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Final Exam Study Guide

Unit 4: This part of the study guide reviews the new material covered in lectures 20 and 21.

1) Describe how bile salts allow TAG to absorb through the intestinal lining.
TAGs are broken down first into monoglycerols, diacylglycerols, free fatty acids, and
glycerol. Then carried using bile salts to be absorbed through the intestinal lining.
- Why can’t fat absorb into the intestinal lining without bile salts? What is the
precursor to bile salts?
Fats are too nonpolar and insoluble to be absorbed without bile salts. The
precursor to bile salts is cholesterol synthesized in the liver. They are micelles
that trap the fat in them.

2) Name the (3) lipases and describe how they are different.
Pancreatic lipase-intestinal lumen that absorbed fatty acids from diet into intestine.
Lipoprotein lipase-capillary walls that absorb FA from lipoproteins into target tissues. Hormone-
sensitive lipase-breaks down cellular fat stores in adipose tissue.
- Where in the body do pancreatic lipases function? What is their target (possible
choices are fats/bile salts in intestinal lining, fats/lipoproteins in target tissues
like muscle, fats stored in adipose tissue)? Where in the body to lipoprotein
lipases function? Where in the body do hormone-sensitive lipases function?

3) Describe a lipoprotein, including its structure, function, and how they are categorized.
- What are the general components of all lipoproteins? What is the general
function of all lipoproteins? What characteristics are they categorized on? What
contributes to this?
Lipoproteins are specific proteins that can transport fat between organs. Made
up of fat in the middle and a single layer of phospholipid molecules. The
hydrophilic heads are on the outside. It’s also got cholesterol esters and
apolipoproteins on the surface to form an overall micelle. Apolipoproteins
determine the fate of the lipoprotein. Characterized based on the density.
4) Contrast the exogenous pathway of lipoproteins metabolism with the endogenous
- Which lipoproteins participate in each? What is the source of fat for each
(dietary or liver)? Track a lipoprotein through each pathway in a stepwise
fashion. How does the HDL participate?
Exogenous-chylomicrons which transport dietary fat to tissue and dietary
cholesterol to the liver. Endogenous-VLDLs deliver endogenous FA and
cholesterol to muscle and tissue. Made from new TAGs and cholesterol made in
the liver.
Exogenous-1. TAGs from intestine packaged with dietary cholesterol into
chylomicrons. 2. Then lipoprotein lipases in the capillaries hydrolyze them into
FAs and glycerol. In muscle, FAs and oxidized for energy. In adipose, they are re-
esterified as TAGs for storage. 3. Remnants of chylomicrons with cholesterol and
apolipoproteins are taken up in the liver.
Endogenous-1. VLDS made in the liver transported to tissue and metabolized by
lipoprotein lipase in the capillaries of tissues to decrease levels of lipids in the
particles(increasing density). 2. VLDL converted to IDL as fatty acids are cleaved
off. 3. 50% of IDL is taken up into the liver and other 50% converted into LDL.
HDL handles reverse transport-scavenges cholesterol from tissues and transports
them to liver for removal.

5) Describe apolipoproteins.
- What is their function? What are the different types? Which apolipoprotein is on
a chylomicron? VLDL? LDL? How do apolipoproteins participate in receptor-
mediated endocytosis?
Apolipoproteins bind lipids for transport.
ApoE-in chylomicron and IDL, catabolism of triglyceride-rich lipoproteins
ApoA1: in HDL, allows for transport of cholesterol to liver/tissues/other
ApoC2: chylomicron and VLDL, activates lipases in capillaries
ApoB100: LDL, weak ligand in the absence of ApoE so hard to bind for breaking
1. As VLDL particles are metabolized, they become more dense and exchange
ApoC2 for ApoE and become IDLs. 2. 50% goes to liver, other 50 turns into LDL.
3. LDL loses ApoE and retains ApoB100.
Liver recognizes the apolipoproteins on lipoproteins and internalize them in
vesicles that fuse with lysosomes which hydrolyze the cholesterol esters. Free
cholesterol and FA are released into the cytosol and the receptors are recycled
to the surface. The released cholesterol goes to the ER: less cholesterol
biosynthesis and less synthesis of LDL receptors from increased cholesterol in ER.

