GENETICS EXAM 3

The mature mRNA transcribed from the human ββ-globin gene is considerably longer than the sequence needed to encode the 146-amino acid polypeptide. Select from the following list the names of three sequences located on the mature ββ-globin mRNA but not translated.

3'-UTR 5'-UTR stop codon

Order the following events from first to last in initiation of translation in prokaryotes.

30S subunit binds near 5' end of mRNA, 16S rRNA base pairs with the Shine-Dalgarno sequence, initiator tRNA charged with fMet binds the P site on the 30S, 50S subunit binds the 30S subunit

Order the following events from first to last in initiation of translation in eukaryotes.

40S subunit binds the 5'-cap region of the mRNA, 40S subunit scans the mRNA for the Kozak sequence, 60S subunit binds the 40S subunit

Identify the features that bacterial ribosomes and eukaryotic ribosomes have in common.

Consist of two subunits. Consist of RNA and protein. Have three tRNA binding sites.

Eukaryotic Initiation of Transcription

Enhancers -30 TATA Box RNA Polymerase II

Why do eukaryotes show more modifications than prokaryotes?

Eukaryotes show more modifications to make the transcript stable and to help the ribosome locate the transcript when it exits the nucleus.

Ribosomal subunits are large complexes composed of numerous polypeptides and at least one rRNA molecule. Which subunits include three rRNA molecules? See Section 9.1 (Page 316) .

Eukaryotic large subunits

Which of the following is characteristic of transcription in eukaryotes but not in prokaryotes?

Exon splicing catalyzed by the spliceosome

Which type of mutation results in a string of altered amino acids at the end of the polypeptide product?

Frameshift

What changes would you recommend to permit expression of this eukaryotic gene in a bacterial cell?

I would place the DNA sequence downstream of a known bacterial promoter. I would place an intrinsic or rho-dependent termination sequence downstream of the DNA. I would modify the coding sequence upstream of the ATG start codon to contain a Shine-Dalgarno sequence. I would make a cDNA copy of the gene which lacks introns.

When a DNA mismatch is detected in E.coli, what mechanism allows the cell to determine which was more likely to be the original nucleotide?

Identification is accomplished by the sensitivity of mismatch repair enzymes to methylation of specific nucleotides in the original DNA strand.

What would you expect to see if the signal sequence has been mutated or deleted?

If the signal sequence is mutated, proteins may not be secreted or processed properly and will begin to accumulate within the cell. Ultimately, this will result in cell death and impaired protein secretion.

________ helps control ribosome formation and binding of the initiator tRNA.

Initiation factor protein

If the first nucleotide in a codon is mutated to a different nucleotide, what would be the effect on the encoded protein?

It depends on what the changed nucleotide is.

You have identified a bacterial protein that has retained the starting fMet in its protein sequence. Which of the following is likely true of this protein?

It is likely nonfunctional, since bacteria use posttranslational cleavage of fMet to make functional proteins.

Which of the following best describe(s) the function of the 5' mRNA cap?

It provides a site for ribosome binding in the cytoplasm. To protect the transcript from degradation

What is necessary for a eukaryotic RNA to be recognized and bound by the small subunit of the ribosome?

Presence of 5' methyl-G cap on the mRNA.

What is the process of protein sorting and how the signal sequence is involved?

Protein sorting is a process that uses signal sequences of amino acids at the N-terminal end of a polypeptide to sort proteins and direct them to their cellular destinations.

Polypeptides must be sorted after translation. Does protein sorting occur in both prokaryotes and eukaryotes?

Protein sorting is used in bacterial cells for many proteins specifically destined for the cell membrane. In eukaryotes, due to protein sorting proteins are dispatched to particular cellular organelles, such as the chloroplast, mitochondrion, lysosome, nucleus, and secreted from the cells.

Which eukaryotic promoters display a high degree of variability in the type, number, and location of consensus sequence elements?

RNA pol II promoters for mRNA

What must eukaryotes do to initiate transcription of a gene?

Recruit the transcription factors and RNA Polymerase that compose the pre-initiation complex.

