked receptor) The
cellular response is reduction in synaptic
vesicle release.
This causes drowsiness by slowing nerve

cell activity. This creates a feeling that you
want to stop and rest or go to sleep.
The longer-term effects of using caffeine
tend to wear off
Once the effect of caffeine stimulation wears off,
you face even greater fatigueand also
depression.
If more caffeine is taken in, the body becomes
jumpy because the neurotransmitters being
released are those present during an emergency
(fight or flight) situation- and they are now there
all day long.
This can cause irritability.
Can we use it to our advantage?
Caffeine speeds up our
metabolism (it can be found as a
main ingredient in most weight-
loss products).
It also increases the breakdown of
fat, freeing fatty acids, which are
used in energy production during
exercise.
Conversion of fat to energy is
about 30% more efficient when
caffeine is consumed prior to
exercise.
Does this mean that caffeine
burns fat?
Not exactly.
The caffeine-enhanced fat breakdown can only
occur during exercise. While the fat is being
burned, glycogen and glucose are being
reserved, allowing blood sugar levels to remain
higher for longer.
Higher glucose levels ward off hunger.
This is why coffee is popular among students
and think tankers. The brain functions
exclusively on glucose, and higher blood sugar
levels facilitate thinking.
Dopamine and acetylcholine
(ACh)
They are neurotransmitters involved in
arousal and happiness and in generating a
response to stressful conditions
If caffeine prevents the restful affects of
adenosine it will consequently increase the
effects of dopamine and ACh thus giving
an arousing, energizing pleasant effect.
ACh (Acetylcholine)
Widely used at synapses
Used at all motor neurons activating
skeletal muscle
Acetylcholine is removed from the synapse
by enzymatic breakdown into inactive
fragments.
The enzyme used is called?
acetylcholinesterase.
Nerve gases
(e.g. sarin gas) achieve their effects by inhibiting
acetylcholinesterase thus allowing ACh to
remain active. In the presence of such inhibitors
ACh keeps stimulating the postsynaptic
membranes and the nervous system soon goes
wild, causing spasms and eventually death.
Atropine is used as an antidote because it
blocks ACh receptors.
organophosphate insecticides
(e.g. parathion)
essentially work the same way as sarin gas
They irreversibly inactivate acetylcholinesterase, which is essential
to nerve function in insects, humans, and many other animals.
parathion, one of the first OPs commercialized, is many times more
potent than malathion, an insecticide used in combatting the
Mediterranean fruit fly (Med-fly) and West Nile Virus-transmitting
mosquitoes.
Even at relatively low levels, these agents may be hazardous to the
brain development of fetuses and young children.
They have been banned from residential use since 2001, but they
are still sprayed agriculturally. They're also used to control pests like
mosquitos in public spaces. They can be absorbed through the
lungs or skin or by eating them on food
Drugs can be involved in a range of
effects on synapses
Mimic a neurotransmitter: would
switch on synapse
Inhibit the Na+K+ATPase pump
-stop action potentials
Open a neuroreceptor channel
-switch on synapse
Inhibit the breakdown enzyme
-switch on a synapse
Block a neuroreceptor channel
-switch off a synapse
Stimulate the release of a neurotransmitter
-switch on synapse
Block the Na+ or K+ channels
-stop action potentials
The role of nearly all drugs that are
commonly abused to produce euphoria is
the nucleus accumbens, the brain's
"pleasure centre"
Neurons in the nucleus accumbens use
the neurotransmitter dopamine, nearly
every drug focused on pleasure either
stimulates dopamine release or enhances
its activity, directly or indirectly
Cocaine
What is it?
An alkaloid extracted from the leaves of the coca
plant (Erythroxylon coca)
a native of the eastern slopes of the Andes.
It is commonly consumed in the form of the
hydrochloride salt, a white crystalline powder
which is usually snorted into the nostrils.
Crack cocaine is pure cocaine liberated from the
hydrochloride (hence known as "free base"),
which makes it smokeable.
How does cocaine work
on the brain?
Dopamine is produced in the brain when you feel happy.

After a given time of feeling happy, the dopamine
decreases because "transporters" mop it up.
The transporters move the dopamine back in the area of
the brain where it is kept until your next happy event.
Cocaine works by keeping the transporters from mopping
up the dopamine. When the dopamine is allowed to stay
free, you have a long-term feeling of great happiness
and well being.
Amphetamines also increases dopamine levels. Again,
the result is over-stimulation of these pleasure-pathway
nerves in the brain.
The effects of cocaine at the
synapse
cocaine
IF dopamine is not removed from the synaptic gap, and it
remains free there, in ever increasing amounts, because
successive nervous stimuli continue to arrive and to
release dopamine.
The prolonged use of cocaine makes the brain adapt to
it, causing the overall synthesis of dopamine by the
neurons to decrease.
Between cocaine doses, or when the use of cocaine is
interrupted, the drug user experiences the opposite of
pleasure, due to the low levels of dopamine now present
in the brain and the result is fatigue, depression and
altered moods (withdrawal).
dopamine
has a number of roles, including muscle control, pain
inhibition and general stimulation.
Some psychosis disorders such as schizophrenia and
depression/bipolar disorder are caused by an excess of
dopamine, and antipsychotic drugs are used to block the
dopamine receptors and so reduce its effects.
Parkinsons disease (shaking of head and limbs) is
caused by too little dopamine compared to acetylcholine
production in the midbrain. The balance can be restored
with levodopa, a drug which mimics dopamine, or with
anticholinergic drugs, which block the acetylcholine
receptors
ADHD and narcolepsy
believed to be linked to sub-performance
of the dopamine and norepinephrine
functions in the brain
responsible for self-regulatory function
(e.g., inhibition, motivation, and memory)
and executive function (e.g., reasoning,
organizing, problem solving, and planning)
Ritalin
mechanism of action - dopamine reuptake
inhibitor.
Blocks the dopamine transporter and
norepinephrine transporter, leading to
increased concentrations of dopamine and
norepinephrine within the synaptic cleft.
Some people use it as in intellectual party
drugmakes you think more clearly and
feel good at the same time.
Caffeine (in coffee, cocoa and cola),
theophylline (in tea), amphetamines,
ecstasy (MDMA) and cocaine all promote
the release of noradrenaline, so are
stimulants.
Antidepressant drugs, inhibit the
breakdown and block the absorption of
neurotransmitters, such as noradrenaline
and dopamine, thereby extending its
effect.
methylenedioxymethamphetamine
or "MDMA -Ecstacy
"feel good drug" - positive feelings of well
being and empathy toward other people,
elimination of anxiety, and extreme
relaxation.
suppresses the need to eat drink and sleep,
allowing club scene users to endure all night
and some times two or three day parties
The drug causes the brain to dump large
amounts of the mood-modulating
neurotransmitter serotonin into the synapses,
and also raises dopamine levels.
Other than withdrawal what is the
problem with taking ecstacy?
Clan labs that make them these people
arent chemists, they are simply following
recipes, often from the internet
Very likely to make a toxic substance
rather than a pleasure drug
Huge number of people end up at
emergency room
FUGU
Tetrodotoxin (from the Japanese puffer fish)

blocks voltage-gated sodium channels.
It is a powerful nerve poison.
tetrodotoxin affects the depolarization part of the
action potential that essentially causes no action
potential to be fired
This means youre muscles cant move
breathing requires muscles!
Curare
Dart Frog
block the acetylcholine receptors in the somatic

nervous system,
and so relax skeletal muscle .
Result: ?
Curare (poison used by S. American
Indians) stops Acetylcholine from
depolarising the post-synaptic membrane,
i.e. become paralysed
botox
Botox
injecting overactive muscles with minute
quantities of botulinum toxin decreases
muscle activity by blocking the release of
acetylcholine at the synpase at the
neuromuscular junction
this stops the muscle from contracting for
a period of 4 to 6 months.
But is there a cost?
Withdrawal
withdrawal syndrome characterized by
dysphoria the opposite of euphoria
as nucleus accumbens activity declines
below normal levels
Subnormal activity in the nucleus
accumbens is often characterized by
depression, anxiety and craving
this can help people to addiction or
even to suicide if they cant get a fix
Some people have very little issue with
withdrawal and are able to quit a drug cold
turkey others arent so lucky
Cell cycle and meiosis
week 11
Text book: Knox 4th edition Chapters 8

