Exam 1

• 31 OH is required for elongation of nucleotides (DNA has OH only at 3 position

while RNA has OH at both 2 and 3 positions)
• Histones inhibit replication
• AT bonds are weaker (2 vs 3 H bonds) than GC bonds
o GC can use higher annealing temps for PCR
• A DNA template, deoxynucleotides, primers, and DNA poly are all required for
DNA replication, replication cannot occur de novo and the 5’ group is a
phosphate, not a hydroxyl
• A transcriptionally active gene is likely to contain acetylated histones and
increased topo II activity
• Phosphorylation of Rb is implicated in cancer
• Base excision uses DNA glycosylase
• Mismatch repair can delineate between the parent and daughter strand as the
parent strand is methylated
• RNA poly synthesizes RNA, not any DNA polys, reverse transcriptase,
telomerase
• PCR does not make use of RNA but DNA replication, telomere elongation, and
retroviruses do require the use of RNA to replicate/elongate
• Topo II helps to unravel bacterial DNA into a single circular strand
• Telomerase extends DNA strands in eukaryotes only
• Telomerase is a specialized DNA poly
• Telomerase is a protein-RNA complex
• Phosphorylation of initiation factors ensures that replication occurs only once per
cell cycle
• ATM/ATR phosphorylate p53
• Xeroderma pigmentosum patients have errors in their nucleotide excision repair
mechanism
• A gain of function mutation of telomerase results in cancer
• p53 phosphorylation leads to transcription of p21, inhibition of E2F, and cell
cycle arrest
• ddNTPs that inhibit retroviral replication also result in depletion of mitochondria
because both preferentially utilize ddNTPs over dNTPs and lack good
proofreading abilities
• Increased rates of C-T mutations are associated with defective photolyase activity
and deaminase activity
• Chargaff’s rule states that A=T and C=G
• A nucleotide strand can only include a single strand with U
• Fluoruracil inhibits thymidylate synthase
• Methotrexate blocks thymidlyate synthesis, is a competitive inhibitor of
dihydrofolate reductase, and is an anticancer drug
• ddNTPs are used to treat HIV and for DNA sequencing
• p21 is not a substrate for phosphorylation
 • ATM/ATR kinases result in stabilization of p53, transcription of p21, and
suppression of E2F activity
• Increased ATM activity leads to increased p53 activity
• Increased p21 leads to decreased cyclin/CDK activity
• Increased p21 results in increased Rb activity
• Increased p53 activity results in increased p21 production
• Telomerase is unique to eukaryotic replication
• Nucleic acid is encoded by nitrogenous bases
• Semi-conservative replication means each strand has 1 parental strand and 1
daughter strand
• DNA poly III has an error rate of 1 x 107
• Ε subunit is the proofreading element of DNA poly III
• DNA synthesis always occurs in the 5’ to 3’ direction
• PCR involves a helicase, primase, and polymerase analogous to replication
• DNA glycosylases generate AP sites, function in base-excition repair, and
preferentially remove T bases
• SOS repair is associated with errors
• Histones are rich in positively charged amino acids which facilitates DNA
binding, acetylation decreases histone affinity for DNA, and histone acetylation
enhances transcriptional activity
• A nucleoside analog must be lacking hydroxyl groups at both the 2’ and 3’
positions
Exam 2
• Removal of an enhancer or changing the spacing of regulatory elements from the
typical -35, and -100 positions will lead to a decrease in transcription
• RNA and DNA polymerases read from 3’ to 5’ so that they can transcribe/translate
in the proper 5’ to 3’ direction
• α-amantin is toxic to humans because it inhibits mRNA synthesis
• Transcription occurs from the “top” to the “bottom” of the Christmas tree
structure, cis regulatory elements are therefore located above the top of the tree
• The cis regulatory elements of the lac operon include the promoter and operator
while the trans elements are RNA poly, the inhibitor, and CAP (promoter that
binds)
• Intron splicing is not involved in the production of diverse proteins by bacteria
which lack introns, but mRNAs can encode multiple genes (operon) and the exons
of the bacteria are densely packed on the chromosome
• RNA synthesis occurs 5’ to 3’ but does not involve a primer as it can occur de
novo and lacks proofreading ability, it does however require the template of DNA
• σ subunit of RNA poly exhibits helicase activity
• Tamoxifen inhibits gene expression in the treatment of cancer (gleevec and