What events occur when one of these codons appears at the A site of the ribosome?

Release factor RF1 or RF2 binds to the A site. The 70S ribosome disassembles into 50S and 30S ribosomal subunits. GTP is hydrolyzed, causing release of the RF from the A site. The ester bond linking the polypeptide to the tRNA in the P site is hydrolyzed.

A full-length eukaryotic gene is inserted into a bacterial chromosome. The gene contains a complete promoter sequence and a functional polyadenylation sequence, and it has wild-type nucleotides throughout the transcribed region. However, the gene fails to produce a functional protein. What are the possible reasons why this eukaryotic gene is not expressed in bacteria?

Sequences required for efficient translation initiation in bacteria are not present. The eukaryotic promoter is unlikely to be recognized by bacterial RNA polymerase holoenzyme. The introns will not be removed from the pre-mRNA, which will result in production of an abnormal protein.

The preinitiation complex forms in bacteria when the start codon is recognized through binding of 16srRNA and what region of mRNA?

Shine-Dalgarno sequence

Prokaryotic Initiation of Transcription

Sigma Subunit -35 Consensus Pribnow Box

Which statements are true involving the initiation of transcription.

Since prokaryotes lack a nucleus, translation can begin before the transcript is fully transcribed. Eukaryotic RNA polymerase II requires general transcription factors for initiation of transcription. Three different RNA polymerases in eukaryotes transcribe different classes of genes.

How might a single base INSERTION into the second codon of the coding sequence of a gene affect the amino acid sequence of a protein encoded by the gene?

The amino acid sequence would be altered.

How does the eukaryotic initiation complex locate the correct start codon?

The initiation complex moves the small ribosomal subunit through the 5' UTR, scanning for the start AUG.

Which of the following statements support the previous conclusion that there are more mRNA bases than amino acids? (NOTE: While there may be some rare exceptions that don't support the conclusion, choose statements that typically support the conclusion.)

The mRNA contains 5' and 3' untranslated regions. The start site of transcription is upstream of the start codon. The stop codon does not code for an amino acid. Each codon contains 3 RNA bases.

Which of the following best describes the first step in the formation of the translation initiation complex?

The small ribosomal subunit binds to an mRNA sequence near the 5' end of the transcript

Alternative splicing can process the same pre-mRNA into different forms of mRNA. Which one of the following reasons best explains why this pre-mRNA can't be processed into a mRNA containing only (Exon 1-Intron A-Exon 3)?

The spliceosome can not excise RNA sequences bounded by two 3' splice sites.

Which of the following statements support the previous conclusion that there are more mRNA bases than amino acids? (NOTE: While there may be some rare exceptions that don't support the conclusion, choose statements that typically support the conclusion.)

The stop codon does not code for an amino acid. The mRNA contains a poly-A tail. The start site of transcription is upstream of the start codon. The mRNA contains a 7-methylguanosine cap. Each codon contains 3 RNA bases. The mRNA contains 5' and 3' untranslated regions.

What result would you expect if a mutation eliminates one of the four arms of a tRNA?

The tRNA will not be recognized by tRNA synthetase and cannot be charged.

In eukaryotes, how does the length of a typical monocistronic mRNA compare to the length of the protein generated from this mRNA?

There are more mRNA bases than amino acids.

In prokaryotes, how does the length of a typical monocistronic mRNA compare to the length of the protein generated from this mRNA?

There are more mRNA bases than amino acids.

What is the role of codons UAA, UGA, and UAG in translation?

They indicate the end of the coding sequence and trigger translation termination.

Which type of DNA damage is repaired by the enzyme photolyase?

Thyminedimers

Which of the following lists steps of mRNA production in eukaryotes in the correct order?

Transcription, 5' cap addition, addition of poly-A tail, exon splicing, passage through nuclear membrane

Thymine dimers are most commonly caused by exposure to:

UV irradiation.

What type of mutagen would you use if you wanted to study the effect of pyrimidine dimers in causing cancer?