Forensic applications of molecular genetics
Suspects blood
samples 1-7
Blood stain
found near the
victim
Plant Breeding
4n X 2n => 3n
Transient sexual mimicry leads to fertilization, Roger T. Hanlon, Mari-Jose Naud, Paul W.
Shaw, Jon N. Havenhand, Nature, January 20, 2005
Eukaryotic chromosomes
Consist of chromatin, a complex of DNA and
protein that condenses during cell division
In animals
Somatic cells have two sets of chromosomes
Gametes have one set of chromosomes
In preparation for cell division

DNA is replicated and the chromosomes
condense
Each duplicated chromosome
Has two sister chromatids, which separate during
cell division
0.5 m
A eukaryotic cell has multiple
chromosomes, one of which is
represented here. Before
duplication, each chromosome
Chromosome
has a single DNA molecule.
duplication
(including DNA
synthesis)
Once duplicated, a chromosome
consists of two sister chromatids Centromere
connected at the centromere. Each
chromatid contains a copy of the
DNA molecule.
Sister
Separation chromatids
of sister
Mechanical processes separate chromatids
the sister chromatids into two
chromosomes and distribute
them to two daughter cells.
Figure 12.4 Centromeres Sister chromatids

Chromosome is tightly package single DNA molecule
Cell cycle
The mitotic phase alternates with
interphase in the cell cycle
Interphase can be divided into subphases
G1 phase
S phase
G2 phase
The mitotic phase

Is made up of mitosis and cytokinesis
Phases of the Cell Cycle
The cell cycle consists of
The mitotic phase
Interphase
INTERPHASE
S
G1 (DNA synthesis)
G2
Figure 12.5
Mitosis consists of five distinct phases
Prophase
Prometaphase
G2 OF
PROPHASE PROMETAPHASE
INTERPHASE
Centrosomes Aster Fragments Kinetochore
(with centriole pairs) Chromatin Early mitotic
spindle Centromere of nuclear
(duplicated) envelope Nonkinetochore
microtubules
Nucleolus Nuclear Plasma Chromosome, consisting Kinetochore

Figure 12.6 of two sister chromatids microtubule
envelope membrane
Metaphase, Anaphase, Telophase
METAPHASE ANAPHASE TELOPHASE AND CYTOKINESIS
Metaphase
plate Cleavage
Nucleolus
furrow
forming
Nuclear
envelope
Centrosome at Daughter forming
Spindle
Figure 12.6 one spindle pole chromosomes
The Mitotic Spindle: A Closer
Look
The mitotic spindle
Is an apparatus of microtubules that controls
chromosome movement during mitosis
The spindle arises from the centrosomes

And includes spindle microtubules and
asters
Spindle microtubules
Attach to the kinetochores of chromosomes and move the
chromosomes to the metaphase plate
Aster Centrosome
Sister
Metaphase
chromatids Plate
Kinetochores
Overlapping
nonkinetochore
microtubules
Kinetochores
microtubules 0.5 m
Microtubules Chromosomes
Figure 12.7 Centrosome

1 m
Anaphase
In anaphase, sister chromatids separate
And move along the kinetochore microtubules
toward opposite ends of the cell
EXPERIMENT
1 The microtubules of a cell in early anaphase were labeled with a fluorescent dye
that glows in the microscope (yellow).
Kinetochore
Spindle
pole
Figure 12.8
2 A Laser was used to mark the kinetochore mircotubles by eliminating the fluorescnce in a region between
one spindle pole and the chromosomes. As anaphase proceeded, researches monitored the changes
in the lengths of the microtubles on either side of the mark.
Mark
RESULTS As the chromosomes moved toward the poles, the microtubule segments on the
kinetochore side of the laser mark shortened, while those on the spindle pole side stayed the
same length.
A group of cells is assayed for DNA
content immediately following mitosis and
is found to have an average of 8
picograms of DNA per nucleus. Those
cells would have __________ picograms
at the end of the S phase and
__________ picograms at the end of G2.
a) 8 ... 8
b) 8 ... 16
c) 16 ... 8
d) 16 ... 16
e) 12 ... 16
A cell containing 92 chromatids at
metaphase of mitosis would, at its
completion, produce two nuclei
containing how many
chromosomes?
a) 12
b) 16
c) 23
d) 46
e) 92
Cytokinesis
Nonkinetechore microtubules from

opposite poles
Overlap and push against each other,
elongating the cell
In telophase
Genetically identical daughter nuclei form at
opposite ends of the cell
Cytokinesis: A Closer Look
In animal cells
Cytokinesis occurs by a process known as
cleavage, forming a cleavage furrow
Cleavage furrow 100 m
Contractile ring of
Daughter cells
microfilaments
Figure 12.9 A (a) Cleavage of an animal cell (SEM)

In plant cells, during cytokinesis a
cell plate forms
Vesicles Wall of 1 m
patent Cell
forming
cell plate New cell wall
cell plate
Daughter cells
(b) Cell plate formation in a plant cell
Figure 12.9 B (SEM)
Mitosis in a plant cell
Nucleus Chromatine Chromosome
Nucleolus condensing
1 Prophase. 2 Prometaphase. 3 Metaphase. The 4 Anaphase. The 5 Telophase. Daughter

spindle is complete,
The chromatin We now see discrete chromatids of each nuclei are forming.
and the chromosomes,
is condensing. chromosomes; each chromosome have Meanwhile, cytokinesis
attached to microtubules
The nucleolus is consists of two separated, and the has started: The cell
at their kinetochores,
beginning to identical sister daughter chromosomes plate, which will
are all at the metaphase
disappear. chromatids. Later are moving to the ends divided the cytoplasm
plate.
Although not in prometaphase, the of cell as their in two, is growing
yet visible nuclear envelop will kinetochore toward the perimeter
in the micrograph, fragment. microtubles shorten. of the parent cell.
the mitotic spindle is
staring to from.
Figure 12.10
Mitosis movie
Go to
www.whfreeman.com/iga8e
Prokaryotic cell cycle
In binary fission
The bacterial chromosome replicates
The two daughter chromosomes actively move apart
Origin of
Cell wall
replication
Plasma
Membrane
E. coli cell Bacterial
1 Chromosome replication begins. Two copies Chromosome
Soon thereafter, one copy of the of origin
origin moves rapidly toward the
other end of the cell.
2 Replication continues. One copy of Origin Origin

the origin is now at each end of
the cell.
3 Replication finishes. The plasma

membrane grows inward, and
new cell wall is deposited.
Figure 12.11 4 Two daughter cells result.

Yesterday:
mitosis and the cell cycle
Today:
Meiosis
Genetics:
the mechanism behind the variation
Meiosis
Offspring acquire genes from parents by
inheriting chromosomes
Genes
Are the units of heredity
Are segments of DNA
Each gene in an organisms DNA has a specific
locus on a certain chromosome
We inherit
One set of chromosomes from our mother and
one set from our father
A karyotype
Is an ordered, visual representation of
the chromosomes in a cell
Pair of homologous
chromosomes 5 m
Centromere
Sister
chromatids
Figure 13.3
Sexual reproduction
In sexual reproduction
Two parents give rise to offspring that have
unique combinations of genes inherited from
the two parents
Fertilization and meiosis alternate in sexual
life cycles
A life cycle
Is the generation-to-generation sequence of
stages in the reproductive history of an
organism
Meiosis
Homologous chromosomes
Are the two chromosomes composing a pair
Have the same characteristics
May also be called autosomes
Sex chromosomes
Are distinct from each other in their
characteristics
Are represented as X and Y
Determine the sex of the individual, XX being
female, XY being male
A diploid cell
Has two sets of each of its chromosomes
In a human has 46 chromosomes (2n = 46)
Meiosis and DNA synthesis
In a cell in which DNA synthesis has occurred
All the chromosomes are duplicated and thus each
consists of two identical sister chromatids
Key
Maternal set of
chromosomes (n = 3)
2n = 6
Paternal set of
chromosomes (n = 3)
Two sister chromatids

of one replicated
chromosome
Centromere
Two nonsister Pair of homologous

chromatids in chromosomes
a homologous pair (one from each set)
Figure 13.4
The Stages of Meiosis
Interphase
Homologous pair
of chromosomes
in diploid parent cell
Chromosomes
replicate
Homologous pair of replicated chromosomes
Sister
chromatids Diploid cell with
replicated
chromosomes
Meiosis I
1 Homologous
chromosomes
separate
Haploid cells with

replicated chromosomes
Meiosis II
2 Sister chromatids
separate
Haploid cells with unreplicated chromosomes

