MCB250 Exam 2
Which of the following statements is accurate? -A single pre-mRNA can undergo only two forms of alternative splicing. -Alternative splicing cannot alter the exons at the far 5' and 3' ends of the gene. -Alternative splicing is a purely stochastic process. -Alternative splicing allows one gene to produce different proteins in different cell types. -Protein isoforms resulting from alternative splicing have identical amino acid sequences.
Alternative splicing allows one gene to produce different proteins in different cell types.
Nucleosomes are _______. -"spool-like" structures around which DNA is wrapped 1.65 times -made up of RNA-protein complexes -the organelles at which proteins are made in the cell -the molecular machinery within the nucleus that carries out transcription of nuclear genes -the regions within bacteria containing genomic DNA
"spool-like" structures around which DNA is wrapped 1.65 times
A complete ribosome has _______ tRNA binding sites. -2 -1 -3 -4 -0
3
The eukaryotic initiation factor eIF4E is also known as the ______. -Shine-Dalgarno protein -polyA-binding protein -18S Ribosomal RNA -initiator tRNA -Cap-binding protein
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 -DNA duplex where the primer provides the single-stranded DNA that directs the addition of each complementary deoxyribonucleotide to the annealed template -DNA duplex where the DNA polymerase catalyzes the phosphodiester bind between the 3'-end of the primer and the 5'-end of the template -DNA duplex where the DNA polymerase catalyzes the phosphodiester bind between the 5'-end of the primer and the 3'-end of the template
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 has 5' exonuclease activity; DNA polymerase III does not. -DNA polymerase III is responsible for the majority of DNA synthesis in E. coli. -The processivity of DNA synthesis is an order of magnitude greater for DNA polymerase III as compared to DNA polymerase I. -DNA polymerase I is able to proofread; DNA polymerase III is not. -DNA polymerase I can replace RNA primers with DNA; DNA polymerase III does not.
DNA polymerase I is able to proofread; DNA polymerase III is not.
The error rate in transcription (1 in 104 nucleotides) is orders of magnitude higher than that of DNA replication. This is not surprising given that ________ . -the organic bases in RNA do not undergo tautomerization to proper base pairing cannot occur. -Genes are permanent elements of inheritance, whereas gene products such as RNA are transient. -RNA lacks thymine (T), which causes RNA polymerase to make irreversible errors when it encounters an adenine (A) in the template strand. -RNAs do not form a double-helix, so that their nucleotide sequences are difficult to read by polymerases that replicate them. -the ribose backbone lacks 5'-to-3' polarity, so that RNA sequences can be read in either direction.
Genes are permanent elements of inheritance, whereas gene products such as RNA are transient.
Base excision repair (BER) differs from nucleotide excision repair (NER) in which of the following ways? -BER involves a DNA synthesis step, while NER does not. -NER involves the removal and replacement of DNA containing altered bases, while BER does not. -BER involves the removal and replacement of DNA containing altered bases, while NER does not. -NER recognizes helix distortions, while BER recognizes specific base damage. -BER recognizes helix distortions, while NER recognizes specific base damage.
NER recognizes helix distortions, while BER recognizes specific base damage.
___________ transcribes only ribosomal RNA genes in eukaryotes. -DNA polymerase III -RNA helicase -RNAse H -RNA polymerase III -RNA polymerase I
RNA polymerase I
The term 'ribozyme' specifically refers to _________. -RNAs that catalyze enzymatic reactions. -RNAs that have a specific secondary structure recognized by proteins. -proteins that catalyze post-transcriptional modification of RNAs. -sequences removed from mRNAs during the process of RNA splicing. -functional RNAs produced by the enzymatic cleavage of larger precursor molecules.
RNAs that catalyze enzymatic reactions.
