BIOL 219 Exam #3

Which of the following molecules serves as the genetic code?

A. DNA

B. RNA

C. protein

D. lipids

A

How many nucleotides make up one codon and therefore represent an amino acid code?

A. 1

B. 2

C. 3

D. 4

C

There are 64 codons, but only 20 amino acids. Which of these is NOT an explanation for this?

A. some codons code for STOP

B. some codons code for the same amino acid. in other words the code is redundant

C. some codons don’t code for anything. they allow random amino acids to be inserted in proteins

C

How would you classify a mutation where one nucleotide is swapped for another and codes for a new amino acid? For example, ATG becomes ATC?

A. nonsense

B. missense

C. frameshift

D. silent

B

True or false: each nucleotide can be used in multiple codons within the same protein. In other words, the code is overlapping.

False

Which statement correctly describes the relationship between the genome and the proteins a cell produces?

A. all cells in the body express the same proteins, since they all contain the same genome

B. the genome changes every time a new protein is needed

C. every nucleotide in the genome is part of a codon that codes for protein

D. only a subset of the genome codes for protein; the rest has other functions or no currently known function

D

Which of the following correctly describes the flow of information described by the central dogma?

A. DNA —> RNA —> protein

B. DNA —> protein —> RNA

C. Protein —> RNA —> DNA

D. RNA —> DNA —> protein

A

chargaff, 1950, base composition analysis

the amount of A always equals the amount of T, and the amount of G always equals the amount of C

watson, crick, franklin, and wilkins, 1953

DNA is a double helix, with the two strands held together by base pairing

griffith, 1928, bacterial transformation

a heritable transforming principle could pass between bacterial strains

If each codon were only 2 nucleotides long instead of 3, how many unique codons would be possible, and would that be enough to specify all 20 amino acids?

A. 8 possible codons; not enough

B. 20 possible codons; exactly enough

C. 64 possible codons; more than enough

D. 16 possible codons; not enought

D

In Crick’s frameshift experiments, inserting one extra nucleotide into a bacteriophage gene disrupted its reading frame and produced a nonfunctional protein (large plaques). Which of the following insertions would you predict would restore a functional reading frame?

A. none of the above would restore the reading frame

B. inserting 2 additional nucleotides

C. subtracting 2 additional nucleotides

D. inserting 1 additional nucleotide

B

Crick also found that combining one insertion (+) with one deletion (-) in the same gene restored a functional reading frame (small plaques), even though neither mutation alone did. Why does a (+)(-) combination restore function when a (+)(-) combination does not?

A. ribosomes can skip over regions with both an insertion and a deletion

B. the deletion repairs the chemical damage caused by the insertion

C. DNA polymerase proofreads and removes both mutations before transcription

D. the insertion and deletion cancel out, so the net number of nucleotides added or removed is zero

D

In Nirenberg’s experiment, a synthetic RNA made entirely of uracil (poly-U) was translated in a cell-free system, producing a protein made entirely of phenylalanine. What can you conclude from this result?

A. uracil is only found in codons that specify phenylalanine

B. all codons made only of one repeated nucleotide code for the same amino acid

C. phenylalanine is the only amino acid that can be added to a growing protein

D. the codon UUU specifies phenylalanine

D

A synthetic RNA built from a repeating three-nucleotide sequence (CCUCCUCCUCCU repeated) can be read starting at three different positions, producing three different results: a chain of all proline, a chain of all serine, or a chain of all leucine, depending on where translation begins. What does this demonstrate about how the genetic code is read?

A. proline, serine, and leucine share a common codon that can be read in any frame

B. RNA polymerase determines which amino acid is added, not the ribosome

C. the code is ambiguous, since the same RNA sequence can code for three different amino acids at the same time

D. the code is read in a single, continuous, non-overlapping reading frame; shifting the starting point changes every codon that follows

D

nirenberg

synthetic RNA translated in a cell-free system

griffith

transformation of bacterial strains

crick, barnett, brenner, and watts-tobin

frameshift mutagenesis in bacteriophagew

chargaff

chemical analysis of base composition

Beadle and Tatum’s one gene, one enzyme hypothesis proposed that each gene codes for exactly one protein. Which of the following is a real exception to this simple model?