Figure 13.7
A cell in G2 before meiosis
compared with one of the four
cells produced by that meiotic
division has
a) twice as much DNA and twice as many chromosomes.
b) four times as much DNA and twice as many
chromosomes.
c) four times as much DNA and four times as many
chromosomes.
d) half as much DNA but the same number of
chromosomes.
e) half as much DNA and half as many chromosomes.
Interphase and meiosis I
INTERPHASE MEIOSIS I: Separates homologous chromosomes
PROPHASE I METAPHASE I ANAPHASE I
Centromere Sister chromatids

Centrosomes
(with kinetochore) remain attached
(with centriole pairs)
Chiasmata Metaphase
Sister
chromatids plate
Spindle
Nuclear
Microtubule Homologous
envelope
Tetrad attached to chromosomes
Chromatin separate
kinetochore
Chromosomes duplicate Tertads line up Pairs of homologous
chromosomes split up
Homologous chromosomes
(red and blue) pair and exchange
Figure 13.8 segments; 2n = 6 in this example
Telophase I, cytokinesis, and meiosis II
MEIOSIS II: Separates sister chromatids
TELOPHASE I AND PROPHASE II METAPHASE II ANAPHASE II TELOPHASE II AND

CYTOKINESIS CYTOKINESIS
Cleavage Haploid daughter cells

furrow Sister chromatids forming
separate
Two haploid cells

form; chromosomes During another round of cell division, the sister chromatids finally separate;
Figure 13.8 are still double four haploid daughter cells result, containing single chromosomes
Meiosis movie
A Comparison of Mitosis and Meiosis
Meiosis and mitosis can be distinguished from
mitosis by three events in Meiosis l
1. Synapsis and crossing over
Homologous chromosomes physically connect and
exchange genetic information
2. Tetrads on the metaphase plate
At metaphase I of meiosis, paired homologous
chromosomes (tetrads) are positioned on the
metaphase plates
3. Separation of homologues
At anaphase I of meiosis, homologous pairs move
toward opposite poles of the cell
In anaphase II of meiosis, the sister chromatids
separate
A comparison of mitosis and meiosis
MITOSIS MEIOSIS
Parent cell Chiasma (site of
MEIOSIS I
(before chromosome replication) crossing over)
Prophase I
Prophase
Chromosome Chromosome
replication replication
Tetrad formed by
Duplicated chromosome 2n = 6 synapsis of homologous
(two sister chromatids) chromosomes
Chromosomes Tetrads
positioned at the positioned at the Metaphase I
Metaphase
metaphase plate metaphase plate
Anaphase Sister chromatids

Homologues Anaphase I
Telophase separate during
separate Telophase I
anaphase
during
anaphase I;
sister Haploid
chromatids n=3
remain together Daughter
cells of
meiosis I
2n 2n
MEIOSIS II
Daughter cells
of mitosis
n n n n
Daughter cells of meiosis II
Sister chromatids separate during anaphase II

Figure 13.9
The human life cycle
Key
Haploid gametes (n = 23)
Haploid (n)
Ovum (n)
Diploid (2n)
Sperm
Cell (n)
MEIOSIS FERTILIZATION
Ovary Testis Diploid

zygote
(2n = 46)
Mitosis and
development
Multicellular diploid
Figure 13.5 adults (2n = 46)
The Variety of Sexual Life Cycles
The three main types of sexual life cycles
Differ in the timing of meiosis and
fertilization
Animal
Plants and some algae
Fungi and some protists
In animals
Meiosis occurs during gamete formation
Gametes are the only haploid cells
Key
Haploid
Diploid
n n
Gametes
n
Zygote
2n 2n
Diploid Mitosis
multicellular
organism
Figure 13.6 A (a) Animals
Plants and some algae
Exhibit an alternation of generations
The life cycle includes both diploid and haploid
multicellular stages
Haploid multicellular
organism (gametophyte)
Mitosis n Mitosis
n n
n n
Spores
Gametes
Diploid
2n
multicellular 2n
organism Zygote
(sporophyte)
Mitosis
Figure 13.6 B (b) Plants and some algae
In most fungi and some protists
Meiosis produces haploid cells that give rise to
a haploid multicellular adult organism
The haploid adult carries out mitosis,
producing cells that will become gametes
Haploid multicellular
organism
n
Mitosis Mitosis
n
n n
Gametes n
2n
Zygote
Figure 13.6 C (c) Most fungi and some protists
Genetic variation
Genetic variation produced in sexual life
cycles contributes to evolution
Reshuffling of genetic material in meiosis
Produces genetic variation
In species that produce sexually

The behavior of chromosomes during meiosis
and fertilization is responsible for most of
the variation that arises each generation
Homologous pairs of chromosomes
Orient randomly at metaphase I of meiosis
In independent assortment
Each pair of chromosomes sorts its maternal and paternal
homologues into daughter cells independently of the other pairs
Key
Maternal set of
chromosomes
Possibility 1 Possibility 2
Paternal set of
chromosomes
Two equally probable

arrangements of
chromosomes at
metaphase I
Metaphase II
Daughter
cells
Figure 13.10 Combination 1 Combination 2 Combination 3 Combination 4

Crossing Over
Crossing over
Produces recombinant chromosomes that carry genes derived
from two different parents
Prophase I Nonsister
of meiosis chromatids
Tetrad
Chiasma,
site of
crossing
over
Metaphase I
Metaphase II
Daughter
cells
Recombinant
Figure 13.11 chromosomes
Random Fertilization
The fusion of gametes
Will produce a zygote with any of about 64 trillion
diploid combinations
Genetic variation
Is the raw material for evolution by natural
selection
Mutations
Are the original source of genetic variation
Sexual reproduction
Produces new combinations of variant genes, adding
more genetic diversity
The imprecise nature of meiosis
Chromosome nondisjunction
When the chromosomes do not segregrate
properly during mitosis or meiosis
In humans, since most such embryos are non-
viable, one might expect that these errors would
be extremely rare.
But identified in at least 5 percent of all
pregnancies, making it the leading known cause
of foetal loss.
only a small proportion foetuses survive to term
but are cause of mental impairment and
developmental disabilities.
At what point in the cell cycle could
this problem occur??
a. Meiosis 1
b. Meiosis 2
c. At either stage
Remember: The first cell division (meiosis I)

separates homologous chromosomes; the
second (meiosis II) segregates the sister
chromatids of each homologue.
Meiotic Nondisjunction
Meiosis I
Nondisjunction
Meiosis II
Nondisjunction
Gametes
n+1 n+1 n1 n1 n+1 n 1 n n