6) Explain the reasons for why LDL is considered “bad” but HDL is considered “good.”
That’s why LDL bad. Receptors bind to LDL and get cholesterol but then receptors for
LDL are decreased as a result. Plus ApoB100 is super weak so the binding power wasn’t
that great to being with. Also, lipid accumulation in blood vessel walls. Triggers
inflammatory response or creates plaques. Overall v bad.
HDL good because it extracts excess cholesterol from cells. Surface membranes do that.
Transports cholesterol to liver to make bile salts.

7) Describe how fatty acids are activated and transported into the mitochondria for 
- Why must a fatty acid be “activated?” How are they activated? What is the role
of carnitine? What is the enzyme that transfers FA to carnitine? Which enzyme
removes carnitine once in the mitochondria?
Fatty acid needs to be activated because they’re too stable. Can’t cross the
membranes. Glucagon and epinephrine mobilize adipose. Releases it using
hormone-sensitive lipase. FA transported to tissue for oxidation and energy
production. Albumin serves as a carrier protein for steroids and FA in the blood.
Hormone sensitive lipases convert TAGs into oxidizable components, glycerol
which can go into glycolysis and 3 fatty acyl groups.
FA activated with Acyl-CoA synthetase. Needs ATP and CoA to make fatty acyl-
CoA, AMP and 2 phosphates.
Acyl-CoA can’t directly enter the mitochondria. 1. Fatty acyl group of FA is
transferred to carnitine. 2. Acyl carnitine enters the matric through a carnitine
transporter. 3. Carnitine acyltransferase inside transfers the fatty acyl group to a
CoA. 4. Carnitine returns to cytosol through the transporter.

8) Know the following about  oxidation:

- What is the starting reactant for transporting FAs across the mitochondrial
membrane? What is the final product of even chain FA oxidation? What are the
final products of odd chain FA oxidation? What are their fates? How does 
oxidation interact with the electron transport chain? How does FA oxidation
influence the citric acid cycle? What are the energy totals for one round of
oxidation (NADH, FADH2, Acetyl-CoA)? How many rounds of beta oxidation are
required to oxidize a FA chain with 20 carbons? 18?
Starting reactant is fatty acyl-CoA. Occurs in the mitochondria. Acetyl-CoA is oxidized
to go into CAC which directly produces 1 FADH2 and 1 NADH to feed electron
transport chain. The acetyl-CoA that goes into the CAC can then make 3 NADH, 1
FADH2, and 1 GTP. 1 round of B oxidation makes 14 ATP as a result.
Each round generates 1 acetyl-CoA and a fatty acyl-CoA that loses 2 carbons. For a
FA chain with 20 carbons, need 9 rounds. And for 18, need 8 rounds.
Odd-chain helps replenish CAC intermediates. You get 1 acetyl CoA and 1 propionyl-
CoA which is turned into succinyl CoA.

9) Explain why one molecule of a fatty acid contains more oxidizable energy than one
molecule of glucose.
Because it has B oxidation and CAC stuff.

10) Describe how glucagon/epinephrine regulates  oxidation.

- What is the effect of glucagon or epinephrine on the activity of hormone
sensitive lipase? The concentration of free fatty acids? What does
glucagon/epinephrine bind to? How is cAMP involved?
Glucagon stimulates Fbase-2 activity and reduces F26BP levels which increases
gluconeogenesis. But also stimulates activity of hormone sensitive lipase, free
fatty acids, and B oxidation.
11) Describe the fate of glucose in the liver when metabolic fuels (ATP) are abundant.
Stored as glycogen in the liver.

12) Describe the fate of lipids and proteins in the liver during a fed vs. fasted state.
- Under what conditions are ketone bodies made?
Produced when fatty acid degradation and starvation.
13) Name the fuel sources used by the brain and under what conditions each are used (fed or
Glucose and ketone bodies. Fed uses glucose, fasted uses ketone bodies.
14) Describe how fuel sources for skeletal muscle change during different periods of exercise.
- What is phosphocreatine and what is its role?
- When does muscle tissue use anaerobic respiration to produce ATP? What about
Skeletal muscle can use FA, glucose, ketone bodies.
Resting muscle: FA major fuels and yields acetyl-CoA
Moderately active muscle: uses glucose from glycogen and FA
Active: glycolysis exceeds CAC and pyruvate is reduced to lactate(back to glucose
through Cori cycle)
Phosphocreatine supplies 2nd wave of ATP. You can cleave off the phosphate to
make ATP and creatine.

15) Describe the fuel sources of the heart.

