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Chapter 8
Energy and Metabolism
 All reactions within the body require energy for metabolism.
-Metabolism includes all of the chemical reactions in an organism.
-These reactions are ordered into metabolic pathways, a sequence of steps, each controlled by
an enzyme, which covert a specific molecule to a product.

 There are 2 primary types of metabolism:

1) Anabolism – building up; synthesis
-Requires energy
-Example: Photosynthesis
2) Catabolism – breaking down; decomposition
-Releases energy
-Example: Cellular respiration
 2 forms of energy
-Energy has been defined as the capacity to cause change
1) Kinetic energy is the energy of motion, of matter that is moving.
-This matter does its work by transferring its motion to other matter.
-Thermal energy (heat) = the kinetic energy of randomly moving molecules
2) Potential energy is the capacity of matter to cause change as a result of location or arrangement
-Chemical Energy = a form of potential energy that is available for release in chemical reactions

The Laws of Energy Transformations

 Thermodynamics is the study of energy and its application to energy systems.
 1st Law of Thermodynamics (Law of Conservation of Energy): Energy can’t be created or destroyed
but can be transferred or transformed
-Energy can be converted from one form to another
-Example: plants convert light energy to the chemical energy in sugar, and cells release this
potential energy to drive cellular processes
 nd
2 Law of Thermodynamics: Every energy transfer or transformation results in entropy and
constant energy loss
-Entropy increases when energy is lost.
-10% rule: only 10% of energy is transferred in a reaction, and the other 90% is lost into the
environment in an unusable form.
-We’re always working against entropy: decrease in entropy means decrease in energy, which
means that organisms must have a constant input of energy in order to compensate for this
energy loss
 Two forces govern energy conversions:
1. Entropy – measure of randomness/disorder
2. Enthalpy – the amount of available heat
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Free Energy
Free Energy Change
 Free energy is the measure of energy available to do work
WORK:
1) Transport and movement
2) Biochemical reaction (synthesis)
3) Reproduction and growth
*Free energy is stored as ATP, in the last high energy phosphate bond
 Gibbs free energy measures the changes in free energy and tells us whether or not the reaction
occurs spontaneously
ΔG = ΔH – TΔS
*Reactions favored are those in which:
a. +Δ S (= entropy: disorder/randomness)
b. – ΔH (=enthalpy: total energy of a system)
 Reactions occur spontaneously when the energy of the products is less than that of the reactants.
-If ΔG is negative = spontaneous
-If ΔG is positive = nonspontaneous
Free energy, Stability, and Equilibrium
 When ΔG is negative, the final state has less free energy than the initial state  the final state is less
likely to change and is more stable
 A system rich in free energy has the tendency to change spontaneously to a more stable state, a
state of equilibrium
-Moving toward equilibrium is spontaneous because the ΔG of the reaction is negative
-At equilibrium, the forward and backward reactions are proceeding at the same right and the -
relative concentrations of products and reactants stays the same
*Equilibrium = equal rates of reaction, but the concentrations do not have to be equal;
the concentrations just stay constant
-Once at equilibrium, a system is at a minimum of free energy and will not spontaneously
change
Free Energy and Metabolism
 Reactions may be either exergonic or endergonic
 Exergonic: releases free energy
- ΔG is negative; it’s spontaneous
-downhill
-Example = CELLULAR RESPITATION (C6H12O6 + O2  CO2 + H2O + ATP)
-All kingdoms of life carry out cellular respiration
-It produces or releases energy
 Endergonic: absorbs free energy
- ΔG is positive; it’s nonspontaneous
-uphill
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-example: PHOTOSYNTHESIS (CO2 + H2O C6H12O6 + O2)

-Only plants, some bacteria, and some protists carry out photosynthesis
-This process uses chloroplasts
-It uses an input of energy to decrease entropy
 Coupled Reaction: exergonic reactions fuel endergonic ones
-In cellular reactions, endergonic reactions are typically coupled with exergonic reactions.
-The exergonic reactions provide the energy to “push” the endergonic reactions “uphill”
-The energy released by an exergonic reaction (–ΔG) is equal to the energy required by the
reverse reaction (+ΔG)
 Metabolic disequilibrium is essential to life
-Metabolic reactions are reversible and could reach equilibrium if the cell did not maintain a
steady supply of reactants and siphon off the products (as reactants for new processes or as
waste products to be expelled)

ATP and Cellular Work

A cell performs 3 primary types of work:
1) Mechanical = involves movement
-moving cilia or flagella, contracting muscles, moving chromosomes
2) Transport
-Active or passive transport
3) Chemical
-coupling endergonic reactions with exergonic reactions
Structure of ATP
ATP = adenosine triphosphate

3 phosphates Adenine
(=highly negative) (purine)
ATP consists of the nitrogenous base adenine
bonded to the sugar ribose, which is connected
to a chain of three phosphate groups.
Ribose
sugar

Hydrolysis of ATP
 ATP isn’t stored within the cell, but is continually converted.
 ATP can be hydrolyzed to ADP (adenine diphosphate) and an inorganic phosphate (Pi)
ATP  ADP + Pi +7.3 kcal/mol
-Energy is a product: the reaction is exergonic
-This equation can be rewritten as:
ATP  ADP + Pi ΔG = -7.3 kcal/mol
-About 10 million molecules of ATP are consumed/regenerated each second per cell.
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-The ΔG of this reaction in the cell is estimated to be closer to 13 kcal/mol

 The system doesn’t reach equilibrium because the product of one reaction (exergonic) becomes the
reactant of the next reaction (endergonic)
-Fuels are continually supplied and wastes are removed.

ATP is the immediate source of cellular energy

 Energy from ATP comes from the high energy 3rd phosphate bond
-The phosphate bonds in ATP are weak and unstable, so they yield a high amount of energy
when broken.
-This instability is the result of the combination of the 3 “crowded” negative charges from the
phosphate groups on the tail of the molecule. The 3 negative charges repel each other.
-This instability results in breakdown and release of energy
 ATP energizes other molecules by transferring phosphate groups to them (=phosphorylation)
-Phosphorylation: addition of a phosphate, which raises a molecule’s energy
-This produces a molecule that is more reactive and less stable
-The free energy released from the hydrolysis of ATP is used to transfer phosphate groups

Regeneration of ATP
 A cell regenerates ATP at a phenomenal rate
 The formation of ATP from ADP and Pi is endergonic, with a ΔG of +7.3 kcal/mol (in standard
conditions)
-This means that making ATP requires an input of energy
 Direct source of energy = sunlight
Indirect source of energy = food
*Glucose by itself isn’t a good source of energy because it packs too much of an energy punch. It
contains more energy than required, and will explode the cell
 Cellular respiration (the catabolic processing of glucose and other organic molecules) provides this
energy for the regeneration of ATP
-Plants can also produce ATP using light energy
-Mitochondria convert glucose into ATP in the process of cellular respiration

Enzymes
The Activation Energy Barrier
 Activation energy: additional energy requirement to start a reaction
-Most reactions (even exergonic ones) require an input of energy in order to initiate a chemical
reaction
-It requires energy to break chemical bonds; and energy is released when bonds form
-The activation energy allows reactants to reach the unstable transition state, where bonds are
likely to break and from which the reaction can proceed
-This is the peak of the graph (see below)
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-The EA (activation energy) barrier is essential to life because it prevents the energy-rich
macromolecules of the cell from decomposing spontaneously
-For metabolism to proceed, the EA must be reached
 The rate of the reaction is dependent upon the amount of activation energy required to initiate the
reaction.
 Catalysts are chemical agents that speed up rates of reaction but are unchanged by the reaction.
-They do not affect the net energy released; they only lower the activation energy barrier
-They are not consumed by the reaction.
 Enzymes are biological catalysts and function by lowering the activation energies so that reactions
can occur more quickly and metabolism can proceed at cellular temperature
-Example: the enzyme sucrose speeds up hydrolysis of sucrose
*Enzymes do not change the ΔG for a reaction

Potential Energy Diagram

Activation energy

Enzymes lower the activation energy

Potential (=temperature at which the reaction occurs)
energy
PE of ΔH = enthalpy = heat of reaction
reactants
PE of products

