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Metabolic pathways unit study guide (chapters 8, 9, 10, 40, 44)

Chapter 8: More about enzymes and chemical reactions
Vocabulary:
metabolism (catabolic vs. anabolic), free energy (ΔG), entropy, exergonic vs. endergonic,
ATP vs. ADP, phosphorylation, activation energy, feedback inhibition

Concepts:
8.1 – Basics of energy transformation
--respiration is one example of a / an catabolic metabolic pathway in metabolism,
while photosynthesis is one example of a / an anabolic metabolic pathway

--principles to keep in mind when thinking about energy:

--1st law of thermodynamics – energy is never be created or destroyed instead it is just
Transferred or transformed from one form to another

--2nd law of thermodynamics – any time this happens above (1st law),
energy is also produced spontaneously

--or, the entropy of the universe always increases – we highly ordered biological systems
must constantly obtain new energy and spend some of it to maintain our order

--so if organisms are constantly transforming energy sources and losing some of
it, where do (most) ecosystems get a new source of energy? Sun/making it.

There are two separate discussions about how chemical reactions work in this chapter:
1) Whether a chemical reaction will happen at all (and how ATP helps) – 8.2 / 8.3
2) How fast a chemical reaction occurs (and how enzymes help) – 8.4

8.2 – Free energy and whether a chemical reaction happens by itself

∆G = ∆H - T∆S
--you will learn more about H and S in a chemistry course, let’s just focus on G

--a reaction with overall (-) ∆G is called an spontaneous/exothermic reaction

--draw an energy diagram of a reaction with (-) ∆G below (fig. 8.6a is the right
idea, though I like a line from fig. 8.14 better – also label what ∆G is)
free energy
(Joules)

progress of reaction
--circle the correct word in each pair:
the products are (higher / lower) in energy and thus (more stable / less stable),
this overall reaction will be (spontaneous / nonspontaneous)
written by Kevin Bleier
Milton High School
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--a reaction with overall (+) ∆G is called an endergonic reaction

--draw an energy diagram of a reaction with (+) ∆G below (label what ∆G is in diagram)

free energy (Joules)

G

progress of reaction
--circle the correct word in each pair:
the products are (higher / lower) in energy and thus (more stable / less stable),
this overall reaction will be (spontaneous / nonspontaneous)

--remember, that does NOT imply anything about how FAST a reaction occurs
ex: 2 H2O2  2 H2O + O2 is exergonic, but very slow if not catalyzed by peroxidase

8.3 – ATP and helping endergonic reactions happen in cells

--from last unit – I can think of two types of proteins that we discussed already that require ATP
energy to function – name them and what they do

carrier proteins- change the shape of some molecules with ATP to allow them into the cell.
pumps- pumps molecules across the concentration gradient.
Motor Proteins-allow vesicles to travel across the cytoskeleton

How ATP’s structure relates to its function:

--what does the abbreviation ATP stand for?
Adenosine triphosphate
--draw a basic diagram of ATP’s structure (figure 8.9a)

Triphosphate Adenine

Pentose ATP  ADP + Pi

--the above equation is very exergonic – why is the ATP reactant so unstable? (relate
ATP’s structure relates to function .. also left middle p. 149)

The three phosphate groups are all negatively charged and want to repell each other.

--review – this is hydrolysis reaction involving the breakup of a phosphate molecule

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--usually cells do not hydrolyze ATP by itself – instead, we will add the broken P group to a
protein or a reactant – this is called phosphorylation intermediate (bottom right p. 149)

--drawing time again! draw a typical endergonic reaction, then re-draw the reaction when
ATP phosphorylates the reactant.

free energy (Joules)

progress of reaction
exergonic / endergonic
--this is called energy coupling (fig. 8.10 caption) – using _______________ ATP
hydrolysis to help power an _________________ chemical reaction
exergonic / endergonic

(make sure to contrast this with what enzymes do – section 8.4)

-enzymes change the activation energy needed, so they do not change the energy
in the products or reactants.
Regenerating ATP:
--if cells are constantly spending ATP as described above, they need to be able to regenerate it

ADP + Pi  ATP

--the above reaction is very endergonic, why?

-This reaction is endergonic because it takes energy to create the bond between the three
phosphates and make ATP more unstable.