- What is the source of lactate?
Heart uses FA as main fuel source but can use glucose, ketones, and lactate.
Lactate from active muscle can be used by the heart directly.
16) Compare and contrast the effect of insulin on the liver, muscle, and adipose tissue.
- How can insulin stimulate both glycolysis and gluconeogenesis in the liver?
Liver: up glycolysis, up glycogen synthesis, up FA synthesis
Muscle: up glucose uptake(GLUT4), up glycogen synthesis, up slycolysis
Adipose: up glucose uptate(GLUT4), down lipolysis.
Can stimulate both because
17) Compare and contrast the effect of glucagon in the liver, muscle, and adipose tissue.
Liver: up glycogen breakdown, up gluconeogenesis, inhibits glycolysis.
Adipose: up lipolysis and FA mobilization
18) Compare and contrast the effect of epinephrine on the liver, muscle, and adipose tissue.
Liver: up glycogen breakdown, up gluconeogenesis
Muscle: up glycogen breakdown, up glycolysis
Adipose: up lipolysis and FA mobilization
Pancreas: up glucagon secretion, inhibits insulin secretion
19) Compare and contrast the fed vs. fasted state in the liver, muscle, and adipose tissue.
Fed: Liver-up glycolysis, FA and glycogen synthesis stimulated. Adipose: lipolysis
suppressed, TAG synthesis stimulated. Muscle: anabolism of proteins and glycogen
Insulin promotes entry of glucose into muscle and adipose which increases
surface expression of GLUT4
Fasted: Liver-increased FA as fuel, gluconeogenesis, glycogen breakdown, release
glucose into blood, protein catabolism. Muscle: decreased entry of glucose, increased
use of FA as fuel to save glucose for brain and not do protein catabolism. Fat: lipolysis
provides free FA for ATP production via B oxidation.
20) Name and describe the two main priorities during starvation.
- When is the 2nd priority ignored? What are the consequences of this?
- Why is the first priority difficult to manage during starvation?
1st priority is to provide glucose to brain or other glucose-dependent tissues like
RBC. 2nd priority is to preserve proteins by shifting fuel source from glucose to
ketone bodies. 2nd priority is ignored when no fat left. Causes degradation of
proteins and autosarcophagy.
21) Describe the cause, metabolic effect, and consequence of type 1 diabetes.
- What is the cause? What is the effect on glucose transport? What is the effect on
glycolysis, gluconeogenesis, and glycogenolysis? What is the effect on lipolysis,
lipid storage, and the rate of oxidation? What is the effect on protein
- What molecules accumulate as a result of increased lipolysis?
- What are the phenotypes associated with T1D?
- What is ketoacidosis and why is it fatal?
- What is the only known treatment for T1D?

22) Describe the progression of type 2 diabetes over the span of many years.
- What is prediabetes and how is it different from mature diabetes?
- How is T2D different from T1D?
- What is insulin resistance? What happens to insulin secretion? What is the
eventual consequence of insulin hypersecretion?

The final exam is cumulative, so for the remainder of the study guide, you should review the
previous three guides you were already provided with. The points below were not covered in
the previous study guide but will be appearing on the final exam.

23) What is the action and purpose of the Cori cycle?

Turns lactate back into glucose. Lactate from the muscle to the liver which is turned into
24) The reactants, enzymes, and product for the first step of the urea cycle (the committed
Transamination. Amino acid. Aminotransferase to make an alpha keto acid. Removes
the NH3. Alpha ketoglutarate accepts the amino group and turns into glutamate.
25) How is DNA used as a template to produce RNA? In what direction is RNA synthesized?

The points below are taken directly from the old study guides. I am putting them here since
these points would be a good place to start. Remember that the points below do not cover
everything that is on the exam, but they are a good starting point for review.
Unit 3:
26) Describe the purpose of lactic acid fermentation and how this differs from aerobic
- Which step of aerobic respiration regenerates NAD/FAD? What is the enzyme
that does this during lactic acid fermentation? What are the reactants and
products for this enzyme? Why is regeneration of NAD different between
aerobic and anaerobic respiration? What is the effect on ATP synthesis?
- What is the action and purpose of the Cori cycle?
Doesn’t regenerate it. Lactate dehydrogenase does that. Forward and back

27) Name the three enzymes in the glycolysis pathway that are directly regulated and
describe the regulatory mechanisms involved.
- What mechanism regulates hexokinase, which is step 1 (allosteric, covalent
mod., genetic control, substrate cycle)? Why can glucose leave the liver before
being phosphorylated? What is the consequence if glucose can’t leave the liver?
- What mechanism regulates phosphofructokinase (PFK-1) (allosteric, covalent
mod., genetic control, substrate cycle)? What molecules regulate PFK-1? What
molecules regulate FBPase? What is meant by the statement: “the committed
step of glycolysis is regulated by the energy state of the cell?” How is F26BP
regulated? What is the role of insulin and glucoagon?
- You do need to know that pyruvate decarboxylase is a regulatory step, but you
do not need to know how it is regulated.