Time

Overview of Enzymes
1. Most are proteins (at their tertiary structure at least)
2. Reduce activation energy without altering energy of products
3. Speed up rate of reaction – reaction takes less time
4. Not consumed by the reaction
5. Can be re-used again and again
6. Can catalyze both synthesis and decomposition reactions
7. Are very specific: substrate must fit active site of enzyme
8. Names of enzymes often end in –ase
9. May be altered by temperature, pH, salinity, or cofactors
10. Inhibitors reduce or prevent enzyme activity (noncompetitive or competitive)

Catalytic Cycle of Enzyme Action

1. Binding of substrate to active sit of enzyme
-Active site: pockets or clefts in the surface of the enzyme protein
-Enzymes must fit precisely into the active site of the substrate
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*Enzyme specificity depends on the shape of the enzyme (specifically, the shape of its
active site)
-When the substrate binds to the enzyme, it forms the enzyme substrate complex

2. Binding of substrate results in induced fit

-The combination of enzyme and substrate often involves induced fit: when the enzyme’s
shape changes slightly, resulting in an even better fit and enhancing the enzyme’s ability to
catalyze the chemical reaction
Mechanisms to lower activation energy & speed up reaction
a. The enzyme stresses the substance by stretching and bending the chemical bonds
-Enzymes are held to substrate by hydrogen or ionic bonds
b. The enzyme distorts the substrate and reduces the amount of free energy needed to
break bonds
c. The binding of the enzyme to the substrate may create a microenvironment that is
more conducive to a reaction by:
1) Transfer of Hydrogen ions
2) Interaction with acid R groups
d. There is brief covalent bonding between the enzymes
3. Substrate is converted to product while at the active site
4. Enzyme releases degraded substance; active site is available for another molecule
-Enzymes are recyclable: can be re-used again and again

Characteristics of enzyme-mediated reactions

1. Most reactions are reversible.
-Enzymes catalyze both forward and reverse reactions.
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-Which reaction is catalyzed is dependent upon the concentration of the substances

present.
-Enzymes catalyze reactions going towards equilibrium
-There is no specific direction to determine which enzymes bind with which substrates.
2. The rate of the reaction is concentration dependent.
-The rate of the reaction is fastest when it first starts because there is a high
concentration of substrates that need to bind with available enzymes
-The rate eventually slows down until it becomes constant as the substrate
concentration decreases. The enzymes have less substrate molecules to react with.
-Reactions may reach the saturation point when all active sites are occupied
Rate of Enzymatic Reactions

Constant reaction rate: all substrates saturated with enzymes

Increase in reaction rate

Factors Affecting Enzyme Activity

1. Temperature
-A slight increase in temperature will increase the kinetic energy of molecules  this
increases the rate of the reaction up to a point
-Enzymes have temperature optimums at which they function best
-Too high or too low of a temperature will denature the enzyme (=alter the shape of its
active site)
Heat: increase beyond optimum T°
 increased energy level of molecules disrupts bonds in enzyme & between enzyme & substrate
 H, ionic = weak bonds
 denaturation = lose 3D shape (3° structure)
Cold: decrease T°
 molecules move slower
 decrease collisions of enzyme & substrate

2. pH
-Enzymes have an optimum pH
-example: pepsin works in the low pH of the stomach (2-3) while trypsin works at a pH of 7-8
in the small intestine
 adds or remove H+
 disrupts bonds, disrupts 3D shape
o disrupts attractions between charged amino acids
o affect 2° & 3° structure and denatures protein
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3. Salinity (salt concentration)

-If the salt concentration is close to zero or really high, the enzyme will denature
-Enzymes have an optimum at intermediate salt concentrations
- adds or removes cations (+) & anions (–) disrupting bonds and 3D shape

4. Presence of cofactors
-Cofactors and coenzymes= nonprotein helpers that help fill in the active site and bind
either permanently or reversibly with enzymes
Cofactors: Coenzymes
-inorganic -organic
-metallic elements like iron -vitamins
Mg in chlorophyll NAD, FAD, CoenzymeA

5. Enzyme inhibitors
a. Competitive inhibitors – bind to the active site and compete with the substrate
-They block the actual enzyme
-Increasing the concentration of substrate molecules may overcome this type of
inhibition
b. Noncompetitive inhibitors – bind to another part of an enzyme, causing the enzyme to
change shape and making the active site less effective
-Example = allosteric enzymes

Metabolic Control Mechanisms

Biochemical pathways
 Biochemical pathways are a sequence of chemical pathways in which the product of one reaction
becomes the reactant of the next reaction.
-Biochemical pathways are the organizational units of metabolism.
Control of Metabolism
 Control of chemical pathways is achieved by making the enzymes involved in the process
catabolically active or inactive
1. Allosteric regulation = noncompetitive inhibition
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-In allosteric regulation, molecules may inhibit or activate enzyme activity when they bind to
a site separate from the active site.
-Many enzymes have an allosteric site: a specific receptor site which is NOT the active site
-Binding of an inhibitor to allosteric site = reinforces the inactive form of the enzyme
-Cooperativity is when the induced-fit binding of a substrate molecule to one subunit
changes the shape so the active sites of all subunits are more active

2. Feedback inhibition
-In feedback inhibition, the end product of a pathway inhibits an enzyme early in the
pathway, preventing the cell from producing an excess of a particular substance
-Metabolic pathways are commonly regulated by feedback inhibition
-Example: Conversion of threonine to isoleucine

Localization of enzymes
 Enzymes are sequestered in mitochondria according to function
o Different locations have different enzymes and different amounts of those enzymes,
based on the process being carried out at that location and how the enzymes need to
function
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Chapter 9: Cellular Respiration

Catabolic pathways yield energy by oxidizing organic fuels

Redox Reactions: Oxidation and Reduction OIL RIG

 Oxidation-reduction or redox reactions involve the partial or complete transfer of one or more
electrons from one reactant to another
 Oxidation = loss of electrons
-The substance that loses electrons becomes oxidized and acts as a reducing agent (electron
donor) to the substance that gains electrons
 Reduction = gain of electrons
-By gaining electrons, a substance acts as an oxidizing agent (electron acceptor) and becomes
reduced
 Oxygen strongly attracts electrons and is one of the most powerful oxidizing agents
-As electrons shift toward a more electronegative atom, they give up potential energy
-Chemical energy is released in a redox reaction that relocates electrons closer to oxygen
*Organic molecules with an abundance of hydrogen are rich in “hilltop” electrons that release
their potential energy when they “fall” closer to oxygen
 In cellular respiration:
o NAD+ picks up electrons and is reduced to NADH
o Energy from respiration is released as electrons are passed from NADH down an
electron transport chain, a group of carrier molecules located in the inner
mitochondrial membrane. These electrons eventually reach a stable location next to
highly electronegative oxygen, forming a water molecule.
The Cell and Energy
 Free energy is stored as ATP in the 3rd high energy phosphate bond
 Activities that require energy:
1) Transport and movement
2) Reproduction and growth
3) Biochemical reaction (e.g. protein synthesis)
 ATP can be broken down to produce ADP and an inorganic phosphate. The phosphate can then
phosphorylate and energize another molecule.
 For organisms, a direct source of energy is sunlight and an indirect source is food
 Glucose cannot be used as a direct source of energy because it contains more energy than required
and will explode the cell
 Instead, glucose must be oxidized to form ATP in the mitochondria of cells
-Mitochondria are similar to chloroplasts: they share an evolutionary history
-Difference between them:
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-Chloroplasts make glucose and use energy (photosynthesis)

-Mitochondria break down glucose and produce energy (cellular respiration)
 Cristae within the mitochondria = infolded membrane that increases surface area
-Enzymes are embedded here, so it increases the number of enzymes, therefore increasing the
rate of reaction
 The circulatory system transports glucose and oxygen to cells

An Overview of Cellular Respiration

C6H12O6 + 6O2  6H2O + 6CO2 + ATP (36–38)