--so what is the source of free energy to help this reaction occur? (figure 8.12 is too
broad, find in the text p. 151 bottom left)

-cellular respiration, catabolic reactions

--note fig. 8.12 carefully, then connect it with fig. 1.9 on pg. 7 – ATP is the common energy
currency for ALL cells (common ancestry)
--extra: are there other carriers besides ATP? yes (GTP, cAMP, but not for this course)
Energy is put into the plant and is converted from ADP and P to make more ATP in cell
respiration, and then which is then expended by reactions within the plant. When energy is used
it is converted back to ADP and P when it is expended as heat.
8.4 – Enzymes and the speed of a chemical reaction
--what determines how fast a reaction occurs? activation energy (Ea) and the transition state (TS)
draw an exergonic reaction below and label TS and Ea (figure 8.14 will help)
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(make sure you see that Ea and ΔG are different)
--now re-draw your reaction diagram to show the effect of an enzyme on energetics
(please note how this is DIFFERENT than the ATP drawing above)
-this reduces the activation energy not the delta G

free energy (Joules)

progress of reaction

--what causes an activation energy barrier? It is caused because an energy state is needed
to be reached for bonds to break becyase that takes energy. When new bonds are made,
energy is released because the molecules are made more stable. Since the amount of
energy is released more than the energy consumed it is exergonic. Activation energy is
determined by the amount of energy needed to reach the state where bonds can break.
why is any transition state so unstable? Transition state is so unstable because it is the
point where reactants have absorbed enough energy for the bonds to break.
(discussed p. 152 and blue captions figure 8.13)

--you can read about how enzymes lower the Ea barrier p. 154, but no details necessary

--regulating enzyme activity: feedback inhibition (figure 8.21, section 8.5) – often the best
inhibitor for a series of enzymes (or a long metabolic pathway) is the product

--this molecule typically binds at the allosteric site site of an early enzyme to
shut the pathway off

--is this a form of negative or positive feedback? Negative.

--we will see an example of this in respiration (pg. 181, fig. 9.20)

Chapter 9: Cell respiration

Vocabulary:
oxidation vs. reduction, NAD+ and NADH, electron transport chain,
substrate-level vs. oxidative phosphorylation, cytochrome, chemiosmosis, ATP synthase, aerobic
vs. anaerobic, respiration vs. fermentation, facultative anaerobe vs. obligate anaerobe

Concepts:
9.1 – Overview of respiration
--write the word equation for the overall summary of respiration
C6H12O6+6O2 6CO2+6H2O
(respiration is a multi-step process)
--write the balanced chemical formula for the overall summary of respiration
p. 164 – identify sugar
+oxygen carbon dioxide+water- oxygen is reduced, and sugar is oxidized.
which reactant is
being reduced
and which is
oxidized
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(respiration is a multi-step process)

--how can you remember these formulas? think about what you take in (food & oxygen) and
what you breathe out (carbon dioxide & water – think about breath fogging up a cold window)
--now let’s explore respiration in more detail:
glycolysis (always)

if no O2 present if O2 present

citric acid cycle

fermentation (or Kreb’s cycle) = respiration

electron transport chain /

chemiosmosis

--respiration / fermentation generate ATP in two broad ways (fig. 9.6 bottom):
1) while cutting up sugar, getting phosphates to attach to ADP
= substate-level phosphorylation

2) (respiration only) using energy from high-energy electrons to combine free-floating

phosphates to ADP = oxidative phosphorylation
--we will track the movement of these high-energy electrons as they are extracted
from glucose … we will talk about one main “shuttle” (fig. 9.4)

--when the shuttle is carrying 2 high energy e-s, it is called NADH

--after the shuttle drops off the 2 high energy e-s, it is called NAD+

(note: there is another molecule that does the same job in the citric acid cycle called
FADH2 – fig. 9.11 – but we will consider them to be the same for our purposes)

9.2 – Cutting up sugar, step 1 – glycolysis glyco =sugar lysis = splitting

--where does glycolysis take place inside ANY cell? (fig. 9.6) cyloplasm
(figure 9.8 net results will help you with table below)
In to glycolysis (no #s needed, net results) Out of glycolysis (no #s needed, net results)
1) glucose becomes 1)2 pyruvate, 2h2o
becomes
2) 4ATP-2ATP 2)2ATP
becomes
3) 2 NAD++4e-+4H+ 3)2NADH+2H+
--skim figure 9.9 to appreciate how many enzymes (note the –ase endings) are required

9.3 – Cutting up sugar, step 2 – citric acid cycle (aka Krebs cycle)
--bottom p.168, only if oxygen is present, then citric acid cycle is next
--if not, fermentation is next (section 9.5)

--in eukaryotes, the citric acid cycle is run by a series of enzymes contained within the
innermost space of the mitochondrea
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--prokaryotes don’t have this organelle – they have these enzymes in their cytosol.

