Biochem Exam 4 Clicker Flashcards
A nucleotide contains which of the following:
a. 6 - carbon sugar
b. at least 3 phosphate groups
c. nitrogenous sugar
d. 4 - carbon sugar
e. nitrogenous base
NITROGENOUS BASE!
The first committed step in pyrimidine biosynthesis is:
a. The action of CPS2 to create IMP
b. The action of ribonucleotide reductase to create dTTP
c. The action of CPS2 to create carbomoyl phosphate
d. The action of Glutamine: PRPP Aminotransferase
THE ACTION OF CPS2 TO CREATE CARBOMOYL PHOSPHATE
The difference between ribose and deoxyribose is:
a. Ribose is a 6 carbon sugar and deoxyribose is a 5
b. At the 2’ carbon position
c. Deoxyribose has more hydrogens
d. Ribose has one nitrogenous base and deoxyribose has two
AT THE 2’ CARBON POSITION
Nucleotides are joined together in a polymer chain via a:
a. Glycosidic Bond
b. Phosphodiester Bond
c. DNA Ligation
d. Hydrogen Bond
e. Nucleophilic Reaction
PHOSPHODIESTER BOND
If a DNA sequence is comprised of 20% adenine, what percent of the sequence is guanine?
30%
Which of the following best defines the nucleosome core particle?
a. Histone octamer + DNA + histone H1
b. Histone octamer + linker DNA
c. Histone octamer + DNA wrapped around octamer
d. Histone octamer + DNA + histone H1 + linker DNA
HISTONE OCTAMER + DNA WRAPPED AROUND OCTAMER
Which is FALSE about DNA polymerase 3?
a. Requires a template strand for synthesis
b. Can use mono, di, and triphosphate nucleotides in synthesis
c. Has polymerase and exonuclease activity
d. Requires a primer - can only addd nucleotides to a growing chain
e. Uses magnesium to stabilize its active site
CAN USE MONO, DI, AND TRIPHOSPHATE NUCLEOTIDES IN SYNTHESIS
What best describes chain elongation during replication?
a. The nucleotide diphosphate is attached to the 5’ hydroxyl of the new strand
b. The nucleotide monophosphate is attached to the 5’ hydroxyl of the new strand
c. The nucleotide triphosphate is attached to the 3’ - hydroxyl of the new strand
d. The nucleotide triphosphate is attached at the 3’ hydroxyl of the template strand
THE NUCLEOTIDE TRIPHOSPHATE IS ATTACHED AT THE 3’ - HYDROXYL OF THE NEW STRAND
Which of these proteins acts ahead of the replisome to ensure efficient DNA replication?
a. helicase
b. DNA polymerase 1
c. topoisomerase
d. DNA polymerase 3
e. primase
TOPOISOMERASE
A DNA sequence is 3’- GCCACCG-5’
What is the sequence of the primer that begins replication?
5’ - CGGUGGC - 3’
Which of these proteins acts ahead of the replisome to ensure efficient DNA replication?
a. helicase
b. DNA polymerase 1
c. Topoisomerase (DNA gyrase)
d. DNA polymerase 3
e. Primase
TOPOISOMERASE
What is the difference between leading and lagging strands?
a. the leading strand is synthesized 5’ to 3’ while the lagging strand is synthesized 3’ to 5’
b. the leading strand is made of DNA only but the lagging strand is DNA and RNA
c. Initially, the leading strand is continuous while the lagging strand is composed of disconnected fragments
d. the leading strand is synthesized by only DNA polymerase 3 and lagging only by DNA polymerase 1
INITIALLY, THE LEADING STRAND IS CONTINUOUS WHILE THE LAGGING STRAND IS COMPOSED ON DISCONNECTED FRAGMENTS
How does DNA replication in eukaryotes and prokaryotes differ?
a. Eukaryotic DNA replication is not bi-directional
b. Eukaryotic replication occurs only in S phase of the cell cycle while bacteria continuously replicate DNA
c. Replication forks in eukaryotes move more slowly
d. There are fewer DNA polymerases in eukaryotes
e. There are fewer replication origins in eukaryotes
EUKARYOTIC REPLICATION OCCURS ONLY IN THE S PHASE OF THE CELL CYCLE WHILE BACTERIA CONTINUOUSLY REPLICATE DNA
Why would an alkylating agent cause cell death?
a. Uracil is incorporated into the DNA
b. Resulting thymine dimers block replication
c. Causes guanine to pair with adenine
d. Crosslinking between strands blocks replication
CROSSLINKING BETWEEN STRANDS BLOCKS REPLICATION
What is the most common source of mutation in DNA?
a. Chemical mutagens
b. Mismatch
c. Replication Slippage
d. Gamma Irradiation
e. Base Insertion
MISMATCH
The MutS/MutL/MutH mismatch repair system in E. Coli can distinguish daughter strand DNA from parent DNA by:
a. An altered conformation of the daughter DNA due to a recent replication
b. Histones have not yet been added to daughter strand DNA
c. Differential incorporation of heavy and light nitrogen
d. Base methylation present on the parental DNA that is not yet added to the daughter strand
e. That new DNA smell
BASE METHYLATION PRESENT ON THE PARENTAL DNA THAT IS NOT YET ADDED TO THE DAUGHTER STRAND
Which of the following does not play a role in base-excision repair?
