Unit III, 810

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Unit III, 8-10
Chapter 8, Energy, Enzymes and metabolism
I.     Energy Section 8.1, p. 146
A. Definitions for discussion kinetic energy,
potential energy, thermodynamics, Kcal
(kilocalorie), joule, first law of
thermodynamics, second law, entropy, free energy,
endergonic, exergonic, catalysis B. Discussion
1. If an enzyme cannot cause a reaction to
occur, of what use is it?
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2. Give an example of entropy that makes sense to
you. 3. A wagon is at the bottom of a hill and
you want it to be at the top of the hill. Give a
one word description of the type of reaction that
must occur for this to happen 4. Explain the
difference between kinetic and potential
energy. 5. The study of energy (heat changes) is
? 6. When an atom or molecule loses an electron
it is oxidized. Why do they call it oxidation?
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C. Energy 1. First law of thermodynamics total
energy in the universe is constant. (energy is
neither created nor destroyed)
2. Second law total usable energy in a system
decreases as energy conversions take place (given
off as heat). This increases entropy
(randomness, disorder)
3.Free Energy a. free energy the amount of
energy available to break and reform bonds.
b. the change in free energy usable energy in
products minus usable energy in reactants ?G
(assuming standard conditions of temp (25C),
pressure (1atm), and pH (approx. 7).
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c. the energetics of reactions 1) -?G
exergonic reaction, energy releasing
2) ?G endergonic reactions, energy requiring
d. Coupled reactions endergonic reactions can
occur when coupled to series or pathways of
reactions that are exergonic (domino effect)
e. Forward and back reactions have a typical
relationship or balance, that is not necessarily
proportional to amount of product or reactant,
but to the energy of the system moving in one
direction or another. This is defined as the
equilibrium constant  Keq Product
concentration (C D)
Reactant concentration (A B)
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If Keq 10, at equilibrium there will be 10
times more CD than AB
4. Activation Energy a. reactions only occur when
there is enough energy to break existing bonds
and from new ones, called activation energy.
b. Catalysts lower activation energies so more
molecules can react but
1) Dont get used up themselves
2) Dont cause unfavorable reactions to happen
3) biological catalysts enzymes
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D. Enzymes, 8.2, p. 150 1. Characteristics and
function how and why they lower activation
energies a. specificity
1) enzymes catalyze only on type of reaction
2) an enzyme interacts with only one type of
molecule, the substrate, example lactase acts on
lactose
b. active sites a place or area on a protein
that is determined by its tertiary structure.
Substrates bind to a specific active site of a
specific protein (old lock and key theory).
After a substrate binds its shifts tertiary
structure which may enhance (or inhibit) farther
bonding at other molecules. Know as induced fit
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c. formation of complexes enzyme substrate
yields enzyme-substrate complex yields product
enzyme E S ?? ES ??E P
d. Enzymes can increase local concentration of
molecules can get two molecules close to each
other so collision more likely.
e. enzymes can position molecules in relation to
each other so they can bond.
f. all characteristics above allow more molecules
to react at any given time and therefore lowers
activation energy
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2. Factors affecting enzyme activity a.
temperature optima is 35-40C after which enzyme
(protein) denaturation occurs. Why? All human
enzymes have same temp. optima
b. pH optima tertiary bonds (especially ionic)
are also affected by H as in pH. 1) pH optimum
for most animals about 6-8 but varies with
location, e.g. plants are usually more acidic
pH 5-9, stomach enzymes have much lower pH optima
(see fig. 8.8, p. 152
c. Enzyme inhibition/activation 1) competitive
inhibition a molecule other than the usual
substrate binds in the active site and blocks
normal product formation
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a) reversible increasing substrate
concentration can change inhibition
b) irreversible same molecules permanently
block active site, e.g. poisons
2) Allosteric effects (alloother, steric site)
Molecules bind on an enzyme somewhere other than
the active site but still affect site by altering
tertiary structure. a) inhibits substrate binding
aka noncompetitive inhibition
b) activators bind and actually enhance enzyme
activity
3. Cofactors molecules that assist in enzyme
function
a) metal ions can pull electrons away from
substrate molecules because of their charge,
example, Zn 2, Fe 2, Mg 2 (in chlorophyll and
stabilizes kinases that make ATP)
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b. coenzymes cofactors that are non-protein
organic molecules. Often operate to transfer
electrons between molecules, therefore are redox
pairs. Example   
(Oxidation)
(Reduction)
4. Other enzyme considerations a. multienzyme
complexes some enzymes are thought to associate
in complexes which increases efficiency of
catalytic events by increasing concentration of
reactants, decreasing competing reactions,
operating as a unit.