Number of chromosomes
(a) Nondisjunction of homologous (b) Nondisjunction of sister
chromosomes in meiosis I chromatids in meiosis II
Other forms
Monosomy a condition in which one
chromosome is missing, abbreviated as 2n-1.
Trisomy has one extra chromosome 2n+1.
Monosomies and trisomies usually result from
nondisjunction during meiosis. They are more
common in meiosis 1 than meiosis 2.
Non-disjunction of sex
chromosomes
Which of the following conditions
do you think can occur and be
viable?
1. XYY
2. YO
3. XO
4. XXY
5 XXYY
Conditions
XXY, XXXY male Klinefelter Syndrome
XYY male XYY syndrome
XO female Turners syndrome
XXX - female Trisomy X
Klienfelter Syndrome
XXY, XXXY
Male
Sterile, smaller genitals,
Some breast enlargement
How would you get Kleinfelters
Syndrome?
Draw it out. XXY
XYY syndrome
Normal male traits
47,XYY
47,XYY boys have an
increased growth velocity
during earliest childhood,
with an average final
height approximately 7
cm above expected final
height
have an increased risk of
learning difficulties (in up
to 50%) and delayed
speech and language
skills
XO Turners Syndrome
Sterile
Short stature
Sex organs lack
maturity
Short stubby fingers
Neck short and
webbed
How would you get
Turners Syndrome?
Draw XO out
Nondisjunction
First discovered in 1913 by Calvin Bridges
Failures may be due to defects in the spindle
integrity or in the motors on the
chromosomes that move them to opposite
poles
Chromosome 21
Chromosome 21 has very few genes
with a million base pair stretch of DNA
with no protein encoding genes, it
contains only 225 genes
Chromosome 22, on the other hand, is
full of genes 545
Which one would you expect to find
more trisomies of?
Dr. John Langdon Down
In 1866, noticed that approximately 10%
of people within asylum resembled
each other
90 years later geneticist determine
these individuals had syndrome called
:Down Syndrome
have 3 copies of the smallest
chromosome, chromosome 21
Trisomy 21
Most common genetic disorder
about 10% of all mentally disabled children
Occurs in about 1/750 live births in all
ethnic groups
About 10% of all mentally disabled
children carry this disorder
Characteristics of Downs
Syndrome
40% of babies with Down's
syndrome will have some sort of
congenital heart defect, such as a
"hole in the heart
some level of learning disorder
immune system which makes them
prone to infections
Vision and hearing problems
1929, the average life span of a
person with Down syndrome was
nine years. 2006, people with Down
syndrome to live to age fifty or more.
Karyotyping
What chromosome might you
expect to lead to the greatest
number of defects?
Chromosome 21
has been shown that not all of chromosome 21 has
to be present in triplicate to produce Down
syndrome
Occasionally only some extra chromosomal material
is present in the distal half of the long arm of
chromosome 21.
This region houses most of the genes including a
gene for an enzyme involved in aging and a leukemia
causing gene
Almost all cases of trisomy 21 are due to
nondisjunction during the first meiotic
division in the mother
male meiosis (sperm production) seems to
have a system that checks that
chromosomes are properly paired, if not that
gamete dies
Female meiosis (Oocyte production) seem
committed to completing meiosis regardless
of what problems arise
male ejaculate contains about 200
million sperm
If a few die during spermatogenesis
due to meiotic failure, there is little cost
to the male
Human female usually makes only
release one egg a month, so the
investment in producing the egg is
quite high
The affect of Maternal Age
Frequency of Down syndrome births
increases with advancing maternal age
Women over 35 years of age produced

about 25% of all the babies born with
Down syndrome
Probability of Downs Syndrome
Age of Mother Risk
20 1:1,340
25 1:1,500
30 1:900
35 1:400
40 1:105
45 1:35
49 1:12
Incidence of Down syndrome increases with
maternal age
Stops in
prophase
1 before
birth
Ovulation:
begins
meiosis II,
but stops
in
metaphase
23/05/2017
Females produce all of their eggs
when they are developing in utero
oocytes begin meiosis before the
female is born
The eggs remain dormant until puberty
and ovulation
the long delay between prophase I and
the first meiotic division in human
oocytes may be responsible for the
high levels of trisomy
Egg ovulated by a 45 year old
female has been so called
dormant for 45 years
Every month several oocytes reinitiate
meiosis, and generally only one of them
completes the first meiotic division
During that time the oocytes may have been
exposed to chromosome damage by
chemicals, viruses or radiation
Males, meiosis on the other hand, is a
continuous process from puberty to death,
sperm are consequently not as susceptible
to environmental hazards
Mendel and the gene
concept
week 12
Gregor Mendel
Documented a particulate mechanism of
inheritance through his experiments with
garden peas
Figure 14.1
Pollen lands on the stigma surface
Crossing pea plants
1 Removed stamens
APPLICATION By crossing (mating) two true- from purple flower
breeding
2 Transferred sperm-
varieties of an organism, scientists can study patterns of
bearing pollen from
inheritance. In this example, Mendel crossed pea plants
stamens of white
that varied in flower color.
flower to egg-
bearing carpel of
purple flower
TECHNIQUE Parental
generation
(P)
Stamens
Carpel (male)
3 Pollinated carpel
(female)
matured into pod
4 Planted seeds
from pod
TECHNIQUE
RESULTS When pollen from a white flower fertilizes 5 Examined
eggs of a purple flower, the first-generation hybrids all have purple offspring:
flowers. The result is the same for the reciprocal cross, the transfer First all purple
of pollen from purple flowers to white flowers. generation flowers
offspring
(F1)
Figure 14.2
Mendels law of segregation, probability and the Punnett square
Each true-breeding plant of the P Generation

parental generation has identical
alleles, PP or pp.
Appearance: Purple flowers White flowers
Gametes (circles) each contain only
one allele for the flower-color gene.
Genetic makeup: PP pp
In this case, every gamete produced
by one parent has the same allele. Gametes: P p
Union of the parental gametes

produces F1 hybrids having a Pp F1 Generation
combination. Because the purple-
flower allele is dominant, all
these hybrids have purple flowers. Appearance:
Genetic makeup: Purple flowers
When the hybrid plants produce Pp
gametes, the two alleles segregate,
half the gametes receiving the P Gametes: 1/ 1/
2 P 2 p
allele and the other half the p allele.
F1 sperm
This box, a Punnett square, shows
P p
all possible combinations of alleles
in offspring that result from an
F1 F1 (Pp Pp) cross. Each square F2 Generation
represents an equally probable product P
of fertilization. For example, the bottom
PP Pp
left box shows the genetic combination F1 eggs
resulting from a p egg fertilized by
a P sperm.
p
Pp pp
Random combination of the gametes
results in the 3:1 ratio that Mendel
observed in the F2 generation. 3 :1
Figure 14.5
Phenotype versus genotype
Phenotype Genotype
Purple
PP
1
(homozygous)
Pp
3 Purple (heterozygous)
Pp
(heterozygous)
Purple
pp
1 White 1
(homozygous)
Figure 14.6 Ratio 3:1 Ratio 1:2:1

Mendel observed the same pattern
In many other pea plant characters
Table 14.1
Important genetic vocabulary
Character: a heritable feature, such as flower color
Trait: a variant of a character, such as purple or white
flowers
Genotype: the genetic constitution of an organism (i.e.
the particular set of alleles present in each cell of an
organism).
Phenotype: the form, or observable manifestation, of a
specific genotype.
Dominant allele: An allele that expresses its phenotypic
effect even when present in a single dose along with a
corresponding recessive allele (heterozygote) or when
present in two doses (homozygote).
Recessive allele: An allele that expresses its phenotypic
effect only when present in two doses (homozygote).
Homozygous: A diploid genotype with two identical
alleles at one locus
Heterozygous: A diploid organism with two non-identical
alleles at one locus
In incomplete dominance
The phenotype of F1 hybrids is somewhere between the
phenotypes of the two parental varieties
P Generation
White
Red CW CW
CRCR
Gametes CR CW
Pink
F1 Generation CRCW
1 1
2 2
Gametes CR CR
1 1 Sperm
Eggs 2 CR 2 CR
F2 Generation
1
2 CR
CR CR CR CW
1
2 Cw
CR CW CW CW
Coat colour in mice is controlled by a single
locus in which B = black and b = brown.
If two Black (Bb) mice are crossed, the progeny
are 3 (black) : 1 (brown). What is the frequency
of the B and b alleles in the eggs and sperm?
1. 1/4 b and 3/4 B.