In E. coli, which protein is central to the process of strand invasion? -RecD -RecC -RecUV -RecA -RecB
RecA
Which of the following statements is not true regarding the mechanism of pre-mRNA splicing? -The excised RNA is called a 'lariat' because the 5' end of the intron is covalently bound to the branchpoint site in the middle. -The splicing of pre-mRNAs involves two successive transesterification reactions. -The first step in splicing is a nucleophilic attack by the 2'-OH group of the conserved A at the branch site. -Splicing is a two-step process that leads to a net loss of two phosphodiester bonds. -Single bases are never lost or gained during splicing to insure that the joined exons are consistently in the same reading frame
Splicing is a two-step process that leads to a net loss of two phosphodiester bonds.
______________is the general transcription factor used by all three of the eukaryotic RNA polymerases? -Mediator complex protein -TATA-binding protein (TBP) -TAF protein -TATA box protein -TFIIH protein
TATA-binding protein (TBP)
True or False: 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
In E. coli, the primary component of the mismatch repair system is the protein MutS. How does MutS recognize mismatched base pairs? -It recognizes purine-purine and pyrimidine-pyrimidine mismatches because they are, respectively, longer and shorter than a purine-pyrimidine pair. -When mismatched base pairs are transcribed, MutS edits the RNA transcript to correct the mutation. -It reads the major groove and counts the number of hydrogen bonds to determine if there is correct base pairing. -It identifies hemimethylated base pairs and methylates the unmodified base. -When subjected to force, mismatched base pairs distort more easily than correctly matched basepairs.
When subjected to force, mismatched base pairs distort more easily than correctly matched basepairs.
In homologous recombination, the term "patch product" refers to _____. -short cDNAs in which the 2nd strand was generated with a random primer. -a region of heteroduplex flanked on either side by sequences that have not experienced recombination. -the product of any Holliday junction resolution. -a localized change in DNA sequence resulting from DNA mismatch repair. -the junction site of chromosomal crossing over.
a region of heteroduplex flanked on either side by sequences that have not yet experienced recombination
For transcription to occur in Escherichia coli, the initiation factor (σ) binds must generally interact with two DNA elements that are __________. -called enhancers because of their ability to bend regulatory regions of singled stranded DNA to the site of transcription initiation -located at the origin of replication -renatures into short stretches of duplex DNA that signals -RNA polymerase to bind where RNA synthesis starts -located near the site of mRNA where the ribosome binds to initiate transcription -approximately 10 and 35 base pairs upstream of the site where RNA synthesis starts
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 _________. -reverses direction, and returns to the promoter of the gene. -arrests and the damage is removed from the DNA by repair enzymes. -gets past the damage by adding a series of A's to the end of the elongating transcript. -repairs the damage with its exonuclease activity, then resumes transcription. -arrests and releases its hold on the DNA.
arrests and the damage is removed from the DNA by repair enzymes.
The primary purpose of RNA splicing is to _________. -remove untranslated regions (UTRs) from the 5' and 3' ends of the pre-mRNA. -cleave the operon transcripts into multiple functional gene products. -shorten mRNAs so that they can be transported to the cytoplasm for translation. -add capping sequences to the 5' and 3' ends of the mRNA to protect against exonucleases. -assemble the protein-coding sequences of the gene into a single continuous reading frame.
assemble the protein-coding sequences of the gene into a single continuous reading frame.
Which one of the following steps in bacterial translation does NOT require hydrolysis of GTP? -delivery of the correct aminoacyl-tRNAs to the ribosomal A site by EF-Tu -EF-G stimulation of ribosome translocation -all of the translation steps mentioned here require GTP hydrolysis -assembly of the 70S initiation complex -assembly of the 30S initiation complex
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 _______. -free in the cytoplasm -attached to the tRNA occupying the A site -is attached through hydrogen bonds to the mRNA -attached to the tRNA occupying the E site -moved to the E site
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 ___________. -DNA helicase unwinding the double helix around the +1 site. -DnaA:ATP complexes binding to and twisting the double helix at the +1 site. -RNA polymerase obtaining the energy to cause separation of strands from ATP hydrolysis. -binding of the DNA complexes to the double helix at the +1 site and twisting of the double helix. -bases at the promoter region flipping outward from the double helix into pockets on the polymerase.
bases at the promoter region flipping outward from the double helix into pockets on the polymerase.