28) Distinguish between the two stages of glycolysis.

- How is the investment phase different from the payoff phase? What is the total
ATP consumed or produced at the end of each stage? What is the net ATP output
from glycolysis? Where is NADH formed? What is the reactant for glycolysis?
What are the products?
Two stages: investment phase and payoff phase.
1-5 is investment where glucose is phosphorylated and cleaved in half. 2 ATP consumed
1. Hexokinase cleaves off a phosphate group from ATP and phosphorylates glucose
so that it can’t leave the cell. Glucose to glucose-6-phosphate
2. Phosphoglucose isomerase isomerizes glucose-6-phosphate to fructose-6-
3. Phosphofructokinase takes a phosphate from ATP to make fructose-1,6-
4. Aldolase cleaves F1,6BP to make two 3-carbon molecules each with a phosphate
(DHAP and G3P)
5. Triose phosphate isomerase isomerizes the dihydroxyacetone phosphate(DHAP)
and glyceraldehyde-3-phosphate(G3P)
6-10 is payoff phase where 2 pyruvate are generated and 4 ATP produced.
6. NAD+ to NAHD (2 made total)
7. 2 ATP made
8. Phosphoglycerate mutase
9. Enolase releases two water
10. 2 phosphoenolpyruvate in and 2 ATP made from pyruvate kinase to make

29) Know the following details of glycolysis:

- Reaction 1: reactants, enzyme, and product. What is the purpose of this first
Glucose, 2 ATP. Hexokinase. Glucose-6-phosphate and 2 ADP. The purpose is to
trap glucose in the cell.
- Reaction 10: reactants, enzyme, and product.
Phosphoenolpyruvate, 2 ADP. Pyruvate kinase. 2 pyruvate and 2 ATP.
- Which reactions involve substrate-level phosphorylation?

- Which reactions involve reduction of NAD?

Reaction 6
- Which step is the committed step? What are the reactants, enzymes, and
products for this?

- What are the products and how many of each are there? How many reactants
were required to generate these products?
2 pyruvates made. 1 glucose required.

30) Describe the similarities and differences between glycolysis and gluconeogenesis.
- Are both exergonic? Why or why not? Are they the same pathways? Why or why
not? Specifically, which enzymes are different? Which enzymes in the glycolysis
pathway do gluconeogenesis enzymes bypass? Where does glycolysis take place
(tissue)? Where does gluconeogenesis take place (tissue)? Where in the cell are
the enzymes for glycolysis? Gluconeogenesis?

31) Describe the transition phase of the citric acid cycle.

- What are the reactants, enzyme, and products? What specifically does pyruvate
dehydrogenase do? What is purpose of linking the acyl group derived from
pyruvate to cofactors like coenzyme A? Why is this phase important for the CAC?
Why is this phase important for oxidative phosphorylation?

32) Know the following about the CAC

- Steps 1, 3, 4, 5, and 6: reactants, enzyme, and product.
- What is the committed step?
- When is GTP generated?
- When is coenzyme A regenerated (there are two steps)? When is it used as a
coenzyme in CAC (excluding the transition phase)?
- When is CO2 released as a result of decarboxylation?
- Where is NAD reduced? Where is FAD reduced?
- Where is OAA regenerated? Where is it consumed?
- Where is carbon lost?
- One cycle of the cycle yields how many CO2, NADH, FADH2, and GTP?

33) Explain the 4 ways in which the citric acid cycle is regulated and give an example of each.
- Give an example of substrate availability, feedback inhibition, allosteric
activation, and competitive feedback in the CAC. Why is NADH so important in
the CAC? What are the enzymes in the CAC that are subject to regulation? Which
molecules that regulate CAC also regulate glycolysis?

