BIO midterm two study set

5' - TAAGCCACT - 3'

What is the complementary sequence to the DNA strand 3' - ATTCGGTGA - 5'

(be sure to pay attention to the orientation of the sequence (5' end, 3' end) in the answer you choose)

5' - TAAGCCACT - 3'

3' - TAAGCCACT - 5'

3' - AGTGGCTTA -5'

5' - AGTGGCTTA - 3'

X-ray diffraction data

Rosalind Franklin's important contribution to solving the structure of DNA was:

Transformation of R-type bacteria with DNA from S-type bacteria

Discovering that the number of adenines matches the number of thymines in all genomes

Piecing together "ball and stick" models of nucleotides to form a double helix

X-ray Diffraction

Purify different types of macromolecule (DNA, RNA, Protein) from lethal bacteria (a strain that kills mice) and test which macromolecule is capable of transforming non-lethal bacteria into lethal bacteria.

Which of the following experimental approaches proved DNA is the genetic material?

- Use radiolabeled nucleotides to show that they are semi-conservatively incorporated into DNA

- Purify different types of macromolecule (DNA, RNA, Protein) from lethal bacteria (a strain that kills mice) and test which macromolecule is capable of transforming non-lethal bacteria into lethal bacteria.

- Determine the structure of different macromolecules using X-ray diffraction

- Heat kill lethal bacteria (a strain that kills mice) and incubate the dead bacteria with live bacteria of a non-lethal strain.

The addition of each nucleotide is powered by hydrolysis of ATP.

Which of the following statements about DNA replication is FALSE?

Each strand within the DNA double helix is used as a template for synthesis of a new strand.

The addition of each nucleotide is powered by hydrolysis of ATP.

It proceeds via the addition of new nucleotides to the 3′ end of a growing DNA strand.

It requires DNA polymerase

Leading strand synthesis only requires a single RNA primer to start, Lagging strand synthesis requires multiple RNA primers

Which of the following statements about leading strand versus lagging strand DNA synthesis is TRUE?

Leading strand synthesis only requires a single RNA primer to start, Lagging strand synthesis requires multiple RNA primers

Leading strand synthesis occurs in the 5' to 3' direction, Lagging strand synthesis occurs in the 3' to 5' direction

Leading strand synthesis generates the coding strand of DNA, Lagging strand synthesis generates the template strand of DNA

Leading strand synthesis requires topoisomerase to remove "knots" ahead of the replication fork, Lagging strand synthesis does not require topoisomerase

in eukaryotes, a single origin of replication forms at one telomere and spreads toward the opposite telomere so that only one origin of replication is required to replicate a chromosome

Which of the following statements about Origins of Replication is FALSE?

in eukaryotes, a single origin of replication forms at one telomere and spreads toward the opposite telomere so that only one origin of replication is required to replicate a chromosome

in eukaryotes, multiple origins of replication form along a chromosome

Origins of replication are bidirectional

each replication fork contains a leading strand and a lagging strand

Helicase

The enzyme that separates the two strands of DNA during DNA replication is:

Topoisomerase

Single Strand Isomerase

Helicase

Primase

the distance between the stop codon and the terminator sequence in the coding strand of DNA

The length of the 3' UTR in a eukaryotic mRNA is determined by:

the position of the TTTTTT sequence that encodes the polyA tail

the open or closed state of chromatin at the 3' end of the gene

the number of stop codons in the mRNA

the distance between the stop codon and the terminator sequence in the coding strand of DNA

In the nucleus

mRNA processing in eukaryotes (including 5' cap addition and splicing), occurs:

only after Dicer converts the RNA from double stranded to single stranded

in the nucleus

in the cytoplasm

only after ribosomes bind the mRNA

5' - AAGCCUGAU - 3'

What mRNA sequence will be transcribed from this DNA template sequence:

3' - TTCGGACTA - 5'

(be sure to pay attention to the orientation of the sequence (5' end, 3' end) in the answer you choose)

3' - AUCAGGCUU - 5'

5' - AAGCCUGAU - 3'

5' - UAGUCCGAA - 3'

3' - UUCGGACUA - 5'

20

How many aminoacyl-tRNA synthetases (the enzyme that attaches an amino acid to tRNAs) exist in a cell?

