Chap 14 Problem Solutions

What is the concept of colinearity, and does it apply to both bacterial and eukaryotic genes?

A) Amino acids code directly for tRNA; applies only to eukaryotes

B) Non-template DNA nucleotides have a direct one-to-one correspondence with the amino acid sequence; applies to bacterial coding regions but not to most eukaryotic genes containing introns

C) Introns code for regulatory proteins; applies to all living organisms

D) Both template and non-template strands are translated simultaneously in bacteria

Non-template DNA nucleotides have a direct one-to-one correspondence with the amino acid sequence; applies to bacterial coding regions but not to most eukaryotic genes containing introns. Colinearity means the continuous nucleotide sequence of a gene corresponds strictly to the amino acid sequence of the protein. Most eukaryotic genes are noncolinear because noncoding introns interrupt the coding sequence and are spliced out.

What are introns, and how does intron frequency relate to organismal complexity?

A) Noncoding intervening sequences removed prior to translation; more complex organisms generally have more introns

B) Coding sequences retained in mature mRNA; found exclusively in bacteria

C) Regulatory sequences in promoters that bind RNA polymerase; present in equal numbers in all species

D) Poly-A tails that stabilize pre-mRNA; absent in multicellular eukaryotes

Noncoding intervening sequences removed prior to translation; more complex organisms generally have more introns. Introns are intervening noncoding regions within eukaryotic genes that must be excised by the spliceosome before translation. Organisms with greater complexity tend to have larger numbers of introns.

What are the three distinct structural regions of a mature mRNA molecule?

A) Promoter, core enzyme, terminator

B) 5' untranslated region, protein-coding region, and 3' untranslated region

C) Exon 1, intron 1, and exon 2

D) TATA box, Shine-Dalgarno sequence, and poly-A tail

5' untranslated region, protein-coding region, and 3' untranslated region. Mature mRNA consists of the 5' UTR (from +1 to the nucleotide before the start codon), the protein-coding region (from start codon to stop codon), and the 3' UTR (from the nucleotide following the stop codon to the cleavage site).

What is the primary function of the bacterial Shine-Dalgarno sequence?

A) Serves as the transcription termination signal

B) Acts as the ribosome-binding site on bacterial mRNA to initiate translation

C) Recruits RNA polymerase holoenzyme to the promoter

D) Directs spliceosome assembly at intron boundaries

Acts as the ribosome-binding site on bacterial mRNA to initiate translation. The Shine-Dalgarno consensus sequence in the 5' UTR of bacterial mRNA base-pairs with rRNA in the small ribosomal subunit, positioning the ribosome properly over the translation start codon.

Which sequence correctly outlines the major processing events undergone by eukaryotic pre-mRNA?

A) DNA replication, transcription bubble collapse, exon cleavage

B) 5' 7-methylguanine capping, cleavage downstream of AAUAAA, 3' polyadenylation, and intron splicing

C) Promoter binding, sigma release, rho termination, export

D) Translation initiation, peptide bond formation, ribosome dissociation

5' 7-methylguanine capping, cleavage downstream of AAUAAA, 3' polyadenylation, and intron splicing. Primary eukaryotic mRNA is modified co-transcriptionally and post-transcriptionally by adding a 5' cap, cleaving downstream of the polyadenylation signal, adding a poly(A) tail, and removing introns via splicing.

What is the eukaryotic 5' cap and what are its key biological functions?

A) A run of adenines that terminates transcription

B) A 7-methylguanine nucleotide that protects against degradation, enables splicing of the first intron, and provides the ribosome binding/scanning site

C) An inverted repeat that forms a stem-loop to pause RNA polymerase

D) A noncoding intron that regulates nuclear export

A 7-methylguanine nucleotide that protects against degradation, enables splicing of the first intron, and provides the ribosome binding/scanning site. The 5' 7-methylguanine cap protects mRNA from exonucleases, facilitates excision of the first intron, and allows the small ribosomal subunit to bind and scan for the start codon.