A. some genes are transcribed into mRNA but never translated

B. some proteins are broken down shortly after they are made

C. a single gene can be alternatively spliced to produce more than one protein

D. some genes are turned off by DNA methylation

C

True or false: if you sequence the genome of a cell, you can tell what kind of cell it is.

false

Which of these is NOT a feature of epigenetic regulation?

A. DNA mutation

B. reversible

C. heritable

D. environmentally responsive

A

True or false: the position of histones/nucleosomes on DNA is fixed. You can’t move them once they are placed.

False

Which of these is most likely to lead to reduction in ionic bonds between DNA and histone proteins?

A. histone acetylation

B. histone methylation

C. DNA methylation

D. X-inactivation

A

Which of these is NOT a unique feature of RNA?

A. a 2’ -OH group

B. the possibility of uracil in the bases

C. a 3’ -OH group

C

Which of these is the “assembler” of RNA?

A. fatty acid synthase

B. ribosomes

C. RNA polymerase

D. glycosyl transferase

C

Which of these is not a feature of RNA polymerase?

A. DNA entry site

B. DNA exit site

C. RNA exit site

D. nucleotide exit site

D

Which RNA polymerase is used to generate mRNA?

A. RNA polymerase I

B. RNA polymerase II

C. RNA polymerase III

D. any of these can make mRNA

B

In eukaryotes, how is transcription terminated?

A. a protein called Rho binds to the new RNA and bumps RNA polymerase off (allostery)

B. a hairpin loop is formed inside RNA polymerase, which weakens the binding affinity and the polymerase falls off

C. a nuclease recognizes a site in the new RNA and cleaves it from the RNA polymerase, which keeps transcribing

D. the RNA polymerase reaches a stop codon

C

If a gene’s transcript is turned up by the removal of a repressor, how would you classify this?

A. positive induction

B. negative induction

C. positive repression

D. negative repression

B

Which of the following cis-factors can be moved closer or further from the transcription start site and still work the same way?

A. core promoter

B. proximal promoter

C. distal promoter

D. only trans-factors can do this

C

Which of these is responsible for determining when (under what circumstances) a gene will be transcribed?

A. general transcription factors

B. regulatory transcription factors

C. core promoter

D. proximal promoters

B

A fibroblast normally does not express muscle genes. Which of the following best explains why, at the chromatin level?

A. fibroblasts actively degrade any muscle gene mRNA that is made

B. muscle genes are packaged in relatively inaccessible chromatin in fibroblasts, limiting transcription

C. fibroblasts lack the DNA sequence for muscle genes entirely

D. RNA polymerase II is not present in fibroblasts

B

Evaluate the following statement: “epigenetic regulation changes the DNA sequence, responds to the environment, and is heritable through mitosis but not meiosis.” Which part of this statement is FALSE?

A. epigenetic regulation is not heritable through mitosis

B. nothing is false; the whole statemen is correct

C. epigenetic regulation does not respond to the environment

D. epigenetic regulation does not change the DNA sequence

D

nucleosome position and density

determines how much DNA is physically wrapped up and inaccessible to transcription machinery

histone tail modification

chemical marks that can be added, read, or removed to change how tightly DNA and histones interact

DNA methylation

a heritable chemical mark, typically on CpG sequences, that can recruit repressive proteins

Which of the following is NOT true of DNA methylation?

A. it typically occurs on CpG sequences in mammals

B. it directly changes the DNA sequence, creating mutations that alter the protein produced

C. it can provide binding sites for histone-modifying enzymes like deacetylases

D. it can provide binding sites for transcriptional repressors

B

Forcing expression of MyoD in a fibroblast is sufficient to activate muscle-specific genes and convert the cell toward a muscle-like identity. MyoD is a protein that binds specific DNA sequences near muscle genes to recruit RNA polymerase. Is MyoD best described as a cis-factor or a trans-factor, and why?

A. cis-factor, because it must be located immediately next to the gene it regulates

B. trans-factor, because it directly synthesizes new RNA without help from RNA polymerase

C. trans-factor, because it is a protein that binds to DNA with sequence specificty to influence transcription

D. cis-factor, because it is built into the DNA sequence itself

C

The DNA sequences that MyoD binds near muscle genes are an example of which type of regulatory element?

A. histone tail modification

B. cis-factor

C. trans-factor

D. general transcription factor

B

Cis-regulatory elements controlling a gene can be located far away from that gene on the chromosome. Which property of DNA makes this possible?