a. DNA polymerase
b. DNA ligase
c. Deoxyribose phosphodiesterase
d. Endonuclease
e. All of these play a role
ALL OF THESE PLAY A ROLE
Which of the following is specific to transcription compared to DNA replication?
a. Synthesis proceeds 5’ to 3’ only
b. Requires a primer during initiation
c. 3’ OH of growing chain attacks inner most phosphate of incoming triphosphate
d. Uses ribose triphosphates when growing the chain
e. Synthesis driven by pyrophosphate hydrolysis
USES RIBOSE TRIPHOSPHATES WHEN GROWING THE CHAIN
Which of these is true for both intrinsic and protein-dependent termination?
a. Requires a protein called rho
b. Contains a G-C rich sequence followed by a stretch of U’s
c. The termination signal is coded in the DNA/RNA
d. Forms a hairpin structure
e. ATPase activity allows a protein to pull down on the newly formed RNA
THE TERMINATION SIGNAL IS CODED IN THE DNA/RNA
The lac operon DOES NOT transcribe downstream genes when…
a. Allolactase binds to the repressor
b. B-galactosidase binds to the Lac promoter
c. Glucose levels are high
d. Lactose levels are high
e. CAP with cAMP binds to the operon
GLUCOSE LEVELS ARE HIGH
What TF2 is responsible for recruiting RNA polymerase 2 to the pre-inititation complex?
a. TF2A
b. TF2B
c. TF2E
d. TF2F
e. TF2H
TF2B
How are coactivators recruited to enhance transcription at Estrogen Response Elements?
a. Estradiol binding to the NHR induces a conformational change in the NHR
b. NHR binds to the DNA-binding domain
c. Chromatin becomes tightly coiled by the addition of acetyl groups by HATs
ESTRADIOL BINDING TO THE NHR INDUCES A CONFORMATIONAL CHANGE
Which of the following would you expect for mRNA’s that have a 5’ cap versus those that do not?
a. Decreased rate of degradation and decreased ability to be transcribed
b. Decreased rate of degradation and increased ability to be translated
c. Increased rate of degradation and decreased ability to be translated
d. Increased rate of degradation and increased ability to be transcribed
DECREASED RATE OF DEGRADATION AND INCREASED ABILITY TO BE TRANSCRIBED
What process requires the presence of the sequence 5’ -AAUAAA-3’ in the eukaryotic mRNA transcript?
a. Capping
b. Editing
c. Polyadenylation
d. Splicing
e. tRNA base modification
POLYADENYLATION
The branch point A residue involved in lariat formation is part of the…
a. Intron
b. Exon
c. 5’ cap
d. 3’ polyA
INTRON
The 5’ end of the intron is marked by_____, where splicing factors bind.
a. GU
b. GG
c. A
d. GT
e. AG
GU
How many reading frames are in a 6 nucleotide stretch of mRNA 5’ - AUACAC - 3’
a. one
b. two
c. three
d. four
e. five
THREE
Within the reading frame of the first start codon (AUG), how many amino acids are in this peptide?
a. 1
b. 2
c. 3
d. 4
e. 5
FOUR
Inosine can be within which part of the tRNA?
a. Acceptor stem
b. Hydrogen bonds
c. CCA 3’ end
d. Anti-codon
ANTI-CODON
Which does NOT contribute to the specific binding of an amino acid into the aminoacyl tRNA synthase binding pocket?
a. size of the amino acid
b. charge of the amino acid
c. GTP bound to the amino acid
d. hydrophobicity of the amino acid
GTP BOUND TO THE AMINO ACID
All nucleotides contain which one of these components?
a. a 6 carbon sugar
b. a minimum of 3 phosphate groups
c. a nitrogenous base
d. a 2’ hydroxyl group
e. an imidazole ring
A NITROGENOUS BASE
The phosphodiester bond:
a. acts between bases on opposite strands to hold the helix together
b. joins nucleotides
c. attaches the nitrogenous base to the sugar backbone
d. is involved in stacking interactions
e. joins the phosphate to the 5’ carbon
JOINS NUCLEOTIDES
A melting curve was run on 2 DNA samples. The Tm of sample A was 55 degrees and the Tm for sample B was 89 degrees. What can be inferred as likely about the nucleotide content of the DNA in these samples?
a. Sample A has more nucleotides than sample B
b. Sample B has a higher GC content
c. Sample B has stronger van der Waals contacts
d. Sample A has fewer adenosine and thymidine nucleosides than sample B
e. Tm does not imply anything about nucleotide content
SAMPLE B HAS A HIGHER GC CONTENT
A chromatosome contains:
a. The nucleosome, H1 histone, and linker DNA
b. Only the H1 histones and DNA
c. The nucleosome and non-histone protein scaffolds
d. Condensed, non-transcribed chromatin
e. The nucleosome and modifications on the histone tail
THE NUCLEOSOME, H1 HISTONE, AND LINKER DNA
In Meselson and Stahl’s experiment showing semi-conservative DNA replication, bacteria were pulsed with 15N and then given a 14N chase. Why did the first round of replication disprove conservative replication?
