Klug ch. 13

Write a sequence of mRNA that codes for five amino acids and the mRNA should contain proper punctuation and polarity.

5′ AUG (any four amino acid coding codons) and (UAA, UGA, or UAG) 3′

Describe how rho-dependent termination occurs in bacteria.

A bacterial protein called rho factor binds to an mRNA at the rut site. It moves along the mRNA in a 5′-to-3′ direction chasing after the RNA polymerase. When it reaches the hairpin loop it removes it and then proceeds to break through the hydrogen bonds holding the RNA-DNA together, which successfully removes the RNA polymerase.

Which of the following is true regarding the genetic code? A) The genetic code is degenerate. B) The genetic code is overlapping. C) The genetic code is considered to not be universal. D) The genetic code has three start codons and one stop codon. E) The genetic code is ambiguous.

A) The genetic code is degenerate.

A particular mRNA is 300 nucleotides long. If a mutation in the middle of the sequence changed a codon from a AAA to a UAA then what would be a reasonable prediction? A) The protein coded by this mRNA would be shorter. B) The protein coded by this mRNA would kill the cell. C) The protein coded by this mRNA would not form due to a failure in initiation. D) The protein coded by this mRNA would be longer. E) The protein coded by this mRNA would be the same size.

A) The protein coded by this mRNA would be shorter.

In 1964, Nirenberg and Leder used the triplet binding assay to determine specific codon assignments. A complex of which of the following components was trapped in the nitrocellulose filter? A) charged tRNA, RNA triplet, and ribosome B) ribosomes and DNA C) sense and antisense strands of DNA D) uncharged tRNAs and ribosomes E) free tRNAs

A) charged tRNA, RNA triplet, and ribosome

Due to the wobble hypothesis, which position in the codon, if changed to a different nucleotide, would be least likely to cause a change in the amino acid encoded? A) third nucleotide of the codon B) any nucleotide of the codon. C) first nucleotide of the codon D) second nucleotide of the codon E) Either the first or second nucleotide of the codon.

A) third nucleotide of the codon

The type of RNA modification that requires guide RNAs is ________. A) addition of the 7-methylguanosine cap to the 5′ end B) splicing together of exons C) RNA editing D) removal of introns E) addition of the 3′ polyadenylated tail

B) Spliceosomal introns are removed using large protein-based enzyme complexes.

Which of the following intron groups is matched appropriately with a true statement? A) Group I introns are removed from rRNAs that are found in mitochondria and chloroplasts. B) Spliceosomal introns are removed using large protein-based enzyme complexes. C) Group I introns are removed from rRNAs using large protein-based enzyme complexes. D) Spliceosomal introns are removed using the catalytic ability of the intron itself. E) Group II introns are removed from mRNA in mammals.

B) Spliceosomal introns are removed using large protein-based enzyme complexes.

If one compares the base sequences of related genes from different species, one is likely to find that corresponding ________ are usually conserved, but the sequences of ________ are much less well conserved. A) chaperons; exons B) exons; introns C) introns; exons D) introns; proteins E) introns; chaperons

B) exons; introns

Eukaryotic transcription is different than bacterial transcription because eukaryotic transcription ________. A) occurs in the cytoplasm B) requires the uncoiling of the chromatin fiber C) only requires one RNA polymerase D) does not require the mRNA to be modified E) does not require general transcription factors to initiate transcription

B) requires the uncoiling of the chromatin fiber

When scientists were attempting to determine the structure of the genetic code, Crick and coworkers found that when three base additions or three base deletions occurred in a single gene, the wild-type phenotype was sometimes restored. These data supported the hypothesis that________. A) AUG is the initiating triplet B) the code is triplet C) the code is overlapping D) there are three amino acids per base E) the code contains internal punctuation

B) the code is triplet

The genetic code is fairly consistent among all organisms. The term often used to describe such consistency in the code is ________. A) exceptional B) universal C) trans-specific D) overlapping E) None of the above

B) universal

A researcher is looking at a cellular sample using an electron microscope. They observe that while mRNA is being transcribed from the DNA that ribosomes are binding to themRNA to make proteins. Is this sample from a bacterial or a eukaryotic cell?

Bacteria. Since bacteria lack a nucleus, the ribosomes can bind to the mRNA as it's being synthesized and initiate translation.

An intron is a section of ________. A) DNA that is removed during DNA processing B) the carbohydrate that serves as a signal for RNA transport C) RNA that is removed during RNA processing D) protein that is clipped out posttranslationally E) the transfer RNA (tRNA) that binds to mRNA codon

C) RNA that is removed during RNA processing

When considering the initiation of transcription, one often finds consensus sequences located in the region of the DNA where RNA polymerase(s) binds. Which of the following is a common consensus sequence? A) TTTTAAAA B) satellite DNAs C) TATAAT D) any trinucleotide repeats E) GGTTC

C) TATAAT

Which transcription factor binds directly to the TATA-box sequence? A) TFIIA B) TFIIB C) TFIID D) enhancers E) TFIIC

C) TFIID

A Mutation in a particular bacterial gene prevents the formation of a hairpin loop. This is most likely to affect which part of transcription? A) This mutation will not affect any aspect of transcription in bacteria. B) This mutation will affect initiation, elongation, and termination. C) This mutation will affect elongation. D) This mutation will affect termination. E) This mutation will affect initiation.

