Homework 5, 6, 7, 8

The genetic code includes

1 start codon and 3 stop codons

Nonsense codons are

Codons that do not code for an amino acid

A protein with a zinc-finger domain most likely has what type of activity?

DNA binding

A neomorphic mutation in the Antennapedia (Antp) gene of Drosophila causes

Growth of a leg from the head region

Which is a true statement about mitochondrial genomes?

In most cases, the mitochondrial genome is transmitted, largely intact, from one parent to offspring

Transcription occurs ________ and translation occurs __________ of eukaryotic cells

In the nucleus; in the cytoplasm

This pedigree shows the segregation of a rare disease in a family. What is the most likely mode of inheritance of this disease? (assume complete penetrance)

Maternal imprinting

A mutation that is characterized by a change in the DNA sequence, but no change in the resulting protein sequence, is a

Silent mutation

The DNA sequence 5′ ATGGGGGACACC 3′ encodes the amino acids Met Gly Asp Thr. A mutation changes the sequence to 5′ ATGGGTGACACC 3′, but the same amino acids are encoded. What type of mutation has occurred?

Silent mutation

A fragment of DNA with a radioactive label is incubated with DNase in the presence and absence of a protein that acts as a positive regulator of transcription. The samples are then run on a gel and visualized with autoradiography. Which statement describes a possible result and conclusion from such an experiment?

Some bands on the gel are absent in the sample with the transcriptional regulator, therefore the protein binds the DNA fragment

A complex of proteins and small nuclear RNAs that form discrete particles to mediate splicing is a

Spliceosome

You have identified a 50 nucleotide deletion that is not within an open reading frame in an otherwise wild-type prokaryotic genome. You identify five mRNAs that are not translated in these mutant bacteria; the five mRNAs are transcribed from five different genes located far from the deletion. Select the most likely explanation for the effect of this deletion.

The deletion prevents expression of a small RNA that regulates translation of all five genes

In plant cells, DNA molecules are found inside which structures?

The nucleus, the mitochondrial matrix, and the chloroplast stroma

In four o'clock plants, reciprocal crosses are performed with a green plant and a white plant. How will the offspring of the reciprocal crosses look?

The offspring will be white if the egg came from the white plant and green if the egg came from the green plant

Why is a variegated plant considered heteroplasmic?

The plant has mutant and wild-type chloroplast DNAs distributed amongst the cells in different ratios

What would you anticipate would be true about the metabolism of a bacterial species isolated from water samples, one at the surface and another from a hot vent on the ocean floor?

The species from the water surface would be more likely to be able to conduct photosynthesis

Which is true of enhancer DNA sequences?

They retain function if their nucleotide sequence is moved/inverted, they can be more than 10 kb away from the genes they regulate, and they may bind to more than one transcription factor at the same time

As a general principle of gene regulation through operons, regulatory genes encode

Trans-acting proteins that interact with cis-acting DNA elements

Which of these processes are coupled in prokaryotes but NOT in eukaryotes?

Transcription and translation

How does tryptophan, the end product of the trp operon, function in the regulation of the operon?

Trp bindings to and changes the conformation of the repressor, which can then bind DNA and block transcription of the operon

Bacteria that live in extreme environments, such as thermal vents on the ocean floor, have evolved genes that allow them to use the resources within that environment.

True

Cells of which bacterial genotype would be able to utilize lactose as an energy source?

l+oCZ+Y-/F'(l+o+Z-Y+)

The action of which small RNA inhibits the movement of transposable elements?

piRNA

A prokaryotic large ribosomal subunit is composed of

rRNA and protein

A mutation creates a dominant negative allele of a particular gene. The gene encodes a protein that forms a trimer within the cell. If one or more of the subunits has the mutant structure, the entire trimeric protein is inactive. In a heterozygous cell, if the proteins of both alleles are present at the same levels, what percent of the trimers present in the cell will be active?