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E. ATP adenosine triphosphate 1. structure a.
one nitrogen base adenine
b. one sugar ribose
c. one three phosphate group
1)phosphate functional group, PO3, 2-, aka
inorganic phosphate, aka Pi
d. a and b adenosine
F. Metabolic Evolution 1. Theory for biochemical
pathway evolution (p. 156) as raw materials
in environment (reactants) run out, others are
added to give products over billions of years
entire pathways evolved.
2. Regulation Feedback. Commonly end product
inhibition but there are variation on the type of
feedback
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3. Proposed evolution of metabolism
F ? H G
E ? F ? H G
D ? E ? F ? H
G
C ? D ? E ? F ? H
G
So over time, what started out as a simple, one
step reaction, turned into a more complex, series
of reactions.
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4. ATP hydrolysis liberates 7 Kcal/bond a. used
to do work of cell
b. drives endergonic reactions
c. phosphorylates
d. can cause couple reactions
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Chapter 9, p. 162-182   I. Cellular Respiration
Overview A. Breakdown of C-H bonds of glucose
and transfer of hydrogen atoms to oxygen yields
energy stored in the form of bonds of ATP.
Overall
C6H12O6 6O2 H2O ? 6CO2 12H2O
Energy
B. Cellular Respiration the big picture see
diagram in notes
Glucose (broken down in cytoplasm) ? thru
glycolysis ? 2 pyruvic acid molecules.
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B. Cellular Respiration the big picture see
diagram in notes
Glucose (broken down in cytoplasm) ? thru
glycolysis ? 2 pyruvic acid molecules.
(With oxygen)
(Without oxygen)
Anaerobic Fermentation - cytoplasm
Aerobic cellular respiration
Gives off
Krebs cycle (matrix of mitochondria)
Ethanol (yeast)
Lactic acid (animal muscle cells)
Electron transport chain (ETC) in cristae of
mitochrondria
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C. The Stages of Cellular Respiration 1.
glycolysis glyco (sugar) lysis (splitting)
a. occurs in the cytoplasm of all cells
b. 10 reactions catalyzed by specific enzymes
c. Energy is obtained from breaking the C-H bonds
of glucose
d. overall glucose (6 carbons) yields 2
molecules of pyruvic acid (3 carbons)
e. Main events in glycolytic pathway 1) Steps 1,
3 require energy (ATP) energy of activation
2) Steps 6, 7, 10 yield energy and there is a net
gain of energy
3) 6 C yields two 3 C molecules (G3P) at steps 4
and 5. This step is important because after this
step, everything happens times two.
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4) Phosphate from ATP are added to sugars
(phosphorylation). Also DHAP yields G3P quickly
f. Energy balance sheet for glycolysis 4 ATP
produced (steps 7, 10) minus 2 ATP used (steps 1,
3) Net yield 2 ATP   Also 2 NADH produced (step
6)   2. Oxidation of pyruvate (pyruvic acid). See
fig. 9.10, p 169 a. the reaction (see
transparency, slide 35)
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b. see hand notes
Acetyl CoA ? High ATP ? Fatty acid synthesis ?
fat storage
Acetyl CoA ? low ATP ? stimulates aerobic
respiration ? proceeds to mitochondria/Krebs
c. Energy yield from oxidation of pyruvate NADH
(2 per molecule of glucose)
3. Aerobic Respiration Mitochondria a. Krebs
cycle aka citric acid cycle aka tricarboxylic
acid cycle
1) occurs in matrix of mitochondria
2) generates 1 ATP (via GTP) per turn by
substrate level phosphorylation
3) generates large amounts of stored energy in
the form of NADH (higher energy) and FADH2 (lower
energy)
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4) Initial reaction (see notes)      Acetyl CoA
(2 carbons) Trioxaloacetate or OAA (4
carbons) ? Citric Acid
5) Cycle gives off carbon dioxide
6) OAA concentration must be high for cycle to
occur because it starts the cycle (primer) and
ends the cycle (must be regenerated).
7) Two turns of Krebs/molecule of glucose.
(because in step 4, 5 of glucose 6 carbon yields
two 3 carbons)
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8) At the end of Krebs all original C-C and C-H
bonds of glucose are broken
9) Energy balance for Krebs only
per turn per
molecule of glucose 1 ATP
2 ATP 3 NADH 6 NADH 1
FADH2 2 FADH2
b. Electron Transport Chain ETC
1) Based on flow of electrons electrons are
passed from glucose (originally) to oxygen
(ultimately) in a series of steps with electrons
falling i.e. releasing stored energy at each
step
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2) This occurs through a series of oxidation
reduction reactions in the inner mitochondrial
membrane, the cristae.