34) Discuss how glucose uptake/transport is regulated, including the specific proteins
- What is GLUT4? How does it change in response to insulin?

35) Know the following about the urea cycle:

- What is the purpose for converting NH3 to urea?
- How many nitrogenous groups must enter the urea cycle to create one molecule
of urea and in what form do they enter the cycle?
- The reactants, enzyme, and product for the production of carbamoyl phosphate.
- The reactants, enzyme, and product for the production of aspartate.
- The reactants, enzymes, and product for the first step of the urea cycle (the
committed step)

36) Name the electron carriers that function in oxidative phosphorylation.

- How many electrons are carried by NAD? FAD? Ubiqinone? Cytochrome C?

37) Know the following about the electron transport chain and chemiosmosis:
- Track the path of an electron through the chain: NADH  Complex I/Fe cofactors
 Q  Complex III  cytochrome c  Complex IV  oxygen = water.
- Track the path of an electron through the chain: FADH2  Complex II  Q 
Complex III  cytochrome c  Complex IV  oxygen = water.
- How are electrons from FAD different from those coming from NAD? How does
this affect the movement of H+ protons?
- Where does a reaction from the CAC directly overlap with the ETC?
- Where in the cell does this happen?
- What is the purpose of moving electrons from a high energy state to a low
energy state?
- What is the proton motive force and how does it relate to ATP synthesis?
- Which complexes are coupled to movement of H+? Is H+ moved down or up its
concentration gradient?
- What is the name of the enzyme that drives ATP production through

38) Describe three functions of protein degradation in cells.

- Amino acids undergo oxidative degradation in three metabolic circumstances.

39) Compare and contrast chaperone-mediated autophagy with lysosomal degradation of

- What are the circumstances that result in chaperone-mediated autophagy?
What are the circumstances that result in proteasome degradation? How are
proteins identified for lysosomal degradation? How are proteins identified for
proteasomal degradation? What is LAMP-2A and what does it do/how does it
work? How is the lysosome different from the proteosome? Do these require
ATP hydrolysis?

40) Contrast a glucogenic amino acid with a ketogenic amino acid.

Unit 2:

41) Label the different parts of a reaction coordinate diagram and explain how an enzyme
will/will not change the plot of this diagram.
- Label: reactants, products, activation energy, transition energy, Greaction. Draw
the difference in free energy over time between a catalyzed and uncatalyzed

42) Connect the functions of an enzyme to the activation energy of a biochemical reaction.
- What is the effect of an enzyme on: activation energy, transition state, Greaction,
equilibrium? How does the enzyme stabilize the TS? What is binding energy and
how does this contribute?
Lowers activation energy. Stabilizes the transition state. Doesn’t change delta G
or equilibrium.
Stabilizes the TS by reducing its free energy. So, the enzyme makes weak
interactions with the substrate to release binding energy(separation energy
required for a chemical to dissociate to its constituent components). Binding
energy released contributes to the activation energy required to reach TS,
making it lower.

43) Draw the relationship between enzyme reaction velocity, substrate concentration, and
enzyme affinity (Km).
- Label: substrate concentration, initial velocity, Vmax, ½ Vmax, Km. What does a
large Km mean? Low Km? What is meant by the phrase “Km is an intrinsic
constant for an enzyme”? How does Vmax change when substrate concentration
increases? How does Vmax change when enzyme concentration increases? How
does Vmax change when enzyme concentration decreases? Why does an
enzyme with low affinity require a higher concentration of substrate to reach ½

Km high means bad affinity. Lower Km means good affinity. The phrase means
that Km is a constant and doesn’t change when enzyme concentration changes.
When substrate concentration increase, vmax increases.

44) Use the Michaelis-Menten equation to solve for enzyme affinity, substrate
concentration, or maximum velocity in a biochemical reaction.

