C485 Review Sheet for Exam II (Fall ’15)
This sheet is intended as a study aid, not a comprehensive list of everything
we covered. This sheet hits the highlights.
Basic Units Covered:
1) Glycogen breakdown (21.1)
2) Regulation of glycogen breakdown and synthesis (21.2-21.3, 21.5)
3) Glycogen synthesis (21.4)
4) Signal Transduction, G-coupled receptors, Insulin receptor (14-14.2)
5) Fatty acid degradation and ketone bodies (22-22.3)
6) Fatty acid synthesis (22.4)
7) Regulation of fatty acid synthesis (22.5)
8) Protein digestion (23.1)
9) Cellular protein turnover (23.2)
10) Amino acid degradation I: transamination and the urea cycle 23.3-23.4
11) Amino acid degradation II: specific degradation of amino acids, ketogenic vs.
glucogenic aa’s (23.5) and class notes.
The exam will generally be similar or identical to questions from the review questions,
practice exams and the questions assigned from the student companion. As a rule, you
should know the names and structures of the intermediates in pathways and the roles of
the specific proteins and cofactors associated with those pathways. You should also
know the roles of regulatory molecules associated with pathways and the logic behind the
regulation (i.e. why is citrate an activator of fatty acid synthesis?). If I gave you a
mechanism in class, you are responsible for knowing it. If I did not cover a mechanism,
you don’t have to know it, but you still have to know the transformation.
1) Gycogen degradation in muscle and liver. Enzyme activities required (phosphorylase,
transferase, glucosidase- i.e. debranching). Differences between end products and
enzyme acitivites in muscle and liver.
2) Regulation of phosphorylase by covalent modification and allosteric interactions.
Understand the interconversion of phosphorylase a and b, and of the R and T states in
both muscle and liver. Be able to explain the logic behind the use of various small
molecules to regulate the enzyme. Know the difference in regulation between the liver
and muscle enzymes. You should be able to diagram the hormone pathways associated
with activation and/or inactivation of the enzyme.
3 Know the structure of glycogen. Be able to describe the enzyme activities required for
glycogen synthesis (synthase and branching enzyme). Explain why branching is
important. Understand the role of UDP glucose and how it is synthesized.
4 Know the basic signal transduction pathways for insulin, and ephinephrine/glucagon
signaling. Understand the basic components of signaling systems (pp382-383).
5) Degradation and transport of dietary triglycerides (lipases, bile salts, chylomicrons).
Storage of triglycerides, hormone activation of lipid mobilization, fatty acid transport in
the blood. Fate of glycerol. Activation of lipids as CoA thioesters. Transport into
mitochondria (role of carnitine and associated proteins). Steps of fatty acid oxidation
(know the structures). Stoichiometry of energy production. Enzyme activities required
for unsaturated and/or polyunsaturated fatty acids. Activity required for odd chain fatty
acids. Role of propionyl CoA, methylmalonyl CoA, and succinyl CoA (please know the
mechanism of the synthesis of both methylmalonyl CoA and succinyl CoA and the role
of required cofactors). Understand the structure of ketone bodies, when they are formed,
from what they are formed, and what their role is.
6) Differences between fatty acid breakdown and synthesis. Role of acyl carrier proteins.
Basic steps of beta oxidation. Be able to draw the sequence of events in the synthesis of
palmitate. Stoichiometry of palmitate synthesis. Mechanism of Acetyl CoA carboxylase.
Regulation of carboxylase by hormones, covalent modification and allosteric effectors.
Citrate shuttle.
7) Sites of dietary protein digestion. Role of pepsin and other peptidases/proteases.
Breakdown to amino acids.
8) Ubiquitinylation. Enzyme activities required for ubiquitinylation. Structure of the
isopeptide bond attachment. Polyubiquitinylation. Recognition factors for ubiquitin
attachment. Function of the proteasome. Outline chemical mechanism of proteolysis
(Thr nuc; acyl enzyme int).
9) Mechanism of transamination. Transport of nitrogen from peripheral tissues (muscle)
to the liver. Glucose-alanine cycle. Role of glutamate in nitrogen excretion. Steps of the
urea cycle.
10) Differences between glucogenic and ketogenic amino acids.
Glutatmate
dehydrogenase. The urea cycle. The alanine-glucose cycle.
11)Breakdown of amino acids to glutamate (gln, his, pro, arg). Catabolism of branched
chain amino acids. (Make sure you know the mechanism of oxidative decarboxylation.)
Breakdown of asn and asp.
12) Breakdown of aromatic amino acids (if we get that far)
13) Dehydration of ser, thr (PLP)
14) Cysteine and methionine and S-adenosyl methionine (if we get that far)
Be aware and up on your cofactor mechanisms. PLP, biotin, B12 and TPP all play
substantial roles in the transformations you have learned. All mechanisms of cofactorassisted transformations are fair game. There is a nice summary of PLP mechanisms on
the web site, as well as information on branched chain amino acid degradation, TPP
mechanisms and B12 mechanisms.