Biochem exam 4 - Smartwork

The processes of DNA replication and RNA transcription in E. coli are similar in some respects and different in others. How are they similar?

- A specific region of the DNA is recognized and bound by the polymerase. - The direction of polymerization is 5' to 3' - The direction of enzyme movement on the template strand is 3' to 5'

translation initiation in eukaryotes:

- ATP and GTP hydrolysis provides energy necessary for formation of the initiation complex. - A 5′ cap and 3′ polyadenylation of the mRNA is necessary. - The 80S ribosomal complex is made up of the 40S and the 60S subunits.

RNA and protein BOTH

- Both can fold into tertiary structures that are important for correct function of the molecule. - Both can interact with other RNA and protein molecules. - Both can be found in the nucleus and cytoplasm.

Which of the following DNA repair mechanisms does NOT require a DNA template? A. Single-strand DNA break repair via short repair gap filling B. Double-strand DNA repair via homologous recombination C. Single-strand DNA break repair via long repair gap filling D. Double-strand DNA repair via non-homologous end joining

- Double-strand DNA repair via non-homologous end joining

Resolvase activity will act upon ______________________ and will generate which of the following? A. only nonrecombinant nucleic acid B. only recombinant nucleic acid C. either recombinant or nonrecombinant nucleic acid

- Holliday - either recombinant or nonrecombinant nucleic acid

part of the miRNA pathway for mRNA degradation

- The RISC complex can serve as a transcription block. - The RISC complex can lead to mRNA cleavage. - Precursor miRNA is transcribed in the cell.

How is the Ames test used to quantitate mutagenic potential of chemical compounds?

- The Salmonella test strain used in the Ames test contains a mutation in the histidine biosynthetic pathway, which is used to identify compounds that induce back mutations to permit bacterial growth on histidine free plates. - The chemical compound to be tested is added to a filter paper disk and placed on agar plates containing the tester Salmonella strain; potent mutagens result in MORE colonies forming on histidine free plates as compared to control plates.

What observation would directly support the idea that co-suppression was caused by RNA interference?

- The levels of chalcone synthase mRNA were lower in plants with an extra copy of the chalcone synthase gene as compared to untreated plants.

Which of the following hypotheses could explain how a ribosome deals with this to always start translation at the start codon?

- The ribosome moves along the mRNA starting at the Shine-Dalgarno sequence and uses the first start codon it finds to initiate translation, so the length does not matter.

Which of the following statements about aminoacyl-tRNA synthetases are true?

- The tRNA-charging reaction they catalyze is irreversible in typical cellular conditions. - They are found in the cytoplasm. - They are found in the mitochondria. - They sometimes charge tRNAs with the wrong amino acid.

property of ribozymes

- They are capable of using metal ions as cofactors - They are capable of acid-base catalysis. - They can catalyze reactions intramolecularly or intermolecularly

Which enzymes are required for the complete process that leads to successful retrotransposon insertion?

- integrase - RNA polymerase - reverse transcriptase

If a protein-coding gene is fused to the lac promoter sequence, then bacteria will produce large amounts of that protein when stimulated with IPTG. As described in the text, this can be accomplished by creating a plasmid that carries the new gene construct. What features other than a promoter must also be present on the plasmid to ensure that the protein is expressed?

- lac repressor binding site - Shine-Dalgarno sequence

A number of different RNAs are required for protein synthesis. Which of the following RNAs are required for the complete process of assembling the protein synthesis machinery as well as translation in eukaryotes?

- mRNA, tRNA, and rRNA - snoRNA and snRNA

Unlike most eukaryotes, prokaryotes make polycistronic mRNAs. These polycistronic mRNAs encode more than one protein. In order to properly synthesize all of the encoded proteins, these prokaryotic polycistronic mRNAs must duplicate which mRNA components?

- stop codon - Shine-Dalgarno sequence

Rank the following events from earliest to latest during the initiation of E. coli DNA replication.

1. oriC becomes separated 2. binding of the primosome 3. Interaction of Pol III via the beta-clamp subunit 4. two opposing replication forks collide 5. resolution of catenated DNA molecules

Which of the following best describes the relationship between the lytic and the lysogenic cycle of bacteriophage λ? A. A lysogenic cycle can revert to the lytic cycle within the same cell. B. A lytic cycle involves recombination and a lysogenic cycle does not. C. A lytic cycle can revert to the lysogenic cycle within the same cell.

A lysogenic cycle can revert to the lytic cycle within the same cell.

Functions with DNA replication to remove incorrect nucleotides from the nascent strand.

Mismatch repair

What accounts for the high fidelity of DNA polymerization?

Active site geometry ensures that only correct sized nucleotide base pairs are formed, and 3' to 5' proofreading removes incorrect nucleotides.

NOT TRUE for RNA and protein

Both require the same amount of time for synthesis. ****** different amount of time for synthesis ********

Repairs nucleotide bases without requiring DNA ligase

Direct repair

Why is it necessary for σ factor to dissociate from the RNA polymerase in order for elongation to occur efficiently?

Dissociation of σ factor increases the affinity of RNA polymerase for general DNA.

hyperphosphorylation

Multiple copies of the heptapeptide repeat are phosphorylated on some combination of serine, threonine, and tyrosine residues.

E. coli replication fork, which protein is responsible for relieving torsional stress?

Gyrase

How high should the concentration of aminoacyl-tRNA synthetases be, compared to the concentration of tRNAs in a cell?

Low: because a single aminoacyl-tRNA synthetase can catalyze many reactions

Why is the trp operon regulated in this manner? why is it evolutionarily favorable?

The production of the tryptophan biosynthetic enzymes is a waste of metabolic energy if tryptophan is available to the bacterial cell from the environment.

The cytoplasm has a reducing environment, while the extracellular space tends to have an oxidizing environment. Based on this information, where would proteins with disulfide bonds most likely be synthesized?

Rough endoplasmic reticulum, because disulfide bonds are more stable in the extracellular space

Pre-spliceosome (SnRNP complexes)

U1 & U2

Precatalytic (SnRNP complexes)

U1, U2, U4, U5, and U6

Active spliceosome (SnRNP complexes)

U2, U5, and U6

If 15N DNA replicated using conservative replication in 14N media, the outcome would be that new DNA has:

one high density and one low density strand.

Requires an endonuclease to remove an abasic nucleotide before DNA Pol I can replace a portion of the strand.

Base-excision repair

Is needed to repair chemical damage in DNA effecting more than one nucleotide, such as cyclobutane pyrimidine dimers.

Nucleotide-excision repair

What is a Holliday Junction?

The location in a DNA recombination intermediate where DNA strands from different DNA molecules are crossed over, which links the two DNA molecules together.

What four amino acid side chains are integral to the DNA binding function of the TATA binding protein?

four phenylalanine residue side chains

AZT is such a good HIV drug because it:

prevents new DNA from being replicated.