45) Describe the catalytic constant kcat and its relationship to Vmax and Km.
- Define kcat. What does a high kcat mean? Define kcat/Km. What does a high
kcat/Km mean? What is meant by the phrase “Kcat is an intrinsic constant for an
enzyme”? How can you calculate Kcat given Vmax and enzyme concentration?
What happens to Vmax when enzyme concentration is decreased, and how does
that affect kcat?
Kcat=how fast TS proceeds to product. When V0=Vmax
Kcat=Vmax/E concentration. unit is s^-1
Higher kcat=faster reaction.
Kcat/km=catalytic efficiency
Vmax goes down when enzyme concentration is reduced and kcat stays the

46) Compare and contrast competitive, uncompetitive, and mixed enzyme inhibition.
- Where does the inhibitor bind in each situation: the active site on the enzyme,
the enzyme-substrate complex, both? How are Km and Vmax affected by each
type of inhibitor? Why does Vmax stay the same during competitive inhibition?
Why does Vmax decrease during uncompetitive inhibition? Why does Km? Why
does Km increase during mixed inhibition?
Competitive: binds to the active site. Km goes up because the substrate
decreases therefore a higher [s] needed to reach ½ vmax. Vmax stays the same
because it can still enter the active site when inhibitor isn’t bound.
Uncompetitive: binds to allosteric. Km decreases proportionally because it
depletes the ES complex causing more S to bind to E. Vmax goes down.
Mixed: binds to both. Vmax decreases, km can either increase or decrease.
Noncompetitive: allosteric. vmax decreases and km doesn’t change.
Allosteric enzymes are modulated through noncovalent binding of regulatory
compounds called allosteric effectors.
Homotrophic enzyme: one molecule acts as both substrate and the
allosteric effector. Hetero: different than the substrate and bind to
different places on the enzyme.
Are sigmoidal saturation curves and don’t follow M-M kinetics.

47) Define cofactor and provide some examples.

Cofactor is an inorganic ion or coenzyme.
Coenzyme: organic factor required for action of some enzymes. Split into
cosubstrates(loosely bound) and prosthetic groups(tightly bound can be organic or
48) Categorize carbohydrates based on: the number of carbohydrate units (mono, di, oligo,
poly), the position of the carbonyl group (aldose or ketose), D/L stereochemistry, and
their anomer designation ( or ).
- What is the overall empirical formula for a carbohydrate? How do you determine
D/L stereochemistry in a linear carbohydrate? What is a reference carbon? What
is the anomeric/hemiacetal carbon?
Reference carbon(second to last one) on the left:L. Hemiacetal carbon that one.
Alpha if opposite, beta if same as CH2OH on reference carbon.

49) Identify reducing sugars.

- What is a reducing sugar? What type of carbon must a sugar have to be a
reducing sugar?
Reducing sugar is free OH on hemiacetal.

50) Compare and contrast the structure and function of homopolysaccharides and
- Why are these polysaccharides and not oligosaccharides? How are glycogen and
starch similar? Different? What is the major structural difference between
cellulose and glycogen? What is the major functional difference between
cellulose and glycogen? What happens to cellulose when it is ingested by an
animal? Why?
They are polysaccharides because they’re a lot of them. Homo:
glycogen/starch/cellulose and one type of monomer. Hetero: extracellular
matrix and multiple monomers.
Starch: alpha 1-6 branched, alpha 1-4 unbranched glucose. Plants.
Glycogen: alpha 1-6 branched, alpha 1-4 unbranched glucose. Liver and skeletal
muscle. Got more branches than starch.
Cellulose: glucose beta 1-4.
It’s not energy supply because we cant break beta 1-4 linkages.

Glycoproteins contain 1+ oligosaccharides. Assist in chaperone

folding(recognition sites for them). Provides tags for protein binding (lectin stuff
tht binds carbs and binds lysosomal enzymes for transport and a bunch of other
stuff). Provides blood group specificity.
Proteoglycans-type of glycoprotein with big polysacc. called glycosaminoglycans.
Chondroitin sulfate is found in cartilage to resist compression. Also makes
aggregates of extracellular matrix.

51) Describe the chemical, structural, and functional differences between deoxyribonucleic
acid and ribonucleic acid. Label the different parts of a DNA molecule.
- Double-stranded or single-stranded? Ribose or deoxyribose? Where is T found?
Where is U found? Why is DNA the keeper of genetic information instead of
RNA? What can RNA do that DNA cannot? Label: phosphodiester bond, a base
pair, the 5’ end, the 3’ end, major groove, minor groove
- How is DNA used as a template to produce RNA? In what direction is RNA

52) List the steps in a polymerase chain reaction and describe the molecular process that is
happening during each step.
- How is DNA denatured and renatured? What types of interactions increase the
melting temperature of DNA? What are the three steps of PCR and what are the
temperature requirements, and why? What is a primer and what does it do?
What makes Taq DNA polymerase unique? What is a dNTP? What is the initial
reactant in a PCR reaction? What is the final product? Be able to determine how
errors in the PCR procedure change the final product of the reaction.
95, 50, 72 REPEAT!