A. cis-elements are copied and moved next to the gene before transcription begins

B. DNA is flexible and can loop in three dimensions, bringing distant sequences into contact with the gene

C. DNA can be transcribed starting from any point along its length

D. RNA polymerase can bind DNA at a distance without any direct contact

B

A gene with several different cis-regulatory elements can be turned on under some conditions but not others, depending on which transcription factors are available in the cell. What is this property called?

A. combinatorial control

B. genetic drift

C. allosteric regulation

D. semi-conservative regulation

A

Which general transcription factor provides the helicase and kinase activity needed to help RNA polymerase II begin transcription?

A. TBP alone, without any other factors

B. TFIIH

C. TFIID

D. Rho

B

cAMP binds CAP, causing CAP to bind the promoter and recruit RNA polymerase

positive induction

allolactose binds the repressor, causing it to fall off the operator

negative induction

True or false: Once a gene is turned “on”, it produces RNA at a fixed, all-or-nothing rate; the amount of RNA made cannot be finely adjusted.

False

RNA polymerase selects each incoming ribonucleotide using a “guess and check” process, similar in logic to enzyme kinetics you learned earlier in this course. What determines whether a given nucleotide is retained long enough to be added to the growing RNA strand?

A. random chance alone; RNA polymerase cannot distinguish between correct and incorrect nucleotides

B. the presence of a 3’ OH group, which is unique to correctly paired nucleotides

C. its binding affinity for the template strand; correctly paired bases have enough affinity to be retained while incorrect ones do not

D. its molecular weight; heavier nucleotides are retained preferentially

C

a nuclease cleaves the RNA at a specific site, separating it from the elongating polymerase

eukaryotes

a hairpin loop plus an AU-rich region weakens the RNA-polymerase interaction, causing the complex to fall apart

prokaryotes

Rho protein travels along the RNA and displaces RNA polymerase from the DNA

prokaryotes

A cell biologist wants to convert a skin cell directly into a muscle cell in a dish, without passing back through a pluripotent state. Which term best describes the skin cell’s potency before this conversion, if it can only become other skin-lineage cell types on its own?

A. multipotent

B. fully committed, with no potency at all

C. totipotent

D. pluripotent

A

Reprogramming a fibroblast toward pluripotency requires turning FGF signaling off while turning on pluripotency factors like Sox2; forcing high MyoD expression instead pushes the same starting cell toward a muscle identity. What does this demonstrate about a cell’s identity?

A. cell identity depends only on the cell’s location in the body, not on its gene expression

B. cell identity is defined by the specific set of genes being expressed, and can be redirected toward different fates by changing which transcription factors are present

C. cell identity is permanently fixed by the genome sequence and cannot be changed once set

D. cell identity can only be changed by altering the DNA sequence of the cell

B

Where does RNA processing occur in eukaryotic cells?

A. in the nucleus, while transcription is still happening

B. in the nucleus, after transcription has been terminated

C. in the cytoplasm, after the RNA has been exported

D. in specialized organelles, depending on their function

A

During mRNA processing, what processing occurs at the 5’ end of the mRNA?

A. several A’s are added

B. splicing occurs to remove the first several nucleotides

C. a 7mG cap is added in a 5’ to 5’ orientation

D. nucleotides are modified so they aren’t recognized by nucleases

C

During exon splicing, which step occurs first?

A. the 3’ end of the intron attacks the branchpoint A

B. the branchpoint A attacks the 3’ end of the intron

C. the branchpoint A attacks the 5’ end of the intron

D. the 5’ end of the intron attacks the branchpoint A

C

Which of the following types of processing is used for RNAs?

A. splicing

B. poly-adenylation

C. nucleotide addition

D. cleavage

E. trimming

F. nucleotide modification

D

Which of the following would you expect n the presence of a perfectly complementary small RNA?

A. transcription termination

B. mRNA cleavage

C. translation initiation

D. translation inhibition

B

Which of the RNAs is the “translator” that reads in RNA and “writes” in protein?

A. mRNA

B. tRNA

C. rRNA

D. miRNA

B

Imagine that the ribosome has just assembled. Where is the first tRNA-amino acid?

A. A-site

B. P-site

C. E-site

D. it is not in a ribosomal site

B

Imagine that the ribosome has just made the first peptide bond. Which of the following is NOT true of the ribosome at this time?