12.5% Wild type allele = Pw Dominant mutant allele = Pm In both cells alleles are present in equal ratio so genotype is Pw/Pm For functional trimers, 3 Pw are needed Probability of getting 3 Pw is (1/2)(1/2)(1/2) = 1/8 1/8 = 12.5% active 100%-12.5% = 87.5% inactive

An anticodon of sequence 5′ GUA 3′ will recognize the codon sequence

5' UAC 3'

The wobble base of a tRNA is

5' base of the anticodon Or 3' base of the codon

Which of the following is required for initiation of eukaryotic translation?

5' cap

In the modification of eukaryotic mRNA, ______ cap and ______ tail are usually added to the transcript

A methylated guanine; a poly adenine

Which of the following mutant alleles is most likely to be dominant to the wild-type allele?

A missense mutation that increases enzyme activity

A strain of penicillin-resistant N. gonorrhoeae that does not have a plasmid is isolated. A lysate made from the bacterium cannot degrade penicillin in an in vitro assay. When a culture of this strain is grown in a solution that contains radioactive penicillin, the amount of penicillin found within cells is less than the amount found within cells from a nonresistant strain. The DNA sequence of the porin gene from the resistant strain does not have any mutations. What is the most likely mechanism of resistance in this strain?

A mutation in the mtr gene has occurred, resulting in fewer efflux pumps

RNA polymerase binds to ______ before beginning transcription

A promoter

An anticodon is a physical component of _______ molecule

A tRNA

Viruses are isolated from wild-type E. coli cells that have been infected with wild-type bacteriophage λ. These viruses are used to infect a Gal− strain of E. coli. A few bacterial colonies that can grow on galactose are obtained, while no bacteria that can grow on galactose are obtained from cells that were not infected. What has happened?

A λ gal+ phage was generated

The ___________ codon is used as the start codon by nearly all organisms

AUG methionine

What is a trans-acting factor that increases transcription above the basal rate called?

Activator

Aminoacyl-tRNA synthetase is the enzyme that

Adds the appropriate amino acid to an uncharged tRNA

The appearance of a novel phenotype resulting from the substitution of a single base pair might be due to

All of the choices are possible consequences of a single base pair substitution; change in amino acid sequence, change in amount of protein expressed, alteration in gene that codes for a non-translated RNA, and a change in the developmental time or location at which a gene is expressed

Which molecules are examples of effector molecules?

Allolactose and Trp

Proteins whose conformations change when they are bound to an effector molecule are called

Allosteric proteins

Which of these types of gene regulation occurs earliest in the process of gene expression?

Alternative splicing

How can one primary mRNA result in several polypeptides with different amino acid sequences?

Alternative splicing of exons

The episome in an Hfr strain is inserted near the trp (tryptophan operon) locus. This Hfr strain is grown with an F- Trp- strain. From this mating, we isolate an F+ Trp+ strain that can readily impart the Trp+phenotype to F- Trp- strains, but no other traits are ever transferred. (When the original Hfr strain is mated with F− strains, traits other than Trp+ can be transferred, although at lower frequency than Trp+.) What most likely has happened?

An F' trp+ plasmid has been generated

When the anticodon of a tRNA and the codon of an mRNA interact, the two sequences are

Antiparallel

What is the primary function of basal transcription factors?

Assist RNA polymerase binding to the promoter

A crucial step in the regulation of most bacterial genes occurs

At transcription initiation

Gene B is usually expressed only in skin cells. To learn about the mechanism by which expression of the gene B is regulated, you make clones that contain a GFP reporter and various parts of the upstream and downstream intergenic regions of genomic DNA that normally surround gene B (black lines) as shown in the figure below. The resulting clones were introduced into frog skin cells growing in the lab and levels of GFP expression was monitored by measuring green fluorescence. The table below shows relative GFP expression, with more +s equal to more expression. (one + = basal expression). Which area contains an enhancer?