C) This mutation will affect elongation.

Which mRNA modification is likely absent if the mRNA is degrading prematurely from the 5′ end of the mRNA? A) RNA editing B) splicing together of exons C) addition of the 7-methylguanosine cap to the 5′ end D) removal of introns E) addition of the 3′ polyadenylated tail

C) addition of the 7-methylguanosine cap to the 5′ end

There is some indication that the code is in some way ordered; a certain pattern exists. Describe an observation that supports this view.

Certain amino acids may be grouped according to the middle base; for example, U or C in the second position often specifies hydrophobic amino acids. Also, codons with the same two starting letters frequently encode the same amino acid.

If there were 75 naturally occurring amino acids then what is the smallest codon size? A) 1 B) 2 C) 3 D) 4 E) 5

D) 4

What is the name given to the three bases in a messenger RNA that bind to the anticodon of tRNA to specify an amino acid placement in a protein? A) wobble B) procodon C) cistron D) codon E) rho

D) codon

The relationship among a gene, a messenger RNA, and a protein is that ________. A) mRNAs make genes, which then make proteins B) mRNAs make proteins, which then make genes C) genes make proteins, which then make mRNA D) genes make mRNA, which then make proteins E) proteins make mRNA, which then make genes

D) genes make mRNA, which then make proteins

The experiments that deciphered the genetic code used an enzyme called polynucleotide phosphorylase. If researchers added this enzyme to a large quantity of only guanine (G)ribonucleoside diphosphates then a RNA molecule would be produced that would code for which amino acid? A) phenylalanine (phe) B) lysine (lys) C) proline (pro) D) glycine (gly) E) arginine (arg)

D) glycine (gly)

In which cellular organelle do the three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes occur? A) mitochondrion B) cytoplasm C) lysosome D) nucleus E) Golgi

D) nucleus

An mRNA that is being produced comes off of the ________. A) template strand in bacteria and the coding strand in eukaryotes B) coding strand in bacteria and the template strand in eukaryotes C) coding or template strand in both bacteria and eukaryotes depending upon the species D) template strand in both bacteria and eukaryotes E) coding strand in both bacteria and eukaryotes

D) template strand in both bacteria and eukaryotes

Describe the direction of information flow in living systems. Use appropriate, scientific terms in your description.

DNA is replicated and passed to offspring through a variety of reproductive processes. Information contained in the base sequences of DNA is transcribed into a variety of RNAs. Certain RNAs (tRNA) carry amino acids to the site of translation where proteins are assembled. Other RNAs (mRNA and rRNA) provide a mechanism for ordering the sequence of amino acids in proteins.

What is the initiator triplet in both bacteria and eukaryotes? What amino acid is recruited by this triplet? A) UAA, UGA, or UAG; arginine B) AUG; arginine C) UAA, UGA, or UAG; methionine D) UAA, UGA, or UAG; no amino acid called in E) AUG; methionine

E) AUG; methionine

The finding that some phage genes have multiple initiation sites is evidence against what characteristic of the genetic code? A) The genetic code is commaless. B) The genetic code is unambiguous. C) The genetic code is a triplet code. D) The genetic code is universal. E) The genetic code is nonoverlapping.

E) The genetic code is nonoverlapping.

It has been recently determined that the gene for Duchenne muscular dystrophy (DMD) is more than 2000 kb (kilobases) in length; however, the mRNA produced by this gene is only about 14 kb long. What is a likely cause of this discrepancy? A) The DNA represents a double-stranded structure, whereas the RNA is single-stranded. B) The exons have been spliced out during mRNA processing. C) When the mRNA is produced, it is highly folded and therefore less long. D) There are more amino acids coded for by the DNA than by the mRNA. E) The introns have been spliced out during mRNA processing.

E) The introns have been spliced out during mRNA processing.

A mutation of what type of sequence is predicted to have the greatest effect on the rate of transcription? A) enhancer B) silencer C) termination sequence D) proximal-promoter element E) core promoter

E) core promoter

The nuclear genetic code is considered universal with a few exceptions. Some of these exceptions are found when comparing the nuclear genetic code of humans to what? A) acterial genetic code B) chimpanzee's genetic code C) angiosperm's genetic code D) phage M2 genetic code E) human mitochondrial genetic code

E) human mitochondrial genetic code

Which of the following bacterial RNA polymerase subunits is found in the holoenzyme, but not the core enzyme? A) β (beta) B) β′ (beta prime) C) ω (omega) D) α (alpha) E) σ (sigma)

E) σ (sigma)

A particular mRNA makes a protein that has a unformylated methionine as its first amino acid. Did this mRNA come from a bacterial or a eukaryotic cell? Explain.