Electron Acceptor Molecules in Respiration

- + +
e + NAD + H ⎯→ NADH
- +
e + FAD + 2H ⎯→ FADH2
- +
e + ½O2 + 2H ⎯→ H2O
Glycolysis –
 All living things carry out glycolysis
-This has led scientists to believe that all living things have a common ancestry. The enzymes of
glycolysis are very similar among all organisms. The genes that code for them are highly conserved.
 In an overview of glycolysis, one molecule of glucose is decomposed into 2 molecules of pyruvate.
This produces 2 molecules of ATP.
 ATP is produced through Substrate Level Phosphorylation (SLP) = phosphate added to ADP
 Glycolysis takes place in the cytosol
-Glucose is stored in the body in liver and muscle tissue as glycogen
-The circulatory system transports both glucose and oxygen to cells
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-Glucose diffuses into the cell through passive transport: facilitated diffusion with a channel
protein
 ATP net gain = 2
-ATP cost = 2
-ATP gain = 4
+
NAD is reduced to form NADH

Glycolysis in anaerobically respiring organisms is followed by fermentation or anaerobic respiration

Glycolysis
2 NAD+ is reduced to form 2 NADH (= higher energy)
Uses 2 ATPs
Glucose 4 ATPs produced by SLP
(6 – C)
2 Pyruvate
2 (3 – C)
Net gain = 2 ATP

Fermentation or Anaerobic Respiration: the partial degradation of sugars to release energy without
oxygen
2 types of fermentation:
1) Alcohol fermentation =pyruvate is converted to ethanol in 2 steps, with the 1st releasing
CO2
*This is for bacteria  Bacteria only carry out glycolysis
-Produces 2 ATP which is okay for tiny bacteria
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-Bacteria can survive with such little energy because they’re small, single-celled,
have no organelles, and no transport -recycles NADH
-Alcohol fermentation by yeast is used in brewing, winemaking, and baking
-Obligate anaerobes = poisoned by O2 and need fermentation or anaerobic respiration
to survive
-Obligate aerobes = need O2 to survive and need cellular respiration
-Facultative anaerobes = can survive using fermentation or cellular respiration
2) Lactic acid fermentation = pyruvate is reduced by NADH, forming lactic acid (=lactate) as
an end product, with no release of CO2
-Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt
-Human muscle cells use lactic acid fermentation to generate ATP when O2 is scarce

 Aerobic respiration: uses oxygen in the breakdown of glucose to yield carbon dioxide and water
and release energy as ATP and heat . Cellular respiration is referred to as the aerobic process

What happens to Pyruvate after glycolysis?

Conversion of Pyruvate to Acetyl CoA

 At the end of glycolysis, the 2 pyruvate molecules are in the cytosol
 First: the 3-carbon pyruvate moves into the matrix of the mitochondria through active transport
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-In the process of moving from one location to another, the 3-carbon pyruvate molecule loses a
carbon and is converted into the 2-carbon Acetyl
-CO2 and NADH are produced
-Anytime carbon is lost, it’s lost in the form of CO2
-NAD+ is reduced to form NADH
 The 2-carbon acetate molecule binds to a molecular complex called coenzyme A. The resulting
compound is called acetyl CoA.
-This compound is present within the matrix of the mitochondria of cell.

Krebs Cycle/ Citric Acid Cycle

 The Krebs Cycle occurs in the matrix of the mitochondria
**It is important to remember that for every one molecule of glucose, the Krebs cycle “turns” 2
times
The 2 carbon acetyl combines with a 4 carbon molecule oxaloacetic acid to form the 6 carbon
product, citrate/citric acid.

 In the process (for 1 glucose=2 turns of the Krebs cycle), 2 ADP are phosphorylated to form 2 ATP.
NAD+ is reduced to form 6 NADH and FADH+ is reduced to form 2 FADH2. 2 CO2 are produced when
carbon is lost.
-Oxygen is the one substance that has not been used yet
Oxidative Phosphorylation
 Takes place between the matrix and inner mitochondrial membrane (2nd membrane)
-The infolded membrane (=cristae) creates more surface area, which allows this process to
occur more often and more quickly
-Thousands of electron transport chains are embedded in the cristae (infoldings) of the inner
mitochondrial membrane
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2 Parts of Oxidative phosphorylation:

1) Electron transport system = electron transport and pumping of protons (H+) which
create an H+ gradient across the membrane
o NADH and FADH2 are high energy electron carriers  they drop off electrons
 NADH and FADH2 are oxidized because they’re losing electrons as they drop
electrons off at electron carrier proteins
 NAD+ and FADH are continually recycled: drop off electrons and come back to
get more (shift between reduced and oxidized states)
o Electrons move to proteins(electron carriers) of greater electronegativity
 Electronegativity = tendency of an atom to attract electrons. When electrons
are passed from lower to higher electronegative atom, energy is released.
 NADH and FADH2 carry electrons from one electron carrier protein to the next
 Each electron carrier in the chain increases in electronegativity to cause release
of energy in steps.
o This released energy goes to pump hydrogen ions across the membrane  creates a
gradient of H+ across the membrane
o Oxygen = “Final electron acceptor”
 Oxygen has the highest electronegativity  accepts electrons from NADH
 Oxygen diffuses into the mitochondria and combines with H+ to form water
2) Chemiosmosis = ATP synthesis powered by the diffusion of H+ back across the membrane
-H+ diffuse back through the membrane, from high to low (passive transport)
-H+ diffuse through the enzyme ATP synthase
-ATP synthase uses the energy of the H+ gradient to allow ADP to be phosphorylated to
form ATP
-Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of
an H+ gradient across a membrane to drive cellular work
The H+ Gradient
I. In mitochondria: endergonic redox reactions produce the H+ gradient that drives the
synthesis of ATP
II. In chloroplasts: light energy is used to create the proton-motive force used to make ATP
by Chemiosmosis, instead of an H+ gradient
III. In prokaryotes: H+ gradients are used to transport molecules, make ATP, and rotate
flagella

Here is the picture we looked at in class:

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Tallying Up the Total

Glycolysis Pyruvate  Krebs ETS (electron Total Total energy
Acetyl CoA Cycle transport system)

CO2 0 2 4 0 6 None

NADH 2 2 6 0 10 10 x3 = 30 ATP

FADH2 0 0 2 0 2 2 x2 = 2 ATP

ATP (by SLP) 2 0 2 4 4 ATP

38 ATPs
produced

Oxidative Phosphorylation
1. Electron transport = NADH and FADH2 pass electrons to the electron transport
chain, from which they combine with hydrogen ions and oxygen to form water
2. Chemiosmosis = The energy released through this electron transport chain of redox
reactions and diffusion of H+ ions is used to synthesize ATP
 Purpose of cellular respiration = to produce energy in the form of ATP
-36 to 38 molecules of ATP may be generated for each molecule of glucose oxidized to
carbon dioxide
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-The reason it varies is because energy might be lost to move pyruvate into
mitochondria
-About 10% of this ATP is produced by substrate-level phosphorylation (SLP) – you SLAP a
phosphate onto ADP
-NADH = 3 ATPs
-FADH2 = 2 ATPs
-All organisms carry out cellular respiration

Comparing Fermentation to Cellular Respiration

 Both use glycolysis with NAD+ as the oxidizing agent to convert glucose to pyruvate
 To oxidize NADH back to NAD+:
-Fermentation uses pyruvate as the final electron acceptor
-Cellular respiration uses oxygen as the final electron acceptor
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Chapter 10: Photosynthesis

Photosynthesis converts light energy to chemical energy of food
The Anatomy of a Leaf
 Photosynthesis occurs in the leaves of plants
 The cuticle is the waxy covering on the top of the leaf.
- Produced by the upper epidermis, it provides protection, prevents water loss through
evaporation, and directs rain water to the roots (like a gutter).
 Mesophyll layer = spongy layer + palisade layer
- Where photosynthesis occurs
 Just below the upper epidermis is the palisade layer. These cells are tightly packed together
and contain lots of chloroplasts.
 Below the palisade layer is the spongy layer. These cells are loosely arranged and have air
spaces.
 This allows for diffusion of gases, especially CO2, within the leaf.
 At the lower epidermis, the underside of the leaf contains stomata which allow transpiration
and gas exchange, allowing CO2 to enter and O2 to exit
 Surrounding each stomate are guard cells, which control the opening and closing of the
stomates
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 Veins carry water from the roots to the leaves and distribute sugar from the leaves to non-
photosynthetic tissue
 Vascular bundles are found in the spongy layer.
 Vascular bundles include xylem and phloem tubes that transport materials throughout the
plant. Xylem tubes transport water, and phloem tubes transport sugars.
Chloroplasts
 Photosynthesis takes place in the chloroplasts of the leaves
 The green color of the leaf is from chlorophyll, the green pigment located within chloroplasts.
*It’s the light energy absorbed by chlorophyll that drives photosynthesis in chloroplast
 Chloroplasts are found mainly in the cells of the mesophyll, the tissue in the interior of the leaf.
 A chloroplast consists of a double membrane surrounding a dense fluid called the stroma and an
elaborate membrane system called thylakoids, enclosing the thylakoid space
 Thylakoid sacs may be stacked to form a granum.
 Chlorophyll is embedded in the thylakoid membrane.

