Exam 4 Practice Questions

Chromatin Remodeling

-Condensed parts of chromatin----------INACTIVE -Decondensed (loosened) parts of chromatin--------- ACTIVE -HAT - histone acetyl transferase (adds acetyl group) -HDAC - histone deacetylase (removes acetyl group) - adding methyl=condense -adding acetyl=decondense

When does gene expression occur?

A gene product is actively being synthesized Used in a cell

. During elongation, which site in the ribosome represents the location where a codon is being read? A. P site B. A site C. E site D. the small ribosomal subunit

B. A site

How does termination of translation take place? A. The poly-A tail is reached. B. A stop codon is reached. C. The end of the mRNA molecule is reached. D. The 5' cap is reached.

B. A stop codon is reached.

positive control

Bacterial gene regulation in which the binding of a regulatory protein (activator) to regulatory DNA sequence stimulates transcription.

Transformation

Cells that take up DNA from the environment and incorporate into their genomes

How can we tell if a gene is being expressed?

Production of RNA Production of a protein

Reverse transcriptase catalyzes the synthesis of DNa from an....

RNA template

lacZ

The first gene in the lac operon of E. coli that codes for enzyme B-galactosidase.

Cells differ due to

differential cell expression

When glucose is present...

does not allow the import of lactose. This phenomenon is called inducer exclusion

lacY

encodes the lactose permease, required for transport of lactose into the cell

arac

gene

What is the role pf lactose in regulating lac operon expression>

it induces transcription by binding to the repressor and causing its release from the operator

When present in a DNA synthesis reaction mixture, a ddNTP molecule is added to the growing chain of DNA. No further nucleotides can be added afterward. Why?

lacks OH- group

Translation directly involves

mRNA, tRNA, ribosomes, GTP

What is needed to make cDNA from RNA?

reverse transcriptase

A gene that contains introns can be made shorter for genetic engineering purposes by

reverse transcriptase to reconstruct the gene from its mRNA

operator

short DNA region, adjacent to the promoter of a prokaryotic operon, that binds repressor proteins responsible for controlling the rate of transcription of the operon

Steps of PCR

(1) heat the DNA strands to about 94 degrees C to separate the strands (2) add the primers to the separated strands and allow the primers to combine (or hybridize) with the strands by lowering the temperature to about 60 degrees C (3) add the DNA polymerase and a mixture of free nucleotides (G,A,T,C) to the separated strands. Heat the test tube to 72 degrees C and the polymerase enzyme directs the rebuilding of a double stranded DNA molecule; the process is repeated 25 to 30 times

Regulation of genes in Euk. in ORDER

1. Chromatin remodeling 2. Transcipion 3. RNA processing 4.mRNA stability 5.Translation 6. post translational *side note first 3 steps occur in nucleus and last 3 occur in cytoplasm

Put the following events of elongation in prokaryotic translation in chronological order. 1. binding of mRNA with small ribosomal subuint 2. recognition of initiation codon 3. complementary base pairing between initiation codon and anticodon of initiatior tRNA 4. base pairing of the mRNA codon following the initiator codon with its complementary tRNA Select one: a. 1,2,3,4,5 b. 2,1,4,3,5 c. 1,2,3,5,4 d. 5,4,3,2,1

1.2.3.5.4

Control of Translation

1.RNA interference 2.By phosphorylation of a certain ribosomal protein

RNA Interference (microRNA)

1.Transcription of genes that code for hairpin RNAs 2.Hairpin RNA transported to cytoplasm where the hairpin loop is cut out. 3.One strand is taken up by the RNA -induced splicing complex (RISC) ...now called a microRNA 4.MicroRNA binds to target mRNA 5.RISC cuts the mRNA and prevents translation!! limits life span

Types of regulatory sequences

1.promotor proximal elements 2. enhancers 3. silencers

Enhancers

A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes. -can work even if the orientation flipped (5'-3'). -positive, NOT next to promoter

Restriction endonuclease

A bacterial enzyme that recognizes a specific DNA nucleotide sequence and that cuts the double helix at a specific site within the sequence. only cut at palindromes

cDNA library

A limited gene library using complementary DNA. The library includes only the genes that were transcribed in the cells examined.