a. The only DNA band seen was 15N
b. The only DNA band seen was 14N
c. A band containing both 14N and 15N labeled DNA was seen
d. A majority of DNA was labeled with 14N and a small percentage with 15N
e. Two rounds of replication were needed to disprove
A BAND CONTAINING BOTH 14N AND 15N LABELED DNA WAS SEEN
DNA polymerase catalyzes which type of bond formation?
a. Hydrogen
b. Glycosidic
c. Peptide
d. Electrostatic
e. Phosphodiester
PHOSPHODIESTER
Which statement is correct regarding lagging strand synthesis?
a. It is synthesized in the 5’ to 3’ direction
b. It requires only one RNA primer to initiate complete replication
c. It is synthesized as a continuous strand
d. It requires a special polymerase
e. None of these
IT IS SYNTHESIZED IN THE 5’ TO 3’ DIRECTION
Which protein is not part of the replisome but plays a critical role in preparing the DNA for replication?
a. Helicase
b. Topoisomerase
c. DNA polymerase
d. Primase
e. Sliding clamp
TOPOISOMERASE
Which of these statements is true comparing prokaryotic and eukaryotic DNA replication?
a. DNA replication only happens in S-phase in both prokaryotic and eukaryotic cells
b. Prokaryotic cells require DNA to be assembled around histones
c. Both prokaryotic and eukaryotic cells replicate their telomeres
d. Eukaryotic cells have multiple origins of replication while prokaryotic cells have one
e. Only prokaryotic cells use DNA polymerase to replicate DNA
EUKARYOTIC CELLS HAVE MULTIPLE ORIGINS OF REPLICATION WHILE PROKARYOTIC CELLS HAVE ONE
What is the most common source of mutation in DNA?
a. Chemical mutagens
b. Mismatch during replication
c. Replication slippage
d. Gamma irradiation
e. Base insertions
MISMATCH DURING REPLICATION
Which type of DNA repair will only happen during cell replication?
a. Direct repair
b. Mismatch repair
c. Homologous recombination
d. Base-excision repair
e. Non-homologous end joining
HOMOLOGOUS RECOMBINATION
How does UV light cause damage?
a. Promotes formation of guanine dimers
b. Breaks phosphodiester bonds
c. Causes deamination of cytosine to uracil
d. Promotes formation of thymidine dimers
e. Breaks glycosidic bonds
PROMOTES FORMATION OF THYMIDINE DIMERS
Which statement is correct about nucleotide excision repair?
a. Excises >13 nucleotides
b. Used to repair deamination of cytosine
c. Does not break the phosphodiester bond
d. Does not require DNA ligase
e. Requires MutH
EXCISES >13 NUCLEOTIDES
Which of the following is an important difference between DNA replication and RNA synthesis?
a. RNA is synthesized 3’ to 5’, but DNA is synthesized 5’ to 3’
b. RNA synthesis is driven by hydrolysis of pyrophosphate, while DNA replication is not
c. Uracil is used as a catalyst in RNA synthesis but not in DNA synthesis
d. RNA synthesis uses deoxyribose triphosphates, but DNA synthesis uses deoxyribose diphosphates
e. RNA synthesis does not require a primer sequence to begin, while DNA replication does
RNA SYNTHESIS DOES NOT REQUIRE A PRIMER SEQUENCE TO BEGIN, WHILE DNA REPLICATION DOES
Which subunit of bacterial RNA polymerase reduces the affinity of the complex for regions of general DNA?
a. Sigma
b. Alpha
c. Beta
d. Beta Prime
e. Gamma
SIGMA
What is the name for specialized sequences in bacterial DNA that are located approximately 35 and 10 base pairs upstream from the transcription start site?
a. Repressors
b. Activators
c. Recruiters
d. Enhancers
e. Promoters
PROMOTERS
In the transcription bubble of RNA polymerase, which strand of DNA has the same sequence as the RNA product (both read 5’ to 3’)?
a. Template Strand
b. Reading Strand
c. Coding Strand
d. Binding Strand
e. Guide Strand
CODING STRAND
During intrinsic termination of transcription, what role does a series of uracil bases immediately following a hairpin structure have?
a. The weak interaction between uracil in RNA and adenine in DNA allows the RNA strand to release from the transcription bubble
b. Uracil repeats form a kink in the RNA strand that causes RNA polymerase to release the new RNA strand
c. This series of uracil bases is what forms the hairpin structure that pauses RNA polymerase
d. Uracil repeats bind to an inhibitory region of RNA polymerase, signaling it to stop transcription
e. The series of uracil bases binds with an upstream series of adenine bases to form the hairpin structure and pause RNA polymerase
THE WEAK INTERACTION BETWEEN URACIL IN RNA AND ADENINE IN DNA ALLOWS THE RNA STRAND TO RELEASE FROM THE TRANSCRIPTION BUBBLE
In the case of the lactose operon, shown here, what molecule binds to the operator site (o) to control the expression of the downstream genes?
a. Activator
b. Enhancer
c. Inducer
d. Repressor
e. Promotor
REPRESSOR
In eukaryotes, the recruitment of the transcription machinery begins with TBP binding to what 4 base series upstream of the initiation site?
