DNA Replication: Helicase Function & Okazaki Fragments

What is the funcHon of helicase?

a. It removes mismatched nucleotides from the 3ʹ end of DNA. b. It eliminates supercoils by cleaving DNA. c. It primes synthesis of DNA. d. It uses ATP to add negative supercoils to DNA. e. It uses ATP to separate DNA strands.

It uses ATP to separate DNA strands.

DNA pieces that are synthesized on the lagging strand are referred as:

a. repliction fork. b. Okazaki fragments. c. polymerase. d.Holliday fragments. e. telomere.

Okazaki fragments.

What is the role of the small RNA primer in DNA replication?

a. It is involved in recognition of the replication origin. b. It provides a free 3ʹ hydroxyl group for DNA polymerase. c. Unlike the leading strand, the lagging strand cannot be replicated without primers d. It provides a free 5ʹ phosphate group for DNA polymerase. e. It is used by RNA-dependent DNA polymerase.

It provides a free 3ʹ hydroxyl group for DNA polymerase

4. What are telomeres?

a. ends of eukaryotic chromosomes b. ends of prokaryotic chromosomes c. replicon ends d. proofreading mechanisms e. replication fork

ends of eukaryotic chromosomes

5. The formation of a phosphodiester linkage between the 5ʹ-phosphate group at the end of one DNA fragment and the 3ʹ-hydroxyl group at the end of the other fragment is catalyzed by:

a. telomerase. b. polymerase. c. gyrase. d. ligase. e. primase.

ligase.

6. What prevents two complementary strands unwound by helicase from forming a double helix?

a. DnaA proteins b. DnaB proteins c. SSB proteins

SSB proteins

7. What is the name of the site of chromosome replication in prokaryotes?

a. origin of replication b. replicon c. prepriming complex d. telomere e. Okazaki fragment

origin of replication

Which DNA polymerase has exonuclease activity in both 5' to 3' and 3' to 5' directions?

a. Pol I b. Pol II c. Pol III d. Pol IV e. Pol V

Pol I

9. Processivity:

a. indicates the error rate for a polymerase. b. is a deletion of one or more bases in the DNA. c. depends on the size of the replicon d. is the ability to catalyze many consecutive reactions without releasing a substrate. e. indicates the observed rate of the lagging strand replication.

is the ability to catalyze many consecutive reactions without releasing a substrate. e. indi

10. All DNA polymerases require which?

a. template b. dNTPs c. primer d. Mg2+ e. all of the above

all of the above

11. Choose the enzyme that primes synthesis of DNA.

a. helicase b. topoisomerase I c. topoisomerase II d. primase e. gyrase

primase

12. In what direction does the DNA strand grow upon replication?

a. 3ʹ → 5ʹ b. 5ʹ → 3ʹ c. 3ʹ → 3ʹ d. 5ʹ → 5ʹ e. both 3ʹ → 5ʹ and 3ʹ → 5ʹ

5ʹ → 3ʹ

13. Which polymerase is responsible for the completion of replication of damaged genomes?

a. polymerase I b. polymerase II c. polymerase α d. error-prone polymerase e. telomerase

d. error-prone polymerase

14. Why are insertions and deletions of DNA more damaging than a mismatched base pair?

a. Replicative polymerases can stall or fall off a damaged template entirely. b. Offspring of the next generation will be sterile c. Synthesized proteins may have low activity. d. The organism will be susceptible to diseases. e. Replicative polymerases will make more mistakes.

Replicative polymerases can stall or fall off a damaged template entirely

What is the name of the reacHon leading to the formation of hypoxanthine from adenine?

a. halogenation b. carboxylation c. deamination d. dehydration e. nitrosation

deamintion

How does the mismatch repair machinery of E. coli determine which of the bases is incorrect?

a. The incorrect base is tagged by a hydroxyl group. b. A newly synthesized strand is vulnerable to exonucleases, so the enzymes work precisely. c. The incorrect base induces protein cascades to activate the repair machinery. d. RAD51 helps to identify the incorrect base. e. The incorrect base is nonmethylated in the newly synthesized daughter strand.