rifampicin do not)
• DNA binding proteins function as dimers because this allows binding affinity to
increase, specificity to increase, and combinatorial complexity to increase
 • Hairpin loops trigger termination of RNA synthesis in prokaryotes
• RNA splicing, polyadenylation, 5’ methyl G capping all occur in the nucleus
• Enhancers are not identical in transcription of eukaryotic mRNA, but RNA poly
II, TFIIF, and TBP are all the same
• Chromatin decondensation, histone acetylation, and mediators all promote
transcription
• Linker scan analysis, DNAse I footprinting, and plasmid vector expression assays
are all useful in identifying regulatory sequences (cis)
• DNA cannot be spliced because it lacks a 2’ OH group
• CAP and Lac I are allosteric binding proteins
• Histone deacetylases and methylation of promoters silence gene expression
• Tamoxifen makes use of the activator domain of the estrogen receptor for a target
• Yeast 2-hybrid screens identifies protein-protein interactions while gel shift assay
and DNAse I fingerprinting identify protein-DNA intxns
• CML is not the result of altered cis regulation while Burkitt’s and Follicular
lymphoma are
• v-SRC and Bcr-abl are both constitutively active kinases
• Not all oncogenes function by directly promoting cell-cycle progression
• Rb is a tumor suppressor while Ras, myc, and bcl-2 are all protooncogenes
• Splicing does not involve DNA
• Altering promoter sequences, interfering with enhancer activity, and inactivating
polyadenylase are all means to reduce gene expression
• In prokaryotes mRNA are roughly equal in size to the DNA that encode them
• In eukaryotes mRNAs are smaller than the DNA that encodes them
• si and micro RNA are effective antibiotic activities
• follicular lymphoma is not directly attributable to trans factors
• Eukaryotes and prokaryotes both include analogous TFIIH, TBP, and exons
Exam 3
• UGA, UAG, and UAA are all stop codons while AUG is the start codon
• Aminoacyl t-RNA synthetases proofread using a dual sieve mechanism that
hydrolyzes amino acids that are too small and excludes amino acids that are too
big
• Poly A binding proteins increase transcriptional efficiency
• Translation of mRNAs can be initiated in the middle of a transcript
• RFLPs can be used to identify genes associated with genes and be caused by the
creation of a new RE site
• Inhibition of nuclear export would negatively regulate RNAi mechanisms and
translation
• A decrease in translation efficiency could be attributed to elevated deadenylase
activity, be a consequence of miRNA activity, and be attributed to secondary
structures associated with the Shine-Delgarno sequence
• RE can be used to identify changes in DNA nucleotide sequences
• miRNA and siRNA can be distinguished from one another because miRNA allows
the production of product RNA while siRNA will cleave the RNA product and
destroy it, thus a Northern blot can be used to delineate between the two
• Point mutations can result from a cause other than frameshift mutations
• Deletion of an M6P site would lead to the aberrant secretion of lysosomal
enzymes
• Ubiquitination, trafficking of proteins to organelles, and diphtheria toxin all target
proteins but IRE-BP activity does not
• Ubiquitination is irreversible
• A site is the aminoacyl; P site is the peptidyl site; E is the exit site
• shRNAs, siRNAs, and miRNAs all participate in gene silencing
• Southern blotting does not evaluate RNA, but in situ hybridization and Northern
blotting do
• If either the 5’ cap or 3’ polyadenylation is not present on an mRNA, a subset of
mRNPs will fail to bind the RNA and its export from the nucleus will decrease
• Endogenous RNAi mechanisms require RNA cleavage in the nucleus
• siRNAs can distinguish between single base-pair differences in target DNA
sequences
• RNAi occurs in the cytoplasm
• RNAi is a catalytic process
• Poly A binding protein is important in mRNA export, stability of the mRNA
transcripts in the cytoplasm, and in promoting translation
• KDEL sequence directs a protein to remain in the ER
• Protein levels can change independently of mRNA levels
• TRAP mediated suppression of translation is analogous to rerritin mRNA intxns
with IRE-BP when iron levels are low
• RNAi is triggered by stem-loops, requires enzyme processing in the nucleus and
cytoplasm, and can result in degradation of mRNAs
• A guide RNA binds to a target mRNA imperfectly and results in suppression of
translation