53) Classify lipids based on their function (storage or structural), backbone (glycerol or
sphingosine), constituents (fatty acid chain or head group), and linkage (ester or amide)
of the constituent to the backbone.
- Do this for triacylglycerol, glycerophospholipid, sphingolipid, sphingomyelin,
gangliosides. What is a ceramide?

54) Apply your knowledge of transport proteins to identify a transport mechanism as active
or passive, carrier or channel, and uniport, symport, or antiport.
- You will be given a general mechanism for a transport protein like in the glucose
transporter or Na/K ATPase slides. Know how to determine if the protein is a
carrier or a channel? Active or passive? Uniport, symport, or antiport?
3 Na out, 2 K in.
55) Label the steps of the -adrenergic receptor/epinephrine signal transduction pathway,
which is a G-protein coupled receptor system.

56) Describe the role of cAMP and protein kinase A in the epinephrine signaling cascade.
- What enzyme generates cAMP? What does cAMP bind to? How does this
activate PKA? How does PKA regulate other proteins?

Unit 1:

57) Recall the abbreviations [three letter and single letter] for each of the 20 amino acids,
recall the chemical nature of the amino acid R groups, and match the name of an amino
acid with its corresponding R group. Do not memorize pKas, hydropathy indexes or
isoelectric points.

58) Describe the different characteristics of a two-stage titration curve for an ionizing amino
- What is an OH equivalent? How many OH equivalents does it take to titrate a
single ionizing group in solution? 2 ionizing groups? How many OH equivalents
does it take to titrate an ionizing group to its pKa? Know how to determine the
net charge of an amino acid in solution as pH increases. Know how to determine
what the predominant form of an amino acid is as pH increases (which groups
are protonated and deprotonated and in what order). What is the isoelectric
point? How do you calculate the isoelectric point of an amino acid with 2 ionizing
groups? 3 ionizing groups? How do you determine the best buffering regions for
an amino acid with 2 ionizing groups? 3 ionizing groups?
Lower pka, stronger acid.
pI=isoelectric point
Calculate isoelectric point using pka! Pi=find point of net 0 charge and calculate
avg of those 2 pks surrounding the 0 charge. Buffering zone=flat area.

59) Describe the primary, secondary, tertiary, and quaternary structures of proteins.
- Which forces – covalent bonds, noncovalent bonds, or both – are responsible
for stabilizing each type of protein structure? How do the parts of the primary
amino acid sequence interact to form secondary structures? Compare and
contrast the different types of secondary structure (Which amino acids are likely
to be in an -helix?  sheet? What is the orientation of the R groups? Which
amino acids are least likely to take up an - helix?  sheet? Which amino acids
are likely to be part of a  turn?  loop?) What is a molten globule? Is the
structure of hemoglobin tertiary or quaternary? How are tertiary structures
different from quaternary structures? What groups in secondary protein
structures interact to form tertiary structures? How are fibrous proteins different
from globular proteins (Give an example of each type).
Primary-covalent bonds. 2dary-noncovalent with the alpha helices and beta
sheets. 3iary-both. 4nary-covalent?

2dary: Proline and glycine least likely to form alpha helix-proline has no rotation
around C-N bond. Glycine too flexible and too much rotation.
Parallel beta sheets=n terminus and c terminus same direction.
Antiparallel=opposite. Glycine and alanine super common in beta sheets because
r groups need to be very small.
Prolines and glycines common in B-turns- antiparallel links. Loops are parallel.

3ary: Collagen is coiled with 3 left-handed helical structure structures wrapped

around each other with a righ-handed twist/ Glycine rich between helices
because glycine is small. Collagen fibrils-triple-helical structures

Globular proteins folded into spheres. Hydrophobic core, hydrophilic surface.

Folded conformation in aqueous environment.

Fibrous-long thin molecules, like keratin or collagen(bone/cartilage/skin).

Insoluble in water. Structural role mostly

Globular-folds 3D. hemoglobin/insulin/enzymes. Soluble in water. Metabolic


Domains regins of protein with a specific function and can usually function
independedntly of the rest of the protein.