UV radiation

You accidentally exposed your cell culture dish to radiation, but you are not sure of the precise wavelength of the exposure. How can you use the induced DNA damage to tell whether the radiation was UV or higher energy? What is the difference between the DNA damage caused by UV radiation compared to higher-energy radiation?

Ultraviolet radiation creates pyrimidine dimers in DNA, and these can lead to base-pair substitution mutations. Higher-energy radiation can induce DNA strand breaks, the most serious being the induction of DNA single-strand or double-strand breaks.

What is the final step of translational initiation in both bacteria and eukaryotes?

Union of the large subunit with the small subunit to form the intact ribosome

In bacteria, the methionine that initiates the formation of a polypeptide chain differs from subsequently added methionines in that _______.

a formyl group is attached to the initiating methionine

Generally speaking, which of the following mutations would most severely affect the protein coded for by a gene?

a frameshift deletion at the beginning of the gene

What would you expect to find bound to the stop codon at the A site?

a translation release factor

What term describes a gene or region of a genome where mutations occur much more often than average?

hotspots of mutation

The Shine-Dalgarno sequence in bacteria ________.

is a purine-rich consensus sequence found in the 5' UTR of the mRNA

When a peptide bond is formed between two amino acids, one is attached to the tRNA occupying the P site and the other _______.

is attached to the tRNA occupying the A site

What event occurs during translocation?

mRNA shifts in the 5' direction along the ribosome.

Agents generating mutation-inducing DNA damage are collectively referred to as ________.

mutagens

Studies of gene mutation frequencies have shown that ______.

mutations are rare, and genomes are generally stable

Only introns

removed from the primary transcript, remain in the nucleus

What proteins bind to silencer sequences, forming a protein "bridge" that bends the DNA over the promoter and prevents transcription?

repressor proteins

Neither

rho DNA Polymerase

Which type of mutation is possible due to the redundant nature of the genetic code?

silent

What is the general name for the components of the spliceosome, which removes introns from mRNAs?

small nuclear ribonucleoproteins

The rat α-tropomyosin (α-Tm) gene produces nine different mature mRNA proteins from a single gene using which three "alternative" mechanisms?

splicing, promoters, and polyadenylation

What process, which is responsible for many trinucleotide repeat disorders, alters the number of DNA repeats?

strand slippage

A second-site mutation that compensates for the mutation in one gene by mutating a second gene and restoring the wild-type phenotype is also known as a ________ .

suppressor mutation

translation

tRNA, rRNA, mature mRNA

mechanisms used by eukaryotes to identify the authentic start codon during translation initiation:

the preinitiation complex recruited to the 5'-cap region of mRNA, scanning in which it uses ATP hydrolysis to move the small ribosomal subunit through the 5' UTR in search of the start codon, the authentic start codon is embedded in a consenses sequence, the kozak sequence

In bacteria:

transcription and translation are coupled, no membrane bound organelles to provide physical seperation of transcription and translation

In eukaryotes:

transcription and translation are uncoupled, mRNA recieves a 5' cap, mRNA recives a 3' tail

Which repair process(es) use(s) a DNA polymerase?

translesion DNA synthesis homologous recombination (synthesis-dependent strand annealing) nucleotide excision repair base excision repair

What are the two basic types of base-pair substitutions?

transversion transition

A mutant DNA polymerase that increases the frequency of strand slippage would increase the frequency of which type of mutation?

triplet-repeat expansion

Which of the following statements about eukaryotic transcription is false?

A polycistronic mRNA may be transcribed if the gene products are used in the same pathway or needed at the same time.

What normally binds to an open A site on the ribosome?

