Molecular Bio Review

Put the steps of PCR cycle in the order they occur: a. denature-anneal-elongate b. anneal-denature-elongate c. denature-elongate-anneal d. elongate-anneal-denature

a. denature-anneal-elongate

The eukaryotic organelle that produces energy for the cell is a. mitochondria b. nucleus c. ER d. cytoskeleton

a. mitochondria

How many H-bonds form between A and T? a. 1 b. 2 c. 3 4. 0

b. 2

Would removing the Shine Delgarno sequence from an mRNA have an effect on eukaryotic translation? a. Yes, the small subunit would not bind b. No, eukaryotic translation relies their cap structure and first AUG c. Yes, the initiator tRNA would not be able to bind to the A site d. No, because eukaryotic translation uses elongation factors to assemble the ribosome

b. No, eukaryotic translation relies their cap structure and first AUG

Choose the characteristic that is NOT found in a plasmid a. origin of replication b. circular c. double-stranded RNA d. double-stranded DNA

c. double-stranded RNA

Which of the following is NOT used in a Western blot? a. antibody b. acrylamide gel c. SDS d. RNA probe

d. RNA probe

All of the following are required for translation except: a. mRNA b. tRNA c. rRNA d. amino acid polymerase

d. amino acid polymerase

All of the following bases are found in DNA except a. adenine b. thymine c. guanine d. uracil

d. uracil

Why is a DNA virus not considered to be a living cell? A. It doesn't carry genetic information B. It cannot replicate without a host cell and its machinery C. Its genome is contained within a proteinaceous capsid D. it does not have any ribosomes

B. It cannot replicate without a host cell and its machinery

Alternative sigma factors RpoH is active at high temp but not at normal temp-why? a. It is targeted for degradation at normal temperatures; at high temperatures, chapteronins degrades misfolded proteins instead b. it is transcribed when temperatures exceed 60C c. It needs the cascade mechanism of activation d. anti-sigma factor binds at lower temperatures while anti-anti-sigma factors is active at high temperature

a. It is targeted for degradation at normal temperatures; at high temperatures, chapteronins degrades misfolded proteins instead

Which method allows a researcher to screen for a protein based on its function, and find its nucelotide sequence too? a. Phage display b. Co-immunoprecipitation c. Rt-PCR d. Intein trapping

a. Phage display

a genome is a. all of the genetic information of an organism b. one of the variants of a gene c. the location of a gene on a chromosome d. the coding sequence of a protein

a. all of the genetic information of an organism

A triplet of three nucleotides found on the tRNA that hybridize with the mRNA sequence in the ribosome is the___: a. anticodon b. codon c. trio d. peptide

a. anticodon

Genes a. are segments of DNA that code for proteins b. are particular versions of alleles c. always have it pair on the homologous chromosomes d. show a mutant phenotype when heterozygous

a. are segments of DNA that code for proteins

Where are hydrophobic residues likely to be found in a cytoplasmic (non-membrane) protein? a. buried in the center of the protein, shielded from the external, aqueous environment b. exposed on the surface of the protein so they can interact with water c. interacting with hydrophillic residues to provides balance to the protein structure d. forming ionic bonds with charged r-groups in the peptide chain

a. buried in the center of the protein, shielded from the external, aqueous environment

What is the difference between dATP and ddATP? a. ddATP is missing a 3'OH group b. dATP is missing a 2'OH group c. dATP has an extra base that interferes with base pairing d. ddATP has double the amount of phosphate groups

a. ddATP is missing a 3'OH group

Introns: a. interrupt the coding sequence of genes b. are found in the spaces between genes c. are repetitive sequences that can identify individuals d. are mutated, non-expressed versions of genes

a. interrupt the coding sequence of genes

If 1000 base-pair pieces of DNA were analyzed on a gel, which piece would you expect to migrate the slowest in a gel? a. linear piece of DNA b. supercoiled plasmid of DNA c. linear piece of DNA with multiple AAA tracts in it d. a relaxed piece of DNA

a. linear piece of DNA

Protein primary structure is the result of a. peptide bonds between adjacent amino acids b. H-bonds forming along the peptide backbone c. covalent bonds between r-groups d. H-bonds between R-groups

a. peptide bonds between adjacent amino acids

What is the purpose of the multiple cloning site (MCS)? a. provides a cluster of unique restriction sites to aid in inserting DNA b. allows for selection by an antibiotic c. sets the origin of replication d. restricts expression of the cloned DNA

a. provides a cluster of unique restriction sites to aid in inserting DNA

What is the proteome? a. the total set of proteins encoded by the organisms genome b. the total set of proteins in the ribosome c. the number of genes that transcribed during a specific growth condition d. the total number of genes that are transcribed into any form of RNA

a. the total set of proteins encoded by the organisms genome

Digestion of a linear piece of DNA with EcoRI yields 3 smaller pieces of DNA. How many recognition sites were in the original piece of DNA? a. 1 b.2 c. 3 d. 4

b. 2

How many replication forks are found in a replication bubble? a. 1 b. 2 c. 4 d. varies

b. 2

Which sequence would have the lowest melting temp? a. TATATATA b. ATATATAT c. CTCTCTCT d. GTGTGTGT

b. ATATATAT

According to the Central Dogma, in what order does genetic info pass? a. RNA-DNA-Protein b. DNA-RNA-Protein c-DNA-Protein_RNA d. Protein-RNA-DNA