a. AATT
b. TTAA
c. TAAT
d. TATA
e. ATAT
TATA
Which transcription factor has these two unique functions: 1) acts as a helicase to open up DNA, and 2) phosphorylates the carboxy-terminal domain (CTD) of RNA polymerase II?
a. TFIIA
b. TFIIG
c. TBP
d. TFIID
e. TFIIH
TFIIH
Which of the following is an example of catalytic RNA?
a. snRNA
b. tRNA
c. miRNA
d. hnRNA
e. mRNA
snRNA
mRNAs produced in a cell with inactive polyA polymerase would most likely be
a. Unable to be transported out of the nucleus
b. More stable
c. Quickly translated
d. Unable to interact with splicing factors
e. Rapidly degraded by exonucleases
RAPIDLY DEGRADED BY EXONUCLEASES
What are the first two bases that mark the beginning of every intron in mRNA?
a. GT
b. GU
c. AT
d. AU
e. None of these
GU
A 1000bp eukaryotic mRNA is found to be translated into 2 different proteins, one being 250 amino acids in length and one being 170 amino acids in length. What best explains this?
a. Shift in reading frame
b. Incomplete splicing
c. Splice variants
d. Alternative initiating codon usage
e. Incomplete transcripton
SPLICE VARIANTS
One reason why the same amino acid can be specified by different codons is:
a. Some bases in the codon can interact with more than one type of anti-codon base
b. Some bases in the codon cause the ribosome to shift the reading frame
c. tRNA synthetase is less specific for tRNA than the amino acid
d. Some bases of the anti-codon can interact with more than one type of codon base
e. Methylation of the tRNA causes the ribosome to shift the reading frame
SOME BASES OF THE ANTI-CODON CAN INTERACT WITH MORE THAN ONE TYPE OF CODON BASE
What type of mutation would have the least negative effect on protein function?
a. Conservative
b. Nonsense
c. Silent
d. Non-conservative
e. Frameshift
SILENT
Which of these statements about the genetic code is false?
a. The code is read 3’ to 5’
b. Most amino acids are specified by multiple codons
c. Three of the codons do not specify an amino acid
d. Each codon corresponds to one amino acid
e. Codons are non-overlapping
THE CODE IS READ 3’ TO 5’
Which best describes the P site of a ribosome?
a. Docking site for incoming tRNA with elongation factor
b. Recognized by release factor
c. Catalyzes peptide bond formation
d. Location of the growing peptide chain
e. Binds uncharged tRNA
LOCATION OF THE GROWING PEPTIDE CHAIN
The role of the Shine-Delgarno sequence in bacterial mRNA is to:
a. Signal the ribosome to stop translation
b. Position the ribosome at the start codon
c. Encode for a hydrophobic peptide chain
d. Position the mRNA at the E site on the ribosome
e. Interact with Initiation Factors to begin translation
POSITION THE RIBOSOME AT THE START CODON
What best describes why a stop codon halts translation?
a. Release factors interact with the stop codon to catalyze dissociation
b. GTP is no longer hydrolyzed to shift the mRNA by a codon
c. The amino acid corresponding to the stop codon is incorporated to the peptide
d. Peptidases interact with the stop codon and cleave the protein from the ribosome
e. The ribosome binds tightly to the mRNA
RELEASE FACTORS INTERACT WITH THE STOP CODON TO CATALYZE DISSOCIATION
Antibiotics like Streptomycin are able to target bacteria and not eukaryotic cells because they:
a. Inhibit Methionine-tRNA , binding at the ribosome
b. Block the function of initiation factors
c. Inhibit formylmethionine-tRNAf binding at the ribosome
d. Stop translation of uncapped mRNA
e. Interfere with ribosome assembly
INHIBIT FORMYLMETHIONINE-TRNAF BINDING AT THE RIBOSOME
Which property of double-stranded DNA does not contribute to its chemical or structural ability?
a. Bases partially buried in the center of the duplex
b. Hydrogen bonding between strands
c. Has a 2’-deoxyribose sugar
d. Able to shift between A-DNA, B-DNA, and Z-DNA forms
e. Many van der Waal’s contacts between bases
ABLE TO SHIFT BETWEEN A-DNA, B-DNA, AND Z-DNA FORMS
Given Chargaff’s Rule, what is the complementary sequence to this nucelotide strand?
5’-ATCAGTC-3’
5’-GACTGAT-3’
Of the following, which contributes most to the low error rate during DNA replication?
a. The replicating DNA polymerase has an exonuclease function
b. DNA endonucleases remove incorrect bases as DNA is being synthesized
c. Homologous recombination is used during replication to remove incorrect bases
d. The replication fork moves very slowly
e. DNA ligase replaces any incorrect bases
THE REPLICATING DNA POLYMERASE HAS AN EXONUCLEASE FUNCTION
Deamination of cytosine to uracil is the most common point mutation in humans. What type of repair is most frequently used to correct this mutation?
a. Direct repair
b. Nucleotide excision repair
c. Mismatch repair
d. Base excision repair
e. Recombination
BASE EXCISION REPAIR
What promoter element in eukaryotes can exist very far away from the site of initiation (thousands of base pairs) and still influence gene expression by recruiting large complexes of transcription factors?