The incorrect base is nonmethylated in the newly synthesized daughter strand.

Ultraviolet light:

a. is able to modify adenine to form hypoxanthine. b. adds a hydrocarbon molecule to nucleoHde bases. c. promotes the formaHon of cross-links between adjacent pyrimidines along one DNA strand. d. converts a G-C base pair into a T-A base pair in a reacHon of DNA with aflatoxin B1 epoxide. e. promotes the formaHon of single- and double-stranded breaks in DNA.

promotes the formaHon of cross-links between adjacent pyrimidines along one DNA strand.

Why does DNA have thymine instead of uracil?

a. It is energeHcally unfavorable to make A-U bonds in DNA. b. The repair system can disHnguish cytosine and methylated cytosine. c. Uracil retains methylated thymine and the repair system excises it from the chain. d. DeaminaHon of cytosine results in thymine, which is recognized by the repair system and excised from the chain. e. DeaminaHon of cytosine results in uracil, which is recognized by the repair system and excised from the chain.

DeaminaHon of cytosine results in uracil, which is recognized by the repair system and excised from the chain.

What is the first step of the DNA repair process?

a. proofreading b. DNA synthesis using DNA polymerase c. cleavage of glycosidic bonds d. excision of wrong bases e. ligaHon of synthesized strands

proofreading

If you could look at individual strands of DNA and you saw a Holliday juncHon, what would that tell you?

a. A region of DNA that contains a thymidine dimer is undergoing repair. b. DNA repair of a double-strand break is occurring via a recombinaHon mechanism. c. DNA with a point mutaHon is undergoing base-excision repair. d. DNA with a point mutaHon is undergoing nucleoHde-excision repair. e. Mutagenic reversal is occurring, as seen in the Ames test.

DNA repair of a double-strand break is occurring via a recombinaHon mechanism

The process whereby two daughter molecules of DNA are formed by the exchange of geneHc material between two parent molecules is known as:

a. chemical modificaHon. b. recombinaHon. c. alkylaHon. d. dimerizaHon. e. replicaHon

b. recombinaHon.

22. What is a gene?

a. Basic unit of informaHon b. Nucleic acid sequence that codes for a protein, tRNA, or rRNA c. Building block for an amino acid d. A and B e. B and C f. A and C

d. A and B

What is transcripHon?

a. DNA-directed RNA synthesis b. RNA-directed DNA synthesis c. RNA-directed protein synthesis d. DNA-directed protein synthesis

DNA-directed RNA synthesis

What are the components of the RNAP holoenzyme?

alpha, alpha, beta, beta' w, sigma

Choose the correct statement(s) about sigma factors:

a. Every cell has a housekeeping sigma factor b. Sigma factors recognize consensus sequences upstream of the transcripHon start site c. A single bacterial species makes a single sigma factor d. A and B e. A, B, C

A and B

Which subunit of E. coli RNAP is required for iniHaHon of synthesis?

sigma

What does RNAP require for transcripHon? a. Template b. AcHvated precursors (rNTPs) c. Divalent metal caHon d. All of the above e. None of the above

d. All of the above

Choose the correct statement(s) about promoters

a. The -10 and -35 sequences direct RNAP to the site to iniHate transcripHon b. Strong promoters closely resemble the consensus c. Sigma factors recognize the promoter and are released at the elongaHon phase d. All of the above are correct

All of the above are correct

IdenHfy and correctly order the phases of transcripHon:

a. IniHaHon, TerminaHon, ElongaHon b. ElongaHon, IniHaHon, TerminaHon c. IniHaHon, ElongaHon, Proofreading d. IniHaHon, ElongaHon, TerminaHon

IniHaHon, ElongaHon, TerminaHo

Which are parts of an operon?

a. Promoter b. Operator c. Polycistronic message d. A and B e. A, B, C

A, B, C

Choose the correct statements about the lac operon:

a. The lac repressor regulates transcripHon based on lactose availability b. It encodes 3 proteins c. It is inducible - allolactose binds the repressor d. All of the above e. None of the above

