Study Guide for Mid-Term Exam #3

Thursday, December 10
4:30-5:50 PM
Structures you should know:
The 20 amino acids
Formyl-methionine
The difference between a proton, a hydride, and a hydrogen
The five nucleotides (ATP, GTP, TTP, UTP, CTP)
The differences in structure between RNA and DNA
The general structure of a chain of RNA and DNA
The structures of aminoacyl-adenylates and aminoacyl-tRNA (only the structure of the aa
attached to the terminal adenosine of the tRNA)
The cloverleaf structure of tRNA
The Watson Crick base pairs
The GU Wobble base pair
You should be able to recognize 8-oxoguanosine
S-adenosylmethionine
Mechanisms you should understand:
DNA replication mechanism for adding one nucleotide (Figure 34.2)
Peptide bond formation in the ribosome
Aminoacyl-adenylate synthesis
Aminoacyl-tRNA synthesis
Methyl transfer reactions with S-adenosylmethionine
Chapter 33: The structure of informational molecules: DNA and RNA
Nucleic acid structures
The differences between a base, a nucleoside, and a nucleotide
The differences between RNA and DNA (Figure 33.3, 33.4, 33.5 and related text)
Watson Crick base pairs
The basics of a double helix (Figure 33.11, 12, and 13 and related text)
You do NOT need to know about Meselson and Stahls semi-conservative experiment
Annealing and denaturing of double stranded DNA and RNA
The major and minor grooves of DNA
Supercoiling
Nucleosomes, chromatin and chromosome general structure, size and protein composition
Very basic information about RNA tertiary structure (figure 33.31)
Chapter 34: DNA replication
Chemical mechanism for replication (Figure 34.2)
General polymerization reaction (Figure 34.1)
Hand shape of DNA Polymerase structure and what the different regions do
Shape selectivity of DNA polymerase (Figures 34.4 and 34.5)
Functions of helicases, topoisomerase, exonuclease, DNA polymerase, DNA ligase in E. coli
DNA polymerase recognition of DNA and binding
Replication forks
Leading and lagging strands
Okazaki fragments
Direction of synthesis.

Figure 34.16, 17, and 18

Very basics of telomeres and telomerase
Chapter 35: DNA repair and recombination
Types of errors that can occur during replication and the errors in replication that arise
Figures 35.2, 35.3, and 35.6
Dont worry about the genetic diseases talked about near Figure 35.1
For aflatoxin, you should be generally aware that it makes a DNA adduct that causes errors in
replication. Dont worry about the structure of the adduct
Mismatch repair (Figure 3.57)
The function of glycosylase and base excision repair (Figure 35.8)
Nucleotide excision repair (Figure 35.10)
Deamination of cytidine to make uracil and uracil repair (Figure 35.11)
Ames Test (General info only, Figure 35.13)
DNA recombination in repair and the big picture of the Holliday junction (Figure 35.15)
Chapter 36: RNA synthesis and regulation in bacteria
RNA polymerase
Genes as transcriptional units
Initiation
Elongation
Termination
Sigma subunits
What it means to transcribe 5 to 3 (as a cartoon and on the level of a chemical structure)
Rho protein
The basics of base modifications (namely recognize modified bases and mechanisms that use
S-adenosylmethionine or other reaction pathways weve studied)
You do not need to worry about antibiotics that inhibit transcription
The lac operon and regulation of transcription
The lac repressor
The big picture of riboswitches
Chapter 37: Gene expression in eukaryotes
Figure 37.1
The products from the three different RNA polymerases
Eukaryotic promoter elements, especially the TATA box
Transcription from the TATA box and the proteins involved including RNA polymerase II
Enhancer sequences
Nuclear hormone receptors
Histone acetylation and transcription

Chapter 38: RNA processing in eukaryotes

Ribosomal RNA modification and processing (Figure 38.1)
Transfer RNA processing (Figure 38.2)
Messenger RNA capping, modification, and splicing (big picture) (Figure 38.5 and 38.3)
Poly A Tail (Figure 38.4)
Two types of introns
That the spliceosome is a ribonucleoprotein and what that means
Figure 38.7 and the mechanism of lariat RNA synthesis
The big picture of alternative splicing to cause disease and to produce multiple forms of a
protein
Coordination of splicing with transcription
RNA as a catalyst and the Group II intron splicing mechanism
Chapter 39: The genetic code
Section 39.1 (Do NOT memorize Table 39.1 but know how to read it)
Do NOT worry about variability in genetic codes, but be aware that it exists
The basic structure of transfer RNAs
The wobble pair in the codon/anticodon interactions
Degeneracy in the genetic code
Pairing of different bases beyond Watson-Crick base pairs
The basics of lysidine recognition of codons
Transfer RNA aminoacylation (both reactions and mechanisms)
The structure of amino acids attached to the 3 end of tRNAs (attached to the terminal A)
The big picture of tRNA aminoacylation, amino acid substrate recognition and editing of
misacylated tRNAs
The ribosome is a ribonucleoprotein (and what this means)
The role of ribosomes in protein translation
Translation goes from 5 to 3 and what this means.
Do NOT worry about the secondary structure of ribosomal RNA
Chapter 40: The mechanism of protein synthesis
Protein synthesis and decoding of mRNA
AUG, the Shine-Delgarno sequence, and initiation of translation
Role of formyl-Met in translation initiation
Formation of the 70S ribosome
Svedberg units and what they mean
The size and components of the different ribosome subunits
The roles of EF-Tu and EF-G in translation
Peptide bond formation, including the mechanism (You do NOT need to worry about how the
ribosome catalyzes deprotonation of the amino acid in the peptidyltransferase center, just the
fact that deprotonation is required)
Figure 40.8 and 40.9
Mimicry in translation
The differences between translation in bacteria and eukarya (In particular, initiation and poly A
tail)
Antibiotics as inhibitors of translation (Table 40.1)
Do NOT worry about diphtheria toxin or ricin
Synthesis of secretory and membrane proteins (the signal recognition particle, the rough
endoplasmic reticulum, signal sequences and Figure 40.19)
Basic mechanisms to regulate protein synthesis