1.1What is Life?

Biology Comes from the Greek bio, meaning life, and logy, meaning
the study of.
Organisms share common characteristics that, taken together, define life:
o Acquire and use materials and energy
o Actively maintain organized complexity
o Sense and respond to stimuli
o Grow
o Reproduce
o Evolve, collectively
Cell
o Basic unit of life
o The cell is the smallest unit of life
o Separated from surroundings by a membrane
o Encloses a variety of structures and chemicals in a fluid environment
Unicellular
o Exists as a single cell
Multicellular
o Exists as a collection of at least two cells
o Although the most abundant organisms on Earth are Unicellular, the
qualities of life are more easily visualized in multicelluar organisms such
as this water flea.
Organisms acquire and use materials and energy
o Important materials (minerals,, water, other simple chemical building
blocks) are acquired from air, water, soil bodies of other living things
o Organisms use energy continuously
o Obtained in two ways: Photosynthesis and consumption
o Photosynthesis - Is the process by which plants and some single-celled
organisms capture sunlight
o Other organisms consume energy-rich molecules in bodies or body parts
The flow of energy and the recycling of nonliving nutrients
o Energy flows in a one-way path from the sun to photosynthetic organisms
to all other forms of life
o Some energy is lost as heat at each transfer from one organism to another,
making less energy available with each transfer.
Organisms actively maintain organized complexity
o Living things continuously use energy to maintain themselves
Cells pump chemicals in and out, allowing necessary chemical
reactions to occur
Cells and organisms maintain relatively constant internal
conditions, or homeostasis
Organization tends to disintegrate unless energy is used to
maintain it.
Organisms maintain relatively constant internal conditions
 Organisms sense and respond to internal and external stimuli
o Sensory organs in animals can detect and respond to external stimuli such
as light, sound, and chemicals
o Internal stimuli in animals are perceived by stretch, temperature, pain, and
chemical receptors
o Plants, fungi, and bacteria respond to stimuli as well
o Animal example: When your brain detects a low level of sugar in your
blood (an internal stimulus), it causes your mouth to water at the smell of
food (an external stimulus).
o Plant example: Plant shoots grow toward light but away from gravity.
Organisms grow
o Every organism becomes larger over time
o Plants and animals grow by producing more cells and increasing cell size
to ultimately increase their mass
o Bacteria grow by enlarging their cells (then divide to reproduce)
o Growth involves conversion of acquired materials into molecules of the
organisms body
Organisms reproduce
o Organisms reproduce by dividing in half, producing seeds, bearing live
young, laying eggs
o Deoxyribonucleic acid (DNA) of parent(s) is passed on to offspring
Organisms, collectively, have the capacity to evolve
o Modern organisms descended, with modifications, from preexisting forms
of life
o Changes in DNA within a population occur over generations, which may
result in evolution
Population = group of the same type of organism living in the
same area
 1.2What is Evolution?

Genetic change in a population over time

o Theory of evolution explains how life on Earth has diversified
Darwin and Wallace (naturalists)
Supported by wide variety of evidence over time
Similarities are found among different types of organisms as a result of
common ancestry
o Similarities between chimpanzees and people
Anatomy
Physiology
DNA (< 5% different)
Embryology
Behavior
DNA of humans differs from that of chimpanzees by less than
5%
o Yeast and bacteria have many of the same genes as humans also.
o At least 65 human genes can be substituted for the same yeast gene-
Ortholog
Three natural processes underlie evolution:
o Mutation can lead to genetic variation among members of a population
o Inheritance of traits by offspring
o Natural selection of traits that allow certain individuals to survive and
reproduce better than others in a given environment
Genetic variation = difference in genes
o Specific segments of DNA
o Basic unit of heredity
o Examples: eye color, hair color, roll tongue
Mutations occur when changes in genes are mistakenly copied
o Mutations are a source of differences in DNA.
o Some mutations are inherited
Occur in parent sperm or egg cells
Are passed on to each offspring cell
o Can result from DNA damaged by
Ultraviolet rays
Toxic chemicals
o Effects of mutations:
Neutral = silent mutation
No effect or harmless
Common
Disadvantageous
Death or poor reproductive success
Advantageous
Enhanced survival/reproduction
Natural selection
o Process or mechanism
 o Organisms with certain inherited traits survive and reproduce better
than others in a particular environment
Organisms that best meet environmental challenges leave the
most offspring
Natural selection preserves genes that help organisms flourish
Natural selection is the mechanism by which evolution most
often occurs. (There are other types of selection.)
Adaptations
o Structures, physiological processes, or behaviors that aid in survival
and reproduction
o May fit in one environment but not in another
o Lack of adaptation can lead to extinction
Complete elimination of a particular species
Dinosaurs (excluding birds) suffered mass extinction when the
environment changed beyond their adaptations.

How did lifes diversity on Earth arise?

o Diversity of habitats coupled with selection produce species variety or
species richness
o Populations become fragmented, and subgroups are subject to different
environmental pressures
May lead to distinct species over time
Species = group of organism of the same type that can
interbreed.