2. 2/3 B and 1/3 b.
3. 1/2 B and 1/2b
4. 3/4 b and 1/4 B.
5. All B.
Coat colour in mice is controlled by a single
locus in which B = black and b = brown.
If the BB genotype is lethal what would the
frequency of black to brown mice in a Black
x Black cross?
1. 1/4 brown and 3/4 black.
2. 2/3 black and 1/3 brown.
3. 1/2 black and 1/2 brown
4. 3/4 brown and 1/4 black.
5. All brown.
In humans; one example is
achondroplasia
A form of dwarfism that is lethal when homozygous
for the dominant allele
The ABO blood group in humans is
determined by multiple alleles
Table 14.2
ABO genotypes of the Anderson family
Bi
Bi
Ai
ii AB
Three babies were recently mixed up in a hospital.
After consideration of the data below, which of the
following represent the correct baby/parent
combinations?
Couple # I II III
Blood groups A and A A and B B and O
Baby # 1 2 3
Blood groups B O AB
1. I-3, II-1, III-2

2. I-1, II-3, III-2
3. I-2, II-3, III-1
4. I-2, II-1, III-3
5. I-3, II-2, III-1
The Law of Independent Assortment
Mendel identified his second law of inheritance
By following two characters at the same time
Crossing two, true-breeding parents differing in two
characters
Produces dihybrids in the F1 generation, heterozygous
for both characters
How are two characters transmitted from

parents to offspring?
As a package?
Independently?
A dihybrid cross
P Generation YYRR yyrr

EXPERIMENT
Two true-breeding pea plants

Gametes YR yr
one with yellow-round seeds and the other with green-
wrinkled seedswere crossed, producing dihybrid F1
plants. Self-pollination of the F1 dihybrids, which are
heterozygous for both characters, produced the F2
generation. The two hypotheses predict different F1 Generation YyRr
phenotypic ratios. Note that yellow color (Y) and round Hypothesis of Hypothesis of
shape (R) are dominant. dependent independent
assortment assortment
Sperm
1 1 Yr 1 1
4 YR 4 4 yR 4
yr
Sperm
Eggs
1 1
RESULTS 2 YR 2 yr
1 YR
4
Eggs YYRR YYRr YyRR YyRr
1
2 YR
F2 Generation YYRR YyRr 1
(predicted 4 Yr
YYrr YYrr YyRr Yyrr
offspring)
1
2
yr
YyRr yyrr
CONCLUSION The results support the hypothesis of 1
4 yR
independent assortment. The alleles for seed color and seed YyRR YyRr yyRR yyRr
3
shape sort into gametes independently of each other. 4
1
4
1 yr
4
Phenotypic ratio 3:1 YyRr Yyrr yyRr yyrr
9 3 3 1
16 16 16 16
Phenotypic ratio 9:3:3:1
Figure 14.8 315 108 101 32 Phenotypic ratio approximately 9:3:3:1

Independent assortment
Each pair of chromosomes sorts its maternal and paternal homologues
into daughter cells independently of the other pairs
Key
Maternal set of
chromosomes
Paternal set of
chromosomes
Y y Y y
R r arrangements of
chromosomes at
r R
metaphase I
Y y Y y
Metaphase II
R r r R
YR YR yr yr Daughter
Yr Yr yR yR
cells

The chromosomal basis of Mendels laws
P Generation
Yellow-round Green-wrinkled
Starting with two true-breeding pea plants, seeds (YYRR) seeds (yyrr)
we follow two genes through the F 1 and F2 Y y
generations. The two genes specify seed r
color (allele Y for yellow and allele y for Y R R r
green) and seed shape (allele R for round y
and allele r for wrinkled). These two genes are
on different chromosomes. (Peas have seven
chromosome pairs, but only two pairs are Meiosis
illustrated here.)
Fertilization
R Y y r
Gametes
All F1 plants produce

yellow-round seeds (YyRr)
R R
F1 Generation y y
r r
Y Y
Meiosis
LAW OF SEGREGATION LAW OF INDEPENDENT ASSORTMENT

R r r R
Two equally
probable
Y y arrangements Y y
of chromosomes
1
at metaphase I Alleles at both loci segregate
1 The R and r alleles segregate in anaphase I, yielding four
R r r R types of daughter cells
at anaphase I, yielding
two types of daughter depending on the chromosome
cells for this locus. Anaphase I arrangement at metaphase I.
Compare the arrangement of
Y y the R and r alleles in the cells
Y y
on the left and right
R r r R
2
Each gamete Metaphase II 2
gets one long Each gamete gets
chromosome Y y a long and a short
y y
with either the chromosome in
R or r allele. one of four allele
combinations.
Y Y
Y Y Y Y y y
Gametes
R R r r R
r r R
1 1 yr 1 1
YR yr yR
4 4 4 4
F2 Generation
Fertilization among the F1 plants
3 Fertilization 3 Fertilization results
recombines the in the 9:3:3:1
R and r alleles 9 :3 phenotypic ratio in
:3 :1
at random. the F2 generation.
A sexually reproducing animal has two unlinked genes,
one for head shape (H) and one for tail length (T). Its
genotype is HhTt. Which of the following genotypes is
possible in a gamete from this organism?
1. HT
2. Hh
3. HhTt
4. T
5. tt
Black fur in mice (B) is dominant to brown fur (b).
Short tails (T) are dominant to long tails (t). What
fraction of the progeny of the cross
BbTt BBtt will have black fur and long tails?
1. 1/16
2. 3/16
3. 1/4
4. 1/2
5. 9/16
Inheritance patterns of particular traits can
be traced and described using pedigrees
First generation
Ww ww ww Ww (grandparents) Ff Ff ff Ff
Second generation
(parents plus aunts
Ww ww ww Ww Ww ww FF or Ff Ff ff Ff Ff ff
and uncles)
Third
ww generation ff FF
WW
(two sisters) or
or
Ww Ff
Widows peak No Widows peak Attached earlobe Free earlobe
(a) Dominant trait (widows peak) (b) Recessive trait (attached earlobe)
Figure 14.14 A, B
If C1 and D1 were to marry, what is the
probability that they will have a Ww
child?
1. 3/4
2. 1/4
3. 1/2
4. 2/3
5. 0
The Chromosomal Basis of Sex
An organisms sex
Is an inherited phenotypic character determined by
the presence or absence of certain chromosomes
In humans and other mammals
There are two varieties of sex chromosomes, X
and Y
44 + Parents 44 +
XY XX
22 + Sperm 22 + Ova 22 +
X Y X
44 + Zygotes 44 +
XX (offspring) XY
(a) The X-Y system
Figure 15.9a
Different systems of sex determination
Are found in other organisms
22 + 22 +
XX X
(b) The X0 system
76 + 76 +
ZW ZZ
(c) The ZW system
32 16
(Diploid) (Haploid)
Figure 15.9bd (d) The haplo-diploid system

Inheritance of Sex-Linked Genes
The sex chromosomes

Have genes for many characters unrelated to sex
A gene located on either sex chromosome
Is called a sex-linked gene
Sex-linkage
A A
X X
genes X Y a
Xa Y Sperm
Ova XA XAXa XAY

XA XAXa XAY
XAXa XAY
XA Sperm
Y
Ova XA XAXA XAY
Xa XaXA XaY
XAXa XaY
Sperm
Xa Y
Ova XA XAXa XAY
Xa XaXa XaY
Human X linked traits
Some recessive alleles found on the X

chromosome in humans cause certain types of
disorders
Color blindness
Duchenne muscular dystrophy
Hemophilia
An achondroplastic male dwarf with normal vision
marries a color-blind woman of normal height. The
man's father was six-feet tall, and both the woman's
parents were of average height. Achondroplastic
dwarfism is autosomal dominant, and red-green color
blindness is X-linked recessive
How many of their daughters might be expected to be color-blind dwarfs
?
A) All
B) None
C) half
D) one out of four
E) three out of four
An achondroplastic male dwarf with normal vision
marries a color-blind woman of normal height. The
man's father was six-feet tall, and both the woman's
parents were of average height. Achondroplastic
dwarfism is autosomal dominant, and red-green color
blindness is X-linked recessive
How many of their sons would be color-blind and of normal height?
A) All
B) None
C) half
D) one out of four
E) three out of four
Linkage
Linked genes tend to be inherited together

because they are located near each other on the
same chromosome
Each chromosome
Has hundreds or thousands of genes
Independent assortment
Key
Maternal set of
chromosomes
Paternal set of
chromosomes
Y y Y y
R r arrangements of
chromosomes at
r R
metaphase I
Y y Y y
Metaphase II
R r r R
Yr Yr yR yR
cells

Non-Independent assortment
Key
Maternal set of
chromosomes
Paternal set of
chromosomes Y y Y y
R r r R
arrangements of
chromosomes at
metaphase I
Y y Y y
R r Metaphase II
r R
Yr Yr yR yR
cells

