biochem test 2

DNA polymerase III is approximately ___________ times faster than DNA polymerase I

10,000

The error frequency of protein synthesis is approximately __________

10^-4

The E. Coli genome contains genes for about _________ proteins.

2000

Z-DNA

A left handed double helix

Aflatoxin B1 is a compound that is converted to a reactive epoxide by cytochrome P450 and causes _______ A) a G-C to T-A transversion. D) All of the above. B) an intrastrand cross-link. E) None of the above. C) deamination of adenine.

A)

The actual three-dimensional structure of tRNA is _______ A) L-shape. D) All of the above. B) cloverleaf. E) None of the above. C) twisted triple helix.

A) L-shape

The λ repressor has the highest affinity for which of the three DNA binding sites? _______ A) OR1 D) All of the above B) OR2 E) Same for A and B C) OR3

A) OR1

What is DNA gyrase? _______ A) A bacterial topoisomerase II D) All of the above B) A bacterial topoisomerase I E) None of the above C) A bacterial helicase

A) a bacterial topoisomerase II

What are the common promoter regions found in bacterial genes? _______ A) a Pribnow box about -10 and a -35 region B) a TATA box about -25 and a CAAT box about -75 C) a Pribnow box about -10 and a TATA box about -25 D) a TATA box about -25 and a -35 region E) None of the above.

A) a pribnow box about -10 and a -35 region

Photolyase functions to _______ A) repair pyrimidine dimers. D) All of the above. B) remove damaged bases. E) None of the above. C) ligate single-strand breaks.

A) repair pyrimidine dimers

Amino acids are attached to tRNA molecules at the ____________________ or _____________________ stem. CCA or acceptor CCA or anticodon anticodon or DHU anticodon or acceptor none of the above

A)CCA or acceptor

The first protein to bind RNA pol II promoter sequences in eukaryotic genes is the A)TATA binding protein (TBP) B)TFIID C)RNA Polymerase D)TFIIA E)None of the above

A)TATA binding protein (TBP)

The key event in eukaryotic transcriptional activation is ______ A) binding of the TATA-box-binding protein (TBP) to the TATA box. B) binding of the SP-1 protein to the CAAT box. C) binding of the RNA polymerase 500 base pairs upstream of the CAAT and TATA boxes. D) All of the above. E) None of the above.

A)binding of the TATA box

Posttranscriptional eukaryotic gene expression can be controlled by_____ A) micro RNAs. B) histones. C) basic-eucine zipper proteins. D) All of the above. E) None of the above.

A)micro RNAs

The start signal for most organisms is ATG AUG AAA UAA AGG

AUG

What are the names of the 3 tRNA binding sites on ribosomes translating mRNA? Applicator, Protein, Entry Anticodon, Peptidyl, Exit Antisense, Peptidyl, Egress Acceptor, Peptidyl, Exit None of the above

Acceptor (aminoacyl), Peptidyl, Exit

the inducer of the lac operon in cells

Allolactose

an assay used to determine carcinogenic potential is called

Ames Test

inosine is often present in this region of DNA

Anticodon loop

a prokaryotic mechanism for gene mediation employed by the trp operon

Attenuation

compounds released by prokaryote to communicate with others in the community

Autoinducers

Structural components of the nucleosome include________ A) transcription factors. B) an octomer of core histones. C) histone H8, which has an amino-terminal tail rich in leucine and isoleucine. D) All of the above. E) None of the above

B) an octamer core of 8 histones

How do coactivators mediate expression? _______ A) By blocking RNA polymerase binding B) By loosening the histone complex formation C) By inhibiting intron splicing D) A and B E) B and C

B) by loosening the histone complex formation

How does the lac repressor inhibit transcription? _______ A) It binds to the RNA polymerase and prevents its association to the DNA. B) It binds to the DNA and prevents the RNA polymerase from unwinding and transcribing the DNA. C) It binds to the mRNA molecule, preventing ribosomes from binding. D) All of the above. E) None of the above.

B) it binds to the DNA and prevents the RNA polymerase fro unwinding and transcribing the DNA

What reaction is carried out by β-galactosidase? _______ A) Lactose is hydrolyzed to galactose and sucrose. B) Lactose is hydrolyzed to galactose and glucose. C) Lactose is hydrolyzed to two molecules of glucose. D) Lactose is hydrolyzed to two molecules of galactose. E) None of the above.

