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2011 BL 426 Study guide test 4 Ch 16, 19, 20, 21 other RNA processing, ribosome,
tRNA, DNA replication, DNA repair telomere
1. The test will be worth 125 pts and will have a number of multiple choice questions, plus some matching
probably, maybe gel or experiment to interpret, and some compare/contrast, or short essay type questions;
maybe also some abbreviations to define.
1. Focus on what was presented in PowerPoints, using your text for additional clarifications and support.
2. Read learning outcomes for each chapter; read summary at end of each chapter for topics covered
3. Review the PowerPoint slides.
4. Focus on understanding important Figures – what is being shown; what type of experiment was done.
5. Consider suggested review and analytical questions at the end of chapters.
6. Make a list of important new terms, concepts, enzymes, DNA sites, RNA sites and what they do
(many are listed below, but the list may not be comprehensive)
7. Complexity: Lots of big protein/RNA and protein/DNA complexes are involved
8. Consider different model systems (bacteria, yeast, mammals) and what they told us. Note that much of
this material is about eukaryotes, although prokaryotic systems were critical for Xray crystallography of
tRNA, of ribosome subunits. viruses (lambda, SV40), Tetrahymena telomeres, trypanosome RNA editing,
Haloarcula, Thermus thermophilus, E. coli, C. elegans, Saccharomyces,
9. Some general comparisons of eukaryotes to prokaryotes – what is similar, what must be different?
Consider RNA processing, DNA replication, repair, ribosomes, tRNA, mRNA; Mg++ was often a cofactor
for cleavages DNA replication (circle, linear, telomeres)
10. Consider some of the types of experimental techniques and assays were used to obtain the
understanding of the molecular mechanisms, many of which we have mentioned before.
in vitro RNA synthesis; RNA and DNA gels; protein-RNA binding; telomerase assay
Purification of proteins and protein complexes (affinity tags, ion exchange chromatography)
EMSA; linker scanning mutagenesis; primer extension RNA synthesis; X-ray crystallography;
mutated RNA sites; Mutant proteins, mutated DNA binding sites,
Chromatin immunoprecipitation; how structure informs funciton
Some new concepts:
rRNA and tRNA processing; tRNA joined to amino acids
trans-splicing vs. cis-splicing
RNA editing
RNAi
Ribosome subunits structure and function; selectivity of aa-tRNA synthetase enzyme ,;
telomerase; telomerase has guide RNA plus proteins
Structures of telomeres and pecific proteins binding to end of telomeres
DNA damage and repair of typical damage; better to repair before replication:
Reversal of damage; Base excision repair, nucleotide excision repair, recombination repair
Alkylating agents, thymine dimers, mismatch, double strand break; SOS repair
Some DNA sequences and signals: oriC, ARS, Telomeres, centromeres, start of transcription
Some jargon/ abbreviations:
Pol II (CTD)
5’-UTR
3’-UTR Upstream downstream
RFLP
NER
BER
ORF
XP
Small subunit
large subunit
RNA start is +1
Some new, some review terms: processivity
semi-conservative
polysome
leading strand
lagging strand,
polycistronic
monocistronic
rolling circle replication
bidirectional replication
sliding clamp
Some protein complexes, what they do and what they contain:
DNA polymerase III holoenzyme, primosome,
primase
RISC
telomerase
DNA polymerases
Some proteins and enzymes:
Ribozyme
RNase T1 RNase III
RNase A
RNase T2
RNase E
RNase P
nuclease S1
DNase I
Antibody
RNaseH
RdRP (RNA-dependent RNA polymerase)
amino acyl tRNA synthetase
TUTase (terminal uridyl transferase) Histone methyl transferase
DNA pol I
DNA pol III (and subcomplexes), Klenow polymerase
DNA ligase
Eukaryotic DNA pol: () main ones
Photolyase
DNA glycosylase
AP endonuclease
helicase
Excinuclease (uvrABC)
recA protease
umuCD (DNA polV)
TERT (telomerase RT)
topoisomerase
o6-meG methyltransferase
T antigen of SV40
Dicer
Ago
peptidyl transferase
Some RNA molecules:
tRNA, rRNA, mRNA,
5S rRNA, snRNA,
hnRNA,
16S
23S
18S
28S
5S
5.8S
Guide RNA (editing) telomerase RNA
siRNA
miRNA
guide RNA (RNAi)