(figure 9.11 will help you with summary below)

Into citric acid cycle (no #s needed) Out of citric acid cycle (no #s needed)
1) 2pyruvate + 4 O2 becomes 1) 4CO2

2) 6NAD+ and 2FAD becomes 2) 2FADH2 and 6NADH

becomes
3) 2 ADP+2P 3) 2ATP
--this is a cycle because the cell can feed in more pyruvate to reconstruct a larger sugar and cut it
up again to harvest more high energy electrons (assuming pyruvate and O2 available)

--again, look how many enzymes are required

--big picture summary: in glycolysis and citric acid cycle, cells start with ___________ energy
and finish with a small amount of _______ energy and a large amount of __________
energy (which is really just carrying energy in the form of high-energy
______________)
--at this point, the cell is finished cutting up sugar – it has been turned into _______,
which just diffuses out of the cell (remember, it is a small, nonpolar molecule)
9.4 – Making lots of ATP – electron transport chain and chemiosmosis
--these steps are run by proteins embedded in membranes
--in eukaryotes, this is in the inner membrane of the mitochondrea
--in prokaryotes, this is in their only membrane: cell membrane

--why is it useful to have such a highly folded inner membrane for respiration (or for some
prokaryotes, a highly folded cell membrane (see fig. 27.8a p. 571)?

It allows for more surface area and more copies of the ETC meaning more cell respiration.

--helpful hint for discussion below: an abbreviation for electrons is e- and an abbreviation
for protons is H+ (so electrons and protons are DIFFERENT particles!)

--electron transport chain: NADH transfers high energy e-s to the electron transport
chain, a series of transport proteins that use the electron energy to power active transport
of H+ (p. 174 right column)

--what happens to NAD+ molecules after dropping off the high energy e-s?
-they return to cytoplasm and the krebs cycle to be used again.

--after the energy of the high-energy e-s has been spent by the transport protein chain,
oxygen must be there at the end to pick up the low-energy electrons and
get rid of them – this molecule becomes H2O after picking them up

(we have to take the electrons away or the assembly line stops (this is why we
need that molecule above in respiration overall)
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--at the end of this step, energy is now stored in the form of a large concentration of
H+ ions that now occupy which area in eukaryotes?

circle one: cytoplasm intermembrane space mitochondrial matrix

--chemiosmosis:
--there is now an imbalance of ions from the step above – they now move back
to the other side through the protein ATP synthase

--recall that moving from high  low concentration through a transport protein
was called passive transport.

--this movement is important because it powers the combination of ADP and

P at this protein to make ATP
(recall that electricity is just the flow of charged particles)

Going in to ETC / chemiosmosis Produced from ETC / chemiosmosis

(no #s needed (no #s needed
1) ADP+P becomes 1) ATP
becomes
2) NADH FADH2 2) NAD+ and FAD+
becomes
3) O2+H+e- 3) H2O
9.5 – Fermentation (the other way to break down glucose)
--fermentation takes place after the broad step of glycolosis if no O2 is present
(see flow chart above or your book)

--if fermentation produces no additional ATP, why do it? (p. 178 mid left)

-when there is no oxygen, or ETC there is still away to produce energy.

--2 possible byproducts of fermentation depending on the type of organism

(contrast this with citric acid cycle … we CANNOT fully break down glucose here):
a) alcohol produced by yeast (many bacteria in anerobic conditions)(what type of
organism)
b) lactic acid produced by humans and certain fungi and bacteria(what type of organism)

--some bacterial / fungal species can function well doing either respiration or fermentation – we
call them facultative anaerobes

--some bacterial / fungal species do respiration but with a different electron acceptor at the end of
the electron transport chain – we call this anaerobic respiration (they are
actually poisoned by oxygen)

--despite some differences, the overall similarities in enzyme pathways for respiration across
almost all species are a major piece of evidence for common ancestry (p. 179-80)

9.6 – The big picture

--figure 9.19 – our bodies can burn other fuels besides glucose (other carbs, fats, proteins even)
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--cells do NOT burn ALL the glucose that enters the cell … what else might cells do with it? (p.
181 left middle)
Synthesize it into other compounds for the body to use.

--fig 9.20 – Phosphructochinase can shut down the respiration enzyme factory (an example of the
concept of feedback inhibition from section 8.5, fig. 8.21)
Chapter 40: Energy budgets of different animals
Vocabulary: negative vs. positive feedback, ectothermy vs. endothermy, hibernation vs.
estivation
Concepts:
Skip 40.1, 40.2 – Feedback in homeostasis
--make sure you are clear about the difference between negative vs. positive feedback responses
--negative feedback general definition:
-a response to stop a action, reduces stimulus.

--positive feedback general definition:

-a response to keep the action going and amplifies stimulus.