B) lactose is hydrolyzed to galactose and glucose

In which pathway is the viral genome incorporated into the bacterial DNA? _______ A) Attenuation B) Lysogenic C) Lytic D) None of the above E) All of the above

B) lysogenic

TATA boxes are part of which RNA polymerase promoter? A)RNA polymerase I B)RNA polymerase II C)RNA polymerase III D)RNA polymerase IV E)RNA polymerase V

B)RNA polymerase II

Which RNA polymerase is responsible for transcribing mRNA from eukaryotic genes? A)RNA polymerase I B)RNA polymerase II C)RNA polymerase III D)RNA polymerase IV E)RNA polymerase V

B)RNA polymerase II

In preparation for attachment to the tRNA, amino acids are activated by: A)methylation. B)adenylation. C)dimethylation. D)all of the above E)none of the above

B)adenylation.

Molecules that bind to a receptor and trigger signaling pathways are called _______ A) antagonists. B) promoters. C) agonists. D) None of the above. E) IRE-binding proteins

B)promoters

high

Bacterial cells produce a truncated trp mRNA when cellular levels of tryptophan are

complex communities of prokaryotes

Biofilms

What are biofilms and why are they medically important?

Biofilms are specialized structures formed on surfaces where many species of prokaryotes may be found. These biofilm structures provide protection for the prokaryotic communities, often rendering them resistant to the immune response of the host and to antibiotics.

Which of the following E. coli proteins is responsible for translocation of the mRNA as a result of a conformation change due to the hydrolysis of GTP? _______ A) RRF D) Shine-Delgarno B) EF-Tu E) None of the above C) EF-G

C) EF-G

How can the leading and lagging strands be synthesized in a coordinated fashion? ________ A) Specific enzymes control the size of the DNA opening. B) Lagging-strand binding proteins inhibit leading-strand replication if the strands become disproportionate in size. C) Pol III is a dimeric holoenzyme, and the looped lagging strand allows the enzyme to proceed in the same direction with each strand. D) All of the above. E) None of the above.

C) Pol III is a dimeric holoenzyme and the looped lagging strand allows the enzyme to proceed in the same direction with each strand

What is the first step in gene expression control? ______ A) Control of translation D) Control of replication B) Control of mRNA processing E) None of the above C) Control of transcription

C) control of transcription

Which of the following conditions leads to the lysogenic state? ______ A) Repressor high, Cro high B) Repressor low, Cro low C) Repressor high, Cro low D) Repressor low, Cro high E) None of the above

C) repressor high, Cro low

DNA footprinting is a technique that allows one to determine _______ A) the homology between various DNA sequences. B) how proteins interact with each other when bound to DNA. C) where proteins bind to DNA. D) All of the above. E) None of the above

C) where proteins binds to DNA

Accuracy during translation occurs because of: codon degeneracy. A)wobble at the third site. B)tRNA specificity in binding the mRNA. C)aminoacyl tRNA charging. D)the structure of mRNA and the stability of that molecule

C)aminoacyl tRNA charging.

Signals that define the beginning and end of protein synthesis are contained in ________ A) rRNA. B) tRNA. C) mRNA. D) ribosome. E) protein.

C)mRNA

For transcription to occur, the structure of DNA must be in A)the closed promoter complex. B)the biphasic promoter complex C)the open promoter complex. D)all of the above E)none of the above

C)the open promoter complex.

This is where the amino acid is attached to the tRNA molecule

CCA3'

the name given to the inhibitory effect of glucose, caused by its effect on cAMP levels

Catabolite Repression

the complex of eukaryotic cells DNA and associated proteins

Chromatin

Class ________ aminoacyl-tRNA synthetases acylate the 2' hydroxyl group of the terminal adenosine of tRNA

Class I

a phenomenon that slows for the generation of multiple distinct types of cells

Combinatorial Control

genes that are expressed at all times and in many cells are subject to this kind of transcription

Constituitive

How does the Cro protein promote the lytic state?