A tRNA that carries the next amino acid to be added to the polypeptide chain

Translation in bacteria is directly dependent on all of the following associations except _______.

complementary base pairing between mRNA and DNA

Only exons

create a spliced RNA, exit the nucleus

Which of the following is able to cause a change in a reading frame?

deletion

Which type of damage is the most likely to be the most lethal to your cells?

double-strand DNA breaks

A signal sequence at the N-terminus of newly synthesized proteins will direct the protein to the ________ for protein packaging.

endoplasmic reticulum

initiation of translation in E.coli Step 2

formation of the 30S preinitiation complex fMet-tRNA fmet bound to IF2-GTP binds to start codon in the Psite and IF1 binds

initiation of translation in E.coli Step 3

formation of the 70S initiation complex 50S ribosomal subunit binds, IF2 cleaves GTP to GDP + phosphate and IF1, IF2-GDP and IF3 leave the complex

Binding of what protein initiates translation-termination events that result in polypeptide release and dissociation of ribosomal subunits?

release factor (RF)

What three rRNAs does processing of the 30S pre-RNA transcript in humans produce after enzymatic cleavage?

28S 18S 5.8S

If you have screened 100,000 pollen grains and identified 5 mutants, what is the mutation frequency?

5 × 10-5

The following portion of the 16S rRNA base pairs with the Shine-Dalgarno sequence found in mRNA.5'...CCUCCU...3'Which mRNA sequence would have perfect complementarity with this rRNA?

5'...AGGAGG...3'

Which of the following steps in translation is NOT facilitated by elongation factors?

Binding of initiator tRNA to the AUG start codon

In the process of eukaryotic pre-mRNA splicing, how is the lariat intermediate formed?

By joining the 5' end of the intron to the 2' carbon of the branch site

Eighteen of the amino acids have two or more synonymous codons. Which two amino acids are the exceptions?

Met and Trp

What type of mutation results in a single amino acid substitution?

Missense

Which of the following statements regarding mutation rates is correct?

Mutation rates are more frequent at the phenotypic level and more variable among organisms; 10-6 to 10-8 per gene are typical.

During translation initiation in bacteria, the amino acid on the initiator tRNA is ________.

N-formylmethionine (fMet)

Is coupling of transcription and translation possible in single-celled eukaryotes such as yeast? Why or why not?

No, because yeast chromosomes are separated from ribosomes by the nuclear envelope and some of their genes contain introns.

Which of the following is an example of the phenomenon termed "RNA editing"?

Posttranscriptional insertion of uracil nucleotides facilitated by a guide RNA

What proteins are bound to enhancers, forming a protein "bridge" that bends the DNA over the promoter to initiate transcription?

activator proteins

How is coupling of transcription and translation possible in bacteria?

bacterial transcripts do not contain introns as soon as an mRNA is transcribed, ribosomal subunits have physical access to it

mechanisms used by bacteria to identify the authentic start codon during translation initiation:

base pairing between the 16s rRNA in the 30s ribosome, a short mRNA sequence located a few nucleotides upstream of the start codon in the 5' UTR of mRNA, a purine rich shine-dalgarno sequence pairs with a complementary pyrimidine-rich segment containing the sequence UCCUCC

In eukaryotes, the initiation factor proteins eIF1A and eIF3 join with ________ to form the preinitiation complex.

charged tRNAMet

Which two repair processes are the most error prone?

nonhomologous end joining translesion DNA synthesis

Which type of mutagen has a structure similar to one of the DNA nucleotides and therefore can work its way into DNA, where it pairs with a nucleotide?

nucleotide base analog

You would like to induce a transversion mutation into a sequence of DNA. Which type of chemical mutagen would give you the best chance of inducing the correct mutation without causing transition mutations as well?

oxidative agent

Which repair process in E. coli uses visible light to repair thymine dimers?

photoreactivation repair

Bacteria group their genes such that they share a single promoter and the mRNA transcript synthesizes several different polypeptides. Collectively, these are referred to as ________ mRNAs, which are part of the operon system.

polycistronic

A polycistronic mRNA contains multiple ________.

polypeptide-producing sequences

transcription/RNA processing:

pre-mRNA, snRNA

initiation of translation in E.coli Step 1

preinitiation complex formation: small ribosomal subunit and IF3 bind to the mRNA, AUG start codon is identified by 16s rRNA base pairing with shine dalgarno sequence, and AUG codon is in the ribosomal P site

Both introns and exons

present in the primary transcript, parts of the transcribed region of a gene