B

Gene B is usually expressed only in skin cells. To learn about the mechanism by which expression of the gene B is regulated, you make clones that contain a GFP reporter and various parts of the upstream and downstream intergenic regions of genomic DNA that normally surround gene B (black lines) as shown in the figure below. The resulting clones were introduced into frog skin cells growing in the lab and levels of GFP expression was monitored by measuring green fluorescence. The table below shows relative GFP expression, with more +s equal to more expression. (one + = basal expression). Which area is likely to bind to proteins that activate gene B (an activator)?

B

Gene B is usually expressed only in skin cells. To learn about the mechanism by which expression of the gene B is regulated, you make clones that contain a GFP reporter and various parts of the upstream and downstream intergenic regions of genomic DNA that normally surround gene B (black lines) as shown in the figure below. The resulting clones were introduced into frog skin cells growing in the lab and levels of GFP expression was monitored by measuring green fluorescence. The table below shows relative GFP expression, with more +s equal to more expression. (one + = basal expression). Which area is likely to contain a cis-acting regulatory element?

B, D

The function of a helix-turn-helix motif in a transcription factor is to

Bind a specific sequence in the major groove of DNA

Small RNAs can regulate gene expression by

Binding target RNAs and inhibiting translation

Transcription in prokaryotes and eukaryotes is similar in that

Both a regulated by binding of proteins to DNA near the gene being transcribed

How do negative regulators such as the Lac repressor prevent RNA polymerase from initiating transcription?

By physically blocking the DNA binding site of RNA polymerase

Horizontal gene transfer

Can accelerate the evolution of a species

DNA sequences that are binding sites for transcription factors are called

Cis-acting elements

One way N. gonorrhoeae became resistant to penicillin was by acquiring a plasmid that carries the penr penicillin resistance gene, which encodes a protein that

Cleaves penicillin to an inactive form

Which is the best method to demonstrate the function of a putative enhancer?

Clone a region of DNA with the putative enhancer into a reporter construct, introduce the construct into eukaryotic cells, and measure expression of the reporter protein

What would be the phenotype of a null mutation in the gene encoding Lac repressor?

Constitutive expression of the lac operon Since there is no repressor to bind/inhibit translation, translation continues

Gene B is usually expressed only in skin cells. To learn about the mechanism by which expression of the gene B is regulated, you make clones that contain a GFP reporter and various parts of the upstream and downstream intergenic regions of genomic DNA that normally surround gene B (black lines) as shown in the figure below. The resulting clones were introduced into frog skin cells growing in the lab and levels of GFP expression was monitored by measuring green fluorescence. The table below shows relative GFP expression, with more +s equal to more expression. (one + = basal expression). Which area contains the gene B promoter?

D

The Central Dogma describes the flow of genetic information as

DNA to RNA to protein

What is the term for a cis-acting DNA sequence that may function at a distance from the gene they are regulating?

Enhancer

A variation in gene function that does not involve a change in DNA sequence but can be inherited is a(n)

Epigenetic phenomenon

The sequences found in a mature eukaryotic mRNAs are

Exons

All the genes in a species' core genome are located on the bacterial chromosome, whereas the genes of the pangenome are carried on plasmids.

False

A mutation that occurs when a base is inserted into or deleted from a DNA sequence, completely altering the subsequent sequence of codons, is a

Frameshift mutation

In an Hfr strain, the F episome is integrated between genes A and B. When this Hfr mates with an F− strain, gene B is always transferred first to the F− cell. What is the last bacterial gene that could possibly (at least in theory) be transferred to the F− from the host chromosome?

Gene A

The enhancer shown in the diagram is able to regulate transcription of which genes?

Gene A, B, C

What describes a situation in which an allele's expression depends on the parent from which it was inherited?

Genomic imprinting

How is glucose involved in catabolite repression of the lac operon?

Glucose caused cAMP levels to decrease, which leads to decreased CRP binding and the lac operon is repressed even when lactose is present

Many cancers have a mutation that changes a valine to a glutamic acid in the RAF kinase protein which phosphorylates proteins that promote cell division. This mutant protein is a constitutively active kinase. What type of allele is this mutant allele?