Cro has the highest affinity for the OR3 site of the λ operator sites. When Cro binds OR3, it blocks transcription for the λ repressor gene. The absence of the λ repressor, leads to the production of phage genes, the production of viral particles and subsequently lysis.

In eukaryotes, DNA-binding proteins bind to DNA by which of the following DNA-binding structures? ______ A) Cys2 His2 zinc-finger domain B) Homeodomain C) Closed loops called lariats E) A, B, and C D) A and B

D) A and B

How does a nucleotide differ from a nucleoside? _______ A) Nucleosides are found in DNA, whereas nucleotides are found in RNA. B) Purines are only found in nucleotides. C) Nucleosides contain only deoxyribose sugars. D) A nucleotide is a nucleoside with a phosphate ester linked to the sugar . E) None of the above.

D) a nucleotide is a nucleoside with a phosphate ester linked to the sugar

Gene regulation by micro RNAs involves ________ A) miRNA binding to Argonaute. B) Argonaute cleavage of mRNA. C) miRNA-Argonaute binding to mRNA. D) none of the above. E) all of the above.

D) all of the above

What are significant features in the development of induced pluripotent stem cells? _______ A) Only four transcription factors are required to induce pluripotency in fibroblasts. B) De-differentiated cells have characteristics of embryonic stem cells. C) Potentially, iPS cells represent a new class of therapeutic agents. D) All of the above. E) None of the above

D) all of the above

The 5´cap present on eukaryotic mRNA molecules has a A)3´ to 3´ linkage B)3´ to 5´ linkage C)5´ to 3´ linkage D)5´ to 5´ linkage E)None of the above

D)5´ to 5´ linkage

Introns begin with the dinucleotide sequence ______ and end with the dinucleotide sequence _________. A)AG and GU B)AG and AG C)GU and GU D)GU and AG E)All of the above

D)GU and AG

A key reaction in gene repression is the deacetylation of this (these) amino acids in histones _____ . A) Serine B) Threonine C) Arginine D) Lysine E) All of the above

D)Lysine

During DNA replication, the RNA primer pieces are removed by

DNA polymerase I

Alternative splicing is important because there are only approximately ____________ genes identified in our genomes but it is estimated that cellular processes require over ___________ proteins. A)75,000 and 25,000 B)25,000 and 1,000,000 C)100,000 and 250,000 D)25,000 and 25,000 E) 25,000 and 100,000

E) 25,000 and 100,000

The DNA strand with the same sequence as the mRNA (except with U in RNA and T in DNA) is called the: A)sense strand B)coding strand C)antisense strand D)template strand E)A and B

E) A and B

The lac operon contains the gene(s) for the protein(s) _______ A) β-galactosidase. B) permease. C) transacetylase. D) A and B. E) A, B, and C.

E) A,B and C

The 70S bacterial ribosome is composed of a 50S and 30S subunit. What is the function of the 30S subunit in translation? a)tRNA recognition b)synthesis of the peptide bond c)alignment of the mRNA on the ribosome to initiate translation d)A and B e)A and C

E) a and c

Which of the following contributes to the attenuation of the trp mRNA transcript? _______ A) High levels of tryptophan B) Plentiful amounts of trp tRNA C) Formation of a stem loop structure at the 5' end of the attenuator region D) Uninterrupted synthesis of the leader peptide E) All of the above

E) all of the above

Functions of RNA polymerase include: A)searching for promoter sites. B)unwinding short stretches of DNA. C)detecting termination signals. D)A and C E)A, B, and C

E)A, B, and C

Eukaryotic translation initiation differs from bacterial translation because A)The ribosomal initiation complex forms on the 5'cap of mRNA. B)translation begins at the first AUG in the mRNA. C)the first amino acid is methionine instead of n-formylmethionine. D)there is no equivalent to the Shine-Delgarno sequence. E)all of the above

E)ALL OF THE ABOVE

Which of the following modifications are made to eukaryotic tRNA transcripts? A)modification of base and ribose moieties B)removal of the 3´ trailer C)cleavage of the 5´ leader by RNase P D)CCA is added E)All of the above

E)All of the above

The triplet "stop" codons that are used to terminate translation are a)AUG b)UGA C)UAA D)UAG E)B, C, and D