Tracking Atoms through Photosynthesis

 The equation for photosynthesis is the reverse of cellular respiration:
CO2 + H2O + Light energy  C6H12O6 + O2
 All photosynthetic organisms need a hydrogen source because plants split water as a source of
electrons from hydrogen, releasing oxygen.
 Photosynthesis is a redox reaction like respiration, but differs in the direction of electron flow.
 The electrons increase their potential energy when they travel from water to reduce CO2
into sugar, and light provides the energy for this endergonic process
 Reduced = gain of electrons
 Oxidized = loss of electrons
 Cellular respiration: NAD+ is reduced to NADH
 Photosynthesis: NADP+ is reduced to NADPH
2 Stages of Photosynthesis:
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1. The Light Reaction: converts solar energy to chemical energy (in thylakoid
membranes; requires light)
 The whole point of the light reaction is to produce 2 things:
1. Energy in the form of ATP
2. Electron carriers, specifically NADPH
 The whole process begins when photons (=energy units) of sunlight strike a leaf, activating
chlorophyll and exciting electrons.
 The activated chlorophyll molecule then passes these excited electrons from water down to a
series of electron carriers, ultimately producing ATP and NADPH.
 The electron acceptor NADP+ is reduced to NADPH and temporarily stores electrons.
 Oxygen is released when water is split.
 ATP is formed during the light reactions, using chemiosmosis in a process called
photophosphorylation
2. The Dark Reaction/ Calvin Cycle: uses ATP, NADPH, and CO2 to make carbohydrates
(in the stroma; doesn’t require light)
 In the Calvin Cycle, carbon dioxide is incorporated into existing organic compounds by carbon
fixation, and these compounds are then reduced to form carbohydrate.
 NADPH and ATP from the light reactions supply the reducing power and chemical energy
needed for the Calvin cycle.

The light reactions convert solar energy to the chemical energy

of ATP and NADPH
The Nature of Sunlight
 The electromagnetic spectrum is the entire range of electromagnetic energy, or radiation
 Visible light consists of wavelengths (including those that drive photosynthesis) that produce
colors we can see
 Light also behaves as though it consists of discrete particles, called photons
Excitation of Chlorophyll by Light
 When a pigment molecule absorbs energy from a photon, one of the molecule’s electrons gains
potential energy, going from the ground state to the excited state
 The excited state is unstable.
 Energy is released as heat as the electron drops back to its ground state
 Isolated chlorophyll molecules also emit photons of light called fluorescence as their electrons
return to ground state
Photosynthetic Pigments: the Light Receptors
 Many light-absorbing pigments participate in photosynthesis, including:
o Chlorophyll a: absorbs most of the light and participates directly in light reactions
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 Its absorption spectrum shows that it absorbs violet-blue and red light best.
o Chlorophyll b
 Absorbs light of different wavelengths and broadens the spectrum of colors useful
in photosynthesis
o Carotenoids
 Absorbs light of different wavelengths and broadens the spectrum of colors useful
in photosynthesis
 These pigments are clustered in the thylakoid membrane into units called antenna complexes.
 All of the pigments within a unit are able to “gather” light, but aren’t able to “excite” the
electrons.
 Only one special molecule – located in the reaction center – is capable of transforming light
energy into chemical energy.
 In other words, the other pigments, called antenna pigments, “gather” light and “bounce”
the energy to the reaction center

Photosystems
 Photosystems contain a number of light-harvesting complexes and a reaction center complex.
 located in the thylakoid membrane
 A reaction center complex is a protein complex with 2 chlorophyll a molecules and a primary
electron acceptor.
 There are 2 types of reaction centers:
1. Photosystem II (PSII)
 The chlorophyll a molecule at the reaction center of PSII is called P680, after the
wavelength of light (680 nm) it absorbs best
2. Photosystem I (PSI)
 There’s a chlorophyll a molecule at the reaction center of PSI called P700
 22

*The primary difference between the two is that each reaction center has a specific type of
chlorophyll a that absorbs a particular wavelength of light: PSI absorbs P700, and PSII absorbs
P680
 When a pigment molecule in a light-harvesting complex absorbs a photon, the energy is passed
from pigment to pigment until it reaches the reaction center. In a redox reaction, an excited
electron of a reaction-center chlorophyll a is trapped by the primary electron acceptor before it
can return to the ground state.

Noncyclic Photophosphorylation/Linear Electron Flow

 Light drives the synthesis of ATP and NADPH by energizing the 2 photosystems
embedded in the thylakoid membranes of chloroplasts.
*Light energy strikes photosystems  activates the electron transport chain
*The direction of electron flow: water  PSII  PSI  NADP+

 The process:
1. A photon of light strikes PSII, boosting electrons to an excited level. These electrons pass on
energy until it excites an electron in the P860 chlorophyll a molecules in the PSII reaction-
center complex.
2. The activated electrons are trapped by P680 and passed to a molecule called the primary
electron acceptor which ejects electrons from PSII. This leaves an electron hole in PSII.
(which will be filled with electrons from splitting water)
3. A water molecule splits into 2 electrons, 2 hydrogen ions (=protons), and an oxygen atom, a
process called photolysis. These electrons fill in the electron hole in PSII.
4. Each photoexcited electron passes from PSII to PSI via an electron transport chain.
 23

 This electron transport chain is similar to that of cellular respiration

 It consists of the proteins acting as electron carrier. These proteins carry the electrons
from PSII to PSI.
5. Some of the energy that dissipates as electrons move along the electron chain of acceptors
will be used to pump protons across the membrane into the thylakoid lumen.
 As electrons are transported, they go from higher to lower energy levels.
 When protons are pumped across the thylakoid membrane, it creates a proton gradient
that is used in chemiosmosis. This is what drives the synthesis of ATP.
6. Meanwhile, photons of light also strike PSI, boosting an electron to its excited state. This
electron then excites other electrons, until this energy reaches the primary electron
acceptor, and is ejected from PSI. This also creates an electron hole. This hole is filled by the
electrons from PSII.
7. Activated electrons are passed from PSI down a second electron transport chain (ETC).
8. The flow of electrons continues along the ETC until it finally reaches the final electron
acceptor NADP+ which is reduced to NADPH.
9. Hydrogen ions (=protons) accumulate inside the thylakoid space (where photolysis occurs),
creating a proton gradient. Protons then diffuse back across the thylakoid membrane into
the stroma through chemiosmosis, passing through the protein ATP synthase. ADP and Pi
are phosphorylized to produce ATP in a process called photophoshorylation.
Cyclic Photophosphorylation
 The cyclic method uses a much simpler pathway to generate ATP.
 What happens in this process:
 The electrons in PSI are excited and leave the reaction center, P700.
 They are passed from carrier to carrier in the electron transport system and
eventually return to P700.
 At the end of this cycle, only ATP is produced.
 This pathway is called cyclic photophosphorylation because the electrons from P700 return to
the same reaction center.
 Unfortunately, this method isn’t as efficient as the noncyclic pathway since it doesn’t produce
NADPH.
 Plants use this method only when there aren’t enough NADP molecules to accept electrons.
 Lots of photosynthetic bacteria only have PSI, so they use this method.
 Photosynthesis may have evolved with cyclic electron flow.
 24