Humans often accelerate the rate of environmental change

o Burning fossil fuels
o Global climate change
o Habitat loss
Since advantageous mutations are relatively rare, human activities often drive
extinction

Questions
1.) Which of the following can evolve?
a. An individual
b. An organism
c. Habitats
d. Populations
2.) In evolutionary biology, adaptation is best
defined as
a. Reversible adjustment by an individual.
b. Evolved traits that enhance an organisms survival or
reproduction.
c. Genetic variation.
d. Neutral mutation.
 1.3 How Do Scientists Study Life?

Life can be studied at different levels

o All matter is formed of elements
o Atom = smallest particle of an element retaining properties of an element
o Atoms combine to form molecules
o Molecules provide building blocks for each cell, the smallest unit of life
o Cells combine to form tissues
o Tissues combine to form organs, which can be united as organ systems
o Multicellular organisms are composed of multiple organ systems
o Group of organisms belonging to the same species and living together =
population
o Interacting populations make up a community
o A community + its nonliving environment = ecosystem
o Entire surface of Earth, including living and nonliving components =
biosphere
Biologists classify organisms based on their evolutionary relationships
o Three major groups, or domains:
Bacteria (prokaryotic)
Bacteria are single, simple cells.
Archaea (prokaryotic)
Archaea are single, simple cells.
Eukarya (eukaryotic)
Eukaryotic organisms have one or more extremely complex
cells.
The domain Eukarya contains four subdivisions or
kingdoms
o Fungi
o Plantae
o Animalia
o Protists
o Fundamental differences among cell types
Cells share common features
o All cells
Plasma membrane = thin sheet of molecules surrounding cell
All cells contain DNA (hereditary material)
Eukaryotic (true nucleus)
o Larger than prokaryotic cells
o Organelles = membrane-bound structures that carry out specific functions
complex
Nucleus = organelle containing cells DNA
o Unicellular and multicellular species
o Domain Eukarya
Protists, plants, fungi, animals
Prokaryotic (before nucleus)
o Smaller than eukaryotic cells
 o Lack membrane-bound organelles simple
o Only unicellular
o Domains Bacteria and Archaea
Biologists use a binomial (two names) system
o Genus (many species) and species
o First letter of genus capitalized
o Both terms italicized
Common name: water flea
Scientific name: Daphnia longispina
 1.4What Is Science

Science
o Systematic inquirythrough observation and experimentinto the
origins, structure, and behavior of living and nonliving environments
Three principles
o Events have natural causes
o Laws do not change over time or distance
o Findings are value neutral; independent of bias
Scientific method
o Important tool of scientific inquiry; six interrelated elements
Observation
Question
Hypothesis
Prediction
Experiment
Conclusion
o Observation of a specific phenomenon
The car wont start.
Observation, in turn, leads to a question.
Why wont the car start?
After referring to prior research, thinking, recalling prior
experience, and/or conferring with colleagues, a hypothesisan
informed explanationis formed.
The battery may be dead.
o A prediction, based on the hypothesis, is made.
If the battery is dead, then a jump-start should start the car.
o The prediction is tested in an experiment.
Attach jumper cables.
o A conclusion refutes or supports the hypothesis.
If the car starts, the hypothesis is supported.

Biologists test hypotheses using controlled experiments

o Two types of situations are established
Control
Baseline
All possible variables are held at a constant
Experimental
One variable is manipulated
Often compared using statistics
o Experiments must
Be repeatable, even by others
Include replicates
o Science is useless unless communicated
o Because it is seldom possible to control for all variables or all possible
effects, science mandates that conclusions are always subject to revision.
 Scientific theory
o General and reliable explanation of important natural phenomena
o Developed through extensive and reproducible observations and
experiments
o New scientific evidence may prompt radical revision of existing theory
o A scientific theory is best described as a natural law, a basic principle
derived from the study of nature that has never been disproven by
scientific inquiry
Law describes a predictable (always the same under given
conditions) phenomenon; does NOT provide an explanation;
often expressed by a mathematical formula
Theory IS an explanation; not expressed by a formula
Examples: Cell Theory, Theory of Evolution
Each creature on Earth was separately created cannot be
subjected to scientific inquiry because it is a belief rooted
in faith
o Cell theory
All organisms are composed of cell(s)
o Scientific theories arise through inductive reasoning
Generalization based on many observations that support it and
none that contradict it
Every organism is made of cells and anything not made of cells are
not organisms
Inductive reasoning (cell theory): All organisms that possess the
characteristics of life are composed of cell(s), AND nothing not
composed of cells shares all of these attributes.
o Scientific theories support deductive reasoning
Generalization used to make predictions
It is an organism so it must be made of cells
Deductive reasoning (cell theory): A newly discovered entity
exhibiting all characteristics of life can be hypothesized to be
composed of cells.
https://www.livescience.com/21569-deduction-vs-induction.html
Science is a human endeavor
o Accidents, lucky guesses, controversies with competitors, curiosity can
contribute to scientific advances
o Alexander Flemings culture became contaminated with Penicillium
(mold), but bacteria did not grow near the mold, leading to the discovery
of the first antibiotic medicationpenicillin.
Spontaneous generation
o Emergence of life from nonliving matter
o Commonly accepted in 1600s that maggots on meat generated
spontaneously
 2.1 What Are Atoms?