E)B,C and D

RNA polymerase requires which of the following for initiation? A)DNA primer B)RNA primer C)Supercoiled DNA D)Nicked DNA E)None of the above

E)None of the above

Which of the following modifications are made to eukaryotic tRNA transcripts? modification of base and ribose moieties removal of the 3´ trailer cleavage of the 5´ leader by RNase P CCA is added. All of the above

E)all of the above

this biomolecule deleivers the aminoacyl-tRNA to the A site in E. coli

Elongation Factor Tu

the existence of stable cell types is due to differences in this

Epigenome

This enzyme has a role in the repression of eukaryotic gene expression

Histone deacetylase

the twofold axis of symmetry of the lac repressor matches the symmetry of the...

Inverted Repeat (DNA)

the name of a peptide containing an abundance of amino acids residues of the type synthesized by the operon

Leader

a pathway that releases approximately 100 virus particles

Lytic

the element in the active site of Argonaute-miRNA complex

Magnesium

A complex of protein subunits that acts as a bridge between transcription factors and RNA polymerase I

Mediator

Proteins are synthesized in ________ direction

N-->C

The first amino acid in bacterial proteins is _____________

N-formyl-methionine

Binding of the lac repressor protein to the lac ___________ sequence blocks transcription initiation and expression of the lac z, y, and a genes.

OPERATOR

UV light causes damage to DNA by forming

Pyrimidine dimers

What role does the protein RecA play in recombination?

RecA, a member of the AAA ATPase family, promotes the formation of the displacement loop, D-loop. This process is often called strand invasion.

these proteins recognize stop codons (UAA,UAG, and UGA) codons

Releasing Factors

this protein is toxic because it hydrolyzes a critical adenine base from he 28SRNA molecule in eukaryotes

Ricin

In E. coli, the signal sequence that proerly aligns the initiation codon in the P site is called the __________ sequence

Shine-Delgarno

The sequence that interacts with a complementary sequence on the 3′ end of the 16S rRNA is the ___________________ sequence.

Shine-degarno

Homeodomain

The DNA binding structure similar to the prokaryotic helix-turn-helix

What is the difference in function between the DNA-binding domain and the activation domain of transcription factors?

The DNA-binding domain identifies and binds regulatory sequences, whereas the activation domain initiates transcription.

What is the function of a mediator in regulating transcription?

The activation domain of the transcription factors act through mediators, which bridge the enhancer-bound activator and the promoter-bound RNA polymerase II

How does a coactivator function in gene expression?

The binding of ligand to the receptor induces a conformational change that allows the recruitment of a coactivator. These coactivators are enzymes that catalyze reactions that lead to the modification of chromatin structure

How does the IRE-binding protein block the initiation of translation when iron levels are low?

The mRNA for ferritin, an iron sequestering protein, includes a stem-loop structure termed an iron-response element (IRE), in its 5' untranslated region. The IRE-binding protein (IRB) binds this stem loop structure under low iron conditions, thus blocking translation.

supercoiling

The tertiary structures of DNA are created in a process called

How do class I and class II aminoacyl tRNA synthetases differ?

There are several differences. They bind ATP differently. Most class I enzymes aremonomeric, in contrast to class II where most are dimeric. Class I enzymes acylate the 2' hydroxyl group of the terminal A at the CCA end of the tRNA, and class II enzymes acylate the 3' hydroxyl group.

This is the term applied to the process of protein synthesis

Translation

Type ______ topoisomerase introduces negative supercoils in DNA while type _______ topoisomerase relaxes supercoils structures.

Type 2; Type I

Type of topoisomerase that does not require ATP

Type I

Type of topoisomerase that can introduce supercoils

Type II

Two copies of each of the four histone proteins H2A, H2B, H3, and H4 form a protein complex called the histone octamer. DNA is then wound around the histone octamer, such that the negatively charged DNA interacts with positively charged lysine and argininie side chains of the histones. In this DNA-protein complex, the nucleosome core particle is connected to the next by linker DNA. Finally, histone H1 seals off the nucloesome at the location at which the linker DNA enters and leaves the nucleosome.

What is the arrangement of histones and associated DNA in a nucleosome?