How is the poly(A) tail added to eukaryotic pre-mRNA, and what is its purpose?

A) Synthesized from a DNA poly-T template by RNA polymerase II to terminate transcription

B) Cleaved ~25 nt downstream of the AAUAAA signal, followed by non-templated addition of 200-250 adenines to enhance stability and assist ribosome binding

C) Added directly to the 5' cap by DNA ligase to prevent degradation

D) Spliced from the branch point to recruit the spliceosome

Cleaved ~25 nt downstream of the AAUAAA signal, followed by non-templated addition of 200-250 adenines to enhance stability and assist ribosome binding. Pre-mRNA is cleaved downstream of the consensus sequence AAUAAA, and poly(A) polymerase adds 200-250 adenines. The tail prevents 3' degradation and interacts with 5' cap proteins to promote translation.

What is the spliceosome and what consensus sites does it recognize on pre-mRNA?

A) A DNA-repair complex that recognizes thymine dimers

B) A ribonucleoprotein complex that removes introns by recognizing the 5' splice site, 3' splice site, and branch point adenine

C) A ribosomal subunit that recognizes the Shine-Dalgarno sequence

D) A termination factor that unwinds RNA-DNA hybrids at Rut sites

A ribonucleoprotein complex that removes introns by recognizing the 5' splice site, 3' splice site, and branch point adenine. Composed of snRNAs and proteins (snRNPs), the spliceosome excises introns and ligates exons by specifically recognizing conserved sequences at both splice junctions and an interior branch point adenine.

Which two mechanisms allow a single eukaryotic gene to encode multiple distinct proteins?

A) Theta replication and rolling-circle replication

B) Semiconservative replication and degenerate codon usage

C) Alternative splicing of exons and use of alternative 3' cleavage sites

D) Polycistronic operons and rho-dependent termination

Alternative splicing of exons and use of alternative 3' cleavage sites. A single pre-mRNA can undergo alternative splicing (splicing different combinations of exons) or alternative 3' cleavage (cleaving at different sites), resulting in mature mRNAs with different coding capacities.

How do mature bacterial and eukaryotic mRNAs differ in their structural features?

A) Bacterial mRNAs have a poly(A) tail; eukaryotic mRNAs have a 5' triphosphate

B) Eukaryotic mRNAs have a 5' cap and 3' poly(A) tail, whereas bacterial mRNAs lack these and utilize a Shine-Dalgarno sequence

C) Bacterial mRNAs contain multiple introns; eukaryotic mRNAs are entirely colinear

D) Eukaryotic mRNAs lack 5' and 3' untranslated regions

Eukaryotic mRNAs have a 5' cap and 3' poly(A) tail, whereas bacterial mRNAs lack these and utilize a Shine-Dalgarno sequence. Both possess 5' UTR, coding, and 3' UTR regions, but only eukaryotic mRNAs have 5' caps and poly(A) tails. Bacterial mRNAs use the Shine-Dalgarno sequence for ribosome recruitment, which eukaryotes lack.

Are the 5' and 3' untranslated regions (UTRs) of eukaryotic mRNAs encoded within the promoter, exons, or introns?

A) In the promoter because they regulate initiation

B) In introns because they are not translated into protein

C) In exons because they are transcribed and retained in the mature mRNA

D) In downstream intergenic spacer regions

In exons because they are transcribed and retained in the mature mRNA. Exons are all sequence regions retained in the mature processed mRNA. The 5' UTR is transcribed in the first exon (upstream of ATG), and the 3' UTR is in the terminal exon; neither is in the non-transcribed promoter or excised introns.

The human dystrophin gene is 2.5 million base pairs long, but less than 1% of its sequence encodes the final protein. What explains this discrepancy?