Polymerase chain reaction

A method of producing thousands of copies of DNA segment using the enzyme DNA polymerase

DNA library

A random collection of DNA fragments from an organism cloned into a vector

plasmid

A small, circular section of extra DNA that confers one or more traits to a bacterium and can be reproduced separately from the main bacterial genetic code.

. In an experimental situation, a student researcher inserts an mRNA molecule into a eukaryotic cell after she has removed its 5' cap and poly-A tail. Which of the following would you expect her to find? A. The molecule is digested by enzymes because it is not protected at the 5' end. B. The cell adds a new poly-A tail to the mRNA. C. The mRNA attaches to a ribosome and is translated, but more slowly. D. The mRNA is quickly converted into a ribosomal subunit

A. The molecule is digested by enzymes because it is not protected at the 5' end.

At which of the following stages does transcriptional control occur? DNA —(a) —> mRNA —(b) —> protein —(c) —> activated protein A. a B. b C. c D. All of the answers represent transcription. E. None of the answers represents transcription

A. a

A promoter is ______ A. a sequence in DNA near the site for transcription, where RNA polymerase bind B. one or more eukaryotic proteins that bind to DNA near the start of a gene C. a sequence in RNA that promotes the release of RNA polymerase from DNA D. a protein that associates with bacterial RNA polymerase to help it bind to DNA

A. a sequence in DNA near the site for transcription, where RNA polymerase bind

An E. coli cell without a functional lacI gene is expected to _____. A. always produce β-galactosidase B. be unable to metabolize lactose within the cell C. be unable to transport lactose into the cell D. never produce β-galactosidase

A. always produce β-galactosidase

David Pribnow studied the base sequences of promoters in bacteria and bacterial viruses. He found two conserved regions in these promoters (the -10 box and the -35 box). These two regions of the promoter _____. A. bind the sigma subunit that is associated with RNA polymerase B. attach the correct nucleotide triphosphate to the template DNA strand C. signal the initiation site D. separate the two DNA strands

A. bind the sigma subunit that is associated with RNA polymerase

The greatest expression of the lac operon occurs when lactose levels are _____ . A. high and glucose levels are low B. low and glucose levels are high C. high and glucose levels are high D. low and glucose levels are low

A. high and glucose levels are low

What does a bacterial RNA polymerase produce when it transcribes a protein-coding gene? A. mRNA B. tRNA C. pre-mRNA D. rRNA

A. mRNA

How can amino acid sequence be used to design a gene specific hybridization probe?

All possible nucleotide sequences that could encode a portion of a polypeptide can be synthesized and used as probes

promoter proximal elements

Are located just upstream of the promoter and the transcription start site -both positive and negative

In the presence of lactose (when glucose is absent) ......

Binds directly to the lacI repressor Causes it to release from the operator (allosteric control) Ends negative control of the operon Lactose is the inducer

What is the most logical sequence of steps for splicing foreign DNA into a plasmid and inserting the plasmid into a bacterium. I. Transform bacteria with a recombinant DNA molecule. II. Cut the plasmid DNA using restriction enzymes. III. Extract plasmid DNA from bacterial cells. IV. Hydrogen-bond the plasmid DNA to nonplasmid DNA fragments. V. Use ligase to seal plasmid DNA to nonplasmid DNA.

C) III, II, IV, V, I

Which one of the following statements about RNA processing is true? A. A primary transcript is often much shorter than the final RNA molecule that leaves the nucleus. B. Exons are cut out before mRNA leaves the nucleus. C. RNA splicing removes introns D. RNA splicing can be catalyzed by tRNA.