Eukaryotic cell. Eukaryotic mRNA code for proteins starts with an unformylated methionine whereas bacterial mRNA code for proteins starts with a formylated methionine.

Describe a difference between the RNA polymerases of eukaryotes and prokaryotes.

In eukaryotes, three polymerases (I, II, and III) have been identified; only one has been described in prokaryotes.

What are four ways that mRNA can be modified?

(1) Adding a modified guanine to the 5′ end, (2) adding a polyadenylation tail to the 3′ end, (3) splicing of introns, and (4) RNA editing.

What are three observations that suggested eukaryotic RNA was an intermediate between DNA and protein.

(1) DNA is found in the nucleus and protein synthesis occurs in the cytoplasm, (2) RNA is synthesized in the nucleus and has a chemical similarity to DNA, and (3) RNA is transported out of the nucleus and into the cytoplasm where protein translation occurs.

List four possible reasons that explain the importance of introns.

(1) introns allow for alternative splicing, (2) exon shuffling, which can aid in evolution of new genes, (3) the intron can be a microRNA itself that can regulated gene expression, and (4) introns can contain enhancer and silencer sequences that aid in gene regulation.

"Breaking the genetic code" has been referred to as one of the most significant scientific achievements in modern times. Describe (in outline or brief statement form) the procedures used to break the code.

(a) use of polynucleotide phosphorylase for the production of synthetic "mRNAs" (b) introduction of synthetic mRNAs into the cell-free protein-synthesizing system(c) frameshift mutations in the rII region of T4 phage to show code is triplet and degenerate (d)triplet binding assay to produce mRNA-tRNA-ribosome complex (e) development of regular copolymers for use in the cell-free protein-synthesizing system

Suppose that in the use of polynucleotide phosphorylase, nucleotides A and C are added in a ratio of 1A:5C. What is the probability that an AAA sequence will occur?

1/6 × 1/6 × 1/6 = 1/216

In a particular bacterial mutant, a specific gene is not producing a mRNA or the corresponding protein. Researchers sequence the gene and determine that there are nomutations in the coding portion of the gene. What could explain these observations?

One of the two consensus sequences are likely mutated. Either the Pribnow box (TATA AT) or the −35 sequence (TTGACA).

Describe the effects of mutating a sigma factor gene in bacteria.

The core RNA polymerase enzyme will form. Since there are more than one sigma factor genes, by mutating a single sigma factor gene there will be some holoenzymes that will not form which will affect specific gene transcription.

In the context of molecular genetics, how does one reconcile the terms overlapping genes and nonoverlapping code?

The genetic code contains codons that are nonoverlapping; however, overlapping genes are observed in some viruses in which, due to differential use of AUG to initiate translation, the same mRNA can yield different protein products.

Explain the "wobble hypothesis" and why it allows a single tRNA to recognize more than one codon.

The relaxed pairing at the third position of the codon and the first position of the anticodon are less constrained and do not need to follow the traditional base pair rules. This allows for a single tRNA to recognize multiple codons.

From the late 1950s to the mid-1960s, numerous experiments using in vitro cell-free systems provided information on the nature of the genetic code. Briefly explain how the use of polynucleotide phosphorylase and the triplet binding assay were used to decipher the genetic code and why the triplet binding assay was more precise.

Use of polynucleotide phosphorylase for the random assembly of nucleotides provided for the assembly of RNA homopolymers and random heteropolymers, which when placed in the cell-free protein-synthesizing system, provided products (polypeptide chains) for analysis. The triplet binding assay along with the use of repeating copolymers were used to verify information provided earlier and to establish the ordered codon assignments.

The finding that virtually all organisms use the same genetic code provides the basis for declaring that the code is universal. Name at least two exceptions to such universality.

mitchondrial DNA Mycoplasma capricolum some protozoans

What is meant by the term heterogeneous nuclear RNA (hnRNA)?

pre-mRNA, primary transcripts before processing in eukaryotes

In eukaryotes, which three factors appear to encourage the specific association of RNA polymerase(s) to a specific region of DNA?

promoters, enhancers, and transcription factors

Reading the RNA sequences in a 5′ to 3′ direction, a base at the first position of an anticodon on the tRNA would pair with a base at the ________ position of the mRNA.

third

Sidney Brenner argued that the code was nonoverlapping because he considered that coding restrictions would occur if it were overlapping. A second major argument against an overlapping code involved the effect of a single nucleotide change. In an overlapping code, how many adjacent amino acids would be affected by a single nucleotide change? In a nonoverlapping code, how many amino acid(s) would be affected?

two one