A Comparison of Chemiosmosis in Chloroplasts and Mitochondria

 Chemiosmosis in mitochondria and in chloroplasts is very similar.
 Electron transport chains (built into a membrane) pump protons across the membrane as
electrons are passed down the chain in a series of redox reactions
 The key difference is that in respiration, organic molecules provide the electrons, and chemical
energy is transferred to ATP. However, in chloroplasts, water provides the electrons as light
energy is transformed to the chemical energy of ATP
 In chloroplasts, the electron transport chain pumps protons from the stroma into the thylakoid
space. As H+ diffuses back through ATP synthase, ATP is formed on the stroma side, where it is
available for the Calvin cycle

The Calvin cycle uses ATP and NADPH to convert CO2 to sugar
 25

The dark reaction uses the products of the light reaction – ATP and NADPH – to make
sugar. CO2 becomes the source of glucose sugars through the process of carbon fixation.
 Carbon fixation simply means that CO2 from the air is converted into carbohydrates.
 Where: occurs in the stroma of the leaf.
 Required: ATP and NADPH
 Produced: G3P which is used to make sugars
The Calvin cycle turns 3 times to fix 3 molecules of CO2 and produces one molecule of
the 3-carbon sugar glyceraldehyde-3-phosphate (G3P).
 Carbon dioxide enters (For 1 turn of the cycle, 3 molecules enter, one at a time)
 The cycle can be divided into 3 phases:
1. Carbon fixation:
 CO2 is added to a 5-carbon sugar called ribulose biphosphate (RuBP) to form an unstable 6-
C compound.
 The enzyme RuBP carboxylase, or rubisco, catalyzes this reaction.
-Rubisco is the enzyme which converts RuBP that has combined with CO2 into a 6-
carbon compound
2. Reduction:
 NADPH is oxidized to produce NADP+
 The electrons lost by NADPH go to convert the 3-carbon compounds into G3P
(glyceraldehyde-3-phosphate).
 For every 3 molecules of CO2 (1 turn of the cycle), there are 6 molecules of G3P.
- One molecule of G3P exits the cycle and will be used to produce sugars.
- The other 5 G3P molecules are recycled to form RuBP again so the cycle can begin.
 The cycle must turn 3 times to create a net gain of 1 molecule of G3P
3. Regeneration of CO2 acceptor (RuBP):
The 5 molecules of G3P are rearranged back into the 3 molecules of RuBP
This requires 3 more ATP

 9 molecules of ATP and 6 of NADPH are required to synthesize 1 G3P

 Since G3P, a 3-carbon molecule, is the first stable product, this method of producing glucose is
called the C3 pathway.
 26

Importance of Photosynthesis: A Review

 About 50% of the organic material produced by photosynthesis is used as fuel for cellular
respiration in the mitochondria of plant cells
 The rest is used as carbon skeletons for the synthesis of organic molecules (proteins, lipids, and
a great deal of cellulose), stored as starch, or lost through photorespiration.
 About 160 billion metric tons of carbohydrates per year are produced by photosynthesis
 27

Photosynthesis:
Sunlight
CO2 + H2O - by process of
Chlorophyll
C6H12O6 + O2
diffusion/
- byosmosis
process of
Enters leaves Enters roots Made in leaves through Made in the light
Chloroplasts
diffusion/ in
through through root photosynthesis in chloroplasts reaction of
thylakoids
osmosis
stomates hairs - Made in the mesophyll photosynthesis
- by process - by process of layer which consists of - Comes from
of diffusion/ root pressure, 1. Palisade layer splitting a
osmosis capillary (condensed) water molecule
action, and 2. Spongy layer (has air - Exits leaves
transpiration spaces) through
- Stored in roots, stems, stomates
and mostly fruits (=the
ovary of the flower; are
fleshy/dry & have seeds )
 28

Ch.11 Study Guide

Components Function Points to remember

of Cell
signaling

Direct cell to Exchange molecules between adjacent cells by direct

cell contact: contact.
e.g.
Plasmodesm
ata

Local Chemical signals are sent to a developing embryo and During the course of
Regulators aid in the formation and specialization of tissues. development, cells of many
tissues differentiate according to
Ex. the positional information that is
Morphogens set by the concentration gradients
of morphogens. Morphogens are
signaling molecules that originate
from a restricted region of a tissue
and spread away from their
source to form a concentration
gradient. Cells differentiate into
different types depending on the
concentration of morphogen
available to them. As the fate of
each cell in the field depends on
the concentration of the
morphogen signal, the gradient
prefigures the pattern of
development. These gradients
drive the process of
differentiation of unspecialized
(stem) cells into different cell
types, ultimately forming all the
tissues and organs of the body.
 29

Local Quorum sensing is when bacterial

Regulators cells secrete tiny molecules that
other cells interpret. The
Ex. concentration of the molecules
Quorum secreted is sensed by other
sensing bacterial cells and allows them as
a group to coordinate their
actions. Quorum sensing lets
groups of bacterial cells perform
activities that require multiple
cells working together in
synchronization. These activities
include conjugation, biofilm
formation, motility, and antibiotic
production.

Reception A receptor recognizes a ligand (signal molecule) from A signal molecule binds to a
another cell. receptor protein, causing it to
change shape.

Transductio Activation of certain cell proteins (kinases), followed Cascades of molecular

n by a chain of activation (signal amplification) and interactions relay signals from
transmission of the signal via relay molecules. receptors to target molecules in
the cell.

Response A final result (physiological response for the cell) in the Cell signaling leads to regulation
chain of activation. of transcription or cytoplasmic
activities.
 30

Ligand A signal molecule is a ligand and ultimately leads to the

cellular response.

Receptor Ligand binds to a receptor

G protein When ligand binds to this receptor, it causes Follow the figure to review how
coupled conformational change in the receptor so that it binds to this receptor works. When
receptor inactivate G protein and activate it. Activated G protein ligand binds to this receptor, it
can now activate an enzyme triggering signal causes conformational change in
transduction. the receptor so that it binds to
inactivate G protein, causing a
GTP to displace the GDP. This
activates the G protein. In step 3
the G protein binds to a specific
enzyme and activates it. When the
enzyme is activated, it can trigger
the next step in a pathway leading
to a cellular response. Note: All
the molecular shape changes are
temporary. To continue the
cellular response, new signal
molecules are required.

Receptor The receptors form a dimer when activated by Follow the figure to review how
tyrosine attachment of ligands. Each tyrosine kinase in a dimer this receptor works.
kinases initiates a unique response when phosphorylated. A
single ligand is able to activate multiple cellular Step 1 shows the binding of signal
responses unlike G protein couple receptor molecules to the receptors and the
subsequent formation of a dimer.
In the dimer configuration, each
tyrosine kinase adds a phosphate
from an ATP molecule.

Step 2 shows the fully activated

receptor protein as it initiates a
 31

unique cellular response for each

phosphorylated tyrosine. The
ability of a single ligand to
activate multiple cellular
responses is a key difference
between G-protein-coupled
receptors and receptor tyrosine
kinases.

Intracellular The receptors inside a cell on a cytoplasm or nucleus. The signal molecule must cross
Receptor Very small molecules like nitric oxide and hydrophobic the plasma membrane and
molecules like testosterone and steroids can cross therefore must be hydrophobic or
plasma membrane and attach to intracellular receptors. very small.

Note: plasma membrane receptors

like G protein and tyrosine
kinases receptors bind to water-
soluble ligands.

Ligand- Specific signal molecules (ligands) cause ligand-gated

gated ion ion channels in a membrane to open or close, regulating
channel the flow of specific ions.
receptor

Protein Enzymes which add phosphate groups to other proteins Signal transduction pathways
kinases and leading to their activation in the chain of signal often involve a phosphorylation
Phosphoryla amplification. Many of the relay molecules in signal cascade. Because the pathway is
tion cascade transduction pathways are protein kinases, and they usually a multistep one, the
often act on other protein kinases in the pathway. possibility of greatly amplifying
Phosphorylation cascade the signal exists. At each step
enzymes called protein kinases
phosphorylate and thereby
activate many proteins at the next
level. This cascade of
 32

phosphorylation greatly enhances

the signal, allowing for a large
cellular response.