All of the above

18S, 5.8S, and 28S genes are transcribed: a. By Pol III b. separately c. as a single transcript d. At the same Hme as they are translated e. In the cytoplasm

c. as a single transcript

EukaryoHc transcripHon occurs in the _________, and translaHon occurs in the _________ a. cytoplasm, nucleus b. nucleus, ER c. cytoplasm, Golgi apparatus d. cytoplasm, cytoplasm e. nucleus, cytoplasm

nucleus, cytoplasm

True/False: EukaryoHc Pol II transcribes mRNA a. True b. False

True

The most commonly recognized cis-acHng element in eukaryoHc promoters is the _______________ a. Upstream promoter element (UPE) b. Enhancer c. Ribosomal iniHator element (rInr) d. TATA box e. None of the above

TATA box

Choose the correct statement(s) about transcripHon iniHaHon: a. TranscripHon factors that bind the promoter are required in eukaryotes b. TranscripHon factors bind to the TATA box and RNAP to open the DNA c. TranscripHon factors are released before RNAP leaves the promoter and start iniHaHon at another promoter d. TranscripHon factors are destroyed aper iniHaHon e. A and B are correct f. A, B, and C are correct

A, B, and C are correct

True/False: Mediators act as a bridge between RNAP and transcripHon factors, etc a. True b. False

True

True/False: ChromaHn is a complex of DNA and histones and its structure plays a major role in controlling eukaryoHc gene expression

True

True/False: Histone deacetylases (HDACs) act to loosen histone-DNA contact a. True b. False

False

True/False: Covalent modificaHons of histone tails are reversible a. True b. False

True

True/False: EpigeneHc modificaHons affect gene expression and alter the DNA sequence a. True b. False

False

In eukaryoHc genes, ________ is the term for intervening sequences that are removed from the mature RNA transcripts a. nonsense b. empty c. intron d. exon

intron

Which type of RNA is the most extensively modified? a. tRNA b. mRNA c. siRNA d. snoRNA e. All RNAs are equally modified

mRNA

EukaryoHc mRNAs are modified in which ways? a. Capped b. Spliced c. Tailed d. A and B are correct e. A and C are correct f. All of the above are correct

All of the above are correct

Splicing must be incredibly precise in order to preserve the reading frame. Which geneHc elements are essenHal for determining where splicing takes place? a. 5' splice site b. 3' splice site c. Branch site d. All of the above are correct

All of the above are correct

What is the spliceosome? a. A massive complex of RNAs and proteins that modify pre-RNAs b. A complex of DNA and histones that control eukaryoHc gene expression c. A bridge between RNAP and transcripHon factors d. A complex between exons and introns e. None of the above are correct

A massive complex of RNAs and proteins that modify pre-RNAs

True/False: the splicing process requires ATP hydrolysis and a pre-mRNA molecule a. True b. False

True

Choose the correct statements about alternaHve splicing a. It's a mechanism for generaHng RNA and protein diversity b. Allows a single gene to code for more than 1 final protein c. Can result in proteins with different funcHons d. All of the above are correct e. Some of the above are correct

All of the above are correct

True/False: mRNA transcripHon and processing are coordinated by the RNAP Pol II carboxy-terminal domain (CTD) a. True b. False

True

Which of the following is the definiHon of RNA ediHng? a. Adding a 5' methylguanosine cap to mRNA b. Adding a 3' poly-A tail to mRNA c. Splicing out internal sequences to mature RNA d. Changing RNA sequence aper transcripHon by processes other than splicing e. Some of the above are correct

Changing RNA sequence aper transcripHon by processes other than splicing

CatalyHc RNAs are called: a. Ribosomes b. Ribozymes c. Introns d. Thermozymes e. None of the above

Ribozymes

Choose the correct statement(s)about the GeneHc Code: a. The code is degenerate or redundant b. The code is universal with few excepHons c. The code is not redundant or degenerate d. There is a single codon for each amino acid e. A and B are correct f. C and D are correct

A and B are correct

True/False: a leader sequence is transcribed but not translated and contains the ribosomal binding site