How Linkage Affects Inheritance
Morgan crossed flies

That differed in traits of two different characters
P Generation Double mutant
(homozygous) (black body,
EXPERIMENT Morgan first mated true-breeding
Wild type x vestigial wings)
wild-type flies with black, vestigial-winged flies to produce Double mutant
heterozygous F1 dihybrids, all of which are wild-type in
(gray body,
(black body,
appearance. He then mated wild-type F1 dihybrid females with normal wings)
vestigial wings) b b vg vg
black, vestigial-winged males, producing 2,300 F2 offspring, b+ b+ vg+ vg+
which he scored (classified according to F1 dihybrid
phenotype). Double mutant Double mutant
(wild type) TESTCROSS
(black body, (black body,
(gray body, x vestigial wings)
vestigial wings)
normal wings)
CONCLUSION b b vg vg
If these two genes were on
different chromosomes, the alleles from the F1 dihybrid
b+ b vg+ vg
would sort into gametes independently, and we would
expect to see equal numbers of the four types of offspring. RESULTS b+vg+ b vg b+ vg b vg+
If these two genes were on the same chromosome,
we would expect each allele combination, B+ vg+ and b vg, 965 944 206 185
to stay together as gametes formed. In this case, only Wild type Black- Gray- Black-
offspring with parental phenotypes would be produced. (gray-normal) vestigial vestigial normal
Since most offspring had a parental phenotype, Morgan b vg
concluded that the genes for body color and wing size
Sperm
are located on the same chromosome. However, the
production of a small number of offspring with
nonparental phenotypes indicated that some mechanism
occasionally breaks the linkage between genes on the b+ b vg+ vg b b vg vg b+ b vg vgb b vg+ vg
same chromosome.
Parental-type Recombinant (nonparental-type)
Figure 15.5 offspring offspring
P Generation
(homozygous) Double mutant
(black body,
x vestigial wings)
Wild type
(gray body, Double mutant
normal wings) (black body,
vestigial wings)
b b vg vg
b+ b+ vg+ vg+
F1 dihybrid Double mutant

Double mutant TESTCROSS
(wild type) (black body,
(black body,
(gray body, x vestigial wings)
vestigial wings)
normal wings)
b b vg vg
b+ b vg+ vg
RESULTS
b+vg+ b vg b+ vg b vg+
965 944 206 185

Wild type Black- Gray- Black-
(gray-normal) vestigial vestigial normal
b vg
Sperm
b+ b vg+ vg b b vg vg b+ b vg vg b b vg+ vg
Parental-type Recombinant (nonparental-type)

offspring offspring
Morgan determined that
Genes that are close together on the same
chromosome are linked and do not assort
independently
Unlinked genes are either on separate chromosomes
of are far apart on the same chromosome and
assort independently
b+ vg+ b vg
X
Parents
in testcross b vg b vg
Most b+ vg+ b vg
offspring or
b vg b vg
Linked genes
Exhibit recombination frequencies less than 50%
Testcross b+ vg+ b vg Black body,
Gray body,
parents vestigial wings
normal wings
(F1 dihybrid) b vg b vg (double mutant)
Replication of Replication of
chromosomes chromosomes
vg b vg
b+
b+ vg+ b vg
vg vg
b b
Meiosis I: Crossing b vg b vg
over between b and vg
loci produces new allele
combinations.
Meiosis I and II:

Meiosis II: Segregation Even if crossing over
of chromatids produces occurs, no new allele
recombinant gametes combinations are
with the new allele Recombinant produced.
combinations. chromosome
Gametes Ova Sperm

b+vg+ b vg b+ vg b vg+
b vg
b+ vg+ b vg b+ vg b vg+ Ova

Testcross
offspring 965 944 206 185
Sperm Wild type Black- Gray- Black-
Recombination 391 recombinants
(gray-normal)
b+ vg+
vestigial
b vg+
vestigial normal
b vg+ frequency
= 100 = 17%
b+ vg+ 2,300 total offspring
b vg
b vg b vg b vg b vg
Figure 15.6 Parental-type offspring Recombinant offspring
Linkage Mapping: Using Recombination
Data:
A genetic map
Is an ordered list of the genetic loci along a
particular chromosome
Can be developed using recombination frequencies
A linkage map
Is the actual map of a chromosome based on
recombination frequencies
APPLICATION A linkage map shows the relative locations of genes along a chromosome.
TECHNIQUE A linkage map is based on the assumption that the probability of a crossover between two
genetic loci is proportional to the distance separating the loci. The recombination frequencies used to construct
a linkage map for a particular chromosome are obtained from experimental crosses, such as the cross depicted
in Figure 15.6. The distances between genes are expressed as map units (centimorgans), with one map unit
equivalent to a 1% recombination frequency. Genes are arranged on the chromosome in the order that best fits the data.
RESULTS In this example, the observed recombination frequencies between three Drosophila gene pairs
(bcn 9%, cnvg 9.5%, and bvg 17%) best fit a linear order in which cn is positioned about halfway between
the other two genes:
Recombination
frequencies
9% 9.5%
17%
Chromosome b cn vg
The bvg recombination frequency is slightly less than the sum of the bcn and cnvg frequencies because double
crossovers are fairly likely to occur between b and vg in matings tracking these two genes. A second crossover
Figure 15.7 would cancel out the first and thus reduce the observed bvg recombination frequency.
Linkage
Many fruit fly genes
Were mapped initially using recombination
frequencies I
Y X IV
II III
Mutant phenotypes
Short Black Cinnabar Vestigial Brown
aristae body eyes wings eyes
0 48.5 57.5 67.0 104.5
Long aristae Gray Red Normal Red

(appendages body eyes wings eyes
on head)
Figure 15.8 Wild-type phenotypes
Human X chromosome
Genetic (Linkage) Mapping: Relative Ordering of Markers
The initial stage in mapping a large genome is to construct a linkage map of
several thousand genetic markers spaced throughout each of the
chromosomes
Cytogenetic map Chromosome
Chromosome banding bands
pattern and location of

specific genes by
fluorescence in situ Genes located
hybridization (FISH) by FISH
1 Genetic (linkage)
mapping
Ordering of genetic
markers such as RFLPs,
simple sequence DNA,
and other polymorphisms Genetic
(about 200 per chromosome) markers
2 Physical mapping
Ordering of large over-
lapping fragments
cloned in YAC and BAC
vectors, followed by
Overlapping
ordering of smaller fragments
fragments cloned in
phage and plasmid
vectors
3 DNA sequencing
Determination of
nucleotide sequence of GACTTCATCGGTATCGAACT
each small fragment and
assembly of the partial
sequences into the com-
plete genome sequence
Figure 20.11
Problem Solving
Mendelian Genetics
Meiosis, Mitosis or impossible??
A B D A b d
a a b d f
A B D
a b d a B d
A b d a b d
b A b d g
A b d
A b d a b d
A B d A A B B D D
c A b d h A A B B D D
a B D a a b b d d
a b D a a b b d d
A B D A a B b D d
d
A b D i
a B d
a B d A a B b D d
e A B D A a B b D d
j
A B D a A b B d D
Tongue Rolling
In humans, there is a gene that controls formation (or

lack thereof) of muscles in the tongue that allow people
with those muscles to roll their tongues, while people
who lack those muscles cannot roll their tongues.
The ability to roll ones tongue is dominant over non-
rolling.
The ability to taste certain substances is also genetically
controlled.
phenylthiocarbamate (PTC for short), which some
people can taste (the dominant trait), while others cannot
(the recessive trait). To people who are tasters, the taste
very bitter, but to non-tasters, there is no obvious taste.
Lets let R represent tongue-rolling, r represent a non-
roller, T represent ability to taste PTC, and t represent
non-tasting.
Taste & Tongue Rolling
Suppose a woman who is both a homozygous tongue-

