Study Guide for Exam 2
Information ESSENTIAL to know:
Ch. 25
Essential & nonessential amino acids (
Salvage pathways (Pro —> Arg, Met —> Cys, Phe —> Tyr)
Deamination (Glu DH)
The UREA cycle!! (Krebs bicycle)
Pathways of degradation to
Ac-CoA (pyruvate) from Thr, Gly, Cys, Ser, Ala
OAA from Asn, Asp
a
-Kg from Arg, Pro, Gln, GluSuccinyl-CoA from Ile & Val
Ch. 26
Structures of bases, nucleosides, and nucleotides
(including xanthine & hypoxanthine)
Pathways of synthesis of AMP, GMP, UMP, CMP
Synthesis of thymidine
Synthesis of deoxyribonucleotides
Purine salvage
Degradation of purines to uric acid
Degradation of pyrimidines to b-Ala
Regulation of purine/pyrimidine metabolism
Synthesis of NAD, FAD, CoA
Ch. 31
Experiments to demonstrate
Semi-conservative replication
Bidirectional replication
Discontinuous replication
Structure & activities of DNA pol I
How replication forks work — integration of all enzymes involved:
DNA polymerases
SSBs
Helicases & topisomerases
Primase
Ligase
Differences/similarities of replication in prokaryotes & eukaryotes
Initiation of replication in E. coli
DNA repair:
Thymidine dimers (photolyase & excision repair)
Excision repair
Mismatch repair (E. coli)
DNA recombination:
RecA functions
RecBCD functions
Holliday junctions
Telomerase
Ch. 32
Vectors & libraries (how they're made, how they work)
Enzymes used (how they work)
Restriction endonucleases
DNA polymerases
Ligases
Screening libraries (hybridization & expression)
Gene replacements & site-directed mutagenesis
Information important to know:
Ch. 25
Tetrapyrrole synthesis (up to d-aminolevulinate)
Ch. 26
Ionized forms of bases
Ch. 31
Mitochondrial DNA replication
SOS repair & lexA/recA system
As usual, I do not expect you to know all the names of enzymes and every intermediate molecule in a pathway. You should be able to draw the structures and know which cofactors are involved.
My exams never simply test how well/much you can memorize & regurgitate. They are also designed to test how much you understand. That is, the WHY of things, the implications of the way things work in biochemical pathways, how things are integrated in the cell, etc.
Some examples (may or may not be on the exam):
1) Why is U only in RNA & and T only in DNA? What is the advantage of this arrangement? How do the biochemical pathways of nucleotide synthesis and DNA/RNA synthesis contribute to maintaining this arrangement?
2) Why does priming pose such a problem for DNA replication (specifially lagging strand synthesis) and how was it solved? Why is this problem even more serious for organisms with linear chromosomes and how was that problem solved?
3) What reasons do we have for believing in an "RNA world"? What would have had to evolve in order to allow the transition to DNA? And why bother with DNA at all?
4) How does amino acid salvage and degradation pathways intersect in mammalian organisms?