Protein Enzymes which remove phosphate group from They help in turning off the
phosphatase phosphorylated protein and inactivate them. cellular response when not needed
s in the absence of signal.

Secondary They are small non protein molecules like cyclic GMP, Not all components of signal
messenger cyclic AMP, calcium ions (Ca2+), and inositol transduction pathway are proteins.
triphosphate (IP3) that can initiate phosphorylation Many signaling pathways involve
cascade activating relay molecules. small, non-protein water-soluble
molecules or ions called
secondary messengers, Once
activated, they can initiate a
phosphorylation cascade resulting
in a cellular response.
 33

Nuclear A signal transduction pathway leads to response, Many signaling pathways

Response regulation of one or more cellular activities. The ultimately regulate protein
response at the end of pathway may occur in the synthesis, usually turning specific
nucleus or cytoplasm of the cell. Once phosphorylated, genes on or off in the nucleus.
the last kinase in the sequence enters the nucleus and Often, the final activated
there activates a gene regulating protein, a transcription molecule in a signaling pathway
factor. This protein simulates transcription of a specific functions as a transcription factor.
gene(or genes) resulting in synthesis of a particular
protein.
 34

Cytoplasmic Sometimes a signaling pathway may regulate the For example, the final step in
Response activity of proteins rather than their synthesis, directly signaling pathway may affect the
affecting proteins that function outside the nucleus. activity of enzymes or cause
cytoskeleton rearrangement.
Cytoplasmic response to a signal: the breakdown of
glycogen to glucose 1-phosphate
 35

Defective or Inhibit neuron control over ion concentrations across

blocked cell the cell membrane or communication between neurons
signals (refer (essentially stops movement of neurotransmitters.)
to Essential
knowledge
3D4 below
and pick one
cause )

Neurotoxins

Apoptosis It is triggered by signals that activate a cascade of An elaborate example of cell

“suicide” proteins (proteases) in the cells. This signaling is a program of
programmed cell death protects neighboring cells from controlled cell suicide called
damage that would occur if a dying cell merely leaked apoptosis. During apoptosis the
out its digestive and other enzymes. cell is systematically dismantled
and digested. This protects
neighboring cells from damage
that would occur if a dying cell
merely leaked out its digestive
 36

and other enzymes.

It is triggered by signals that

activate a cascade of “suicide”
proteins in the cells.

In vertebrates apoptosis is a
normal part of development and is
essential for a normal nervous
system, for the operation of the
immune system, and for normal
morphogenesis of hands and feet
in humans.

Specificity of Different cells respond differently to same signaling Explanation for different
cell signaling molecule. Consider two different cells in your body-a responses: Because different
liver cell and a muscle cell for example. Both are in kinds of cells turn on different
contact with your bloodstream and are therefore sets of genes, different kinds of
constantly exposed to many different signal molecules. cells have different collections of
Yet the liver cell responds to some signals but ignores proteins. The response of a
others, and same is true for heart cell. And some kinds particular cell to a signal depends
of signals trigger responses in both cells-but different on its particular collection of
responses. For instance, epinephrine stimulates the liver signal receptor proteins, relay
cell to break down glycogen, but the main response of proteins, and proteins needed to
the heart cell to epinephrine is contraction, leading to a carry out the response.
more rapid heartbeat.
37
 38

Chapter 12: The Cell Cycle

Cell division results in genetically identical daughter cells.
Importance of the cell cycle
*It makes 2 new identical cells
1) Reproduction
-In unicellular organisms: it makes a whole new organism
-Multicellular organisms: use reproduction to grow
2) Growth/development
3) Repair and replacement
- The cell cycle extends from the creation of a new cell by the division of its parent cell to its own
division into 2 cells
- Mitosis: somatic cells (=normal body cells)
-2 identical diploid cells: same # of chromosomes
-Diploid = 2n
- Meiosis: gametes (=sex cells)
-2 identical haploid cells: half the # of chromosomes
-Haploid = n
- DNA is involved in:
1) Protein synthesis
DNA (only part of the DNA, one gene, is copied) RNA (mRNA, rRNA, or tRNA) 
polypeptide (chain of amino acids)
2) The Cell Cycle
DNA (all is copied)  chromosomes replicate (Interphase in S-phase)  chromosomes
separate (mitosis)  2 nuclei within 2 daughter cells (cytokinsesis)

Cellular Organization of Genetic Material

 Nucleotides: the genetic code/information within the genes of chromosomes
 39

1. Sugar (deoxyribose)
2. Phosphate
3. Nitrogenous base (Adenine --- Thymine ; Guanine ----Cytosine)
 DNA: polymers of nucleotides that contain genetic information
-Double helix
-DNA is the chemistry of chromosomes
 Chromosomes: structure that contains lots of genetic information. Chromatin condense into
chromosomes.
 Genes: bits of genetic information; sections of chromosomes
 Chromatin: DNA + proteins
-proteins = histones and nucleosomes  they aid in the coiling of DNA so that it can fit inside the
cell
Distribution of Chromosomes During Eukaryotic Cell Division
 Prior to cell division, a cell copies its DNA and each chromosome densely coils and shortens, forming
sister chromatids.
 Sister chromatids: 2 identical replicated chromosomes
-Centromere: where the 2 chromatids are most closely attached
-“Arms:” the side of the chromatid on either side of the centromere
 The 2 sister chromatids separate during mitosis and then the cytoplasm divides during cytokinesis,
producing 2 genetically identical daughter cells with equal numbers of chromosomes

Interphase: the period between division where the cell grows and duplicates its chromosomes
**lasts 90% of the cell cycle
-the individual chromosomes are not visible in the nucleus
-3 stages:

1. G1: “first gap” or prereplication

 Cell is assimilating: grows in terms of cytosol, membrane, organelles; takes in
nutrients; gets rid of waste
 Increases in size: the surface area to volume ratio gets smaller
 Genetic material appears in the form of chromatin (DNA +proteins)— appears as a
dark granular mass, so chromosomes can’t be seen individually
2. S phase: “synthesis”
 40

 Two centrosomes have formed by replication

-Centrosome = microtubule-organizing center
-In animal cells, each centrosome features 2 centrioles. But centrioles aren’t required for
normal spindle operation.
-Even though plants don’t have centrioles, they still produce spindle fibers which help to pull
the chromosomes apart
 Doubles the number of genes in the nucleus by DNA replication
3. G2: “second gap” or premitosis
 Organelles within the cell replicate
 Other materials needed for cell division are produced, like RNA, proteins, etc.
 Further condensation of chromatin happens but sister chromatids are still long and
skinny

M phase or Mitosis: the nucleus divides

Stages: prophase, prometaphase, metaphase, anaphase, telophase

1. Prophase
 The chromatin fibers become more tightly coiled, condensing into visible chromosomes.
 Each duplicated chromosome appears as 2 identical sister chromatids attached at their
centromeres
 The nucleoli “disappear” – it disperses during cell division
 Spindle fibers begin to form
-It is composed of the centrosomes and protein microtubules that extend from
them.
-Aster = the radial arrays of shorter microtubules that extend from centrosomes
 41

 Centrosomes move away from each other to opposite poles of the cell, propelled by the
lengthening microtubules between them