True

Choose the correct statements about genes: a. The DNA coding sequences for tRNAs and rRNAs are considered genes b. tRNA and rRNA sequences are separated by spacers c. Have a start and a stop codon d. tRNAs can act as spacers between rRNAs e. All of the above are correct f. Some of the above are correct

All of the above are correct

Which is not a binding site in the ribosome for a tRNA? a. Acceptor site b. PepHdyl-tRNA site c. Exit site d. Shine Dalgarno site e. A, B, and C answer the quesHon

Shine Dalgarno site

True/False: Polysomes can be observed only in prokaryotes a. True b. False

False

Which are the 3 stages of translaHon in order? a. IniHaHon, ElevaHon, TerminaHon b. InnovaHon, ElongaHon, TerminaHon c. IniHaHon, ElongaHon, TranscripHon d. IniHaHon, ElongaHon, TerminaHon e. None of the above are correct

IniHaHon, ElongaHon, TerminaHon

Choose correct statements about translaHon elongaHon in prokaryotes a. Aminoacyl-tRNA binding is the 1st step b. In transpepHdaHon, the amino acid in the A site interacts with the amino acid in the P site c. In translocaHon, the ribosome moves down 1 codon and the empty tRNA leaves the P site d. ElongaHon factors (EFs) are involved e. All of the above are correct

All of the above are correct

Which statement(s) about translaHon are true for both prokaryotes and eukaryotes? a. Both use iniHaHon factors b. Both use ribosomes c. Both have polysomes d. Both use release factors e. All of the above

All of the above

TRUE/FALSE: MOLECULAR CHAPERONES HELP PROTEINS FOLD CORRECTLY a. True b. False

True

True/False: SecreHon is the movement of proteins within cells to the plasma membrane or periplasmic space, while translocaHon is movement of proteins out of the cell a. True b. False

False

True/False: Proteins going to the mitochondria are translated in the cytoplasm, then delivered to the organelle a. True b. False

True

Choose the incorrect statement about regulatory RNAs: a. They can inhibit translaHon b. They can acHvate translaHon c. They can promote mRNA degradaHon d. They do not prevent mRNA degradaHon e. They typically operate post-transcripHonally

They do not prevent mRNA degradaHon

True/False: asRNA originate in protein-coding genes and affect expression of only that gene a. True b. False

True

RNAi... choose the correct answer a. May have evolved as a protecHve measure against dsDNA viruses b. Uses Dicer to produce short ds RNA fragments c. Argonaute generates short ssRNA fragments from the dsRNA d. The RISC complex uses the ssRNA to degrade target mRNA e. All of the above are correct

All of the above are correct

True/False: Some anHbioHcs inhibit translaHon a. True b. False

True

Choose correct statements about translaHon iniHaHon in prokaryotes a. The 1st tRNA added is fmet-tRNA (N-formylmethionine-tRNA) b. The 16S rRNA and ribosomal binding sites align c. IniHaHon factors (Ifs) are involved d. All of the above are correct e. Some of the above are correct

All of the above are correct

Choose the correct statements about translaHon terminaHon in prokaryotes a. There are 3 stop codons b. Release factors (RFs) help recognize stop codons c. The ribosome falls off the mRNA and is recycled d. At the stop codon, a terminaHon amino acid is added to the protein e. Some of the above are correct

Some of the above are correct

Effects of asRNA on gene expression do not include: a. Stopping transcripHon b. PrevenHng mRNA translaHon c. PromoHng mRNA degradaHon d. PromoHng mRNA translaHon e. None of the above

PromoHng mRNA translaHon

True/False: RISC is an acronym for RNA-induced silencing complex a. True b. False

True

Which enzyme separates the DNA strands during replication?

ligase

gyrase

topoisomerase I

helicase

primase

helicase

Where is telomerase active?

at the ends of eukaryotic chromosomes

On Klenow fragments

At the helicase complex

In the prokaryotic chromosome

On Okazaki fragments

at the ends of eukaryotic chromosomes

Choose the enzyme that primes synthesis of DNA.

helicase

topoisomerase II

primase

gyrase

topoisomerase I

primase

The step-by-step addition of deoxyribonucleotides to a DNA strand is catalyzed by:

helicase.

polymerases.

gyrase.

topoisomerases.

endonuclease.

polymerases.