64

61 !

20

between 20 and 61

Peptidyl transfer - when the polypeptide is transferred from the P site and forms a peptide bond with the single amino acid attached to a tRNA in the A site

During translation elongation, what stimulates the ribosome to move down one codon?

A stop codon entering the A site.

A new tRNA entering the A site.

The hydrolysis of ATP.

Peptidyl transfer - when the polypeptide is transferred from the P site and forms a peptide bond with the single amino acid attached to a tRNA in the A site

the small ribosomal subunit directly binds to a ribosome binding site in the 5' UTR

Which of the following is unique to translation initiation in bacteria (does not occur in eukaryotes)?

the small ribosomal subunit directly binds to a ribosome binding site in the 5' UTR

the first amino acid added is Met (Methionine)

the start codon is AUG

only the small ribosomal subunit initially "scans" the mRNA

2, 1, 3, 4, 5

Which sequence of events CORRECTLY describes the initiation and elongation steps of translation in bacteria?

(1) initiator tRNA binds start codon on mRNA

(2) small ribosomal subunit binds to mRNA

(3) large ribosomal subunit binds

(4) tRNA entry and peptidyl transfer reaction

(5) translocation of ribosome and release of tRNA

2, 3, 1, 5, 4

1, 3, 2, 4, 5

2, 1, 3, 4, 5

1, 2, 3, 5, 4

aminoacyl-tRNA synthetases attach the correct amino acid to tRNAs

Which of the following does NOT occur during translation elongation?

Charged tRNAs (with the next amino acid to be added to the polypeptide) enter the A site of the ribosome.

Base pairing between tRNAs and the mRNA.

both the large and small ribosomal subunits are assembled on the mRNA

aminoacyl-tRNA synthetases attach the correct amino acid to tRNAs

release factor protein

What recognizes the codon UAA in the ribosome "A" site?

nothing - the A site is not filled when those codons are present

tRNAs that are not charged with an amino acid

release factor protein

any tRNA charged with Met

Only some nucleotides within a microRNA base pair with their target mRNA - the mutated nucleotides are outside this region

A scientist is studying a microRNA believed to play a role in cancer. She mutates two nucleotides of DNA in the gene encoding this microRNA. This mutation does not affect the cancer cells in any way and all of the microRNA targets are expressed normally. What is a possible explanation for this result?

Mutating DNA has no effect on microRNAs, she would have to mutate the RNA

The mutated nucleotides are not within the 5' UTR of the microRNA

MicroRNAs work together with siRNAs, so the siRNA can make up for the loss of microRNA function !

Only some nucleotides within a microRNA base pair with their target mRNA - the mutated nucleotides are outside this region.

HOTAIR could still bind target DNA sequences but would not bind to histone modifying proteins

Mutations in the HOTAIR gene that remove the secondary structures ("stem loops" or "hairpins") of the ncRNA but maintain the normal RNA sequence would likely cause what result?

HOTAIR could still bind target DNA sequences but would not bind to histone modifying proteins

HOTAIR would lose its ability to bind to DNA but could still bind histone modifying proteins

HOTAIR does not require secondary structures, it would still function normally

HOTAIR would lose its ability to bind to both target DNA and to histone modifying proteins

a microRNA that inhibits ey mRNA translation is expressed after the embryonic stage of development

