BIO 350 Quizzes

The first ribonucleotide in a nascent RNA would correspond with the ______ position along the _____ strand.

+1; template

In a hypothetical scenario, a deletion mutation in gene X blocks its ability to activate gene Y which is responsible for activating gene Z. Which answer choices represent plausible scenarios for how activation of gene Z could be restored?

-A hypermorphic mutation could activate gene Z independent of genes X and Y -A gain-of-function mutation in gene Y could make Y able to activate gene Z without it having to interact with gene X.

Which types of DNA damage are likely to inhibit replication and/or transcription? (select all that apply)

-A nick in the phosphate backbone -A double strand break -A pyrimidine dimer -A benzo[a]pyrene adduct

How is it possible for a gene to encode more than one gene product without changing the genome sequence? Select all correct answers.

-A single gene can code for multiple different polypeptides by utilizing alternative transcriptional start and stop sites. -Genes (in eukaryotes) can be alternatively spliced to generate RNAs for unique polypeptides.

A eukaryotic Type 2 promoter contains several cis regulatory sites including: (select all that apply)

-BoxB -BoxC

Why might E. coli with a hypomorphic DAM methylase have higher mutation rates than wildtype E. coli? (select all that apply)

-DNA repair machinery may mistakenly replace the base on a parent strand that is mismatched with its daughter. -DNA repair machinery will have a hard time distinguishing parent from daughter stands.

Which molecules are trans-acting during replication? (select all that apply) -DnaA -DAM methylation site -SSB -ter -ori

-DnaA -SSB

What are some features (cis or trans) that differ between eukaryotic and bacterial transcriptional systems? In other words which answers are unique to bacteria or unique to eukaryotes. (Select all that apply).

-Downstream promoter -Sigma factor - -35 box -TBP -RNA polymerase I

In an open complex RNA polymerase:

-Has locally unwound a small region of double helix. -Will create short nascent RNAs.

What molecules improve processivity during replication?

-Helicase -SSB

Which scenarios are possible in non-homologous end joining? (select all that apply)

-Ligase activity joins broken strands -Integration of INDELs to the DNA. -DNA is trimmed back. -Nucleotides may be added to one or both strands.

The replication of the bacterial chromosome is an example of:

-Single copy replication control -Bidirectional replication

Which molecules make up a transcriptional ternary complex?

-Template strand -Ribonucleotide -RNA polymerase

Researchers using the diploid frog species Xenopus tropicalis, isolated an interesting strain that have orange eyes instead of black eyes (their normal eye color). If a male and female pair both with orange eyes are bred together 3/4 of the resulting offspring have orange eyes and 1/4 have black eyes. If two offspring with black eyes are raised to adults and bred with each other all offspring have black eyes. On the other hand if an orange eyed frog is bred with a black eye frog all offspring develop orange eyes. Interestingly, a proportion (i.e., not all) of the orange eye frogs also have unusual white foot pads on their fore and hind limbs. For example a breeding pair of orange eye frogs produced offspring for which 3/4 have orange eyes, but only 1/4 of them also had white foot pads. Furthermore none of the black eyed frogs had white foot pads. Which statements are true? Select all that apply.

-The original parent frogs must have been heterozygotes fo the "orange allle". -If a male orange allele heterozygote is bred with a female orange allele homozygote we would expect all offspring to have orange eyes. -The orange allele and white pad allele are linked. -The orange allele is dominant whereas the white pad allele is recessive. -The orange eyes are a trait derived from a dominant allele.

During replication the replication bubble expands and the opposing replication forks move away from each other. Which statements are true (select all that apply):

-Topoisomerase must cut and rejoin DNA to relieve tension. -Helicase is actively unwinding DNA as the forks move apart. -The double helix becomes tighter outside the replication bubble.

