MCB 250 Exam 2

Suppose you wish to identify potential Rh-independent transcription terminators in the genome of E. coli. Which of the following sequence motifs would you search for?

A G/C rich inverted repeat immediately followed by a run of T-A base pairs

Peptide bonds are formed in the ribosome when the peptide is transferred from the peptidyl-tRNA to the amino acyl-tRNA. What is the ultimate source of energy for this reaction and what enzyme is responsible for providing this energy

ATP and an Aminoacyl-tRNA synthetase

The "GAX" codons encode Asp and Glu. Which of the following function as appropriate anticodons for the GAX Aso and Glu tRNAs?

Asp: IUC Glu: UUC

27

look at figure

Eukaryotic DNA replication

occurs at a slower rate than in prokaryotes

DNA supercoiling is the

over or under-winding of a DNA duplex

During the process of translation, which component has the responsibility of ensuring that the tRNA is correctly charged, i.e. carries the amino acid that corresponds to its anti-codon

the aminoacyl-tRNA synthetase

Type I topoisomerases

cleave and reseal phosphodiester bonds in the DNA backbone

Nucleosomes are

"sppol-like" structures around which DNA is wrapped 1.65 times

What is the LK0 for a covalently closed, circular B-form of DNA of 1050 base pairs that is free from supercoiling

+100

look at number 20

...

look at 33

......

the human genome contains approximately ______ genes

25,000

a complete ribosome has ____ tRNA binding sites

3

correct statements

Bacteria use formyl-Met-tRNA to initiate translation while eukaryotes use Met-tRNA In bacteria but not eukaryotes, translation can be initiated at multiple sites in a single mRNA in both eukaryotes and bacteria each mRNA is translated by many ribosomes in both eukaryotes and bacteria the mRNA is translated in a 5' to 3' direction

correct statements about translation in E. Coli

Binding of the large subunit leads to hydrolysis of the GTP bound to IF2 IF3 bound to the E site of the small ribosomal subunit prevents the 50S subunit from binding to the 30S subunity the IF1-IF2-GTP complex carries the initiator fMet-tRNA to the P site the mRNA associates with the initiation complex by forming base pairs with the 16S RNA of the small ribosomal subunit

Guanine is sometimes modified by oxidative damage to 8-oxoguanine, as shown. Based on your knowledge of the structures of bases found in DNA, which base pairing could 8-Oxoguanine participate in

C or A

the eukaryotic initiation factor elF4E is also known as the

Cap-binding protein

During DNA replication, the primer:template junction refers to the

DNA duplex where the template provides the single-stranded DNA that directs the addition of each complementary deoxyribonucleotide to the annealed primer

In E. coli, DNA polymerases I and III differ in many regards. Which of the following statements is not accurate

DNA polymerase I is able to proofread; DNA Pol III is not

The error rate in transcription (1 in 10^4 nucleotides) is orders of magnitude higher than that of DNA replication. This is not surprising given that

Genes are permanent elements of inheritance, whereas gene products such as RNA are transient

Which of the following statements regarding translation initiation in E. Coli is NOT CORRECT

Hydrolysis of GTP leads to IF3 leaving the D site, allowing the small subunit to bind

Which of the following statements is not correct

In both eukaryotes and bacteria, the AUG codon can only be used at the beginning of the open reading frame not within the protein coding sequence

which of the following statements regarding RNA structure is NOT correct?

In high pH, RNA will spontaneously degrade to 5'-phosphate-ribonucleotides

Base excision repair (BER) differs from nucleotide excision repair (NER) in which of the following ways

NER recognizes helix distortions, while BER recognizes specific base damage

Which of the following statements is not correct

Newly replicated DNA is hemimethylated in both eukaryotes and bacteria

Which of the following statements regarding DNA replication in D. coli is CORRECT

Pol 1 can replace RNA primers with DNA

_____ transcribes only ribosomal RNA genes in eukaryotes

RNA Pol I

RNA rather than DNA possesses catalytic activity because

RNA possesses greater conformational flexibility than DNA

The term "riboenzyme" specifically refers to

RNAs that catalyze enzymatic reactions

In E. coli, which protein is central to the process of strand invasion

RecA

______ is the general transcription factor used by all three of the eukaryotic RNA polymerases

TATA-binding protein (TBP)

Which of the following sets of enzymatic activities would most likely be used to repair sites of cytosine deamination in DNA

Uracil N-glycosylase, AP endonuclease, Pol 1, DNA ligase

in homologous recombination, the term "patch product" refers to

a region of heteroduplex flanked on either side by sequences that have not experienced recombination