Elements
o Cannot be broken down into simpler substances
o Cannot be converted into other substances by ordinary chemical reactions
Processes that form or break binds between atoms
o Form all matter
o 92 occur naturally
Atom
o Smallest unit of an element
o Retains all the chemical properties of that element
o Composed of subatomic particles
Uncharged neutrons
Positively charged protons
Negatively charged electrons
o As a whole, neutral, as charges balance each other
Subatomic particles are measured in atomic mass units
o Protons and neutrons each have a mass unit of 1
o Mass of electrons is negligible (so small)
Mass number
o Total number (equal to total mass) of the protons and neutrons contained
in the nucleus of an atom
Electrons are in constant motion about the nucleus
Atomic number
o Number of protons in the nucleus
For example, hydrogen atoms have one proton, so the atomic
number for hydrogen is one
o Defines each element
For example, carbon has six protons and oxygen has eight
Periodic Table of the Elements
o Every hydrogen atom has one proton, every carbon atom has six, and
every oxygen atom has eight, giving these atoms atomic numbers of 1, 6,
and 8, respectively. The periodic table (Appendix II) organizes the
elements according to their atomic numbers (rows) and their general
chemical properties (columns).
Isotopes
o Atoms of the same element with different numbers of neutrons
o Distinguished by different mass numbers
o Some are radioactive (spontaneously break apart, releasing energy) and
are used in research
o Radioactive isotopes are used in radioactive dating (of mummies, ancient
trees, skeletons, artifacts), tracing physiological pathways, treating cancer
(radiation therapy), and imaging.
Nuclei and electrons play complementary roles in atoms
 o Nuclei provide stability by resisting external forces (energy, heat,
electricity)
o Electrons are dynamic
Can capture and release energy
Can forms bonds, linking atoms
For example, the stable nuclei of a carbon atom (12C) keeps its
carbonic identity regardless of the different structures in which it
may be found.
Electrons occupy electron shells
o Three-dimensional regions around nucleus
o Each has a specific energy
o The farther from the nucleus, the greater the amount of energy stored in
the electrons occupying that shell
Energy (heat, light) can excite an atom
o Can cause an electron to jump from a lower-energy electron shell to a
higher-energy shell
o Soon afterward, the electron falls back into its original shell, releasing the
extra energy
o Life depends on electrons capturing and releasing energy
Examples: incandescent light bulb, photosynthesis (photosystems).
Each electron shell holds a specific number of electrons
o Shell nearest the nucleus can hold up to two
o More distant shells can hold up to eight (some more)
Electrons fill the lowest-energy shell (nearest nucleus) first
As atomic number increases, electrons fill shells increasingly distant from the
nucleus
o Protons and electrons are balanced
o The two electrons in helium occupy the first electron shell. A carbon
atomwith six electronswill have two electrons filling its first shell and
four occupying its second shell, which can contain a total of eight
electrons.
 2.2 How Do Atoms Interact to Form Molecules?