Following replication of a circular chromosome in a bacterium, segregation of the two chromosomes to the two daughter cells requires _________. -conversion of the DNA into linear chromosomes just prior to mitosis -decatenation of the replication products by Type II topoisomerases -the action of telomerase to complete to complete synthesis of the lagging strand -compaction of the separate chromosomes into 10 nm and 30 nm strands -interactions of the chromosomal DNA with nucleosomes
decatenation of the replication products by Type II topoisomerases
Promoter escape occurs when RNA polymerase enters into the _________ phase of the transcription cycle. -closed complex. -initiation -open complex -elongation -termination
elongation
During homologous recombination, strand invasion involves all of the following except ______. -two nearly identical DNA sequences -excision of abnormal bases -alignment of DNA on different chromosomes -formation of a heteroduplex sequence -a double stranded break in the DNA
excision of abnormal bases
One common type of DNA mutation is the thymine dimer. These dimers result from ______. -exposure to UV radiation. -exposure to reactive oxygen species. -errors in DNA replication. -spontaneous deamination of thymine. -incorporation of base analogs.
exposure to UV radiation
The structure of RNA does NOT have _________. -a ribose ring with a hydroxyl (-OH) group on its 2' carbon. -extended regions of base-pair complementarity adopt a helical form identical to B-type DNA. -adenine-thymine (A-T) base pairs. -bases in RNA that can form non-Watson-Crick base pairs. -base-pairing between short complementary sequences that can fold a single-stranded RNA into a stable 3-dimensional structure.
extended regions of base-pair complementarity adopt a helical form identical to B-type DNA.
In the figure below, the letter C indicates _____. -supercoils -a DNA double helix -histones -a nucleosome -loops
histones
The primary mechanism used to repair double-stranded DNA breaks is ______. -nucleotide excision repair -homologous recombination -mismatch excision repair -arm-linking -crossover during meiosis
homologous recombination
Transfer RNAs (tRNAs) contain a number of unusual bases (not A, U, C or G) 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 -methylguanine -pseudouridine -dihydrouridine -hypoxanthine
inosine
The interaction of DNA with histones in nucleosomes _______. -does not affect or influence expression of genes -requires binding to the zinc-finger motifs of the histones -occurs only during replication of the chromosome -is dynamic -stores energy through positive supercoiling
is dynamic
The 30 nm fiber of chromatin ____________. -contains DNA that is more accessible to the enzymes that regulate DNA function than the 10 nm fiber. -is formed by a mechanism that requires the amino-terminal tail domains of the core histones for stabilization of the 30 nm fiber -decreases the compaction of linear DNA relative to the 10 nm fiber so that DNA can be more readily transcribed -is formed by lining up three 10 nm fibers of different chromosomes next to each other -can be formed by the addition of histone H2 to the 10 nm fibers
is formed by a mechanism that requires the amino-terminal tail domains of the core histones for stabilization of the 30 nm fiber
Transcription termination in eukaryotes ___________ . -occurs by a Rho-dependent mechanism -is dependent on ribosomes binding RNA polymerase off the transcript -is linked to RNA destruction by a highly processive RNAse -requires a highly accessible stop codon -requires the formation of 5' hairpin structures
is linked to RNA destruction by a highly processive RNAse
DNA sequencing methods that involve "chain termination" result from ________ . -lack of a base on the previously incorporated nucleotide on the DNA chain being extended. -lack of a 2'-OH on the previously incorporated nucleotide on the DNA chain being extended. -lack of a 3'-OH on the previously incorporated nucleotide on the DNA chain being extended. -lack of a 5'-Pi on the previously incorporated nucleotide on the DNA chain being extended. -lack of a 4'-OH on the previously incorporated nucleotide on the DNA chain being extended.
lack of a 3'-OH on the previously incorporated nucleotide on the DNA chain being extended.