Nucleosomes consist of __a___ basepairs of ds DNA wrapped around a circular disc of proteins called __b___. By assembling into nucleosomes, DNA is compacted approximately ___c___.

a: 147 b: histones c: 6 fold

RNA structure correct statements

all hydrogen bonding groups on the bases will be hydrogen bonded to water or other groups in the RNA RNA can contain G:U base pairs RNA can contain triple base pairs RNA structure is not constrained by the shape of the helix

which of the following statements is accurate?

alternative splicing allows one gene to produce different proteins in different cell types

which of the following statements is CORRECT

alternative splicing of eukaryotic pre-mRNAs can lead to many different protein products from a given gene

For a covalently closed circular double-stranded DNA, the linking number is

an invariant topological property of that DNA molecule

For transcription to occur in E. coli, the initiation factor (sigma) binds must generally interact with two DNA elements that are

approximately 10 and 35 base pairs upstream of the site where RNA synthesis starts

In E. coli, if a molecule of RNA polymerase encounters DNA damage in a gene that it is actively transcribing, then the polymerase

arrests and the damage is removed from the DNA by repair enzymes

Eukaryotic transcription factors

assemble into a pre-initiation complex in order to attach RNA polymerase to specific sites on the DNA

the primary purpose of RNA splicing is to

assemble the protein-coding sequences of the gene into a single continuous reading frame

which of the following steps in bacterial translation does NOT require hydrolysis of GTP

assembly of the 30S initiation complex

when a peptide bond is formed between two amino acids, one is attached to the tRNA occupying the P site and the other is

attached to the tRNA occupying the A site

The initiation of transcription requires melting of the DNA double helix, i.e. separating hydrogen-bonded base pairs, immediately upstream of the +1 site. In E. coli this melting is accomplished by

bases at the promoter region flipping outward from the double helix into pockets on the polymerase

DNA gyrase DIFFERS from other Type II topoisomerases because gyrase

can catalyze the formation of negative supercoils in negatively supercoiled DNA

Aminoacyl t-RNA synthetases

can frequently use more than one type of tRNA as substrate

the E. coli DNA polymerase III core

catalyzes the formation of a phosphodiester bond between the 3'-hydroxyl group of the growing DNA strand and the 5'-phosphate of the incoming dNTP

You isolate a mutation in the open reading frame encoding Helicase. Careful analysis reveals that the resulting protein is full length but has the interesting property that it works at 30 C and 42 C. the general term for this is a temperature sensetive mutation. upon sequencing the gene you determine that the mutation, located in approx the middle of the ORF, resulted in the change of a codon to UGG encoding Trp in the mutant protein. Assuming this mutation was the result of a single base change what were the possible amino acids that could have been in the wild-type protein?

cys, ser, leu, arg, or gly

Following replication of a circular chromosome in a bacterium, segregation of the two chromosomes to the two daughter cells requires

decatenation of the replication products by Type II topoisomerases

Promoter escape occurs when RNA polymerase enters into the _____ phase of the transcription cycle

elongation

during homologous recombination, strand invasion involves all of the following except

excision of abnormal bases

one common type of DNA mutation is the thymine dimer. these dimers result from

exposure to UV radiation

The structure of RNA does NOT have

extended regions of base-pair complementarity adopt a helical form identical to B-type DNA

During transcription in eukaryotes, an important function of the pre-initiation complex is to _______

form an open transcription complex

correct statements about histones

histone proteins are rich in Lys and Arg residues the histone core of the nucleosome contains two copies each of histones H2A, H2B, H3, and H4 the N-terminal tails of the core histones can be postranslationally modified to regulate chromatin structure wrapping DNA around the nucleosome is equivalent to adding negative supercoils

The primary mechanism used to repair double-stranded DNA breaks is

homologous recombination

_______ can stabilize loop structures within a single RNA molecule

hydrogen bond formation between the ribose -OH groups and nitrogenous bases

Which of the following changes will probably NOT affect the strength of an E. coli S70-dependent promoter

increasing the spacing between the +1 and the ribosome-binding site

tRNAs contain a number of unusual bases that result from post-transcriptional chemical modifications. ____is an unusual base that contributes to "wobble" base-pairing between certain pairs of codons and anticodons

inosine

The 5' cap of eukaryotic mRNAs

involves an unusual triphosphate linkage between the 5' carbons of the two ribose molecules linking the cap to 5' end of the mRNA chain

the interaction of DNA with histones in the nuclosomes

is dynamic

The 30nm fiber of chromatin

is formed by a mechanism that requires the amino-terminal tail domains of the core histones for stabilization of the 30nm fiber