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The sequence elements in the bacterial promoter act in [1] to instruct RNA polymerase holoenzyme to transcribe RNA. Sigma factor acting in [2] enables specificity for promoter interaction and initiation of transcription. A [3]-acting intrinsic terminator often results in a hairpin that causes RNA polymerase to disassociate from the transcript. Alternatively Rho factor acting in [4] interacts with the transcript causing termination.

1) Cis 2) Trans 3) Cis 4) Trans

The three major stages of DNA replication are...

1) Initiation 2) Elongation 3) Termination

In an animal cell [_____1_____] is responsible for transcribing tRNA, [____2_____] is responsible for transcribing 18S and 28S rRNA, and [____3_____] is responsible for transcribing mRNA. (not case sensitive, but spelling counts)

1) RNA Polymerase III 2) RNA Polymerase I 3) RNA Polymerase II

Find the linkage map of trait loci in Drosophila (it's in the lecture slides), using the map how often do you think the "black body" trait will appear with the "hairy body" trait?

50% of the time

Sigma factor ________ is responsible for interacting with the most promoters in a bacterial genome.

70

If a bacterial mRNA is colinear with its expressed polypeptide product and the mRNA is 255 nucleotides long (from start codon to stop codon), how many amino acids would you expect in the final protein?

84

cDNA

A DNA copy of an expressed mRNA

Mutation

A change in nucleotide sequence

Interrupted gene

A gene in which the sequence of DNA or RNA does not continuously encode the gene product. For example, genes that contain introns are interrupted.

RT-PCR

A method to create a DNA copy of an expressed gene followed by a polymerase chain reaction

The origin-of-replication in a bacterial chromosome is functionally similar to:

A mitochondrion D-loop

Suppression mutation

A mutation in a separate gene that suppresses the effect of the first mutation

Second site reversion

A mutation in the same gene that suppresses the effect of the first mutation

Forward mutation

A mutation that causes a phenotype

Transition mutation

A mutation that results in a A<->G or C<->T change in DNA sequence

Transversion mutation

A mutation that results in a A<->T or G<->C change in DNA sequence

Null mutation

A mutation that results in no functional gene product

Alternative splicing

A process of adding and/or excluding exons/introns from a primary transcript

RNAse

A ribonuclease

Closed reading frame

A sequence of RNA that contains frequent and early translational stop sites.

SNP

A single nucleotide polymorphism

Overlapping gene

A situation in which more than one gene sequence share the same region of DNA sequence such that reading frame and/or read direction determines which gene is transcribed.

What is the primary distinction between a second site reversion and a true reversion?

A true reversion restores the original sequence whereas a second site reversion may only restore function.

The recombination frequencies for a hypothetical set of genes that all reside on the same chromosome are: A-B: 32 A-D: 40 E-B: 14 C-D: 18

A,E,C,B,D

A trans-acting mutation in a regulatory protein is likely to...

Affect activation of all target genes

Which choice best represents a complete gene region (genic DNA)?

All sequence contained in the precursor mRNA.

What class of vertebrate organisms exhibit the largest genome sizes? insects pandas amphibians cartilaginous fishes marsupials blue whales

Amphibians

Ligase

An enzyme that catalyzes joining of one polynucleotide chain with another at the 5' and 3' ends.

DNAse

An enzyme that degrades DNA

Phosphatase

An enzyme that removes a phosphate from its substrate

Find the linkage map of trait loci in Drosophila (it's in the lecture slides), using the map how often do you think the "cut wings" trait will appear with the "ruby eyes" trait?

Approximately 12% of the time

Mutation rates in hotspots are:

At least an order of magnitude higher than average

Why is it fair to say that sigma factor is the primary regulator for RNA polymerase?

Bacterial systems use a single RNA polymerase that can recognize multiple promoters by association with different sigma factors.

Why would a mutation altering RNA polymerase subunit ⍺ result in failed transcriptional initiation?

Because ⍺ is responsible for physically interacting with the promoter.