3) Enzymes take 2 e- and 2 H (i.e. 2 H atoms)
from glucose
Glucose
2 electrons H
1 H goes into surrounding area, or intermembrane

NAD, becomes NADH (has 2 electrons to give)
ETC
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4) The etc is a series of 5 membrane associated
proteins embedded in the cristae. Electrons from
NADH and FADH2 move from protein to protein in a
series of redox reactions
5) Mechanics of ETC fig. 9.15, p 174 Summary of
events -Electrons from NADH go to NADH
dehydrogenase
-Electrons are passed to next molecule,
ubiquinone (Q) while protons, H are released in
intermembrane space
-FADH2 starts at Q (misses first step therefore
begins at lower energy level)
- Electrons are passed through the series of
enzymes and molecules (Ccytochrome) until are
given to oxygen, yielding water
-Protons, H, build up in intermembrane space,
creating a proton gradient or electrochemical
gradient.
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6) ATP production result of chemiosmosis
-ATP synthase (aka ATP synthetase and ATP
coupling factor and ATPase) is a channel protein
i.e. embedded in crisate
-H ions move with the concentration gradient
(i.e. osmosis of H or chemiosmosis from outside
the cristae (inner matrix)
-Energy released in this process enables ADP
become phosphorylated ADP Pi yields ATP, called
oxidative phosphorylation
-For every 2 e- from NADH, 3 ATP -For every 2 e-
from FADH2, 2 ATP
D. Summary of Aerobic Respiration (Know fig.
9.18, p 176, the theoretical ATP yields at each
step
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E. Regulation of Aerobic Respiration Feedback
signals from both ADP and ATP. Overall, high ADP
levels and/or citrate levels stimulate
phosphofructokinate (glycolysis). High ATP
levels and/or high NADH levels inhibits
glycolytic enzymes
II. Catabolism of proteins and fates (the other
food molecules) fig 9.3, p 178 A. Proteins (see
transparency)
Polypeptide ? AA (deamination or taking off a NH2
group) ? carbon chain ? kreb and glycolysis
intermediaries
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B. Cellular Respiration of fats (see
transparency)

• In the matrix lipids either become
• Gylcerol or
• 2. Broken down into fatty acids (chains) ? 2
  carbon pieces (acetyl groups) ? acetyl CoA.

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III. Fermentation Anaerobic respiration A.
Characteristics 1. Occurs in the cytoplasm
2. is pathway for the conversion of pyruvic acid
to either ethanol or lactic acid
3. small amount of ATP are generated (indirectly
through the oxidation of NADH to NAD, which
drives the reaction)
4. Includes strict anaerobes (bacteria) and
facultative anaerobes i.e. cells that can
switch from aerobic to anaerobic respiration
(animal muscle cells)
B. Examples of Fermentation overhead 1. Yeast
(bacteria) yields beer, wine (ethanol) Why does
balloon wine work?
2. Animal muscle cells in oxygen debt yields
lactic acid
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Chapter 10 photosynthesis   I. Definitions for
discussion absorption spectrum, carotenoids,
carbon fixation, photorespiration, CAM, C3, C4,
photosystem, reaction center, antenna complex,
cyclic phosphorylation, photosystem II, I   II.
Discussion 1. Blackman (1905) discovered 2 phases
to photosynthesis first dependent on light not
affected by temperature   second dependent on
temperature but only up to about 35 C   In each
phase, the reactions involve the interaction of
what substances that could account for these
results?
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2. Originally, it was believed that in the
overall equation for photosynthesis that O2
product came from CO2 i.e.   CO2 H2O light
? Carbohydrate (CH2O) oxygen (given
off)   Later it was discovered (Van Niels) that
the oxygen came from water and could actually be
substituted for by other oxidizable substances
like sulfur.   CO2 H2S light ? Carbohydrate
(CH2O) S2 (given off)   How did they figure
that out? Using what technique?
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III. Photosynthesis A. Light characteristics
of 1. Light is both particles of energy (or
photons) AND waves of electromagnetic radiation.
The two models together are used to explain the
behavior of light organisms.
2. White light is a mix of colors and forms
making up the visible spectrum
3. Wavelengths of light, ?(lambda), are
reflected, absorbed or transmitted by plants
4. Only light in the visible spectrum contains
the right amount of energy to transfer electrons
(p. 188) between molecules in living
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5. radio waves and infrared waves dont have
enough energy, electrons dont move enough
6. UV, Xrays, and gamma rays have too much energy
knocks electrons out of orbit
7. Specific atoms absorb only certain photons of
light relative to their own available energy
levels. this can be seen in its characteristic
absorption spectrum.
B. Pigments molecules that absorb light well 1.
chloroplasts the only pigment that directly
converts light energy to chemical energy by
boosting electrons to higher energy levels. See
fig. 10.6, p 190. The phosphorylation of Chl a
b is like the heme group in RBCs. In Hb-Fe is
cofactor, in chlorophyll ?
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2. Other pigments chlorophyll b, carotenoid,
xanthophyll are accessary pigments- they absorb
light at other ? and shift it to chl a.
C. Photosynthesis the big picture 1. The
photosynthetic reaction 6CO2 12H2O light ?