Molecules
o Two or more atoms
o From the same or different elements
o Held together by interactions among their outermost electron shells
o Comprise matter
For example, hydrogen and oxygen are linked to form water (H2O
is two atoms of hydrogen and one atom of oxygen).
Table salt is another example (NaCl); it is one atom of sodium and
one atom of chloride).
An atom will not react with other atoms if the outermost shell is completely
empty or full
o Stable, inert
An atom will readily react if the outermost shell is only partially full (features a
vacancy)
o Reactive
o Somefree radicalsare so reactive that they pull other molecules apart
Can contribute to aging, even death
Example: Neon, with eight electrons in the outermost shell,
is full and, therefore, inert. Oxygen, with six electrons in its
outermost shell, can hold two more electrons, and so is
susceptible to reacting.
Chemical bonds hold atoms together in molecules
o Three major types
Ionic bonds
Covalent bonds
Hydrogen bonds
Atoms, including those that are reactive, have equal
numbers of protons and electrons. The equal number of
protons and electrons gives atoms an overall neutral charge,
but that does not make them stable.
An atom with an almost empty outermost electron shell can
become more stable by losing electrons and completely
emptying the outer shell; this gives it a positive charge. An
atom with a nearly full outer shell can become more stable
by gaining electrons and filling the shell completely, giving
it a negative charge. Hydrogen and oxygen atoms gain
stability by interacting with each other. Single electrons
from each of two hydrogen molecules fill the outer shell of
an oxygen atom to form a water molecule.
Ion
o An atom that has lost or gained electron(s), acquiring an overall positive
or negative charge
 Oppositely charged ions that are attracted to each other are bound into molecules
by ionic bonds
o Giving and taking of electrons
o Usually a metal and a non-metal
Atoms that have lost electrons become positively charged ions
(e.g., sodium: Na).
Atoms that have gained electrons become negatively charged ions
(e.g., chlorine: Cl).
Atoms with partially full outermost electron shells will likely form covalent
bonds
o Most biological molecules
o Sharing of electrons
o Generally stronger than ionic bonds
o Two types
Nonpolar covalent bonds
Polar covalent bonds
Because biological molecules must function in a watery
environment where ionic bonds rapidly dissociate (break
down), the atoms in most biological molecules, such as
those found in proteins, sugars, and fats, are joined by
covalent bonds.
Nonpolar covalent bonds
o Can be formed between atoms of the same element
o May also form between some atoms of different elements with a similar
electronegativity
o No charge on any part of the molecule formed
o Equal or nearly equal sharing of electrons
Nuclei pull equally
o O2, N2, H2, CO2
Polar covalent bonds
o Form when one nucleus attracts electrons more strongly
o Molecule has charged poles
o Unequal sharing of electrons
o H2O
o Often between H and O or H and N in biological molecules
Hydrogen bonds
o Attraction between slightly positive and slightly negative poles of adjacent
polar moleculeslike water
Partially positive H atom of one water molecule is attracted to the
partially negative O atom of another
Give water unique properties
o Comparatively weak but collectively strong
o Polar biological molecules can form hydrogen bonds with water, with
each other, or even within the same molecule.
 2.3 Why Is Water So Important to Life?

Hydrogen bonds among water molecules cause cohesion

o Molecules of a single type tend to stick together
o Droplet formation; flow
o Produces surface tension
Surface of water tends to resist being broken
Water exhibits adhesion
o Molecules of a different types tend to stick together
Water adheres to molecules with charged regions (ions, other polar
molecules)
o Responsible for capillary action
Movement of water into very narrow spaces
Large plants, like trees, depend on cohesion and adhesion to supply water to all
parts of the plant
o Hydrogen bonds cohering water molecules inside the vessels of the tree
allow the water to overcome gravity
o Hydrogen bonds adhering water molecules to the walls of vessels allow
capillary action against gravity
Solvent
o Completely surrounds and disperses individual atoms or molecules of
another substance
Dissolves, yielding a solution
Water is an excellent solvent
o Positive and negative poles of water attract other polar molecules and ions
Hydrophilic (water-loving)
Water as a solvent
Table salt is held together by ionic bonds between
positively charged sodium ions and negatively charged
chloride ions. When a salt crystal is added to water, the
positively charged hydrogen poles of water molecules are
attracted to the chlorine ions, and the negatively charged
oxygen poles are attracted to the sodium ions. Water
molecules surround the ions, preventing them from
interacting with each other: the salt dissolves.
Water is an excellent solvent but not a universal one
o Larger, nonpolar molecules will not dissolve in water
Hydrophobic (water-fearing)
Fat, oils
Phospholipids
Water moderates the effects of temperature changes
o Water has a high specific heat
Energy input must be high enough to break hydrogen bonds and
excite hydrogen molecules
Water resists temperature change
Water moderates the effects of temperature changes
 o Water has a high heat of vaporization
Heat of vaporization = amount of heat needed to cause a
substance to evaporate (change from liquid to vapor).
Energy input must be high enough to break hydrogen bonds and
allow liquid to evaporate
o Water in sweat absorbs excess body heat, cooling us as it evaporates
Water forms an unusual solid: ice
o Most substances become denser when they solidify from a liquid
o Ice is unusual because it is less dense than liquid water
Water molecules spread farther apart than their average distance in
liquid
o Icebergs and ice cubes float
Water-based solutions can be acidic, basic, or neutral
o Small fraction of water molecules break apart into hydroxide and
hydrogen ions
H2O OH + H+
o Pure water contains equal concentrations of OH and H+ (neutral)
o When substances that release OH or H+ are added to water, the solution
no longer has an equal concentration
Solutions in which H+ > OH are acidic
An acid releases H+ when dissolved in water
o For example, hydrochloric acid ionizes in water
HCl H+ + Cl
o H+ exceeds the concentration of OH in the solution
o Lemon juice, vinegar
Solutions in which OH > H+ are basic
A base combines with H+ when dissolved in water
o For example, sodium hydroxide ionizes in water
NaOH Na+ + OH
OH exceeds the concentration of H+ in the solution
Baking soda, chlorine bleach, ammonia
pH scale measures the H+ concentration of a solution
o pH 06 is acidic (H+ > OH)
o pH 7 is neutral (H+ = OH)
o pH 814 is basic (OH > H+)
Buffer
o Molecule that helps maintain nearly constant pH of a solution
Accepts or releases H+ in response to small changes in H+
concentration
In excess H+, a buffer combines with H+
In excess OH , a buffer releases H+
A change in pH can alter the structure and function of biological
molecules.
pH of body fluids is maintained by several different buffers (e.g.,
bicarbonate).
 If the blood becomes too acidic, bicarbonate accepts (and absorbs)
H to make carbonic acid:
HCO3 H H2CO3
bicarbonate + hydrogen ion carbonic acid
If the blood becomes too basic, carbonic acid liberates hydrogen
ions to combine with OH to form water:
H2CO3 OH HCO3 H2O
carbonic acid + hydroxide ion bicarbonate + water
 3.1 Why is Carbon So Important in Biological Molecules?