During Minion development, the Ey protein is only produced during embryonic stages - it is not detected in the adult stage. You measure ey mRNA levels in embryonic and adult stages and find that the mRNA is present at high levels in both embryos and adults. This could be explained by:

a lack of ribosomes in the adult stage

loss of an activator required for ey gene transcription after the embryonic stage of development

a microRNA that inhibits ey mRNA translation is expressed after the embryonic stage of development

deletion of the ey gene after the embryonic stage of development

Histones are a major component of chromatin

Which of the following statements about chromatin is TRUE?

chromatin is only found near regulatory sequences and promoters

Histones are a major component of chromatin

chromatin modifications only occur during DNA replication

Nucleosomes are not considered part of chromatin

a ribosome binding site, a start codon, a stop codon

To produce multiple proteins from a polycistronic mRNA, each translated region must have:

a ribosome binding site, a start codon, a stop codon

a splice site before the next protein coding region

a start codon, a stop codon

a start codon, a stop codon, a termination sequence

Can't say what the effect on transcription will be - some histone modifications activate transcription, some histone modifications inhibit transcription

You discover a non-coding RNA (ncRNA) that contains domains which likely bind to histone modifiers. Even though the exact histone modifiers that bind this ncRNA are unknown, what can you predict about the function of this ncRNA?

- this ncRNA likely inhibits transcription since histone modifications always inhibit transcription

- Can't say what the effect on transcription will be - some histone modifications activate transcription, some histone modifications inhibit transcription

- this ncRNA likely does not bind to DNA since histone modifications mainly regulate mRNA translation

- this ncRNA likely activates transcription since histone modifications always activate transcription

transcription is only regulated via activator proteins and positive control

Which of the following statements about transcription regulation in bacteria is FALSE?

RNA polymerase binds to DNA at the promoter

transcription may be regulated by a combination of activator and repressor proteins

regulatory DNA sequences are often located close to the promoter

transcription is only regulated via activator proteins and positive control

alternative splicing of Gene x pre-mRNA

Fibroblast cells (a eukaryotic cell type) contain 1,000 different proteins. You predict that "Gene X" is involved in fibroblast formation and delete the gene. You discover that fibroblasts lacking Gene X contain 997 proteins. The three missing proteins contain an identical structural domain but are otherwise unique. This result could be explained by:

Three different microRNAs regulate Gene X translation

alternative splicing of Gene x pre-mRNA

Three different ribosome binding sites in the Gene X mRNA

A frameshift mutation in Gene X

A chromatin remodeler that makes the ey promoter accessible to RNA polymerase is only present in anterior / "head" cells

In Minion embryos, the ey gene is only expressed in anterior or "head" cells. This could occur because:

A microRNA that targets the ey mRNA is only present in anterior / "head" cells

A chromatin remodeler that makes the ey promoter accessible to RNA polymerase is only present in anterior / "head" cells

The TATA sequence is missing from the core promoter of the ey gene in posterior / "tail" cells

During development, DNA polymerase does not replicate the ey gene in posterior / "tail" cells

The lac operon would always be transcribed at very low rates, the levels of lactose and glucose would not matter

If lacI were mutated so that the Lac Repressor ALWAYS binds to the operator DNA sequence (regardless of small effector molecule levels), this would cause:

The lac operon would be transcribed at very high rates when lactose levels are low and glucose levels are high

The lac operon would be transcribed at very low rates when lactose levels are low, but would be transcribed at very high rates when lactose levels are high

The lac operon would be transcribed at very high rates when lactose and glucose levels are low

The lac operon would always be transcribed at very low rates, the levels of lactose and glucose would not matter

A transcription activator that is only expressed in fibroblasts and binds to an enhancer sequence in the collagen promoter

The collagen gene is transcribed in fibroblast cells but is never transcribed in neurons. This differential transcription could be regulated by:

a silencer DNA sequence that is only present in the collagen promoter of neurons

an enhancer DNA sequence that is only present in the collagen promoter of fibroblasts