Choose CORRECT statements about E. coli DNA polymerases. Select all that apply.

 

All catalyze the same reaction, which requires a metal ion cofactor.

 

All have finger and thumb domains that wrap around the DNA.

 

All of them possess exonuclease activity.

 

There are five structural classes.

 

Only some of them require a primer.

All catalyze the same reaction, which requires a metal ion cofactor.

All have finger and thumb domains that wrap around the DNA

There are five structural classes.

Choose reactions that always require hydrolysis of ATP. Select all that apply.

formation of the phosphodiester linkage by DNA ligase

unwinding of DNA strands by helicase

formation of the phosphodiester linkage by DNA polymerase I

unwinding of DNA strands by β2 subunits

sliding along template strands

formation of the phosphodiester linkage by DNA ligase

unwinding of DNA strands by helicase

sliding along template strands

Select all that apply. Polymerase I of E. coli has:

 

a 5′ → 3′ exonuclease site.

 

primase activity.

 

a 3′ → 5′ exonuclease site.

 

a magnesium binding site.

 

an oriC locus binding site.

a 5′ → 3′ exonuclease site.

a 3′ → 5′ exonuclease site.

a magnesium binding site.

Select all that apply. The Klenow fragment:

 

has exonuclease activity.

 

has polymerase activity.

 

is an E. coli DNA polymerase fragment.

 

has primase activity.

 

is RNA-dependent DNA polymerase.

has exonuclease activity.

 

has polymerase activity.

 

is an E. coli DNA polymerase fragment.

What does DNA polymerase accuracy depend on?

Watson-Crick base pairings

double helices formation

length of DNA

type of polymerase

Watson-Crick base pairings

In what direction does the DNA strand grow upon replication?

3′ → 5′

both 3′ → 5′ and 3′ → 5′

5′ → 5′

5′ → 3′

3′ → 3′

5′ → 3′

How does the mismatch repair machinery of E. coli determine which of the bases is incorrect?

 

A newly synthesized strand is vulnerable to exonucleases, so the enzymes work precisely.

 

The incorrect base is tagged by a hydroxyl group.

 

RAD51 helps to identify the incorrect base.

 

The incorrect base is nonmethylated in the newly synthesized daughter strand.

 

The incorrect base induces protein cascades to activate the repair machinery.

The incorrect base is nonmethylated in the newly synthesized daughter strand

Ultraviolet light:

promotes the formation of cross-links between adjacent pyrimidines along one DNA strand.

converts a G-C base pair into a T-A base pair in a reaction of DNA with aflatoxin B1 epoxide.

is able to modify adenine to form hypoxanthine.

promotes the formation of single- and double-stranded breaks in DNA.

adds a hydrocarbon molecule to nucleotide bases.

promotes the formation of cross-links between adjacent pyrimidines along one DNA strand.

How are pyrimidine dimers formed?

deamination

alkylation

reactive oxygen species

exposure to UV light

inserting intercalating agents

exposure to UV light

Replication polymerases can fall off DNA when they encounter indels

True

False

True

Why does DNA have thymine instead of uracil?

The repair system can distinguish cytosine and methylated cytosine.

Deamination of cytosine results in uracil, which is recognized by the repair system and excised from the chain.

It is energetically unfavorable to make A-U bonds in DNA.

Deamination of cytosine results in thymine, which is recognized by the repair system and excised from the chain.

Uracil retains methylated thymine and the repair system excises it from the chain.

Deamination of cytosine results in uracil, which is recognized by the repair system and excised from the chain.

Which enzyme cleaves pyrimidine dimers in the direct repair system?

helicase

DNA polymerase I

DNA photolyase

DNA polymerase III

DNA ligase

DNA photolyase

Choose the CORRECT statement about the recombination of DNA.

Single-strand breaks can be repaired by recombination.