A) The gene replicates over 100 times before transcription

B) The gene contains massive noncoding introns that are removed during RNA splicing

C) The promoter occupies over 99% of the gene's sequence

D) More than 99% of the mRNA consists of ribosomal binding sites

The gene contains massive noncoding introns that are removed during RNA splicing. Eukaryotic genes often have huge introns spanning thousands of base pairs. When spliced out, only the small percentage corresponding to exons remains in the mature mRNA.

Which statement correctly contrasts the promoter and the transcription start site (+1)?

A) The promoter is transcribed into the 5' UTR; +1 is non-transcribed

B) The promoter lies upstream of +1 and is not transcribed, while +1 is the exact location of the first transcribed nucleotide

C) The promoter is an intron; +1 is an exon

D) The promoter binds ribosomes; +1 binds DNA ligase

The promoter lies upstream of +1 and is not transcribed, while +1 is the exact location of the first transcribed nucleotide. The promoter is a DNA sequence upstream of +1 that directs RNA polymerase binding. It is not copied into the RNA transcript itself; RNA synthesis begins precisely at the +1 start site.

What happens if the Shine-Dalgarno sequence is deleted from a bacterial mRNA?

A) Pre-mRNA fails to undergo splicing

B) The mRNA is cleaved downstream of AAUAAA

C) Ribosomes cannot bind the mRNA, preventing translation and protein synthesis

D) RNA polymerase cannot terminate transcription

Ribosomes cannot bind the mRNA, preventing translation and protein synthesis. Because the Shine-Dalgarno sequence is required for initial base-pairing with the 16S rRNA of the small ribosomal subunit, its deletion halts translation initiation entirely.

What is the primary cellular consequence if the AAUAAA polyadenylation signal sequence is deleted from pre-mRNA?

A) Introns are translated into protein

B) Cleavage and polyadenylation fail to occur, leading to degradation of the pre-mRNA transcript

C) The transcript is immediately translated without a cap

D) The promoter becomes nonfunctional

Cleavage and polyadenylation fail to occur, leading to degradation of the pre-mRNA transcript. Without the AAUAAA signal, cleavage factors cannot recognize the site, preventing cleavage and subsequent poly(A) addition, which destabilizes the pre-mRNA and causes degradation.

What are the consequences if a eukaryotic pre-mRNA completely lacks a 5' cap?

A) Splicing of the first intron fails, the pre-mRNA is rapidly degraded, and ribosomes cannot bind for translation

B) DNA polymerase stalls at the replication fork

C) Only the poly(A) tail is translated into protein

D) Transcription terminates prematurely at the Pribnow box

Splicing of the first intron fails, the pre-mRNA is rapidly degraded, and ribosomes cannot bind for translation. The 5' cap is required for stability against 5' exonucleases, facilitates splicing of the first intron, and serves as the docking site for ribosomal scanning during translation initiation.

A point mutation occurs inside an intron sequence away from the 5' splice site, 3' splice site, and branch point. What is the expected effect on the protein?

A) The protein becomes completely nonfunctional due to a frameshift

B) The entire intron is retained and translated into extra amino acids

C) No effect on the protein because the mutation does not disrupt splicing consensus sequences and introns are excised

D) Splicing of all downstream exons is permanently inhibited

No effect on the protein because the mutation does not disrupt splicing consensus sequences and introns are excised. If the mutation spares the essential consensus sequences (5' splice site, 3' splice site, and branch point A), the spliceosome excises the intron normally, leaving the coding exons unaffected.

A single gene encodes two distinct functional proteins measuring 56 and 82 amino acids in length. What molecular mechanism best explains this?

A) Alternative splicing of pre-mRNA exons or the use of alternative 3' cleavage sites

B) Random nucleotide deletions caused by DNA polymerase errors

C) Failure of RNA primase during DNA replication

D) Polycistronic transcription from two different promoters

Alternative splicing of pre-mRNA exons or the use of alternative 3' cleavage sites. Alternative splicing joins different combinations of exons, and alternative 3' cleavage produces transcripts of different lengths, allowing a single gene to yield distinct mRNAs and protein products of different sizes.