2. Prometaphase
 The nuclear envelope fragments.
 The spindle has formed from the centrosomes and microtubules
 Chromosomes are short and thick –have coiled back on themselves so it’s easier to move
around
 Each of the 2 chromatids of each chromosome now has a kinetochore, a specialized protein
structure located at the centromere.
 Kinetochore microtubules: attach to the kinetochores of chromosomes and jerk
the chromosomes back and forth
 Nonkinetochore microtubules (polar microtubules): don’t attach to
chromosomes and help to lengthen the cell
3. Metaphase
 The longest stage of mitosis, often lasting 20 minutes
 The centrosomes are now at opposite poles of the cell.
 Sister chromatids align at the equator or metaphase plate.
-The chromosomes’ centromeres lie on the metaphase plate.
-Chromatids move to the center due to the alternate tugging by the kinetochores
microtubules.
 For each chromosome, the kinetochores of the sister chromatids are attached to
kinetechore microtubules coming from different poles of the spindle
4. Anaphase
 The shortest stage of mitosis, lasting only a few minutes
 Begins when centromeres that join the sister chromatids spit and cohesin proteins are
cleaved
 Sister chromatids split to form separate chromosomes
 The 2 new chromosomes move towards opposite ends of the cell as their kinetochore
microtubules shorten.
 42

-Tubules depolymerize (=disassembled by enzymes) at their kinetochore end

-They look like V’s because the centromere is pulled towards the poles first
-The chromosomes continue to move until they have separated into two groups that are
each found near the poles of each of the spindles
 Ends when the chromosomes have stopped moving: now both ends of the cell have
equivalent and complete collections of chromosomes
5. Telophase
 Two daughter nuclei form in the cell.
 Nuclear envelopes reform from the fragments of the parent cell’s nuclear envelope and
other portions of the endomembrane system.
 Nucleoli reappear.
 The spindle breaks apart, forming centrosomes.
 Chromosomes become less condensed and uncoil to form a tangle of chromatin
 This marks the completion of mitosis.
Cytokinesis
 This is when the cytoplasm divides. It often occurs during telophase, so the 2 daughter cells
appear shortly after the end of mitosis.
 This results in the production of 2 identical daughter cells.
 In animal cells:
-cleavage furrow: pinches the cell in two
 In plant cells:
-cell plate: forms from the fusion of membrane vesicles derived from the Golgi
apparatus. The membrane of the enlarging cell plate joins with the plasma membrane,
separating the 2 daughter cells. The cell plate forms from the center of the cell outward.
-A new cell wall develops between the cells from the contents of the cell plate.
All cells don’t undergo cytokinesis. For example, skeletal muscle cells have multiple nuclei in
order to make more proteins and more ATP for movement and support.

Binary Fission
 Single-celled eukaryotes reproduce asexually by a process known as binary fission, which includes
mitosis.
 43

 The binary fission of prokaryotes does NOT include mitosis.

 The bacterial chromosome, a single circular DNA molecule, beings to replicate at the origin of
replication. One of these duplicated origins moves to the opposite pole of the cell.
 Replication is completed as the cell doubles in size, and the plasma membrane grows inward to
divide the 2 identical daughter cells.
-The mechanism of chromosome movement is not fully understood.

The Cell Cycle Control System

 The cell cycle control system coordinates the sequential events of the cell cycle
-Also called the “molecular clock”
-Important internal and external signals are monitored to determine whether or not the cell
cycle will proceed.
 The cell cycle has specific checkpoints where the cell cycle stops until a go-ahead signal is
received
1) G1 checkpoint:
-If a cell receives a go-ahead signal at this checkpoint, the cell continues on in the
cell cycle. Most cells go through this point because they have the necessary
chemicals to receive the signal.
-If a cell doesn’t receive a go-ahead signal, the cell exits the cell cycle and goes into
the G0 stage.
-the nondividing stage: cells don’t reproduce
-Example: brain and nerve cells
-Liver cells go into G0 but exit G0 and reproduce when the liver is damaged
2) G2 checkpoint:
-involves cyclins and Cdks (see below)
3) M checkpoint:
-requires an internal signal to pass through: the cohesins holding sister chromatids
together are not cleaved until all chromosomes are attached at their kinetochores
to spindle microtubules.

 2 types of regulatory proteins involved in cell cycle control:

 44

1) Cyclins
2) Cyclin-dependent kinases (Cdks)
-The combination of cyclin and Cdk allows the cell to pass through the G2 checkpoint and
into mitosis
-The activity of cyclin and cdk fluctuates during the cell cycle: it increases then drops off and
is produced in different amounts throughout the cycle

 Growth factors are certain nutrients and regulatory proteins that are essential for cells to divide
 Density-dependent inhibition: involves the binding of cell-surface proteins of adjacent cells, which
sends a growth-inhibiting signal to both cells
-aka: cells like to be next to each other
 Anchorage dependent: cells must attach to a substratum (=lower layer) in order to divide
-aka: cells need to be in layers

Loss of Cell Cycle Controls in Cancer Cells

 Cancer cells don’t respond normally to the body’s control mechanisms
 They don’t need growth factors to grow and divide:
- May make their own growth factors
- May convey a growth factor’s signal without the presence of a growth factor
- May have an abnormal cell cycle control system
 May be caused by environmental factors (chemicals and carcinogens) or genetic factors
 Benign tumor: harmless and noncancerous; can be surgically removed
 Malignant tumor: invades surrounding tissues and metastasize, exporting cancer cells to other
parts of the body through the blood and lymph systems, where they may form a secondary
tumor.
 45

Chapter 13
Offspring acquire genes from parents by inheriting chromosomes
Inheritance of genes
 The inheritance of traits from parents to offspring involves the transmission of discrete units of
information coded in segments of DNA known as genes
- Most genes contain instructions for synthesizing enzymes and other proteins that then
guide the development of inherited traits.
 Precise copies of an organism’s genes are packaged into gametes (=sperm and eggs)
 Upon fertilization, genes from both parent are passed on to offspring
 The DNA of a eukaryotic cell is packaged along with various proteins into a species-specific
number of chromosomes
- The genome is the entire complement of DNA.
- A gene’s locus is its location on a chromosome.
Comparison of Asexual and Sexual Reproduction
 In asexual reproduction, a single parent passes copies of all its genes to its offspring
- A clone is a group of genetically identical offspring
 In sexual reproduction, an individual receives a unique combination of genes inherited from 2
parents

Fertilization and meiosis alternate in sexual life cycles

Sets of Chromosomes in Human Cells
 In somatic cells there are 2 chromosomes of each type, known as homologous chromosomes or
homologs.
- A gene controlling a particular character is found at the same locus on each chromosome
or homologous pair
 A karyotype is an ordered display of an individual’s condensed chromosomes
- Isolated somatic cells are stimulated to undergo mitosis, arrested in metaphase, and
stained
- A computer uses a digital photograph to arrange chromosomes into homologous pairs by
size and shape
 Sex chromosomes determine the sex of a person:
- Females = 2 homologous X chromosomes
- Males = nonhomologous X and Y chromosomes
 Autosomes are chromosomes that aren’t sex chromosomes
 Somatic cells contain a set of chromosomes from each parent and are diploid cells.
 Gamete cells are haploid cells and contain a single set of chromosomes.

Behavior of Chromosome Sets in the Human Life Cycle

 46

 Fertilization is the fusion of sperm and ovum(=egg)

- Fertilization produces a zygote containing both paternal and maternal sets of
chromosomes
- The diploid zygote then divides by mitosis to produce the somatic cells of the body, all of
which contain the diploid number (2n) of chromosomes
 Meiosis is a special type of cell division that halves the chromosome number and provides a
haploid set of chromosomes to each gamete.
- Gametes are produced by meiosis from specialized germ cells in the gonads.
 An alternation between diploid and haploid numbers of chromosomes, involving fertilization
and meiosis, is characteristic of sexually reproducing organisms
 In sexual reproduction, meiosis and fertilization are complementary processes:
meiosis produces haploid gametes, while fertilization restores the diploid
chromosome number
Meiosis
 Nuclear division that results in gamete formation
 Converts diploid somatic cells (2n) to haploid gametes (n)
 Involves replication of chromosomes one time (during interphase)
 Crossing over may occur
-Homologous pairs may exchange pieces of DNA  mixing of maternal and paternal
genes when homologs are held together by the synaptonemal complex (synapsis)
**Allows unique gametes and increases variation
Homologous pairs: code for the same gene and same basic information, but the specific information
may be different. Homologous pairs carry the same genes, though they may have different alleles.
-Crossing over is visible in regions called the chiasmata where sister chromatids are held
together by sister chromatid cohesion
-Only occurs during prophase I

 Sister chromatids = identical (must be attached at centromere)