roller and a non-PTC-taster marries a man who is a
heterozygous tongue-roller and is a PTC taster, and they
have three children: a homozygous tongue-roller who is
also a PTC taster, a heterozygous tongue-roller who is
also a taster, and a heterozygous tongue-roller who is a
non-taster.
If these parents would have a bunch more children so
that they had 12 in all, how many of those 12 would you
expect to be non-tasters who are homozygous for
tongue-rolling?
If the first child (the homozygous tongue-roller who is
also a PTC taster) marries someone who is
heterozygous for both traits, draw the Punnet square that
predicts what their children will be.
Barr bodies
The formation of Barr bodies is the strategy
that humans use for what is called dosage
compensation.
For many genes encoded on the X
chromosome, cells from both males and
females are designed to work with a single
dose of the genes.
Therefore, in females, one of the Xs is
inactivated, meaning that it is put into a state
where most of its genes cannot be
expressed. In the inactivation process, the
"spare" X chromosome condenses and
becomes the Barr body that can be seen by
staining cells.
Barr Bodies
Barr Bodies
females turn off one of their two X
chromosomes in each cell
(= X inactivation).
This happens early in development and
once the X has been inactivated, the same
X chromosome stays silent throughout cell
divisions, leading to clusters of cells with
the same X on in the adult.
Timing of X inactivation
- 500-1000 cell stage
- Each decision of each cell lineage is independent
31/05/2017
In calico cats where the X chromosome codes for
hair colour there will be a patch of cells with the
yellow X and another patch with the black X.
Calico Cats
Because males only have one X
chromosome, they cant get these
patches.
Occasionally (1/3000), a male cat is born
with an extra X chromosome (XXY) so he
is able to get the patches of colour but
he is usually sterile.
Calico Cats
Interestingly, it is very difficult to breed
calico cats because the process of X
inactivation is random.
You cant predict what type of patches
you will get.
The first cat to be cloned was a calico cat
and the resulting clone (Cc) was all one
colour. Either her X inactivation was not
re-set from the one cell that was cloned, or
all of the cells decided to inactivate the X
in one way during her development.
Problem
Coat colour in cats is located on the X
chromosome. Cats can be black, yellow or
calico. A calico cat has black and yellow
splotches.
If a XCXc female mates with an XcY male
what would be the colour of their
offspring?
A calico cat has a litter of eight kittens --
one yellow male; two black males; two
yellow females; and three calico females.
Assuming there is a single father for the
litter, what is his probable colour?
A yellow cat has a litter of four kittens --
one yellow and three calico. Assuming
there is a single father for the litter, what is
the probable sex of the yellow kitten?
Which of the following matings can never
produce a child with blood type O? The
letters refer to blood types (phenotypes)
AxB
O x AB
AxO
OxO
AxA
A woman with type O blood marries a man
with type AB blood. The chance that their
first child will have blood type A is
_____%.
0%
100%
50%
25%
75%
A woman heterozygous for blood type B is
expecting a child. Her partner is type A.
Her mother-in-law is type B. What are the
chances that their baby will have type AB?
0%
75%
25%
50%
100%
If a female was a carrier for sex-linked
color blindness, what percentage of her
male children would also be color blind?
0%
25%
50%
100%
What pattern of inheritance is shown in the pedigree below?
A) Autosomal dominant
B) Autosomal recessive
C) X-linked dominant
D) X-linked recessive
E) Y-linked dominant
Clouded leopards are a medium sized, endangered
species of cat, living in the very wet cloud forests of
Central America.
Assume that the normal spots (XN, pictured here) are a
dominant, sex-linked trait and that dark spots are the
recessive counterpart (Xn).
Suppose as a Conservation Biologist, you are involved in
a clouded leopard breeding program.
One year you cross a male with dark spots and a female
with normal spots. She has four cubs and, conveniently,
two are male and two female. One each of the male and
female cubs have normal spots and one each have dark
spots. What is the genotype of the mother?
1. XNXN 2. XNXn 3. XnXn
Wolves sometimes have black coats and blue
eyes. Assume that these traits are controlled by
single locus genes and are located on different
chromosomes.
Assume further that normal coat colour (N) is
dominant to black (n) and brown eyes (B) are
dominant to blue (b). Suppose the alpha male is
black with blue eyes and alpha female normal
coloured with brown eyes. The female is
heterozygous for both traits.
What will be the genotypes of their offspring?
In northeast Kansas there is a creature known
as a wildcat. It comes in three colours, blue, red,
and purple. This trait is controlled by a single
locus gene with incomplete dominance.
A homozygous (BB) individual is blue, a
homozygous (bb) individual is red, and a
heterozygous (Bb) individual is purple.
What would be the genotypes and phenotypes
of the offspring if a blue wildcat was crossed with
a red one?
DNA Technology
and Genomics
Week 13
Text book: Knox 5th edition Chapter 15

Gene cloning
Overview of gene cloning with a bacterial plasmid, showing various
uses of cloned genes
Bacterium Cell containing gene
1 Gene inserted of interest
into plasmid
Bacterial Plasmid
chromosome Gene of
Recombinant interest DNA of
DNA (plasmid) chromosome
2 Plasmid put into

Recombinate bacterial cell
bacterium
33 Host cell grown in culture,
to form a clone of cells
containing the cloned
gene of interest
Gene of
Protein expressed
interest
by gene of interest
Copies of gene Protein harvested
Basic Basic
4 Basic research and
research research
various applications
on gene on protein
Gene for pest Gene used to alter Protein dissolves Human growth
resistance inserted bacteria for cleaning blood clots in heart hormone treats
Figure 20.2 into plants up toxic waste attack therapy stunted growth
Using Restriction Enzymes to Make Recombinant DNA
A restriction enzyme will usually make many

cuts in a DNA molecule
Yielding a set of restriction fragments
The most useful restriction enzymes cut
DNA in a staggered way
Producing fragments with sticky ends that
can bond with complementary sticky ends
of other fragments
DNA ligase is an enzyme
That seals the bonds between restriction
fragments
Using a restriction enzyme and DNA ligase
to make recombinant DNA
Restriction site
DNA 5 GAATTC 3
3 CTTAAG
5
1 Restriction enzyme cuts

the sugar-phosphate
backbones at each arrow
G
G
Sticky end
G
G
2 DNA fragment from
another source is added. Fragment from different
Base pairing of sticky DNA molecule cut by the
ends produces various same restriction enzyme
combinations.
G AATT C G AATTC
C TTAA G CTTAA G
One possible combination

3 DNA ligase
seals the strands.
Figure 20.3 Recombinant DNA molecule

Producing Clones of Cells
APPLICATION Cloning is used to prepare many copies of a gene of interest for use in sequencing the gene,
in producing its encoded protein, in gene therapy, or in basic research.
TECHNIQUE In this example, a human gene is inserted into a plasmid from E. coli. The plasmid contains
the ampR gene, which makes E. coli cells resistant to the antibiotic ampicillin. It also contains
the lacZ gene, which encodes -galactosidase. This enzyme hydrolyzes a molecular mimic of
lactose (X-gal) to form a blue product. Only three plasmids and three human DNA fragments
are shown, but millions of copies of the plasmid and a mixture of millions of different human
DNA fragments would be present in the samples.
Bacterial cell lacZ gene

1 Isolate plasmid DNA and human DNA. (lactose Human
breakdown) cell
Restriction
site
2 Cut both DNA samples with the same restriction
ampR gene
enzyme (ampicillin Bacterial Gene of
resistance) plasmid interest
Sticky
ends Human DNA
3 Mix the DNAs; they join by base pairing. fragments
The products are recombinant plasmids and
many nonrecombinant plasmids.
Figure 20.4 Recombinant DNA plasmids

4 Introduce the DNA into bacterial cells that have a
mutation in their own lacZ gene.
Recombinant
bacteria
5 Plate the bacteria on agar containing

ampicillin and X-gal. Incubate until
colonies grow.
Colony carrying non- Colony carrying

recombinant plasmid recombinant plasmid
with intact lacZ gene with disrupted lacZ gene
Bacterial
clone
RESULTS Only a cell that took up a plasmid, which has the ampR gene, will reproduce and form
a colony. Colonies with nonrecombinant plasmids will be blue, because they can
hydrolyze X-gal. Colonies with recombinant plasmids, in which lacZ is disrupted, will be
white, because they cannot hydrolyze X-gal. By screening the white colonies with a
nucleic acid probe (see Figure 20.5), researchers can identify clones of bacterial cells
carrying the gene of interest.
Storing Cloned Genes in DNA Libraries
A genomic library made using bacteria
Is the collection of recombinant vector
clones produced by cloning DNA fragments
derived from an entire genome Foreign genome
cut up with
restriction
enzyme
or
Bacterial Recombinant
plasmids Recombinant
clones phage DNA Phage
clones
Figure 20.6 (a) Plasmid library (b) Phage library