Transcription termination in eukaryotes

is linked to RNA destruction by a highly processive RNAse

RNA splicing in eukaryotes

is typically characterized by a 5' Gu splice junction and a 3' AG splice junction at the Exon/intron boundaries

DNA sequencing methods that involve "chain termination" result from

lack of a 3'-OH on the previously incorporated nucleotide on the DNA chain being extended

____________ is most likely to occur almost very soon after replication of DNA at the replication fork?

mismatch repair

You isolate a mutation in the open reading frame encoding Helicase. Careful analysis reveals that the resulting protein is full length but has the interesting property that it works at 30 degrees C but not at 42 degrees C. The general term for this is a temperature sensative mutation. upon sequencing the gene you determine that the mutation, located in approx the middle of the ORF, resulted in the change of a codon UGG encoding Trp in the mutant protein. what do we call this type of mutation

missense mutation

DNA polymerase ensures that the correct nucleotide is incorporated into the growing strand of DNA by

monitoring the ability of the incoming nucleotide to form the appropriate base pair

The prokaryotic protein Rho

moves along ssRNA in a 5' to 3' direction towards the RNA-DNA duplex

To escape the promoter during eukaryotic transcription, RNA polymerase II sheds most of the general transcription factors used for transcription initiation by

multiple phosphorylation events at the carboxyl-terminal domain of RNA polymerase II

In cells, DNA supercoiling is almost always negative because

negative supercoiling stores energy for cellular processes that require strand separation

Which of the following statements in NOT CORRECT

nucleosomes must be disassembled for DNA replication but not for transcription

as a result of DNA helicase activity, topoisomomerases are also required during replication. topoisomerases help DNA helicases function more efficiently by

preventing formation of positive supercoils

Eukaryotic transcription

produces mRNA that is capped and polyadenylated prior to translation

E. coli RNA Polymerase haloenzyme

recognizes specific initiation sequences in double stranded DNA

a mutation in the sequence of bacterial DNA encoding the ribosome-binding side (RBS) may result in

reduced initiation of translation

It is NOT true that telomerase

replaces the final RNA primer with DNA during DNA replication

The sliding DNA clamp

requires ATP hydrolysis to be loaded onto the DNA

Rho-dependent transcription termination

requires that the ATPase Rho hops on elongating transcripts and translocates along them until they reach RNA polymerase

The snRNP is best described as

small RNAs associated with protein complexes in the nucleus

all of the following statements are accurate except:

snRPS are an important component of the ribosome

Which of the following statements regarding modified bases in tRNAs is CORRECT

specific enzymes create modifications post-transcriptionally

During DNA replication, the initiator protein

specifically recognizes a DNA element in the replicator and activates the initiation of replication

which of the following statements is not true regarding the mechanism of pre-mRNA splicing?

splicing is a two-step process that leads to a net loss of two phosphodiester bonds

Huntingtons disease is an incurable, adult onset neurological disorder. The disease occurs as a result of a trinucleotide repeat expansion believed to be caused by

strand slippage during DNA replication

The role of telomerase in eukaryotic cells is to

synthesize new DNA (using an RNA template) at the 3' end of the chromosome

Repetitive sequences at the ends of eukaryotic chromosomes are added by

telomerase following DNA replication

In eukaryotic cells, the wrapping of DNA around nucleosomes introduces negative supercoiling becasue

the DNA double helix is right-handed, and wrapping of DNA around the nucleosome is left-handed

correct statements

the E. coli chromosome has a single origin of replication while most eukaryotic chromosomes have multiple origins DNA replication is bi-directional from replication origins in both eukaryotes and bacteria the initiation of DNA replication is tightly controlled in both eukaryotes and bacteria in both eukaryotes and bacteria the primer used for initiating leading strand synthesis is an RNA molecule

Which of the following represents a major difference between transcription in bacteria and eukaryotes

the cellular location at which mRNAs are synthesized

The Shine-Dalgarno sequence is

the part of a bacterial mRNA that recruits the 16S rRNA

a nucleosome interacts with DNA by forming hydrogen bonds predominantly with

the phosphodiester backbone and with bases via the minor groove

as part of the SOS response, ______ synthesizes DNA across the lesion within the double helix to fill in the gap

translesion polymerase

Single-stranded DNA molecules are said to be anti-aligned when they are lined up next to each other but oriented in opposite directions

true

the role of DNA helicase is to

unwind the DNA at the replication fork

In E. coli, the primary component of the mismatch repair system is the protein MutS. How does MutS recognize mismatched base pairs

when subjected to force, mismatched base pairs distort more easily than correctly matched basepairs

a nucleosome forms hydrogen bonds with ____ of DNA

with the phosphodiester backbone and with the bases in via the minor groove