a. Enhancers
b. Initiation sites
c. Coactivators
d. Downstream promoter elements
e. Nuclear hormone receptors
ENHANCERS
Why can an organism tolerate RNA polymerase’s high error rate during transcription compared to DNA polymerase in replication?
a. All errors made by RNA polymerase are corrected by enzymes during splicing
b. Errors made by RNA polymerase do not affect the protein eventually produced from the RNA product
c. RNAs and the proteins they encode for are degraded and remade constantly, while chromosomal DNA is not
d. The cell has no mechanism to correct errors made by DNA polymerase during replication
e. The ribosome has a mechanism to recognize and avoid errors in mRNA during translation
RNAS AND THE PROTEINS THEY ENCODE FOR ARE DEGRADED AND REMADE CONSTANTLY, WHILE CHROMOSOMAL DNA IS NOT
The U6 and U2 snRNP’s in the spliceosome catalyze which reaction?
a. RNA ligation
b. Transesterification reactions
c. Debranching of the lariat intron
d. Cleavage of a glycosidic bond with a nucleotide base
e. Binding of other proteins to the RNA
TRANSESTERIFICATION REACTIONS
Inosine is a deamination of guanine, and is useful in tRNA because:
a. It stabilizes the tRNA
b. It is the site of amino acid binding in the tRNA
c. It allows the tRNA to recognize more than one codon
d. It is recognized by the tRNA synthetase
e. It allows the reading frame to be shifted as needed
IT ALLOWS THE TRNA TO RECOGNIZE MORE THAN ONE CODON
What technique allows genetic testing to be completed using only a small amount of DNA?
a. DNA probe synthesis
b. Generation of gDNA library
c. Reverse transcription
d. Polymerase chain reaction
e. Sanger sequencing
POLYMERASE CHAIN REACTION
The role of formylmethionine tRNAf in protein synthesis is to
a. Bring methionine to the correct codon (AUG) during protein synthesis
b. Prevent the premature binding of the large ribosomal subunity to the small subunit
c. Catalyze peptide bond formation
d. Utilize GTP at the A site to move the mRNA through the ribosome by one codon
e. Bind to the initiation codon (AUG) in the P site and set the reading frame
BIND TO THE INITIATION CODON (AUG) IN THE P SITE AND SET THE READING FRAME
Which is most likely to inhibit pyrimidine biosynthesis?
a. ATP and GTP
b. Glutamine
c. CMP and UMP
d. CPS2
e. PRPP
CMP AND UMP
Synthesis of adenosine monophosphate (AMP) from inosine monophosphate (IMP) requires which amino acid?
a. Glutamate
b. Aspartate
c. Glycine
d. Tetrahydrofolate
e. Uric acid
ASPARTATE
What type of bond joins the base to the sugar in a nucleotide?
a. Glycosidic bond
b. Hydrogen bond
c. Phosphodiester bond
d. Peptide bond
e. Ionic bond
GLYCOSIDIC BOND
Hershey and Chase used 32P in their experiments to identify that the DNA was the inherited genetic material because 32P will radioactively label:
a. Phosphorylated methionine in proteins
b. All bases in DNA
c. The sugar-phosphate backbone in DNA
d. The cap of the mRNA
e. The carboxy terminus of proteins
THE SUGAR-PHOSPHATE BACKBONE IN DNA
Euchromatin is mostly packaged as chromatosomes (beads on a string). What are the next two levels of DNA compaction?
a. Nucleosome then chromatin
b. 30 nm fiber then looped domains
c. 30 nm fiber then nucleosome
d. Looped domain then chromatin
e. Chromatin then looped domain
30 NM FIBER THEN LOOPED DOMAINS
DNA polymerase catalyzes which type of bond formation?
a. Hydrogen
b. Glycosidic
c. Peptide
d. Electrostatic
e. Phosphodiester
PHOSPHODIESTER
Which of the following is true regarding DNA replication?
a. Chain elongation occurs from the 5’ end only
b. Exonuclease activity of DNA polymerase 3 catalyzes phosphodiester bond formation
c. DNA polymerase 1 has reverse transcriptase activity
d. DNA polymerase 3 cannot initiate new strand synthesis
e. Deoxynucleotide monophosphates are required
DNA POLYMERASE 3 CANNOT INITIATE NEW STRAND SYNTHESIS
Replication of the lagging strand requires:
a. DNA polymerase 3 to release from the sliding clamp
b. The 5’ to 3’ exonuclease activity of DNA polymerase 1 to remove primers
c. DNA helicase to hydrolyze GTP and loop the strand towards the replisome
d. DNA ligase to join the primer to the end of the growing strand
e. The 3’ to 5’ polymerase activity of DNA polymerase 3
THE 5’ TO 3’ EXONUCLEASE ACTIVITY OF DNA POLYMERASE 1 TO REMOVE PRIMERS
Which of the following is true about telomerases?
a. Uses ATP to unwind the DNA
b. Comprised of GC-rich sequence
c. Causes DNA to loop back on itself to protect the ends
d. Prevents exonucleases from degrading the ends of DNA
e. Has reverse transcriptase activity
HAS REVERSE TRANSCRIPTASE ACTIVITY
Why is rat liver extract used in an Ames test?