The substrate that forms a colored product for the laboratory study of beta-galactosidase

X-Gal

Quorum Sensing

a type of chemical language that allows prokaryotic cells to deduce population densities

CAP is an example of a protein that _____________ transcritption

activates

The activation of tRNA involves the formation of _________ intermediate

aminoacyl-AMP

Release factors (RF) are small proteins that A)bind ribosomes at stop codons and terminate translation. B)dissociate ribosomal subunits from mRNA. C)release ribosomes from DNA. D)hydrolyze GTP to release nascent proteins. E)release uncharged tRNA molecules from the exit site.

bind ribosomes at stop codons and terminate translation.

Enhancers

binding sites in DNA for regulatory proteins, which increases the transcription of a particular gene from a distance

Enhancer sites are often located _______ A) near the poly A tail site. B) within introns. C) at a distance from the transcription start site. D) All of the above. E) None of the above.

c) at a distance from the transcription start site

Proteins destined for extracellular release must first bind to the ___________ in the lumen of the ER

cargo

RNA self-splicing demonstrates the role of RNA as a ______

catalyst

This is another name for an amino acid ester of tRNA

charged tRNA

the template strand has the __________ sequence to the RNA transcript (except T instead of U)

complementary

a ___________ sequence is determined by an alignment of multiple DNA base sequences and is a recurring pattern or motif

consensus

Aminoacyl-tRNA synthetases contain both an activation site and a(n) __________ site

editing (hydrolytic)

mRNA of higher organisms are formed by splicing together _______ after removal of intervening sequences.

exons

The Rho (p) protein terminates transcription by acting as a _________

helicase

Proteins that use ATP to melt the DNA at specific sites are called

helicases

The Pribnow box is found +10 base pairs from the start site of an operon. is found −10 base pairs from the end site. is the site where RNA polymerase binds. serves to regulate translation. none of the above

is the site where RNA polymerase binds.

the lambda repressor protein promotes transcription of _________ encoded by the virus

lambda repressor protein

The DNA strand that is replicated continuously is known as the ______ strand

leadings

The ____________ number is the number of times a DNA strand winds around the helix when it is constrained

linking

________ causes an increase in transferrin receptor levels and a decrease in ferritin levels.

low iron

in the helix-turn-helix motif of DNA binding proteins, the amino acid side chains of one helix binds to the _________ and the other to the _____________

major groove, DNA backbone

The role of EF-G in translation is to displace uncharged tRNA molecules. catalyze peptide bond formation. move the mRNA and peptidyl-tRNA one codon. terminate translation. A and B

move the mRNA and peptidyl-tRNA one codon.

The small DNA pieces observed during DNA replication are called ________

okazaki fragments

the pur repressor behaves _____________ compared to the lac repressor

opposite to

The primer for DNA synthesis is an RNA molecule formed by the enzyme

primase

Coactivators

proteins that act in a coordinated manor with hormone receptors to mediate gene expression

The enzyme that is capable of synthesizing DNa from an RNA template is _____________

reverse transcriptase

The ________ subunit of RNA polymerase recognizes promoters during heat shock conditions

sigma32

the sequence identifies a protein for translocation across the ER

signal

What is the name of the class of ribonucleoprotein particles that catalyze splicing of mRNA molecules? snRP miRNA snoRNA RNAses IncRNA

snRP

the ends of chromosomes are called

telomeres

DNA can serve as a _________ to direct synthesis of the complementary strand or DNA or RNA

template

Iron

this causes a decrease in transferrin receptor levels and an increase in ferritin levels

Polycistronic

this is another term that refers to the polygenic nature of prokaryotic mRNA

The proteins that bind DNA at eukaryotic promoters to form the initiation complex are called enhancers mediator proteins transcription factors chromatin ribosomes

transcription factors

The strands of DNA must be __________ for replication

unwound

The ___________________ hypothesis explains why some tRNA molecules can bind to more than one codon

wobble

The hypothesis that explains why some tRNA molecules can bind to more than one codon

wobble

Eukaryotic RNA polymerases differ in their sensitivity to the mushroom toxin _____________________.

α-amanitin

What is the name of the protein that binds the core RNA polymerase complex that is used for promoter recognition and initiation of transcription? A)α B)β C)β´ D)σ E)ω

σ