Hypermorphic allele Increase in normal gene function

Mutations that result in the production of much less of a protein or a protein that functions less efficiently than wild type are

Hypomorphic mutations

The ChIP technique can be used to identify putative DNA binding sites for various transcription factors because it

Identifies DNA sequences bound to specific proteins

Inhibitors of bacterial translation, such as chloramphenicol and erythromycin, usually

Inhibit mitochondrial protein synthesis and chloroplast protein synthesis

Insulators act to

Interfere with the association between enhancers and specific promoters

During maturation of a eukaryotic mRNA, sequences that are spliced out are

Introns

What is a property of a pathogenic bacterium?

It may produce a protein that interferes with basic cellular functions

When a bacteriophage carrying bacterial DNA infects a new bacterium,

It transfers bacterial DNA from the donor bacterium to the recipient bacterium

Catabolic pathways that break down complex substances into more usable units are usually regulated in response to the

Levels of the molecule that is to be broken down

A strain of E. coli is trp− his− lac−. Which medium would this bacterium grow on?

Minimal media with glucose as the sugar, supplemented with histidine and tryptophan

A mutation that changes a codon sequence, and subsequently changes the amino acid that should have been placed at that point in the polypeptide chain, is a

Missense mutation

What would be the most likely result if a scientist removes mitochondria from a human cell and attempts to grow them in culture?

Mitochondria require the products of nuclear genes to function, so the mitochondria will die soon after being removed from the cell

Transcription and translation can be coupled in bacteria but not eukaryotes because

No nuclear membrane exist in prokaryotes

A mutation that changes a codon that originally coded for an amino acid into a stop codon is a

Nonsense mutation

A large deletion removes the promoter and first three exons of a gene. No mRNA or protein is detected. What type of allele is this mutant allele?

Null allele

Mutations that completely abolish the function of a wild-type allele are

Null mutations

Which enzyme forms peptide bonds between adjacent amino acids during polypeptide synthesis?

Peptidyl transferase

A bacterium is found that is resistant to the antibiotic gentamicin. The bacterium was isolated in a hospital where patients were routinely given gentamicin for a variety of infections. What was the pressure that selected for this resistant population?

Presence of gentamicin in the environment

A neomorphic mutation could result in an allele that

Produces a novel protein that gives rise to a new phenotype

Extranuclear genes show a biparental inheritance pattern in yeast since

Progeny from diploid vegetative growth can have the parent phenotype of either the a or α parent

The pattern or sequence in which a molecule of mRNA is deciphered by a ribosome is the

Reading frame

Which of these is NOT a step in transcription?

Replication

The retroviruses, including HIV, are unique because they use

Reverse transcription

The cellular organelle responsible for protein synthesis is the

Ribosome

What characteristics make bacteria like E. coli attractive as model organisms?

Short generation time, simple genome relative to that of humans, easily mutagenized, haploid

Initiation of transcription by RNA polymerase involves the binding of which of the following subunits to the core enzyme?

Sigma

What did comparing the sequence of the mitochondrial genome in trypanosomes with the sequence of mature mitochondrial RNAs demonstrate?

The RNA sequences are similar to the genome sequence, but have insertions and deletions of uracil residues

Anabolic pathways involved in the synthesis of essential molecules are usually regulated in response to

The end product of the pathway

Three genes (X, Y, and Z) are in the same region of a bacterial chromosome. To determine the order of these genes, you infect X−Y− Z− cells with a lysate from wild-type cells infected with a generalized transducing phage. When X+ cells are selected, 70% of cells are also Y+ and 5% of cells are Z+. When Y+ cells are selected, 68% of cells are also X+ and 1% are Z+. What is the relative arrangement of the three genes?

X is in the middle, but closer to Y

Which is a type of DNA-binding domain found in transcription factors?

Zinc finger

A codon is a three-base sequence of

mRNA that codes for an amino acid