a. To allow bacteria to grow on nutrient agar lacking histidine
b. To revert the mutagen to a non-toxic compound
c. To mimic the metabolic effects of the body on the suspected mutagen
d. To kill the bacteria that can synthesize histidine
e. To make the bacteria histidine dependent
TO MIMIC THE METABOLIC EFFECTS OF THE BODY ON THE SUSPECTED MUTAGEN
What is the role of AP endonuclease in base-excision repair?
a. Nicks the sugar phosphate backbone
b. Hydrolyzes the glycosidic bond to release the base
c. Excises the deoxyribose phosphate
d. Unwinds the DNA at the site of repair
e. Seals the nick after DNA polymerase 1 adds the correct base
NICKS THE SUGAR PHOSPHATE BACKBONE
Recombination, used in double strand break repair, involves:
a. Homologous chromosome pairing during G2 phase of the cell cycle
b. The parent DNA strand serving as a template for the broken strand
c. Homologous chromosome pairing
d. Alignment of heterochromatin
e. Rapid filling in and joining of broken ends
HOMOLOGOUS CHROMOSOME PAIRING
The role of sigma in prokaryotic transcription is best defined as:
a. Recognizes enhancers at distant sites from genes
b. Binds to the TATA box ahead of the AUG to correctly place the polymerase
c. Brings enhancers into close proximity to RNA polymerase by looping DNA
d. Halts transcription
e. Decreases the affinity of DNA polymerase for the DNA
DECREASES THE AFFINITY OF RNA POLYMERASE FOR THE DNA
Protein dependent termination of RNA transcription in bacteria depends on:
a. A stretch of uracils in the DNA sequence
b. The formation of a hairpin that binds to Rho
c. The ATP activity of Rho
d. The formation of hairpin followed by multiple uracils in the RNA
e. TF2H reforming the double helix after the replication bubble has passed
THE ATP ACTIVITY OF RHO
A mutant strain of E. coli cannot product allolactose. This strain will most likely:
a. Will only strongly express the lac operon when glucose is completely absent
b. Will be unable to sense lactose levels, and the lac operon will not be expressed
c. Will have high expression of the lac operon at all times
d. Will regulate the lac operon based on glucose levels only
e. Will have the same expression of the lac operon as normal (wild-type) bacteria
WILL BE UNABLE TO SENSE LACTOSE LEVELS, AND THE LAC OPERON WILL NOT BE EXPRESSED
The role of TFIIB in eukaryotic transcription is to:
a. Serve as a helicase to unwind DNA at the transcription bubble
b. Dephosphorylate the carboxy terminal domain (CTD) of the RNA polymerase
c. Start formation of the PIC at the TATA box
d. Recruit RNA polymerase II to the pre-initiation complex (PIC)
e. All of these
RECRUIT RNA POLYMERASE II TO THE PRE-INITIATION COMPLEX (PIC)
What role does estrogen play in the eukaryotic nuclear hormone receptor system?
a. Promotes binding of the nuclear hormone receptor to DNA
b. Binds to ligand bound nuclear hormone receptor and regulates transcription
c. Causes a conformational change in the nuclear hormone receptor resulting in coactivator binding
d. Serves as a mediator between transcription factors and RNA polymerase
e. Resets the nuclear hormone receptor to its original conformation after co-activator binding
CAUSES A CONFROMATIONAL CHANGE IN THE NUCLEAR HORMONE RECEPTOR RESULTING IN COACTIVATOR BINDING
Which type of RNA does not undergo processing after transcription?
a. Prokaryotic ribosomal RNA
b. Eukaryotic messenger RNA
c. Prokaryotic transfer RNA
d. Prokaryotic messenger RNA
e. Eukaryotic transfer RNA
PROKARYOTIC MESSENGER RNA
Which of the following is false regarding the 5’ cap of mRNA?
a. occurs in eukaryotes only
b. plays a role in splicing
c. increases mRNA stability
d. is comprised of an “upside down” amino acid
e. is the site of ribosome binding down during translation
IS COMPRISED OF AN UPSIDE DOWN AMINO ACID
In splicing, the role of the branch point adenosine is to:
a. Base pair with U2 snRNA and serve as the site of the first transesterification reaction
b. Signal the end of the exon
c. Base pair with the U6 snRNA and serve as the site of the second transesterification reaction
d. Signal the end of the intron
e. Interact with the debranching enzyme
BASE PAIR WITH U2 SNRNA AND SERVE AS THE SITE OF THE FIRST TRANSESTERIFICATION REACTION
What best describes the effect of a silent mutation?
a. Alters amino acid sequence but does not cause an observable phenotypic cleavage
b. Causes an early termination of the protein
c. Does not change the amino acid sequence of a protein
d. Results in a functionally similar amino acid being used in the protein
e. Only changes one nucleotide in the DNA sequence
DOES NOT CHANGE THE AMINO ACID SEQUENCE OF A PROTEIN
What best explains why some codons are synonomous?
a. There is overlap between the codons
b. The code is not degenerate
c. Wobble allows tRNAs to recognize more than one codon
d. Reading frame can switch mid-translation
e. None of these
WOBBLE ALLOWS TRNAS TO RECOGNIZE MORE THAN ONE CODON
Where is inosine most often found?