C. RNA splicing removes introns

Which of the following mutations is most likely to cause a phenotypic change? A. a nucleotide substitution in an exon coding for a transmembrane domain B. a frameshift mutation one codon away from the 3' end of the nontemplate strand C. a single nucleotide deletion in an exon coding for an active site D. a duplication of all or most introns E. a large inversion whose ends are each in the same region between genes

C. a single nucleotide deletion in an exon coding for an active site

Translation requires _____ A. mRNA, DNA, and rRNA B. mRNA, tRNA, and DNA C. mRNA, tRNA, and rRNA D. mRNA, tRNA, DNA, and rRNA

C. mRNA, tRNA, and rRNA

In E coli If RNA polymerase is missing _____, then transcription initiation would not occur at the appropriate initiation sites. A. amino acids B. the core C. the sigma factor D. mRNA

C. the sigma factor

cDNA

Complementary DNA. DNA produced synthetically by reverse transcribing mRNA. Because of eukaryotic mRNA splicing, cDNA contains no introns.

Put the following events of transcription in chronological order. 1 Sigma binds to the promoter region. 2 The double helix of DNA is unwound, breaking hydrogen bonds between complementary strands. 3 Sigma binds to RNA polymerase. 4 Sigma is released. 5 Transcription begins. A. 3, 2, 1, 4, 5 B. 2, 3, 4, 5, 1 C. 2, 3, 1, 4, 5 D. 3, 1, 2, 5, 4

D. 3, 1, 2, 5, 4

In eukaryotic cells, transcription cannot begin until _____. A. the 5' caps are removed from the mRNA B. the DNA introns are removed from the template C. the two DNA strands have been cleaved by topoisomerase D. Several transcription factors have bound to the promoter E. DNA nucleases have isolated the transcription unit

D. Several transcription factors have bound to the promoter

Which of the following is the first event to take place in translation in eukaryotes? elongation of the polypeptide A. covalent bonding between the first two amino acids B. base pairing of activated methionine-tRNA to AUG of the messenger RNA C. binding of the larger ribosomal subunit to smaller ribosomal subunits D. the small subunit of the ribosome recognizes and attaches to the 5' cap of mRNA

D. the small subunit of the ribosome recognizes and attaches to the 5' cap of mRNA

Flow of information

DNA ---> mRNA ----> protein ----. activated protein

For application in gene therapy, what is the most favorable characteristic of retroviruses?

DNA copies of retroviral genomes become integrated into the genome of the infected cell.

Dideoxy sequencing

DNA is made in the lab, but some of the bases are altered, and cause the growing DNA chain to end at that base. These altered bases are dideoxy nucleotides

activators bind to regulatory sequences in ___ and to___ polymerase

DNA;RNA

A ribozyme is _____. A. a catalyst that uses RNA as a substrate B. an enzyme that synthesizes RNA as part of the transcription process C. an enzyme that synthesizes RNA primers during DNA replication D. an enzyme that catalyzes the association between the large and small ribosomal subunits E. an RNA with catalytic activity

E. an RNA with catalytic activity

Post Translational

Folding and assembling into the tertiary and quaternary structures by chaperone proteins. 2. Transportation to the final destination 3. Modifications by adding various groups (eg: phosphates, sugars, lipids) 4. Degradation of the protein - get a ubiquitin tag and a proteasome destroys it.

The cells in a multicellular EUKARYOTE express different genes in response to changes in the...

INTERNAL environment

. How is a mutation in a bacterial cell that deletes three base pairs 10 base pairs upstream from the +1 site likely to affect transcription and why? A. Initiation will be inhibited because RNA polymerase core enzyme cannot bind to the promoter. B. Termination will not occur because hairpin secondary structure cannot form. C. A three-base-pair deletion is too small to have an effect. D. Initiation will be inhibited because sigma cannot bind to the promoter

Initiation will be inhibited because sigma cannot bind to the promoter

What makes up the lac operon?