Organic molecules
o Always contain carbon
Often many carbon atoms are connected in a skeleton or backbone
In this backbone, carbon atoms are the vertebrae.
o Often also contain oxygen and hydrogen
o Many are synthesized by organisms
o Many are quite complex (chains, sheets, rings, helices)
Inorganic molecules
o Lack a carbon backbone
o Many lack carbon altogether
o Many are simpler than organic molecules
Biological molecules
All molecules produced by living things
o Both organic and inorganic
o Nearly all are based on carbon
o Biologically important
Function groups
o Commonly occurring atoms or groups of atoms
o (Attachment on a power tool)
o Attached to carbon backbone of organic molecules
o Less stable than carbon backbone
More likely to react
Hydroxyl
Carbonyl
Carboxyl (Ionized form)
Amino
Sulflydryl
Phosphate (Ionized form)
Methyl
3.2 How Are Large Biological Molecules Synthesized?

Monomers
o Small organic subunits
Polymers
o Chains of monomers
o Formed by dehydration synthesis reactions
o Broken by hydrolysis reactions
Dehydration synthesis
o Removing water to put together
o Monomers joined
One monomer loses a hydrogen ion (H+)
Second loses a hydroxide ion or hydroxyl group (OH-)
 Monomers link covalently at open electron sites and water is
formed
Hydrolysis
o Water break apart
o Polymer broken apart into its original subunits
o Water donates a H+ to one subunit and a )H- to the other
o Energy stored in chemical bonds is released
o Digestion
Biological molecules fall into one of four categories
o Carbohydrates
o Proteins
o Nucleotides/nucleic acids
o Lipids
 3.3 What Are Carbohydrates?

Carbohydrate molecules
o Approximate ratio of 1C:2H:1O
o Monomers are small, hydrophilic sugars
Monosaccharide = just one sugar
Disaccharide = two Monosaccharides
Polysaccharide = many Monosaccharides
The plasma membrane that surrounds each cell is studded with
proteins to which carbohydrates are attached
Monosaccharides
o Backbone of three to seven carbon atoms, most with both H+ and OH-
attached
o Approximate chemical formula (CH20)
o Glucose (six carbons): Most common sugar In organisms and primary
energy source of cells
o Fructose (six carbons): energy in fruit
o Galactose (six carbons): energy in milk
o Ribose and deoxyribose (five carbons): RNA, DNA
Disaccharides
o Two Monosaccharides linked by dehydration synthesis
o Often used for short-term energy storage in plants
o Hydrolyzed and converted into glucose when energy is needed
o Sucrose (table sugar) = Glucose + Fructose
o Lactose (milk sugar) = Glucose + Galactose
o Maltose (malt sugar) = Glucose + Glucose
Polysaccharides are chains of monosaccharides
o Do not dissolve readily
Polar hydroxyl groups are lost during dehydration
o Starch
Energy storage; formed in roots and seeds
Branched
Up to 500,000 glucose subunits
o Glycogen
Primarily in animals
Energy storage; found in liver and muscles
Muchmore branched than starch
Polymer of glucose (like starch)
o Cellulose
Primarily in plants
Structural support
Comprises plant cell walls, cotton bolls
May be the most abundant organic molecule
Polymer of glucose
Some vertebrates harbor cellulose-digesting microbes
Cows
 Passes through as roughage in others
o Chitin
Structural support
Comprises arthropod exoskeletons, fungal cell walls
Similar to cellulose but also bears nitrogenous function groups
 3.4 What Are Proteins?