A. the e-site is empty

B. the p-site has a tRNA, but no amino acids

C. the a-site has a tRNA connected to 2 amino acids

D. the p-site has a tRNA connected to 2 amino acids

D

Which of these protects mRNA from degradation at the 3’ end?

A. the 7mG cap

B. splicing

C. polyA tail

D. cleavage

C

Which of these is NOT a mechanism by which translation of individual mRNAs is regulated?

A. small RNA binding to mRNA

B. stem loops in the structure of the mRNA

C. translation repressors that bind to mRNA

D. availability of EF-Tu

D

alkylation

targets to membranes

glycosylation

used for er and golgi processing

acetylation

neutralizes + charges, reduces ionic bonding between proteins

polymerization

combines proteins together in quaternary structures

phosphorylation

adds - charges, creates potential for new ionic bonds`

ubiquitylation

targets proteins for degradation

During ribosome assembly, which of these binds the mRNA first?

A. large ribosomal subunit

B. tRNA

C. small ribosomal subunit

D. small RNAs

C

EF-Tu

assists entry of a new aminoacyl-tRNA into the A-site

release factor

binds the stop codon and triggers termination

EF-G

drives translocation of the ribosome to the next codon

IF2

assists assembly of the ribosome at the start codon

A new aminoacyl-tRNA entering the ribosome’s A-site is selected using a “guess and check” process, similar in logic to how RNA polymerase selects nucleotides during transcription. What determines whether a given tRNA is retained long enough for its amino acid to be added to the growing chain?

A. EF-Tu physically checks the amino acid identity before allowing entry

B. correct codon-anticodon pairing provides enough binding affinity for the tRNA to be retained; incorrect pairing does not

C. only tRNAs carrying the largest amino acids are retained

D. retention is random and does not depend on the codon being read

B

In cells treated with clindamycin, proteins in production are trapped in the ribosome’s A-site and full-length proteins are never completed. Which process does clindamycin target?

A. translation

B. protein degradation

C. transcription

D. mRNA processing

A

In cells treated with rifampicin, only 2-3 RNA nucleotides can be added to a growing chain, and no full-length RNAs are produced. The drug binds RNA polymerase, but not at its active site. Which process does rifampicin actually target?

A. translation elongation

B. transcription

C. translation initiation

D. mRNA processing

B

mRNA processing (capping, splicing, and the polyA tail) typically begins before RNA polymerase II has even finished transcribing the gene. What coordinates the timing of this co-transcriptional processing?

A. a separate enzyme that waits in the cytoplasm until the finished mRNA arrives

B. the ribosome, which signals back to the nucleus once translation begins

C. phosphorylation of RNA polymerase II’s C-terminal tail (CTD), which recruits different processing machinery at different stages of transcription

D. processing cannot begin until transcription is fully complete; it only appears simultaneous

C

The ribosome itself catalyzes peptide bond formation during translation. Which component of the ribosome is actually responsible for this catalytic activity?

A. the mRNA being translated

B. ribosomal RNA

C. ribosomal proteins

D. tRNA alone, independent of the ribosome

B

Which of the following is FALSE about mRNA splicing?

A. the 3’ OH of exon 1 attacks the 3’ splice site, joining the exons and releasing the lariat

B. the proteins of the spliceosome are the catalytic components of the reaction

C. splicing is coordinated by snRNPs within the spliceosome

D. the 2’ OH of the branchpoint A attacks the 5’ splice site to form a lariat

B

A small RNA that is fully complementary to a target mRNA typically leads to mRNA degradation. What is the typical outcome when a small RNA is only partially complementary to its target mRNA?

A. partial complementarity has not effect on the mRNA at all

B. the mRNA is exported from nucleus more quickly

C. translation of the mRNA is inhibited, but the mRNA itself is not necessarily degraded

D. the mRNA is degraded just as efficiently as with full complementarity

C

Which cellular machine is responsible for degrading proteins that have been marked with ubiquitin?

A. ribosome

B. degradosome

C. spliceosome

D. proteasome

D

KRAS is a protein that requires a lipid modification localize to the membrane. Which category of post-translational modification is most likely to localize a protein to the membrarne in this way?

A. phosphorylation

B. glycosylation

C. alkylation

D. acetylation

C

FoxP1 is a transcription factor that activates genes for cell growth and division. Normally, a small RNA called miR150 represses FoxP1. The transcription factor Myc represses miR150. In many cancers, Myc is unregulated. Based on this regulatory chain, what happens to FoxP1 levels, and why?