A transcription activator that is only expressed in fibroblasts and binds to an enhancer sequence in the collagen promoter

the absence of a core promoter in the collagen gene of neurons

Germline cells

Huntington's disease is caused by a mutation in a single gene. The mutant gene is passed from a parent with Huntington's disease to 50% of their children. For this type of inheritance to occur, the mutation must be present in:

Germline cells

Cells that lack nucleotide excision repair

Somatic cells

Cells that lack DNA proofreading

is in the core promoter of the gene

A mutation in a gene in the fruit fly Drosophila was found to affect eye color. The relevant protein is normal in its molecular weight and amino acid sequence, although much less of the protein is made in mutant flies. A reasonable explanation for the change in levels of protein is that the mutation:

is in a splice site and causes alternative splicing of the pre-mRNA

is in the core promoter of the gene

introduces a premature stop codon

changes a single codon but is a silent mutation

Base excision repair

Cytosine can be converted to uracil by reactive nitrogen molecules. If this occurs within a gene, the uracil is removed by which mechanism:

Proofreading by ribosomes after the gene is transcribed into mRNA

Base excision repair

Proofreading by RNA polymerase when the gene is transcribed

Accurate base pairing by DNA polymerase when that gene is replicated

oncogenes

Mutations in the Ras gene can cause production of a hyperactive Ras protein that promotes cell proliferation / cell divisions. These mutant forms of Ras are:

proto-oncogenes

cell cycle genes

tumor suppressor genes

oncogenes

All of these choices are correct

A proto-oncogene may become an oncogene due to:

Gene amplification, so that the number of copies of the gene increases

Translocation of the gene to a new position within a chromosome, so that it's rate of transcription increases

Point mutation within the protein coding sequence, so that the protein becomes hyperactive

All of these choices are correct

Binding to and inhibiting a transcription factor, E2F, that in the absence of Rb binding "turns on" transcription of genes that promote cell division

The Rb (Retinoblastoma) protein functions as a tumor suppressor by:

Directly binding to enhancer elements that regulate proto-oncogenes

Directly binding to silencer DNA elements in genes that promote cell division

Binding to and inhibiting the activity of the Ras protein

Binding to and inhibiting a transcription factor, E2F, that in the absence of Rb binding "turns on" transcription of genes that promote cell division

a covalent phosphoester bond

During DNA synthesis, nucleotides are added to the 3' end of the DNA strand via formation of:

a double helix

a covalent phosphoester bond

hydrogen bonds between deoxyribose sugars

ionic bonds between phosphates

A DNA polymerase removes the RNA primer and replaces it with DNA

What happens to RNA primers during DNA replication?

The nucleotide excision repair pathway removes the RNA primer

A RNA transisomerase converts the RNA into DNA

RNA can't base pair with DNA, so the RNA primer doesn't stay associated with the template DNA

A DNA polymerase removes the RNA primer and replaces it with DNA

The addition of each nucleotide is powered by hydrolysis of ATP.

Which of the following statements about DNA replication is FALSE?

It requires DNA polymerase

The addition of each nucleotide is powered by hydrolysis of ATP.

Each strand within the DNA double helix is used as a template for synthesis of a new strand.

It proceeds via the addition of new nucleotides to the 3′ end of a growing DNA strand.

DNA synthesis only occurs in a 5' to 3' direction, which causes lagging strand synthesis to "restart" as new 3' regions of template DNA become available

During DNA replication, why is the lagging strand synthesized in a discontinuous fashion (multiple Okazaki fragments)?

DNA synthesis only occurs in a 5' to 3' direction, which causes lagging strand synthesis to "restart" as new 3' regions of template DNA become available

The lagging strand can't be synthesized until the leading strand is completed

There isn't any topoisomerase on the lagging strand

The DNA polymerase that synthesizes the lagging strand can only synthesize short sequences of DNA before it falls off the template.

The ends of chromosomes would become shorter (DNA sequence would be lost) after each round of DNA replication

What would happen if actively dividing cells were treated with a chemical that inhibits telomerase activity?