Proteins have a variety of functions

o Enzymes catalyze specific chemical reactions
o Structural proteins (keratin)
o Notational (albumin, casein)
o Transport (hemoglobin)
o Contractile (actin, note)
o Hormones (insulin, growth hormone)
o Antibodies
o Toxins (snake venom)
o Proteins are polymers of amino acids
Each with a central carbon bonded to a hydrogen atom and three
functional groups
Amino group, -NH2
Carboxylic acid group, -COOH
One of 20 different R groups
o R group is similar functional groups
o R group gives each amino acid distinctive
properties
Hydrophilic
Hydrophobic
Form disulfide bonds
The amino acid cysteine is unique in
having a sulfur-containing
(sulfhydryl) R group that can form
covalent disulfide bonds with the
sulfur of another cysteine molecule.
Proteins are formed by dehydration synthesis
o N in amino group of one amino acid covalently bonded to C in carboxylic
acid group of another
Peptide bond
Peptide
Up to 50 amino acids
Polypeptide
Polypeptide chains can be up to thousands of amino acids in
length. A protein consists of one or more polypeptide chains.
Interactions among amino acids and R groups cause twists, folds, interconnections
o Give protein a 3D structure; up to four levels
Primary: sequence of amino acids; determined by DNA
Secondary: Hydrogen bonds within polypeptide; helix or pleated
sheet
Tertiary: Further folded; determined by structure and environment
Quaternary: Linked tertiary subunits
Function is determined by structure
 o Precise position of amino acids determines secondary and tertiary
structure
Determines how regions of protein interact with each other as well
as other molecules
o Intrinsically disordered proteins have exceptionally flexible structures
Versatile functions
Function is determined by structure
o Denatured proteins
Disruption of tertiary or secondary structure
Primary structure left intact
Function lost
 3.5 What Are Nucleotides and Nucleic Acids?

Nucleotide
o Five-carbon sugar (Ribose or deoxyribose)
o Phosphate group
o Nitrogenous base
Single ring
Thymine, uracil, cytosine
Double ring
Adenine, guanine
o Nucleotides may act as
Genetic storage
Critical energy carries
Intracellular messengers
Subunits of nucleic acid polymers
Adenosine Triphosphate (ATP)
o Ribose nucleotide with three phosphate groups
o Formed by reactions that release energy
Breakdown of carbohydrates and sugars
o Stores energy in bonds between phosphate groups; releases energy when
one of those bonds is broken
Energy drives reactions
Polymerization
NAD+ and FAD
o Transport energy in the form of high-energy electrons
o Active in ATP synthesis, when cells break down sugars
Cyclic adenosine monophosphate (cAMP)
o Messenger molecule
o Initiates series of biochemical reactions
Nucleic acids are polymers of nucleotides
o Formed by dehydration synthesis
o The oxygen in the phosphate group of one nucleotide is covalently bonded
to the sugar of another
Deoxyribonucleic acid (DNA)
o Two strands, twined and linked by hydrogen bonds
o Double Helix
o Genetic material of all cells
o Sequence of deoxyribose nucleotides spells out the recipe for proteins
Ribonucleic acid (RNA)
o Single strands of ribose nucleotides
o Copied from DNA
o Direct protein synthesis
 3.6 What Are Lipids

Lipids
o Diverse group of molecules that contain hydrophobic regions composed
almost entirely of H and C
Insoluble in water
o Not formed by linking monomers into polymers
o Lipids serve a variety of functions
Energy storage
Waterproofing
Primary component of cellular membranes
Hormones
o Lipids fall into three major groups
Oils, fats, waxes
Contain only C,H, and O
Contain one or more fatty acid chains
o Long chains of C and H with a carboxylic acid
functional group at one end
Phospholipids
Steroids
o Fats and oils
Formed by dehydration synthesis
Three fatty acid chains
One molecule of glycerol
o Triglycerides
Energy-rich
o More than twice as many calories per unit as
carbohydrates and proteins
o Fats
Produced primarily by animals
Solid at room temperature
C atoms of fatty acid chains are linked by single bonds
Saturated
o As many H atoms as possible
Straight and closely packed
o Oils
Produced primarily by plants
Liquid at room temperature
Some C atoms of fatty acid chains are linked by double bonds
Unsaturated
o Fewer than maximum H atoms possible
Kinked and more loosely packed
The commercial process of hydrogenationwhich breaks some of
the double bonds and adds hydrogens to the carbonscan convert
liquid oils to solids, but with health consequences.
o Hydrogenation
 Artificially breaks some double bonds and adds hydrogens
Converts liquid oils to solids
Trans fat
Extends shelf life, but encourages arterial cholesterol deposition
o Waxes
Chemically similar to fats
Most animals lack enzymes to digest waxes
Highly saturated
Solid at outdoor temperatures
Water-repellant
Leaves and stems, bird feathers, honeycomb
o Phospholipids
Comprise plasma membranes
Chemically similar to oil but with dissimilar ends
Two hydrophobic fatty acid tails
Hydrophilic phosphate-nitrogen head
o Steroids
Four rings of carbon atoms sharing one or more sides, with various
functional groups attached
Example: Cholesterol
Vital component of nerve cell insulation
Used to synthesize other steroids
o Estrogens
o Testosterone
 4.1 Cell Structure and Function

Cell theory
o Every organism is made up of at least one cell
o The smallest organisms are unicellular, and cells are the functional units of
multicellular organisms
o All cells arise from preexisting cells; this means that cells are the basic units
of life