60) Describe the chemical properties of water and the significance of non-covalent bonds in
aqueous chemistry.
- Is water polar or nonpolar? Does it have a (+) or (-) charge? What types of
substances dissolve in water? What is the hydrophobic effect? Describe the way
water is arranged around soluble (polar, charged) and insoluble (nonpolar)
molecules. How is thermodynamics related to the hydrophobic effect? How are
the bonds that keep a molecule of water together different from the bonds that
keep water as a liquid together? How is cohesion different from adhesion?

61) Explain how the laws of thermodynamics are related to biochemical reactions and the
synthesis of biological molecules (proteins, lipids).
- What is a spontaneous reaction and how is this related to G? If a reaction
increases order in a system, what is the effect on G? If a reaction releases heat,
what is the effect on G? Explain why nonpolar molecules aggregate in aqueous
solution. Explain why polar molecules dissolve in aqueous solution. Describe the
relationship between Gibbs free energy, enthalpy, and entropy. If folding a
disordered polypeptide from primary structure to a secondary ordered structure
violates the laws of thermodynamics, how does it still happen?
Spontaneous reaction is negative delta G=free energy of the products is less than
the free energy of the reactants.

62) Predict the tendancy of a weak acid (HA) to lose a proton and form its conjugate base (A-
) using the acid dissociation constant.
- If two acids have two different Ka, how do you determine which will lose its
proton first during titration? Know how to read the pH scale: how are the
concentrations of [H+] and [OH-] related? What happens to a strong acid or base
in aqueous solution? How is this different from a weak acid or base in aqueous
solution? As [H+] increases, what happens to pH? How does pH affect the
concentration of acid [HA] and its conjugate base [A-]? When given the pKa of an
acid, you should be able to determine the pH at which: the acid (protonated)
form is dominant, the base (deprotonated) form is dominant, and both acid and
base forms are equal in concentration. Be able to identify changes in net charge
of an aqueous solution as a weak acid (such as an amino acid) is titrated with

63) Interpret the relationship between pH, Ka, and pKa.

- How are the Ka and the pKa of an acid related? If a weak acid is placed at a pH
equal to its pKa, what is the result? If an acid has two ioniizable groups, which
will deprotonate first? At what pH is a weak acid a good buffer? Define buffer.
64) Describe the process of separating, purifying, and sequencing a protein using laboratory
- Distinguish between size exclusion, ion exchange, and affinity chromatography.
What properties of amino acids do each rely on? What are the 2 dimensions of a
2D gel electrophoresis procedure? What is SDS and what does it do to a protein?
What does mercaptoethanol do to a protein? Describe the 2-step process of
Western blotting. Why is it also referred to as immunoblotting? What three
steps are critical for protein sequencing? What does alignment mean? Describe
the process of Edman degradation.

65) Describe how the structure of myoglobin is related to its functional role in oxygen
- Does Mb have a high or low affinity for oxygen in tissue? How is this measured?
Does Mb concentrate in the lungs or the muscle (explain why)? How many heme
groups does Mb contain? How does this relate to its function as an oxygen
storage molecule? Why do we need oxygen storage proteins? Describe the
structure of a heme group.

66) Describe how the structure of hemoglobin is related to its functional role in oxygen
- Where does Hb have the highest affinity for oxygen (lungs or tissue)? Why? How
many heme groups are within Hb? Why is Hb better at oxygen transport than
storage? What is cooperative binding? How does this relate to oxygen binding
and release? What is the structure difference between the T and R state? How
does this affect the solubility of oxygen in the blood? Why do we need an oxygen
transport protein? How does the presence of Mb affect the stability of Hb to
bind oxygen?

67) Compare and contrast the oxygen binding curves for myoglobin and hemoglobin.
- What do each look like? How does this relate to the number of oxygen binding
sites contained in each protein? Why is binding of oxygen to Hb slow at first,
then very fast? What does fractional saturation mean? What percentage of Hb is
saturated by oxygen in the lungs versus the tissues?

68) Use binding curves to predict the affinity of a ligand for a protein. What is p50? How is it
related to ligand affinity of a protein?
69) Explain the role of H+, CO2, and CO in controlling the affinity for oxygen binding to
- Where on Hb does CO2 bind? Where on Hb does H+ bind? In which state, T or R
does Hb bind CO2? Why? Is affinity for CO2 higher in the lungs or in the
tissue/bloodstream? Where in the body does Hb bind CO2? How does binding of
CO to Hb affect its affinity to bind oxygen? Does Hb have a higher affinity for
oxygen or CO? What is the effect of Hb binding to CO on oxygen release in the