Roslind Franklin

Captured photo 51 an X-ray photograph of DNA double helix

A mutation in a bacterial promoter sequence that causes significant deviation from the consensus will most likely:

Cause an overall decrease in transcription because the RNA polymerase holoenzyme will not efficiently recognize the promoter.

A ________________ -acting mutation in the regulatory sequence of a gene results in complete loss of transcription.

Cis

A nonsense mutation in a gene results in the inability for that gene to produce a complete protein. The mutation is therefore acting in _____________ essentially blocking the functional gene product from being produced.

Cis

Methylated GATC motifs in the ori of a bacterial chromosome act in ________ to regulate replication.

Cis

The origin-of-replication is a _____ acting element.

Cis

Except for the exclusive use of uracil instead of thymine, an RNA sequence is identical to its _______ .

Coding strand

In a human, which type of DNA damage is most likely a consequence of cigarette smoking?

DNA chemical adduct

In humans, which enzyme can fill in nucleotide sequence that has been removed do to damage?

DNA polymerase ẟ

Transformation

Delivery of exogenous DNA into a bacterium

Transfection

Delivery of exogenous DNA into a eukaryotic cell

Avery, McCleod, McCarty

Determined DNA was the transforming principle in bacteria by conducting a series of enzymatic digestions and transformation attempts.

Erwin Chargaff

Determined that the proportion of all other bases in a genome can be predicted by knowing the proportion of only one base.

Charles Darwin

Developed the theory that traits are inherited and serve a purpose.

Base excision repair pathway is triggered by:

Directly removing the damaged base.

The initiator in bacteria is:

DnaA

Walther Flemming

Dyed salamander cells with aniline dye enabling the visualization of chromosomes.

UTR

Exonic RNA sequence that is not translated

The number of nucleotide bases that RNA polymerase physically interacts with at the promotor:

Expands when sigma factor associates with the complex.

T/F: A bacterial nucleoid is a membrane bound compartment that is near identical to a eukaryotic nucleus.

False

T/F: A chromosome and a gene are structurally the same.

False

T/F: A forward mutation, may or may not have an effect.

False

T/F: A genome's collection of genic DNA is always protein coding.

False

T/F: A mutation in the -10 region of a bacterial promoter will generally affects initial binding of RNA polymerase.

False

T/F: A positioning factor and an assembly factor are just two names for the same protein.

False

T/F: A transition mutation is more likely to distort DNA structure than a transversion mutation.

False

T/F: AUG is an example of a stop codon

False

T/F: Agarose gel electrophoresis can separate linear nucleic acid fragments by length. Under normal conditions the longest DNA fragments migrate faster through the gel than shorter fragments.

False

T/F: All eukaryotic promoters need a TATA box in order to be transcribed.

False

T/F: An RNA sequence can only contain one open reading frame.

False

T/F: Antitermination protein acts in cis by blocking the effect of the terminator sequence element.

False

T/F: Cdc6 is the licensing factor that signals for replication to commence by methylation of GATC motifs in the yeast genome.

False

T/F: DNA endonucleases cut single nucleotides from the ends of DNA strands

False

T/F: DNA exonuclease cuts at specific nulceotide sequences throughout the genome.

False

T/F: During mitosis, microtubules bind directly to the DNA at the centromere.

False

T/F: Gene linkage describes a scenario in which the proteins from two or more different genes assemble into a multimeric complex.

False

T/F: Genes are most likely to be linked when they are on non-homologous chromosomes.

False

T/F: In BER the phosphate backbone of the damaged DNA must be cut prior to base removal.

False

T/F: In a eukaryote a core promoter is the complete package of cis regulatory units that instructs transcription.

False

T/F: In a frog cell promoter cis elements are always upstream of the transcription startpoint.

False

T/F: In an animal cell transcription and translation occur in the same cellular compartment.

False

T/F: In bacteria the single protein, Uvr, can remove damaged DNA.

False

T/F: In eukaryotes the proximity of promoters to enhancers is crucial for regulating transcription, which is why enhancers are always positioned around 10-100 nucleotides from the promoter sequence.