A. FoxP1 increases, because more Myc means less miR150, and less miR150 means less repression of FoxP1

B. FoxP1 decreases, because more Myc means more miR150, which directly degrades FoxP1 protein

C. FoxP1 is unaffected, because Myc only regulates miR150 in non-cancerous cells

D. FoxP1 decreases, because Myc directly represses FoxP1

A

True or false: All ribosomes start out free.

true

How are transmembrane proteins put into membranes?

A. They are fully translated in the cytoplasm, then float to the correct organelle and are inserted in the membrane

B. They are inserted in the membrane during the process of translation when the translocon opens in the ER

C. They are fully translated in the cytoplasm. Then put into vesicles to be delivered to the correct membrane

B

Which of these does NOT happen in the ER?

A. N-linked glycosylation

B. O-linked glycosylation

C. Quality check by calnexin

D. Packaging into vesicles bound for the Golgi

B

Which of the following is TRUE of the glycosylation that happens in the Golgi?

A. Sugars are added to the oxygens. A complex sugar is built one sugar at a time

B. Sugars are added to nitrogens. A complex sugar is built one sugar at a time

C. A complex sugar is built first. Then, that sugar is added to oxygens

D. A complex sugar is built first. Then, that sugar is added to nitrogens

A

Imagine a vesicle is returning from the Golgi to the ER. Which protein is coating the vesicle?

A. Clathrin

B. COPI

C. COPII

D. None. These vesicles are uncoated

B

Vasopressin receptor (V2R) is a membrane protein that must be targeted to the ER during its synthesis. Which of the following signal types would you expect to find on V2R, but NOT on a protein that functions in the cytoplasm?

A. A start codon

B. A signal sequence bound by SRP

C. A nuclear localization signal (NLS), bound by importin

D. A nuclear export signal (NES), bound by exportin

B

True or false: All ribosomes begin translation as free ribosomes in the cytoplasm; whether a ribosome ends up at the ER depends on signals in the protein being made.

true

When are membrane proteins embedded into membranes?

A. During vesicle formation

B. During processing in the Golgi

C. When they reach their final, functional destination membrane

D. During production at the ER

D

Which of the following is NOT a function that occurs in the ER?

A. Addition of sugars one at a time to build an O-linked glycosylation pattern

B. N-linked glycosylation of newly synthesized proteins

C. Quality control of protein folding by calnexin

D. Sensing misfolded proteins and signaling problems to the cell

A

In the Golgi, which face is on the same side as the ER, and which is on the opposite side?

A. Cis is on the same side as the ER; trans is on the opposite side

B. Trans is on the same side as the ER; cis is on the opposite side

C. The Golgi has no distinct faces; sugars are added randomly throughout

D. Cis and trans both face the ER equally

A

A protein’s final destination can be determined by the specific combination of sugars added to it in the Golgi. What recognizes this sugar combination to begin sorting the protein into the correct vesicle?

A. A start-transfer sequence

B. SRP

C. A cargo receptor

D. Calnexin

C

COPII

ER to cis-Golgi

COPI

cis-Golgi to ER

clathrin

trans-Golgi to other cellular destinations

Vesicle budding depends on G-proteins that adopt a curved shape when bound to GTP, helping to physically deform the membrane into a vesicle. What role does GTP hydrolysis play once a vesicle reaches its destination?

A. It helps linearize (uncurve) the vesicle coat proteins, which is needed for membrane fusion

B. It prevents the vesicle from ever fusing with its target membrane

C. It provides the energy for the vesicle to be transcribed into a new protein

D. It reforms the vesicle coat so the vesicle can bud again

A

Several mutations in V2R are known to cause Nephrogenic Diabetes Insipidus. Researchers compared wild-type V2R to several mutant versions, alongside calnexin, and looked for overlap between the two signals. If a mutant V2R shows strong overlap with calnexin while wild-type V2R does not, what would this suggest about the effect of that mutation?

A. The mutant receptor is being degraded by the proteasome before translation is complete

B. The mutant receptor has an unusually strong affinity for its ligand at the plasma membrane

C. The mutant receptor is likely misfolded and retained in the ER by quality control, rather than reaching the plasma membrane like the wild-type receptor

D. The overlap indicates the mutant receptor is functioning completely normally

C