Lac Z,Y,A

mRNA Stability Alternative Splicing

More than one kind of mature, processed mRNA Consisting of different combinations of transcribed exons

What is the fastest form of control?

Post-Translational.... why.... USES MORE ENERGY

Probe

Single stranded fragment that will bind to a particular sequence in a mixture of DNAs. By binding to the target sequence, the probe marks the fragment containing that sequence distinguishing from the other fragments

Replica Plating

The process of growing bacteria on an agar plate, then transferring a copy of that growth to other plates using a sterile velvet pad. Analysis of growth patterns on the secondary plates gives information about the genetic properties of the growing bacteria. -screens for mutants!!!!!!!!

Global Gene Regulation

The regulation of multiple bacterial genes that are not part of one operon.

In eukaryotes, what allows only certain genes to be expressed in certain types of cells?

The set of reg. transcription factors

What is true about enhancers?

They are found in a variety of locations and are functional in any orientation

What is the most energy efficient type of control?

Transcriptional

In gene regulation, which type pf control is the most efficient?

Transcriptional control

single nucleotide polymorphisms

Variations in DNA sequence that occur when a single nucleotide in the genome is changed

Operon

a group of genes that operate together

lacA

acetyl transferase

The inducer (lactose) in the lac operon binds to the repressor which causes a shape change. What type of regulation is this?

allosteric

AraC protein is ____ when bound to arabinose

an activator

Example of positive control

ara operon

silencers

bind to DNA sequences and inhibit the start of transcription. -negative control, NOT next to promoter

What happens when glucose begins to deplete?

cAMP sends a signal "HEY WE ARE DYING ,SOS!!" binds to (CAP), which in turn allows the CAP to bind to upstream of the promoter which assists the RNA Polymerase in binding to the DNA. Transcription is on.

replica plating is used to isolate mutants that

cannot grow in a particular environment

Regulon

collection of genes or operons that are transcriptionally co-regulated

lacI

controls lacZ, lacY and lacA; that codes for a repressor protein

Although the expression of most genes is tightly regulated, some genes are expressed at roughly constant rates. Which of the following genes would you predict to be constitutively (constantly) expressed?

genes that code for reg. proteins

Negative control

genetic expression occurs unless it is shut off by some form of a regulator molecule

vector

make copies of foreign DNA

Chromatin is arranged into...

nucleosomes

a regulon is a set of genes controlled by

one type of regulator of transcription

The product of the lacI genes functions as the cars

parking break

Epigenetic changes

pass from one cell generation to the next but do not alter the DNA sequence -Histone acetylation Histone methylation DNA methylation

Transcriptional control can be regulated via

positive and negative control

DNA cloning

producing many copies of a gene

Arac

protein

What types of proteins bind to the promoter- proximal elements?

reg. transcription factors such as activators

Transcriptional Regulatory transcription factors are proteins that bind to ....

regulatory sequences on the DNA.

Arac protein is a ___ when arabinose is absent

repressor

In the absence of lactose the lacI gene product.....

shuts down expression of lacZ and lacY

What is chromatin?

the complex of DNA and proteins found in eukaryotic nuclei

According to the lac operon model proposed by Jacob and Monrod, what is predicted to occur if the operator is removed from the operon ?

the lac operon would be transcribed continually

in the lac operon, the repressor inhibits transcription when

the repressor is not bound to the inducer

Predict what would happen if the lac repressor protein were altered so it could not bind to the inducer

the repressor would always be bound to DNA

Why are the genes involved in lactose metabolism considered to be an operon?

they are all controlled by the same promoter

If a scientist needs to put a new DNA into bacterium she must___ the bacterium

transform

How does inducer exclusion control gene expression in the lac operon

when glucose and another sugar is present in the environment, inducer exclusion prevents the use of the other sugar and allows only use of glucose