False

T/F: In general BER pathways are more error-prone than NHEJ.

False

T/F: Intrinsic termination does not depend on RNA structure.

False

T/F: Lampbrush chromosomes are found in most two winged insects.

False

T/F: Luckily for humans, DNA damage caused by sun exposure can be fixed by photoreactivation.

False

T/F: Methylation of cytosine to 5'-methyl-cytosine is essentially a mutation

False

T/F: Non-homologous chromosomes frequently form chiasmata with each other.

False

T/F: Promoters and enhancers both operate bidirectionally

False

T/F: RNA is synthesized by adding rNTPs to the growing 5' end of the nascent RNA.

False

T/F: Reverse transcriptase activity is unique to prokaryotes.

False

T/F: Similar to bacteria, a single RNA polymerase holoenzyme is responsible for all of the transcription in an animal cell.

False

T/F: Similar to bacteria, transcription and translation are coupled in a plant cell.

False

T/F: TATA binding protein (TBP) will only bind to TATA boxes to regulate transcription.

False

T/F: The RNA polymerase core enzyme cannot interact with DNA in the absence of sigma factor.

False

T/F: The promoter sequence will not regulate transcription if it does not match the consensus sequence perfectly.

False

T/F: The replication fork and replisome are equivalent structures.

False

T/F: The right macrodomain in a bacterial chromosome is the site where replication will begin.

False

T/F: The transcription factor TFIIH only participates in DNA repair that is coupled with transcription.

False

T/F: Under normal circumstances a deletion mutation can be corrected by a true reversion.

False

T/F: Unlike bacteria the transcriptional startpoint for a eukaryotic gene is assigned the -1 position.

False

T/F: Unlike chromatin in a eukaryote, the bacterial genome does not require proteins to package the DNA.

False

T/F: Elongation of a daughter strand occurs by adding nucleotides to the 5' end.

False, 3' end

T/F: The sequence in the ori where the initial replication bubble forms is generally A and G rich.

False, A and T

T/F: Helicase is responsible for initiating the formation of the replication bubble at the ori.

False, DnaA is responsible for this

T/F: The sequence within an exon always contributes to the protein product.

False, Exon sequences may be untranslated. e.g., UTR

T/F: During replication a single template strand is replicated

False, two strands

Gregor Mendel

First to describe the rules of inheritance.

Anneal

Form hydrogen bonds between nucleotide bases

A bacterial genome contains:

Four macrodomains

Which hexameric sequence is likely to be the target of a restriction enzyme? (hint: palindrome)

GATATC

Genic DNA

Genomic sequence of DNA that encompasses the sequence of a primary transcript.

What enzyme is responsible for removing a damaged nitrogenous base from a DNA sequence?

Glycosylase

A point mutation in the coding sequence of a gene that encodes a protein kinase results in a kinase that is more efficient at phosphorylating substrates than the wildtype kinase. The mutation would be best described as a...

Hypermorph

A Dalmatian gets its coat color pattern from a mutation in a pigmentation gene that results in a protein that is poorly functional. We would say the mutation is an example of a...

Hypomorph

Beadle and Tatum

Hypothesized that one gene is responsible for one enzyme.

The three general steps in transcription are ________to ________to ___________.

Initiation to elongation to termination

RNA pol III binding to a promoter:

Is directed by TFIIIB

Frederich Miescher

Isolated a substance from bloody bandages and named it nuclein

Hershey and Chase

Labeled bacteriophages with 32P and 35S, and demonstrated that the transforming principle is nucleic acid.

Heterochromatin is:

Less transcriptionally active than euchromatin

Assuming the DNA shown in the accompanying pictures are all the same Mass and are run alongside each other on a DNA gel. What is your expectation, with regard to the order of DNA fragments on the gel, from top to bottom?

Linear at the top, relaxed in the middle, and supercoiled at the bottom

The eukaryotic equivalent of DnaB is _______.