Okazaki fragments could not be properly joined together

Large portions of the middle of chromosomes would be single-stranded.

The ends of chromosomes would become shorter (DNA sequence would be lost) after each round of DNA replication

Origins of replication could not form in the middle of the chromosome.

core promoter

Eukaryotic transcription begins at a site in the DNA called the:

enhancer

operator

core promoter

start codon

the tRNA that was previously in the P site and no longer has any amino acid attached exits the ribosome

The Exit Site or "E" Site in a ribosome is where:

the 5' end of mRNA that has already been translated exits the ribosome

the finished polypeptide exits the ribosome

the tRNA that was previously in the P site and no longer has any amino acid attached exits the ribosome

the tRNA that was previously in the A site but has donated it's amino acid and moved to the E site exits the ribosome

30%

30 percent of the Minion genome is composed of the base guanine (G). Therefore, the base cytosine (C) must make up what percent of the genome?

30%

60%

20%

10%

All of these choices are correct

Which of the following enzymes are required for Leading Strand DNA synthesis?

all of these choices are correct

DNA primase

DNA polymerase

Helicase

three

How many nucleotides are in a codon?

three

four

two

one

pre-mRNA

Which of the following types of RNA is NOT produced in bacteria?

pre-mRNA

rRNA

mRNA

tRNA

the 3' UTR is not translated

Which of the following statements about the 3' UTR of eukaryotic mRNAs is FALSE?

the 3' UTR is not translated

the last nucleotide in the 3' UTR is followed by a series of adenines (the "polyA tail")

the nucleotides at the end of the 3' UTR always form a stop codon

microRNAs bind to the 3' UTR of their targets

Glucose causes cAMP levels to decrease and cAMP is the small molecule effector required by CAP to activate lac operon transcription

E. coli exposed to high levels of lactose and glucose (lactose high + glucose high) will transcribe the lac operon at a low rate because:

Glucose causes cAMP levels to decrease and cAMP is the small molecule effector required by CAP to activate lac operon transcription

High levels of lactose cause decreased expression of CAP, regardless of glucose levels

Glucose causes Lac Repressor levels to increase. Lac Repressor binds to the operator sequence, inhibiting lac operon transcription.

High levels of lactose lead to high levels of allolactose. Allolactose binds to the the Lac Repressor and causes it to bind an operator sequence, inhibiting lac operon transcription.

The complexity allows precise control over the timing of transcription and the type of cell where transcription occurs

Which statement best describes why multicellular eukaryotes typically use more complex combinations of regulatory elements to control gene transcription compared to bacteria?

the complexity allows more than one protein to be produced from a single gene

the complexity ensures that a single mutation won't affect gene transcription

the complexity is caused by DNA duplication events that don't occur in bacteria

The complexity allows precise control over the timing of transcription and the type of cell where transcription occurs

DNA is a double helix, so once a damaged region is removed, the correct sequence can be synthesized by using the opposite DNA strand as a template

What characteristic of DNA makes the nucleotide excision repair (NER) pathway possible?

DNA is wrapped around histone proteins that can influence its accessibility to proteins.

DNA may have its own enzymatic activity.

DNA is a double helix, so once a damaged region is removed, the correct sequence can be synthesized by using the opposite DNA strand as a template

DNA is a molecule with directionality, with a free 5' phosphate and a free 3' hydroxyl group.

3' -> 5' exonuclease

DNA polymerase uses which activity to remove a mismatched base pair?

3' -> 5' exonuclease

protease

5' -> 3' exonuclease

RNase

A missense mutation that increases the activity of a protein encoded by a tumor suppressor gene

Which of the following is NOT likely to contribute to cancer formation

A nonsense (loss of function) mutation in a tumor suppressor gene

Increased expression of telomerase

A mutation within the promoter of a proto-oncogene that causes an increased rate of transcription

A missense mutation that increases the activity of a protein encoded by a tumor suppressor gene