4.2 What Are the Basic Attributes of Cells?

Most cells range in size from about 1 to 100 micrometers (millionths of a meter) in
diameter
Cells are so small to ensure access to their environment
Many nutrients and wastes move in and out of cells by diffusion
o Molecules dissolved in fluids disperse from regions where their
concentration is higher to regions where their concentration is lower
All cells share common features
o Plasma membrane
o Cytoplasm
o DNA as hereditary blueprint
o RNA to copy the genetic blueprint and guide construction of proteins
Plasma membrane
o Phospholipid bilayer interspersed with cholesterol
Barrier between interior and exterior of cell
o proteins
Communication portals
Regulate passage of molecules and ions
Cytoplasm
o All the fluid and structures inside the plasma membrane but outside the
nucleus
o Site of most biochemical reactions that support life
Cytosol
o Fluid portion of cytoplasm
o Water, salts, organic molecules
Cytoskeleton
o Protein filaments
o Assists in support, transport, shape, locomotion, cell division
Deoxyribonucleic acid (DNA)
o All cells
o Hereditary blueprint
o Gene segments
Store information
Construction of proteins
Production of new cells
 Ribonucleic acid (RNA)
o Chemically similar to DNA
o Copies genes
o Helps construct proteins
On ribosomes
Cellular workbenches of specialized RNA
o Ribosomal RNA
Two basic types of cells:
o Prokaryotic (before nucleus) cells form the bodies of bacteria and
archaea, the simplest forms of life
No nuclei
o Eukaryotic (true nucleus) cells form the bodies of animals, plants, fungi,
and protists
Far more complex
Nuclei
 4.3 What Are the Major Features of Prokaryotic Cells?

Prokaryotic cells
o Unicellular
o Relatively simple internal structure
Not compartmentalized like eukaryotic cells
o On average, 100x smaller than eukaryotic cells
Domain Archaea
o Many Archaea are extremophilic
o None are known to cause disease
Domain Bacteria
o Even more diverse
Prokaryote shapes include rod-shaped bacilli, spiral-shaped spirilla, and spherical
cocci
Prokaryotic cells have specialized surface features
o Nearly all have a cell wall
Stiff protective coating
Contains peptidoglycan in bacteria
o Some produce adhesive capsules, slime layers, and/or attachment pili
o Pili are surface proteins projecting from the cell wall; they may be short and
numerous (attachment pili) or long and few (sex pili).

o Many form sex pili for transfer of plasmids
o A plasmid is a small ring of DNA.
o Some feature flagella for propulsion
Prokaryotic cells have specialized cytoplasmic structures
o Nucleoid
A region that is not enclosed by a membrane
Contains a single circular strand of DNA
o Most also feature plasmids outside the nucleoid
o Food granules
o Some have internal folds to harness light energy
 4.4 What Are the Major Features of Eukaryotic Cells?