MCM complex

Denature

Melt

Southern blot

Method for probing DNA sequence using hybridization

What protein is responsible for recognizing a stalled RNA polymerase?

Mfd

Frederick Griffith

Microbiologist that discovered the Transforming Principle.

A mutation in a gene's coding region caused an amino acid change in the resulting peptide. Which term best describes the mutation type?

Missense mutation

A mutation that alters one amino acid in the peptide product but does not affect protein function is an example of a...

Neutral mutation

Nucleoside

Nitrogenous base and pentose sugar

Pyrimidine

Nitrogenous base with single ring structure

Purine

Nitrogenous base with two ring structure

Nucleotide

Nitrogenous base, pentose sugar, and phosphate

Which method of DNA repair is most error prone?

Non-homologous end joining

In a eukaryote transcription occurs in the...

Nucleus

Chemical modifications to core histones predominately occur:

On histone tails

Which method of DNA repair is most likely going to result in a perfect fix (identical to the wildtype sequence)?

Photoreactivation

PCR

Polymerase chain reaction

Precursor RNA

Preprocessed mRNA or primary transcript.

The eukaryotic TATA-box is most similar to the _____ sequence element.

Pribnow box

A transcriptional unit in a bacterium extends from the _____ to the ______.

Promoter, terminator

Watson and Crick

Proposed the double helix model for DNA.

Linus Pauling

Proposed the triple helix model for DNA.

A and G are...

Purines

In a human, which type of DNA damage is most likely a consequence of sun exposure?

Pyrimidine dimer

C and U are...

Pyrimidines

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Exon

RNA sequence that is retained in the mature mRNA.

Intron

RNA sequence that lies between exons and generally excluded from the mature mRNA.

Primary transcript

RNA transcript that has undergone no processing.

Flap endonuclease 1 is responsible for:

Removing 5' overhanging flaps in DNA repair.

The positioning factor for RNA pol I is ______.

SL1

Coding region of mRNA

Sequence of codons in a transcript that encode the amino acids sequence of the gene product

Walther Sutton

Showed that chromosomes segregate to daughter cells.

If the N-terminal domain of sigma factor were to be removed we might expect:

Sigma factor to bind promoters without association with RNA polymerase.

A mutation that does not alter the amino acid sequence of the gene product is an example of a(n)...

Silent mutation

Imagine a female mouse with six digits per appendage (normally there are five) is bred with a completely normal male mouse. The pair produces a littler of 10 pups all with 6 digits per appendage. Which statement best describes the mechanism underlying the outcome?

Six digit phenotype is a consequence of a dominant mutant allele.

Which phrase best describes hybridization in terms of nucleic acid base pairing?

Strands of nucleic acid will form double stranded molecules by base pairing, and in some cases the base pairing my occur between strands of different types or origins.

Which sequence in the form of a double helix will melt first?

TAGCTATTAG (The sequence with the least amount of Gs and Cs in it)

The key positioning factor for RNA pol II is ______.

TFIID

The positioning factor for RNA pol III is ______.

TFIIIB

The "puffs" on a polytene chromosome mark areas:

That are active in gene expression

A mutation in the mitfa gene of a zebrafish leads to an albino phenotype. That is to say, mitfa is required for normal pigmentation. If a mitfa loss-of-function mutant female fish mates with a male albino fish (mutation unknown) and the offspring are all born with normal pigmentation then we can conclude...

The albinism in the male fish must be a result of a mutation in a gene other than mitfa.

Which phrase is most likely true if a nucleotide in a polynucleotide chain undergoes a transition mutation?

The mutated nucleotide is an A or G

When comparing gene structure across eukaryotes it is common for...

The number and length of exons to be similar.

During replication in a bacterial cell, newly synthesized daughter strand that carries a mutation can be distinguished from the parent strand and corrected due to the following feature:

The parent strand can be identified by the presence of methylated nucleotides.