- The number of chromosomes varies in eukaryotes, but they all have an even number
because the set of chromosomes is divided in half: an individual gets a set of haploid
chromosomes from each parent which makes a diploid set of chromosomes for the
individual
- The cells of most organisms that reproduce sexually have pairs of similar chromosomes
called homologous pairs
 47

- Each parent provides one member of each homologous pair: they have 1 chromosome from
each set
- In humans, 22 homologous pairs are autosomes and there is 1 pair of sex chromosomes
-Sex chromosomes in males are NOT similar and are called nonhomologous  males
technically have 22 homologous pairs and 1 nonhomologous pair of chromosomes
 Sexual reproduction is when two different parent cells come together to produce one cell
and each parent cell gives half of their DNA
- most organisms are produced this way
- In asexual reproduction, the cells of parent and offspring carry identical sets of
chromosomes, but in sexual reproduction, two parents contribute chromosomes to
offspring.
-For this reason, the gametes that fuse during sexual reproduction are haploid and
carry half the normal number of chromosomes. If gametes were diploid, the number
of chromosomes would double in each generation
- Provides variation which is important because it helps a species survive. It allows at least
some of the species to survive if the environment changes
-Variation = the differences of individuals of the same species
-Traits that are beneficial to a species pass to offspring through fertilization
-Over time, it is possible for characteristics of a population to change over time: this
process is called evolution
 Meiosis occurs in 2 stages:
1) Meiosis I:
- Often called reductional division because it reduces the chromosome sets from two
(diploid) to one (haploid).
- **Homologous pairs separate**
- Results in 2 HAPLOID cells
- Phases: prophase I, metaphase I, anaphase I, telophase I/cytokinesis I
2) Meiosis II:
- Often called equational division because the chromosome number stays the same
- **Sister chromatids separate**
- Results in 4 HAPLOID cells
- prophase II, metaphase II, anaphase II, telophase II/cytokinesis II

The Stages of Meiosis

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Meiosis I
1. Interphase
 Chromosomes replicate  produces identical sister chromatids that remain attached at the
centromere.
- Sister chromatid cohesion is when sister chromatids are attached along their length
2. Prophase I
 Chromosomes begin to condense for the 1st time and homologous pairs form: they loosely
pair along their lengths, aligned gene by gene
 Tetrads may form – tetrads are sister chromatids that are homologous
 Crossing over may occur (=the exchange of corresponding segments of DNA molecules by
homologous pairs)
- Is completed while homologs are in synapsis, held together by proteins along their length
- Forms chiasmata = points where crossing over has occurred
 Synaptonemal complex: “mesh” of spindle fibers to exactly align the chromosomes
-Synapsis ends mid-prophase and chromosomes in each pair move apart slightly
 Centrosomes move apart, the spindle begins to form, and nuclear envelope breaks down
 Each homologous pair has 1 or more chiasmata and the homologs are still associated due to
cohesion between sister chromatids (=sister chromatid cohesion)
 In late prophase I, microtubules attach to the 2 kinetochores (=protein structures at the
centromeres of the 2 homologs). The homologous pairs then move toward the metaphase
plate
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3. Metaphase I
 Pairs of homologous chromosomes line up on the metaphase plate (NOT individual
chromosome) with their kinetochores attached to spindle fibers from opposite poles.
- one chromosome in each pair faces each pole
 Both chromatids of one homolog are attached to kinetochore microtubules  those of the
other homolog are attached to microtubules from the opposite pole

4. Anaphase I
 HOMOLOGOUS PAIRS SEPARATE
 Breakdown of proteins responsible for sister chromatid cohesion along chromatid arms
allows homologs to separate
 The homologs move toward opposite poles, guided by the spindle apparatus
 Sister chromatid cohesion persists at the centromere causing chromatids to move as a unit
toward the same pole
5. Telophase I and Cytokinesis
 RESULTS IN 2 HAPLOID CELLS
 Each chromosome is a sister chromatid
 Cytokinesis usually occurs simultaneously with telophase 1
 In some species, chromosomes de-condense and the nuclear envelopes re-forms
 No replication occurs between meiosis I and meiosis II
Meiosis II
1. Prophase I
 A spindle apparatus forms
 In late prophase II, chromosomes (=2 sister chromatids attached at the centromere) move
toward the metaphase II plate
2. Metaphase II
 The chromosomes are positioned on the metaphase plate as in mitosis
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 Because of crossing over in meiosis I, the 2 sister chromatids of each chromosome are NOT
genetically identical
 The kinetochores of sister chromatids are attached to microtubules extending from opposite
poles
NOTE the difference between Metaphase I and II

3. Anaphase II
 SISTER CHROMATIDS SEPARATE
- These sister chromatids aren’t genetically identical because of crossing over
 Breakdown of proteins holding the sister chromatids together at the centromere allows the
chromatids to separate
 The chromatids move toward opposite poles as individual chromosomes
4. Telophase II and Cytokinesis
 Nuclei form, the chromosomes begin decondensing, and cytokinesis occurs
 The meiotic division of 1 parent cell produces 4 haploid daughter cells
 The 4 daughter are not identical cells – they’re genetically distinct
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A Comparison of Mitosis and Meiosis

Meiosis Mitosis
 Produces HAPLOID daughter cells that  Produces DIPLOID daughter cells that
differ identically from their parent cell are genetically identical to the parent
and from each other cell
 Involves 2 nuclear divisions  Involves 1 nuclear division
 Crossing over may occur during  Crossing over does not occur, so
prophase I chromosomes are IDENTICAL
 In metaphase I, chromosomes line up in  In metaphase I, chromosomes line up as
pairs on the metaphase plate individuals on the metaphase plate
 During anaphase I, homologous pairs  During anaphase, sister chromatids
separate separate
 Homologs separate in anaphase I. Sister  Sister chromatids separate during
chromatids are held together till anaphase I.
anaphase II.

Genetic Variation
Meiosis introduces variation in 3 ways:
1. Crossing over – allows genes from the mother to be exchanged with genes from the father
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-Forms recombinant chromosomes in gametes with new genetic combinations of

maternal and paternal genes on the same chromosome  **chromosomes are no
longer identical
2. Independent assortment – the random distribution of maternal and paternal chromosomes
from each homologous pair
-Chromosomes can separate in different combinations because each parent provides
one member from each homologous pair, but we don’t know which one will be used.
-Each homologous pair lines up independently at the metaphase plate – but the
orientation of the maternal and paternal chromosomes is random.

-The number of possible combinations of maternal and paternal chromosomes in

gametes is 2n (where n is the haploid number)
- In humans with n=23 there are over 8 million possible different gametes (223).
3. Random fertilization – the random pairing of one out of many sperm to one egg
Any 2 human parents will produce a zygote with over 70 trillion (223 x 223) diploid combinations
4. Mutations – any change in the sequence of nitrogenous bases in DNA
*This is not always from meiosis – it is the original source of genetic variation

Evolutionary Significance of Genetic Variation within Populations

 In Darwin’s theory of evolution by natural selection, genetic variations present in a population
result in adaptation
 The individuals with the best variations best suited to an environment produce the most
offspring (=survival of the fittest)
 The process of sexual reproduction and mutation are the sources of this variation
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Human Gametogenesis
 Gametogenesis is the production of gametes by meiosis. It differs in males and females.
Human Spermatogenesis
 Results in 4 equal haploid spermatids  cell division is equal and continuous
 Sperm cells are haploid
 Occurs continuously in the seminiferous tubules of the testes as spermatogonia.
- The primary spermatocyte divides in MEIOSIS I into 2 secondary spermatocytes which
divide in MEIOSIS II to form 4 spermatids.
Human Oogenesis
 Meiotic cytokinesis in unequal: results in 1 large ovum and up to 3 small polar bodies
- The primary oocyte divides into 2 unequal cells in MEIOSIS I: the 1st polar body and the
secondary oocyte
- The secondary oocyte divides into 2 unequal cells in MEIOSIS II: the 2nd polar body and
the ovum or egg
- The ova or egg cell is haploid and survives; the haploid polar bodies will disintegrate
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