In homologous recombination, parent DNA duplexes align at regions of sequence similarity.

A displacement loop is a three-stranded structure.

Holliday junction is a common intermediate of DNA recombination, which consists of two strands of DNA.

Recombination is the exchange of segments between two DNA molecules.

Holliday junction is a common intermediate of DNA recombination, which consists of two strands of DNA.

In DNA repair pathways, which strand is used as template and why?

it's random and unpredictable

daughter strand due to the methylation

parental strand due to the methylation

lagging strand due to the RNA primers

leading strand due to the continuous synthesis

parental strand due to the methylation

Constitutive:

expression is peculiar to all bacteria. Regulated expression is peculiar only to eukaryotes.

genes are continually transcribed at a relatively constant rate. Regulated expression may depend on the availability of substrates.

expression depends on the position of the cell cycle. Regulated expression may depend on the availability of substrates.

expression may depend on the levels of gene products. Regulated expression is activated only by the environmental challenge.

expression ensures continual transcription under particular circumstances. Regulated expression depends only on the availability of substrates.

genes are continually transcribed at a relatively constant rate. Regulated expression may depend on the availability of substrates.

A transcription bubble in E. coli does NOT contain:

 

RNA polymerase.

 

RNA primer.

 

DNA.

 

nascent RNA.

 

RNA-DNA hybrid helix.

RNA primer.

Select all that apply. The lactose operon consists of the:

three structural genes.

control sites.

operator site.

promoter site.

terminator site.

three structural genes.

operator site.

promoter site.

When allolactose binds to the lac repressor, the affinity of the:

 

repressor for RNA polymerase decreases.

 

RNA polymerase for the promoter site decreases.

 

repressor for the operator DNA decreases.

 

repressor for the operator DNA increases.

 

RNA polymerase for the promoter site increases.

repressor for the operator DNA decreases.

The single σ subunit of E. coli RNA polymerase:

 

unwinds a 17-bp DNA segment.

 

catalyzes hydrolysis of a single pyrophosphate.

 

tightly binds to the β' subunit of a particular RNA polymerase.

 

can assist many polymerases to find the UP element.

 

can assist many polymerases to find the –10 and –35 promoter sequence.

can assist many polymerases to find the -10 and -35 promoter sequence.

In transcription, the 3′-hydroxyl group:

attacks the γ-phosphorous group on an incoming nucleotide.

binds to the 5′ ribose.

attacks the α-phosphorous group on an incoming nucleotide.

attacks the 5′ hydrogen of the incoming nucleotide.

binds to Mg2+ in the active site.

attacks the α-phosphorous group on an incoming nucleotide.

Select all that apply. When phosphorylated, the carboxyl-terminal domain of RNA polymerase II:

recruits other factors.

enhances transcription.

inhibits transcription.

transcribes ribosomal RNA.

recruits other factors.

enhances transcription.

Eukaryotic promoters:

 

are referred to as trans-acting elements.

 

are referred to as cis-acting elements because they can be located at a distance from the genes they control.

 

are referred to as cis-acting elements because they are located on the same molecule of DNA as the genes they control.

 

have approximately the same composition.

 

are positioned near the genes they control.

are referred to as cis-acting elements because they are located on the same molecule of DNA as the genes they control.

How does acetylation of histones influence transcription? Select all that apply.

initiating dense packaging of chromatin

increasing affinity of histones to DNA

recruiting chromatin-remodeling engines

decreasing affinity of histones to DNA

recruiting TBP-associated factors (TAFs)

recruiting chromatin-remodeling engines

decreasing affinity of histones to DNA

recruiting TBP-associated factors (TAFs)

Transcription activators can be linked with the RNAP complex by the:

enhancer.

mediator.

transcription factor.

promoter.

CTD.

mediator.

What part of nucleosome is crucial to the activation of transcription through remodeling of chromatin?

linker DNA

nucleosome core particle

histone tails

histone H2B

major DNA groove

histone tails

The _______ links the sequence of bases in DNA (or its RNA transcripts) and the sequence of amino acids in proteins.

genetic code