Gene expression

The process of making gene products (e.g., mRNA, protein)

Amplicon

The product of a polymerase chain reaction

A partially replicated bacterial chromosome is also known as:

Theta structure

If two traits in a diploid animal are observed together about 50% of the time and it's known that the genes for the traits are on the same chromosome, it's likely that the genes are:

They are separated by 50 or more map units from each other.

The major function of the -35 box is:

To enable promoter binding

Recently replicated bacterial chromosomes are often catenated, what enzyme is generally responsible for separating the chromosomes?

Topoisomerase II

Chemical modifications to core histone proteins that affect transcription are acting in...

Trans

DnaA-ATP exerts its activity in ______

Trans

What type of mutation would prevent both alleles of a gene from being expressed?

Trans-acting mutation

A bacterial chromosome has been isolated and linearized by a single double strand cut with an endonuclease. If the cut chromosome and an uncut but otherwise identical chromosome are run on a gel the prediction would be that the linear chromosome will:

Travel slower through the gel than the non-linearized molecule.

T/F: 5'-methyl-cytosine nucleotides are particularly susceptible to transition mutations

True

T/F: A centimorgan is equivalent to map unit (in terms of gene mapping).

True

T/F: A double strand break in DNA can be repaired by recombination repair mechanisms.

True

T/F: A genome size of 50 Kb is less than a genome that is 1 Mb.

True

T/F: A mutation in the -35 region of a bacterial promoter will generally affects initial binding of RNA polymerase.

True

T/F: Blunting ends of a double strand break is a crucial step in non-homologous end joining.

True

T/F: Chemical modifications to a core histone octamer can affect how tightly DNA is wrapped around the histone complex.

True

T/F: During mismatch repair of a G-T mismatch, the thymine is preferentially replaced with a cytosine.

True

T/F: Formation of a daughter strand requires the presence of a free 3' OH as would be present on a nucleotide.

True

T/F: Helicase is an ATP dependent enzyme.

True

T/F: Histone H2B forms a heterodimer with histone H2A

True

T/F: In E. coli it is possible for more than one protein to be translated from a single transcriptional unit.

True

T/F: In E. coli, it is common for a transcriptional unit to be transcribed and translated simultaneously.

True

T/F: In general methylation of a histone correlates with DNA that is less transcriptionally active.

True

T/F: It is possible for an mRNA to have more than one open reading frame.

True

T/F: Recombination events for two genes on a chromosome is proportional to their distance from each other.

True

T/F: The RNA polymerase II must form a complex with additional transcription factors for transcription to proceed.

True

T/F: The bacterial RNA polymerase is a holoenzyme comprised of several subunits.

True

T/F: The mass of DNA in a chromosome is about equal to the mass of protein in that chromosome.

True

T/F: The promoter is a cis element that regulates transcription of a gene.

True

T/F: The protein, xeroderma pigmentosum, complementation group C, is responsible for surveying the genome for distorting DNA damage.

True

T/F: Translesion synthesis is error prone.

True

T/F: Upstream and downstream refer to sequence that is located 5' or 3' from an expressed sequence, respectively.

True

Deamination of a cytosine in DNA results in a:

U-G base pair

Provide a 3 nucleotide sequence (i.e., codon) that determines a translational termination site. Please provide your answer in three letters with no spaces or punctuation (e.g., ABC).

UGA UAA UAG TGA TAG TAA

The 5' sequence before the translational start site in a mature mRNA is...

UTR

Thomas Hunt Morgan

Used fruit flies (Drosophila) to demonstrate that genes reside on chromosomes.

The origin-of-replication is licensed to replicate:

When the GATC motifs in the ori are fully methylated

__________ is responsible for global genome surveillance and initiating global genome repair.

XPC

Mature transcript

mRNA that has been processed and is ready for translation.

Which protein subunits make up the primary catalytic component of the RNA polymerase in E. coli?

ββ'