DNA polymerase ensures that the correct nucleotide is incorporated into the growing strand of DNA by ________ . -selecting the correct nucleotide in an exonuclease active site in the DNA polymerase -specifically allowing only the correct nucleotide to enter the active site -incorporating random nucleotides and then subsequently removing the wrong ones -monitoring the ability of the incoming nucleotide to form the appropriate base pair
monitoring the ability of the incoming nucleotide to form the appropriate base pair
To escape the promoter during eukaryotic transcription, RNA polymerase II sheds most of the general transcription factors used for transcription initiation by ___________ . -inducing supercoiling before the transcription fork -multiple phosphorylation events at the carboxyl-terminal domain of RNA polymerase II -synthesis of a DNA primer that is incompatible with the general transcription factors -undergoing cellular ubiquitination leading to degradation -synthesis of a polyA tail
multiple phosphorylation events at the carboxyl-terminal domain of RNA polymerase II
A mutation in the sequence of bacterial DNA encoding the ribosome-binding site (RBS) may result in _____________. -pausing of the ribosome during elongation -shortening of the peptide as it is being translated -pausing of the RNA polymerase during elongation -reduced transcription of the mRNA for the gene in which the mutation has occurred -reduced initiation of translation
reduced initiation of translation
It is NOT true that telomerase ___________. -has reverse transcriptase activity. -generates a new primer:template junction by providing its own template. -acts to elongate the 3' end of linear DNAs. -is a ribonucleoprotein. -replaces the final RNA primer with DNA during DNA replication.
replaces the final RNA primer with DNA during DNA replication.
Rho-dependent transcription termination __________. -is signaled by a stop codon within the DNA sequence encoding the RNA -involves the stalling of RNA polymerase as two replication forks converge -requires the formation of hetero-duplex DNA which stalls RNA polymerase -takes place at the end of each chromosome -requires that the ATPase Rho hops on elongating transcripts and translocates along them until they reach RNA polymerase
requires that the ATPase Rho hops on elongating transcripts and translocates along them until they reach RNA polymerase
All of the following statements are accurate except: -snRNPs are an important component of the ribosome. -snRNPs are short nuclear RNAs complexed with splicing proteins. -Some snRNPs function as ribozymes, i.e. they catalyze chemical reactions in the splicing process. -Some snRNPs orchestrate splicing by complementary base pairing with conserved sequences in the pre-mRNA. -snRNPs are an important component of the splicesosome.
snRNPs are an important component of the ribosome.
During DNA replication, the initiator protein _________. -is the cis-acting DNA sequence that are sufficient to direct the initiation of the of DNA -specifically recognizes a DNA element in the replicator and activates the initiation of replication -is recruited to the chromosome by other factors, and therefore is not a sequence-specific binding protein. -physically separates the two strands so that replication can occur -is the physical site on DNA where DNA is unwound and DNA synthesis initiates
specifically recognizes a DNA element in the replicator and activates the initiation of replication
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 -the peptidyl transferase center of the ribosome -the messenger RNA -the decoding center of the ribosome -the peptidyl-tRNA
the aminoacyl-tRNA synthetase
DNA supercoiling is ___________. -the number of helical turns of one strand of DNA about the other. -the over- or under-winding of a DNA duplex -not important for compacting DNA & regulating gene expression -affected in bacteria by the winding of DNA around nucleosomes -negative only when DNA is circular
the over- or under-winding of a DNA duplex
The Shine-Dalgarno sequence is _____________. -the extended AUG sequence that serves as a translation start site in eukaryotes. -any of the three sequences that serve as translation stop codons. -the conserved 3' end of tRNAs where amino acid charging occurs. -the part of a bacterial mRNA that recruits the 16S rRNA. -the part of a tRNA that base pairs with a codon.
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 major groove -only with bases via the minor groove. -the phosphodiester backbone and with bases via the minor groove -the side chains of residues pointing outward from the alpha helix -only with bases via the major groove
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 -DNA polymerase II -DNA polymerase I -DNA ligase -reverse transcriptase
translesion polymerase
The role of DNA helicase is to ___________. -relax positive DNA supercoils -bind single stranded DNA and keep it from re-annealing -unwind the DNA at the replication fork -confer processivity to DNA Pol III. -load clamps
unwind the DNA at the replication fork