Eukaryotic cells
o Unicellular and multicellular species
o Organelles within cells
Specialized membrane-enclosed structures
o Domain Eukarya
Extracellular matrix (ECM)
o Reinforces plasma membrane
o Sits just outside the plasma membrane
o In animals, includes supporting and adhesive proteins as well as chemical
signals in a polysaccharide gel
o The ECM may differ from one tissue to another and from one species to
another.
o In plants, the ECM is the cell wall
Overlapping cellulose fibers
Perforated by plasmodesmata
Connect adjacent cells
Cytoskeleton proteins
o Within the cytoplasm
o Three major types
Thin microfilaments of actin protein
Medium-sized intermediate filaments of various proteins
Thick microtubules of tubulin protein
Cytoskeleton proteins
o Can alter cell shape
By shortening, lengthening, or sliding past each other
Requires energy (ATP)
o In animal cells, a scaffolding of intermediate filaments supports the cell, helps
determine its shape, and links cells to one another and to the ECM. An array
of microfilaments concentrated just inside the plasma membrane provides
additional support and also connects with the surrounding ECM.
o Can elicit movement
May lengthen one end while shortening the other
May act as railroad tracks for motor proteins moving molecules or
organelles within the cell
May be pulled by motor proteins (as in muscle cells)
o Participate in cell division
Guide chromosome movements
Pinch dividing cell into two daughter cells
Cilia and eukaryotic flagella
o Beating hair-like structures
o Coated in plasma membrane
o Supported and moved by cytoskeletal and motor
proteins
 o Each contains a ring of nine fused pairs of microtubules
surrounding an unfused pair
Basal body = uncoated portion extending into cytoplasm
Composed of nine fused triplets and no central pair
Produced by centrioles
o The structure of prokarytotic and eukaryotic flagella differs greatly.
Cilia
o Beat in unison, like oars
o Shorter and more numerous than flagella
Flagellum
o Rotate in a corkscrew motion, like a propeller
o When present, there are usually one or two
Protists use cilia or flagella to swim through water
In animals, cilia usually move fluids past a surface
o Gills of oysters
o Female reproductive tract of vertebrates
o Respiratory tract of most terrestrial vertebrates
Most animal sperm cells are propelled by flagella
Nucleus
o Large organelle
o Houses DNA
o major parts
Nuclear envelope
Chromatin
Nucleolus
Nuclear envelope
o Isolates nucleus from rest of the cell
o Double membrane
o Perforated by nuclear pores
Passage of large molecules is regulated by the nuclear pore complex
(gatekeeper proteins lining each pore)
o Studded on outer surface by ribosomes
o Continuous with membranes of endoplasmic reticulum
Chromatin
o Nuclear material within nucleus
o Composed of chromosomes
DNA molecules and their associated proteins
Extremely long, indistinguishable strands when a cell is not dividing
(most of the time)
Condensed, distinct during cell division
Genes
o Specific sequences of nucleotides
o Molecular blueprint for synthesis of proteins and ribosomes
Some proteins provide structure
Some regulate movement of materials through membranes
Some act as enzymes
 Protein synthesis occurs in the cytoplasm, but DNA is confined
to the nucleus
o Copies of genes must be ferried from nucleus to cytoplasm
Genes are copied from DNA to messenger RNA (mRNA)
mRNA moves through nuclear pores into cytosol
mRNA is translated into protein on ribosomes
Nucleolus (plural, nucleoli; meaning little nuclei)
o At least one per nucleus
o Site of ribosome synthesis
o Composed of ribosomal RNA (rRNA), DNA, proteins, and ribosomes
Ribosomes
o Small particles of rRNA and proteins
o Workbench for protein synthesis
o Some appear as singletons in cytoplasm
o Some (polyribosomes) are strung together in cytoplasm
o Some stud the membranes of the nuclear envelope and rough endoplasmic
reticulum
Endomembrane system
o Internal membranes loosely connecting compartments
o Segregates molecules and orders biochemical processes
o Includes the nuclear envelope, vesicles, endoplasmic reticulum, Golgi
apparatus, and lysosomes
Vesicles
o Temporary sacs, tagged with mailing label amino acids by rough
endoplasmic reticulum, that ferry molecules with the help of motor proteins
o Bud from and fuse with the endomembrane system and plasma membrane
Exocytosis = fusion with plasma membrane to export the vesicles
contents outside the cell
Endocytosis = in-pocketing of plasma membrane to surround material
with a vesicle and import it
Endoplasmic reticulum (ER)
o Labyrinth of narrow channels forming interconnected sacs and tubules
o Typically makes up at least 50% of the total cellular membrane
o Important in the synthesis, modification, and transport of molecules
o Has both rough and smooth membranes, continuous with each other
Rough ER
o Continuous with nuclear envelope; both are ribosome-studded
As proteins are synthesized on ribosomes, some are extruded into the
ER
Some proteins remain within
Many proteins are modified, properly folded, and sent to the
Golgi apparatus (via vesicles)
Others, on the outside of the rough ER, function in synthesis of
new phospholipid membrane
Smooth ER
o Lacks ribosomes
 o Also involved in synthesis of new membrane
o In some cells, produces other lipids, converts glycogen, stores ions, or breaks
down harmful molecules
Golgi apparatus (or simply Golgi)
o Flattened, interconnected sacs
o Gives final touches to synthates
Sorting
Mailing labels
Placement into vesicles
o Vesicles from the rough ER fuse with receiving face; vesicles carrying final
product bud off shipping face
Lysosomes
o Membrane-bound sacs
o Hydrolyze various biological molecules when fused with a food vacuole
Food vacuoles are relatively large sacs formed during endocytosis of
nutrients
o Also digest old or defective organelles
Vacuoles
o Some are temporary
o Others persist for the life of the cell
Contractile vacuoles in freshwater protists prevent lysis
Central vacuoles in plant cells
Large
Involved in osmoregulation, storage, concentration of
pigments, turgor pressure
Endosymbiont hypothesis
o Mitochondria and chloroplasts evolved from prokaryotic bacteria roughly 1.7
billion years ago
Prokaryotes gained entry into other prokaryotes without being digested
and, over time, became interdependent and inseparable
Evidence
o Both organelles are surrounded by a double membrane, the inner membrane
more akin to modern-day prokaryote plasma membrane and the outer
membrane more akin to modern-day eukaryotic plasma membrane.
o Mitochondria, chloroplasts, and average prokaryotic cells fall into the same
size range.
o Both feature their own circular DNA, void of introns and histones, like
prokaryotes.
o Both feature small ribosomes, like prokaryotes.
o Mitochondria, chloroplasts, and prokaryotes all reproduce via binary fission.
Mitochondria
o All eukaryotic cells contain mitochondria
o Powerhouses of the cell
o Store energy from food molecules in bonds of ATP
Chloroplasts
o Sites of photosynthesis
o Contain chlorophyll
Light-capturing pigment
Energy is used to drive synthesis of sugar from CO2 and water
Plastids
o Synthesize and/or store pigments or food molecules
Fruit color
Flower color
Starch
Lipids
o Only found in plants and photosynthetic protists
o Chloroplasts, elaioplasts (lipid-storing), and amyloplasts (starch-storing) are
types of plastids.