a. The 3’ base of the codon
b. The 5’ base of the anti-codon
c. The acceptor stem
d. The CCA 3’ end of the tRNA
e. The P site of the ribosome
THE 5’ BASE OF THE ANTI-CODON
Which of the following is true about prokaryotic ribosomes?
a. Comprised mostly of protein
b. rRNA in them acts as a catalyst
c. Initiate translation from the first start codon
d. Bind to the polyA tail of mRNA
e. Translates mRNA 3’ to 5’
RRNA IN THEM ACTS AS A CATALYST
Which property is the same in both prokaryotic and eukaryotic translation?
a. The ribosome binds the Shine-Delgarno sequence
b. Translation starts at the first AUG from the 5’ end of the mRNA
c. Peptidyl transferase catalyzes peptide bond formation
d. tRNA f-met recognizes the start codon
e. Translation occurs in the nucleus
PEPTIDYL TRANSFERASE CATALYZES PEPTIDE BOND FORMATION
Where on the ribosome does EF-Tu bring aminoacyl (or charged) tRNAs?
a. A site
b. P site
c. Translocon
d. Endoplasmic reticulum
e. E site
A SITE
What organelle is bound by ribosomes translating proteins that have signal peptides at their N-terminus?
a. Endoplasmic reticulum
b. Golgi
c. Nucleus
d. Plasma membrane
e. Mitochondria
ENDOPLASMIC RETICULUM
The role of ribonucleotide reductase in purine and pyrimidine synthesis is to:
a. convert dUMP to dTMP
b. Process tetrahydrofolate
c. Remove the oxygen on the 2’ carbon of the ribose
d. Add phosphate groups to nucleotides
e. Catalyze glycosidic bond formation
REMOVE THE OXYGEN ON THE 2’ CARBON OF THE RIBOSE
The glycosidic bonds in DNA and RNA”
a. Join the sugar and the base
b. Can be hydrolyzed by a magnesium ion
c. Stabilize hydrogen bonding
d. Are the site of chain elongation
e. Connect the phosphate to the sugar
JOIN THE SUGAR AND THE BASE
Transcription differs from DNA replication in what way?
a. Transcription occurs in the 3’ to 5’ direction
b. Transcription does not require a primer
c. Transcription does not require a polymerase
d. The 2’ -OH of the growing chain attacks the incoming nucleotide
e. Transcription is not driven by phosphodiester bond hydrolysis
TRANSCRIPTION DOES NOT REQUIRE A PRIMER
Which statement about protein synthesis is true?
a. Aminoacyl-tRNA synthetases add CCA to the 5’ end of the mRNA
b. Peptide bond formation occurs in the P site
c. Peptidyl transferase activity is catalyzed by mRNA
d. The Shine Dalgarno sequence is found in the 3’ UTR
e. The tRNAs possess peptidyl transferase activity
PEPTIDE BOND FORMATION OCCURS IN THE P SITE
Which of the following is not a component of a single nucleotide?
a. Pentose sugar
b. Hydrogen bonds
c. At least one phosphate group
d. Nitrogenous base
e. All of the above are part of a nucleotide
HYDROGEN BONDS
The role of 5-phosphoribosyl-1-pyrophosphate (PRPP) in nucleotide biosynthesis is to:
a. Supply the sugar group
b. Remove the hydroxyl on the 2’ carbon
c. Remove the base from the sugar
d. Convert hypoxanthine to inosine monophosphate
e. Serve as the first committed step in pyrimidine biosynthesis
SUPPLY THE SUGAR GROUP
Which statement is true regarding DNA stability?
a. Deoxyribose is easily hydrolyzed
b. Different melting temperatures between bases stabilize the helix
c. The additive effect of van der Waals interactions creates stability
d. Bases are on the outside of the helix to create a hydrophobic effect
e. Thymidine is readily converted to uridine
THE ADDITIVE EFFECT OF VAN DER WAALS INTERACTIONS CREATES STABILITY
What best describes a nucleosome?
a. A histone octamer and DNA
b. A histone octamer, DNA, and histone H1
c. DNA and histones condensed on a protein scaffold
d. Many octamers with DNA would around them, associating via the H1 histone
e. Areas of condensed chromatin
A HISTONE OCTAMER AND DNA
Why does DNA polymerase 3 have an inherently low error rate in DNA replication?
a. 5’ to 3’ exonuclease activity
b. DNA repair enzymes are part of the replisome
c. Polymerase falls off the DNA to stop replication at a mismatch
d. Induced fit at the active site
e. Endonuclease activity
INDUCED FIT AT THE ACTIVE SITE
What would be the impact if DNA polymerase 1 had no 5’ to 3’ exonuclease activity?
a. Lower mutation rate in the DNA
b. Okazaki fragments would not be synthesized
c. Increased tension caused by DNA unwinding, leading to breaks in the DNA
d. Telomeres would not be extended
e. RNA primers would not be removed from DNA
RNA PRIMERS WOULD NOT BE REMOVED FROM DNA
Why is rat liver extract needed in an Ames test for chemical mutagens?