40.3 – Thermoregulation in ectotherms and endotherms

--top left p. 878 – why is thermoregulation important? (for any organism, not just an animal)

- Because abnormal temperatures can change the fluidity of membranes, reduce efficiency
of enzymes, and anything else in the body related to temperature which can lead to death.

--p. 878 – how must ectotherms regulate their body temperature?

- get their heat from external sources.

--endotherms can also do what ectotherms do above, and also regulate body temperature how?
-with heating and cooling mechanisms, such as

--ALL mammals and birds are endotherms (and a few species in

other major groups), and name groups that are mostly ectothermic

-nonvian reptiles, fishes, amphibians, and invertabrates.

--discuss a major advantage to endothermy (bottom left p. 878), and an advantage to ectothermy
(top right p. 878)

Ectotherm: there is a broader temperature range meaning they can fluctuate more in temperature,
and they also need less energy so less food.
Endotherm: They can withstand more severe temperature because of heating and cooling
mechanisms.

--summarize endothermic strategies – “circulatory adaptations”, “evaporative heat loss”,

“adjusting metabolic heat production”, and strategies for both – “behavioral responses”
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-vasodialation dialiates blood vessels on the skin allowing for blood to go there and for
heaet to be transferred out. Vasoconstriction constricts the vessels on the skin causing the
warm blood not to be transferred to the environment. –countercurrent heat exchange to
allow the heat to be spread out through the body, and maximizes rate of exchange.

-warm water from the body goes to the surface of the skin and is lost because it is
evaporated leaving the water on the surface of the skin cooler because kinetic energy is
lost, panting as well
-behavioral: move to cooler areas, bathe, turn away from the heat source.

-adjustung metabolic heat production: shivering to produce heat

40.4
--p. 883 –– what do all organisms
use chemical energy to broadly accomplish?

1) Homeostasis: thermoregulation 2) ATP production: cellular respiration to

power cell work

3) biosynthesis: body’s growth and repair, synthesis or fat, production of gametes

-- what happens to organisms when they take in more calories (food energy) than
they spend?
-It is stored, often as starch or fat

--what happens to organisms when they spend more energy budget than they take in?

-they begin to take from the stored fat/ starch and eventually will die if they have no more feul to
maintain breathing hearbeat, and cell maintenance.

--p. 884 – what is overall metabolic rate? (do not worry about BMR vs. SMR)
-the sum of all the enrgy an animal uses in a given amount of time.

--p. 884 / fig. 40.19 – identify multiple ways scientists quantify an organism’s metabolic rate
-heat loss, CO2 lost orO2 consumed, food consumption, and chemical energy lsot
--p. 885 – (circle one) an (endotherm / ectotherm) uses far more energy per gram of body
weight and therefore must take in more food energy

--(circle one) a ( smaller / larger ) animal uses more energy per gram of body weight
(note the per gram of body weight … of course a bigger animal will use a larger
amount of total energy calories)

--p. 886 – some organisms can even change their overall metabolic rate in certain conditions –
explain the benefits of hibernation and estivation (and when they occur) in some animals

-hiberantion and estivation allow the organisms body temperature to drop or rise, causing them
to expend less energy in cases where temperatures are too cold or too high because they are not
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being active because if they were active it would take a lot of energy to maintain their body
temperature.

Chapter 10: Photosynthesis

Vocabulary: autotroph vs. heterotroph, chlorophyll, stroma vs. thylakoid, NADP+ vs. NADPH,
light reactions, Calvin cycle, carbon fixation, photosystem, rubisco
Concepts:
10.1 – Overview
--circle one: (autotrophs / heterotrophs / both) do photosynthesis,
while (autotrophs / heterotrophs / both) do respiration

--write the chemical equation for photosynthesis (I’m fine with net equation middle p. 188)
p. 189 – identify 6CO2+CH20 C6H12O6+6O2
which reactant is
being reduced
and which is (photosynthesis is a multi-step process)
oxidized

--write the word equation for photosynthesis

carbon dioxide+water glucose+ oxygen
(photosynthesis is a multi-step process)

--fig 10.5 – if we radiolabel the oxygen atom in water molecules (H2O) and give that water to a
plant, we will find the radiolabeled oxygen atoms existing as what molecule? O2

--is photosynthesis exergonic or endergonic? endergonic

--two steps in photosynthesis (figure 10.6 is an excellent summary):

a) light reactions: converting solar energy to O2 and chemical energy

--once again, this process is completed by many membrane-embedded proteins …

in eukaryotes, this occurs in the inner membrane of the
chloroplast organelle (also called the thylakoid membrane)

--producer bacteria have these membrane proteins in their only membrane:

Photosystems, and ETC

b) Calvin cycle: converting CO2 and chemical energy to chemical energy

--this process involves enzymes floating freely nearby the membrane where the
light reactions take place – this liquidy environment inside the
eukaryotic organelle is the stroma

--for producer bacteria, the Calvin cycle takes place outside the folding of
the membrane.
10.2 – Light reactions in-depth
Into light reactions (no #s needed) Out of light reactions (no #s needed)
1) water becomes 1) O2 e- and H+
becomes
2) ADP + P 2) ATP
becomes
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3) NADp+ 3) NADPH

Sunlight energy

--plants absorb the 380-750 nm visible light part of the overall electromagnetic spectrum

--within that type, why do plants absorb green light the least? I thought plants were green?!?
Because the green light is reflected by chlorophyll the main pigment in plants.

--why do autotrophs have a variety of pigments (why chlorophyll a, chlorophyll b, carotenoids)?

-to absorb different variations of light, broaden the spectrum of light able to be absorbed.
Carotenoids, get rid of excess light energy that would damage the chloryphyll.

--the pigment molecules absorb the light energy to do the first energy conversion.
These are embedded within a larger protein complex called photosystem Thousands of
these proteins are embedded within the thylakoid inner membrane that is folded over and over
again to make room for all these proteins (in eukaryotes). This membrane sits within the
organelle called the chloroplast.
(figures 10.13a and 10.18 may help you with the blanks above)

--absorbing light energy: pigments absorb light and use it to excite electrons within
--the photosystem (technically, the “primary acceptor”) grabs these excited
particles and takes them away from the pigment, delivering them
to the reaction-center complex
--these particles never return to the initial photosystem (see figure 10.14),
so autotrophs cut up a water molecule and take its low-energy
electrons to give back to the pigments

--we use the term catalyze to describe the splitting of this

molecule – it becomes oxygen gas (and H+ that joins solution)

--electron transport chain: just as in respiration, a chain of transport proteins use the energy of
high-energy electrons to do active transport of H+ions

--slight difference from respiration – here, the ETC is concentrating these ions where?
circle one: cytoplasm stroma inner thylakoid space

--another difference – O2 is NOT required in light reactions as in respiration because the

low-energy electrons go where? NADPH
(hint: follow the yellow arrows in figure 10.14 / 10.18) (type of cell transport)

--chemiosmosis: the concentration of H+ ions undergo phosphorylation

through the ATP synthase protein to make lots of ATP
nd
--2 electron excitation: the next photosystem excites electrons by absorbing light
a) noncyclic electron flow – e-s do NOT travel in circle because NADP+ grabs them
(and becomes NADPH) and takes them to the Calvin cycle (fig. 10.14)
OR
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b) cyclic electron flow – e-s travel in circle, traveling back to ETC / chemiosmosis to
produce more ATP before the e-s return to photosystem (fig. 10.16)

10.3 – Calvin cycle in-depth

Into Calvin cycle (no #s needed) Out of Calvin cycle (no #s needed)
becomes
1) RuBp+CO2 1) G3P(sugar)
becomes
2) NADPH 2) NADP+
becomes
3) ATP 3) ADP + P

10.4 – Alternative mechanisms in hot climates

--some plants have adapted to still do photosynthesis well even in hot weather

challenge: if the weather is too hot, plants close stomata to prevent water loss
--this can be a problem because now the Calvin cycle loses access to the CO2 gas
in the atmosphere that it needs, and the light reactions still produce
O2 gas that can no longer escape (and actually interferes with Calvin cycle)

--read about CAM plants (skip C4 plants) – explain how they store CO2 so they can still
keep their stomata closed during the hot day to prevent excess transpiration
they open stomata during the night and build up on CO2 which they then give to
the calvin cycle to process during the day, and during the day the stoma is closed and
sugars are produced.
(note: please do NOT tell me they do photosynthesis at night … photosynthesis
requires sunlight!)

Comparing and contrasting electron transport chain and chemiosmosis steps in respiration versus
the light reactions of photosynthesis (assume in a eukaryotic cell)

Respiration Light reactions of photosyn

Original source of high-energy electrons Sugars water
that power ETC
What delivers high-energy electrons to the NADH photosystem 2
ETC note: NOT NADPH!
Type of particles pumped by ETC with H+ H+
electron power
Direction the particles are Intermembrane space lumen of chloroplast
pumped in ETC
What happens to low-energy electrons after They are given to O2 and They are taken to form NADPH,
being spent in ETC make water and used in the Calvin Cyle
Name of protein that allows particles to ATP synthase ATP synthase
diffuse in chemiosmosis