C6H12O6 6H20
2. Photosynthesis occurs in two main phases a.
light reaction (light dependent reactions)
consists of light capturing, electron transport,
chemiosmosis (ATP production)
b. Light independent reactions energy made in
light reactions used to systematically reduce CO2
to make sugars (Carbon fixation).
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D. The stages of photosynthesis 1. The light
reactions a. light is trapped in photosystems (2)
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b. photosystems are embedded in the inner
chloroplastic membranes (thylakoids) of most
organisms. EXCEPTION bacteria have no
chloroplast, but can be photosynthetic. Why?
Photosynthesis take place in the plasma membrane
c. Two photosystems (ps) PS II (lower energy)
P680 PS I (higher energy) P700 P pigment 680,
700 ? of light in nm absorbed by each pigment
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d. cyclic photophosphorylation purple sulfur
bacteria
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d. The stages of photosynthesis   1) Light hits
the photosystem
2) Pigments absorb light and pass it to Chla in
the reaction center P870
3) Electrons are boosted to a higher energy level
4) As electrons are passed through a series of
oxidation reduction reactions, energy to form ATP
is released (same mechanism as etc)
 5) Electrons return to the photosystem
6) This presumably gave rise to a 2-step system
called the Z scheme seen in modern plants
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e. The z scheme modern plants
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1) water splitting water is broken down by a
water splitting enzyme (z). The e- from hydrogen
are donated to reaction center of PSII and
oxygen is given off. Light hits the reaction
center, chla boosts electrons to a higher energy
level
2) Electrons are passed through a series of
oxidation-reduction reactions to lower energy
levels while a proton (H) gradient forms in the
stroma on the INSIDE of the thylakoid membrane.
3) Electrons are donated to PSI, light hits PSI
and the process repeats itself. Note that PSI is
at a higher energy level than PSII
4) The final electron acceptor is NADP which is
converted to NADPH NADP H ?
NADPH occurs in the presence of NADP reductase
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5) For every 2 e- from water, 1 ATP is produced
in the light reaction by photophosphorylation.
NADPH is generated and sent to Calvin cycle
(light independent reactions)
6) ATP production is by chemiosmosis same as
etc except the ATPsynthase is oriented in the
opposite direction (i.e. H flows from inside to
outside)
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f. Light Independent Reactions aka calvin cycle
aka carbon fixation 1. Overall (see notes)
3CO2 (1 carbon) 3 RuBP (5 carbons
ribulosebiphosphate) In presence of rubisco or
RuBP carboxylase
6 PGA (phosphglycerate)
(Over multiple reactions)
G3P (glyceraldehyde 3 phospate) ? ? Glucose
RuBP (5c, regenerated)
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2. Summary of events of Calvin cycle a) The
Carbon source is CO2 therefore is a 1-1 ratio for
every 3 carbon molecules, 3 CO2 need to go into
the system. RVBP (5C0 must be regenerated.
b) This process uses a lot of energy (9ATP for
every 3 CO2), energy is stored in the bonds of
glucose which translates into very good
efficiency
c) The key enzyme, rubisco or RUBP carboxylase
fixes CO2. This is a key regulatory enzyme and
has some unusual properties -adds a carboxyl to
RUBP
-can bind both CO2 and O2 as substrate
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E. Photorespiration rubisco binds oxygen
instead of carbon dioxide. If the sun is hot and
stomates are closed, O2 builds up inside the
plant. (Recall water splitting with evolution of
oxygen is the first reaction of the light
reaction). If O2 binds, no CO2 bind, no sugars
produced therefore decline and/or death of plant.
Two strategies have evolved in plants to deal
with
1. Crassulacean acid metabolism (CAM). Stomates
stay closed during day, but open at night
(opposite of normal) CO2 is taken from organic
molecules at night. Examples succulents (water
storing, like cactus, pineapple, etc)
2. C4 pathway normal intermediates in Calvin
cycle are 3 carbons (C3) in this pathway 4C
pieces help out, hence the name c4 metabolism.
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a) Mechanism spatial separation of light
dependent and independent reactions
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1) chloroplasts of mesophyll cells carry on
light-dependent reactions, while chloroplasts of
bundle-sheath cells carry on Calvin cycle
2) Advantage a different carboxylase, PEP (not
Rubisco) picks up CO2 in mesophyll cells of C4
plants. PEP carboyxlase does not bind O2,
therefore it can easily pick up CO2 and carry it
to bundle sheath cells without being inhibited
b) Hot conditions, stomates closed see drawing on
board
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c. The 4 C pieces move to chloroplasts of bundle
sheath cells and clip off CO2
d. CO2 goes into regular Calvin cycle where
rubisco catalyzes CO2 fixation. There is no O2
present down here so no inhibition
F. Summarize energy cycle and relationship
between those life cycles
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