a. Helps bacteria survive in the presence of the chemical
b. Prevents excess colonies from growing on the agar plate
c. Causes the mutation in the bacteria to revert so they can grow without histidine
d. Processes the chemical to determine if the chemicals metabolites are mutagenic
PROCESSES THE CHEMICAL TO DETERMINE IF THE CHEMICALS METABOLITES ARE MUTAGENIC
Which statement about sigma factor is false?
a. Recognizes prokaryotic promoters
b. Is part of the RNA polymerase core enzyme
c. Reduces RNA polymerase’s ability to non-specifically bind DNA
d. Release from the holoenzyme marks the beginning of elongation
e. One subunit can be reused to assist many polymerases in finding promoters
IS PART OF THE RNA POLYMERASE CORE ENZYME
What would happen in a strain of bacteria that cannot produce allolactose?
a. The repressor remains on the operator and lac mRNA is never produced
b. cAMP will not bind to CAP on the promoter
c. The repressor is never transcribed
d. The repressor can never bind to the operator and lac mRNA is always produced
e. Enhancers would turn on lac mRNA production from the operon instead
THE REPRESSOR REMAINS ON THE OPERATOR AND LAC MRNA IS NEVER PRODUCED
What is one function of TFIIH in eukaryotic transcription?
a. Moves the RNA polymerase to the initiator element
b. Signals for the polymerase to stop transcription
c. Relieves tension on the DNA via gyrase activity
d. Binds to the TATA box and recruits other transcription factors
e. Phosphorylates the CTD on the RNA polymerase
PHOSPHORYLATES THE CTD ON THE RNA POLYMERASE
Enhancers are:
a. Special RNA transcripts that are translated more efficiently
b. DNA sequences that recruit transcriptional activators to modulate transcription
c. A transcription factor that binds to downstream promoter elements (DPEs)
d. The TATA box -35 from the transcription start site
e. The site of RNA polymerase II binding
DNA SEQUENCES THAT RECRUIT TRANSCRIPTIONAL ACTIVATORS TO MODULATE TRANSCRIPTION
How are coactivators recruited in the nuclear hormone receptor system?
a. Estradiol binding acetylates histones to expose promoter regions
b. The nuclear hormone receptor binds to the DNA
c. The nuclear hormone receptor interacts with an enhancer
d. Nuclear hormone binding induces a conformational change in the nuclear hormone receptor
e. None of the above
NUCLEAR HORMONE BINDING INDUCES A CONFORMATIONAL CHANGE IN THE NUCLEAR HORMONE RECEPTOR
Which is false regarding the RNA polymerase II carboxy terminal domain (CTD)?
a. Phosphorylation marks the transition from transcription initiation to elongation
b. Coordinates splicing
c. Found on both bacterial and eukaryotic RNA polymerase II
d. Binds proteins involved in 5’ cap formation
e. Recruits the endonuclease that cleaves the pre-mRNA for polyA addition
FOUND ON BOTH BACTERIAL AND EUKARYOTIC RNA POLYMERASE II
What type of reactions do snRNAs catalyze in splicing to join exons?
a. Transesterification
b. Glycosylation
c. Ligation
d. Alkylation
e. Polymerization
TRANSESTERIFICATION
What type of mutation likely has the less impact on protein function?
a. Nonsense
b. Frameshift of one amino acid
c. Conservative
d. Frameshift of two amino acids
e. Non-conservative
CONSERVATIVE
Where is inosine most likely to be found on the tRNA?
a. First base of the anti-codon
b. Acceptor stem
c. Third base of the anti-codon
d. 3’ end of the CCA
e. Third base of the codon
FIRST BASE OF THE ANTI-CODON
Where does fMet-tRNAf enter into the ribosome during initiation?
a. Peptidyl (P) site
b. On the Shine Delgarno sequence
c. Aminoacyl (A) site
d. With initiation factor 3
e. Exit (E) site
PEPTIDYL (P) SITE
What statement best describes the central dogma in molecular biology?
DNA IS REPLICATED AND TRANSCRIBED TO MRNA; MRNA IS TRANSLATED TO PROTEIN
Which type of DNA repair can only happen during the S phase of cell cycle?
a. Non-homologous end-joining
b. Base excision repair
c. Homologous recombination
d. Mismatch repair
e. Nucleotide excision repair
HOMOLOGOUS RECOMBINATION
Which statement is true about transcription?
a. Bacterial mRNA is heavily processes as it is transcribed
b. mRNA in eukaryotic cells moves to the ribosome immediately after transcription
c. Enhancers regulate transcription in prokaryotic and eukaryotic cells
d. Transcription factors bind to the promoters in eukaryotic cells
e. Prokaryotic and eukaryotic transcription are exactly the same
TRANSCRIPTION FACTORS BIND TO THE PROMOTERS IN EUKARYOTIC CELLS
Why does streptomycin target bacteria and not eukaryotic cells?
a. Interferes with production of the bacterial large ribosome subunit
b. Prevents Met-tRNAi binding to the bacterial ribosome
c. Blocks Shine Delgarno sequence recognition
d. Interferes with binding of fMet-tRNAf to the bacterial ribosome
e. Blocks the 5’ cap from interacting with the bacterial ribosome
INTERFERES WITH BINDING OF FMET-TRNAF TO THE BACTERIAL RIBOSOME