Dideoxy chain-termination method for sequencing
DNA DNA
(template strand)
Primer
T 3
Deoxyribonucleotides Dideoxyribonucleotides
(fluorescently tagged)
G
5 T
C dATP ddATP
T
T 5
G dCTP ddCTP
APPLICATION The sequence of nucleotides in any cloned DNA A
C
DNA dTTP ddTTP
T polymerase
fragment up to about 800 base pairs in length can T dGTP ddGTP
be determined rapidly with specialized machines C
G
that carry out sequencing reactions and separate A P P P P P P
C G G
the labeled reaction products by length. A
A OH H
3
TECHNIQUE
This method synthesizes a nested set of DNA strands
Labeled strands
complementary to the original DNA fragment. Each 5
DNA (template 3
strand starts with the same primer and ends with a C strand) ddG
T ddA A
dideoxyribonucleotide (ddNTP), a modified G ddC C C
A ddT T T T
nucleotide. Incorporation of a ddNTP terminates a C ddG G G G G
growing DNA strand because it lacks a 3OH group, T
T ddA
ddA A
A
A
A
A
A
A
A
A
A
A
the site for attachment of the next nucleotide (see C ddG G G G G G G G
G C C C C C C C C
Figure 16.12). In the set of strands synthesized, each A ddC T T T T T T T T
T G G G G
nucleotide position along the original sequence is C
A G
G G
T
G G
T T T T T
T T
represented by strands ending at that point with the A T
T
T T T T T T T T
3
complementary ddNT. Because each type of ddNTP
is tagged with a distinct fluorescent label, the identity Direction
of movement
of the ending nucleotides of the new strands, and
of strands
ultimately the entire original sequence, can be
determined.
RESULTS The color of the fluorescent tag on each strand indicates

Laser Detector
the identity of the nucleotide at its end. The results can
be printed out as a spectrogram, and the sequence,
which is complementary to the template strand, can then
G
be read from bottom to top. (Notice that the sequence A
here begins after the primer.) C
T
G
A
A
G
Figure 20.12 C
Sanger Dideoxy Sequencing
The results are provided in the form of a

chromatogram
Amplifying DNA in Vitro: The Polymerase
Chain Reaction (PCR)
The polymerase chain reaction, PCR

Can produce many copies of a specific target
segment of DNA
Uses primers that bracket the desired
sequence
Uses a heat-resistant DNA polymerase
The PCR procedure
5 3
Target
sequence
APPLICATION With PCR, any specific segmentthe target Genomic DNA 3 5
sequencewithin a DNA sample can be copied many times
5 3
(amplified) completely in vitro.
1 Denaturation:
Heat briefly
to separate
DNA strands 3 5
TECHNIQUE The starting materials for PCR are double-
2 Annealing:
stranded DNA containing the target nucleotide sequence to be Cycle 1
Cool to allow
yields
copied, a heat-resistant DNA polymerase, all four nucleotides, 2 primers to Primers
and two short, single-stranded DNA molecules that serve as molecules hydrogen-bond.
primers. One primer is complementary to one strand at one end

of the target sequence; the second is complementary to the 3 Extension:
other strand at the other end of the sequence. DNA polymerase New
adds nucleotides nucleo-
to the 3 end of tides
each primer
RESULTS During each PCR cycle, the target DNA

sequence is doubled. By the end of the third cycle, one-fourth
of the molecules correspond exactly to the target sequence, Cycle 2
yields
with both strands of the correct length (see white boxes 4
above). After 20 or so cycles, the target sequence molecules molecules
outnumber all others by a billionfold or more.

Cycle 3
yields 8
molecules;
2 molecules
(in white boxes)
match target
sequence
Figure 20.7
Genome sequencing
Current estimates are that the human genome
contains about 20-40,000 genes but the number
of human proteins is much larger
Genetic (Linkage) Mapping: Relative Ordering of
markers
construct a linkage map then make a library of overlapping
clones and then determine the contiguous sequence
Chromosome
Cytogenetic map bands
Chromosome banding
pattern and location of
specific genes by
fluorescence in situ
hybridization (FISH)
Genes located
by FISH
1
Genetic (linkage)
mapping
Ordering of genetic
markers such as RFLPs,
simple sequence DNA,
and other polymorphisms
(about 200 per chromosome)
Genetic
markers
Physical mapping
Ordering of large over-
lapping fragments
cloned in YAC and BAC
vectors, followed by
ordering of smaller Overlapping
fragments cloned in fragments
phage and plasmid
vectors
3
DNA sequencing
Determination of
GACTTCATCGGTATCGAACT
nucleotide sequence of
each small fragment and
assembly of the partial
sequences into the com-
plete genome sequence
Figure 20.11
Practical applications of DNA technology
The practical applications of DNA
technology affect our lives in many ways
Numerous fields are benefiting from DNA
technology and genetic engineering
Diagnosis of disease
Forensic science
Gene therapy
Environmental and agricultural applications
Diagnosis of Diseases
Even when a disease gene has not yet been
cloned
The presence of an abnormal allele can be
diagnosed with reasonable accuracy if a
closely linked RFLP marker has been found
RFLP marker
DNA
Restriction Disease-causing
sites allele
Normal allele
Figure 20.15
The segment of DNA shown in the figure below has
restriction sites I and II, which create restriction
fragments A, B, and C. Which of the gels produced
by electrophoresis shown below would represent the
separation and identity of these fragments?
This restriction
fragment contains a
gene whose recessive
allele is lethal. The
normal allele has
restriction sites for the
restriction enzyme PstI
at sites I and II. The
recessive allele lacks
restriction site I. An
individual who had a
sister with the lethal
trait is being tested to
determine if he is a
carrier of that allele.
Indicate which of these
band patterns would be
produced on a gel if he
is a carrier
(heterozygous for the
gene)?
Forensic science
A DNA fingerprint is a specific pattern of
bands of RFLP or PCR markers on a gel
Blood from
Defendants defendants Victims
blood (D) clothes blood (V)
4 g 8 g
D Jeans shirt V
Figure 20.17
Gene therapy
Gene therapy using a retroviral vector
Cloned gene
(normal
allele, 1 Insert RNA version of normal allele
absent into retrovirus.
from
patients
cells) Viral RNA
2 Let retrovirus infect bone marrow cells

that have been removed from the
Retrovirus patient and cultured.
capsid
3 Viral DNA carrying the normal

allele inserts into chromosome.
Bone
marrow
cell from
patient
4 Inject engineered
Figure 20.16 cells into patient.
Transgenesis and cloning animals
P geneX T
Environmental Cleanup
Genetic engineering can be used to modify the metabolism
of microorganisms
So that they can be used to extract minerals from the environment
or degrade various types of potentially toxic waste materials
BP: Deepwater horizon, 5 million barrels of oil

Genetic Engineering in Plants
P geneX T
BT toxin and how it works
1. Insect eats Bt
crystals and spores.
2. The toxin binds to
specific receptors in the
gut and the insects stops
eating.
3. The crystals cause the
gut wall to break down,
allowing spores and
normal gut bacteria to
enter the body.
4. The insect dies as
spores and gut bacteria
proliferate in the body.
Next generation Genetics
Epigenetics
Next generation sequencing
What is epigenetics?
Epigenetics is the study of heritable

changes in gene activity that occur in the
absence of any changes to the DNA
sequence itself.
Identical twins dont look identical later in life

Epigenetics: The ghost in your genes.
Study 1
Small isolated region verkalix, Sweden
Prone to famine and excellent birth and death records for centuries
Mortality of the children linked to food supply of parents and
grandparents
When the father was exposed to famine during pre-puberty, his children
and grandchildren exhibited protection against cardiovascular disease and
diabetes.
When grandmother experienced a famine the opposite was found, ie her

children and grandchildren had a lower life expectancy.
Study 2
PTSD from September 11 disaster
Pregnancy in 3rd trimester
Changes in stress hormone levels in child's saliva
EPIGENETIC Changes
Changes to chromatin that are passed on from
generation to generation
Next-generation sequencing
2nd generation 3rd generation

Next generation genetics; pros and cons
The potential benefits?
Potential concerns?

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