b. DNA-RNA-Protein

During transcription the info in ____ is transferred into _____ a. DNA;DNA b. DNA; RNA c. RNA; DNA d. RNA; protein

b. DNA; RNA

Co-immunoprecipitation is used to a. Determine if two proteins interacts with the same antibody b. Determine if two protein interacts with each other c. Analyze DNA sequence of a protein d. Identify chemical groups that have been added to the protein post-translationally

b. Determine if two protein interacts with each other

Protein secondary structure is the result of a. peptide bonds between adjacent amino acids b. H-bonds forming along the peptide backbone c. covalent bonds between r-groups d. H-bonds between R-groups

b. H-bonds forming along the peptide backbone

Prokaryotic genes: a. are all transcribed individually and are never on the same mRNA b. can cluster together and share the same regulatory region c. are transcribed in the nucleus d. contain introns that are removed before translation starts

b. can cluster together and share the same regulatory region

Topoisomerases a. are antibiotics that kill bacterial cells b. change the amount of supercoiling in DNA c. copy DNA sequence d. digest DNA 1000 bases from their recognition sites

b. change the amount of supercoiling in DNA

Adding chemical groups to an antibiotic can provide resistance to a cell by a. modifying its activity and preventing transcription b. changing the shape of the antibiotic so that it no longer fits in the ribosome and blocks translation c. sequestering the antibiotic in the cytoplasm d. shattering the antibiotic

b. changing the shape of the antibiotic so that it no longer fits in the ribosome and blocks translation

Why must DNA be denatured during PCR? a. DNA polymerase works best at high temp b. denaturing DNA separates the strands of DNA and allows primers to bind to complementary sequences c. the degraded DNA nucleotides are recycled during the synthesis step of PCR d. DNA does not need to be denatured for PCR to work

b. denaturing DNA separates the strands of DNA and allows primers to bind to complementary sequences

Primer extensions is used to a. locate the binding of RNA polymerase b. determine the transcriptional start site c. determine the interaction of RNA and proteins d. generate primers for PCR

b. determine the transcriptional start site

How are okazaki fragments joined to form a continous strand? a. gyrase twists the fragments together b. dna polymerase removes the primer, fills in, and then ligase seals the nick c. single stranded binding protein holds the two ends close together d. methylation reforms the phosphodiester bond

b. dna polymerase removes the primer, fills in, and then ligase seals the nick

Homologous chromosomes a. share the same nucleotide sequence b. have the same genes in the same order c. recombine during mitosis d. are homozygous for all gene alleles.

b. have the same genes in the same order

In eukaryotes, negative regulation occurs by a. obstructing RNA polymerase II b. interfering with activators c. interfering with repressors d. binding of repressors to operators

b. interfering with activators

Euchromatin _______ a. is only found in prokaryotes b. is loosely packed chromatin c. does not allow gene expression to occur d. is densely packed chromatin

b. is loosely packed chromatin

What is the point go a multiple cloning site in a vector? a. codes for an antibiotic resistance gene, which will allow for selection b. makes cloning easier by having a collection of restriction sites grouped in one place in the vector c. is the start site for replication d. distributes copies of the vector evenly between dividing cells

b. makes cloning easier by having a collection of restriction sites grouped in one place in the vector

Reporter systems are most useful for______ a. determining DNA-protein interactions b. monitoring gene expression c. identifying the product of biochemical reactions d. constructing large numbers of clones in bacteria

b. monitoring gene expression

Levels of transcription for a specific gene are measured using all of the following except: a. SAGE b. primer extension c. quantitative PCR d. reporter genes

b. primer extension

Which component of the PCR reaction mixture determines what part of the target sequence gets amplified? a. DNA polymerase b. primers c. nucleotides d. templates

b. primers

Insulator regions in DNA can be bound by insulator binding proteins, and a. extend the reach of enhancers to distant promoter sequence b. restrict enhancers to acting upon local genes c. deacetylate histone tails and cause compaction d. inactivate transcription by blocking activator binding sites

b. restrict enhancers to acting upon local genes

In eukaryotic chromosomes, nucleosomes are a. supercoiled circular pieces of DNA b. segments of DNA wrapped around a core of histone proteins c. the enzyme that makes copies of all genomic information before mitosis d. the protective ends of the chromosomes that contain non-coding DNA

b. segments of DNA wrapped around a core of histone proteins

During translation, elongation factors a. assist stalled ribosomes by providing a stop codon b. shift the tRNA in the A and P sites to the P and E sites, respectively c. Add additional sequence to the mRNA and increase the size of the protein d. Act as internal ribosome entry sites and allow translation of a second cistron

b. shift the tRNA in the A and P sites to the P and E sites, respectively

For an operon, turning on transcription at the promotor a. initiates transcription of non-coding RNA b. starts transcription of a polycistronic mRNA c. Turns off translation of monocistronic DNA d. Activates transcription of a single gene

b. starts transcription of a polycistronic mRNA

If 1000 base-pair pieces of DNA were analyzed on a gel, which piece would you expect to migrate the furthest in a gel? a. linear piece of DNA b. supercoiled plasmid of DNA c. linear piece of DNA with multiple AAA tracts in it d. a relaxed piece of DNA

b. supercoiled plasmid of DNA

Using blue/white screening, what do the white colonies tell us? a. that the lac Z is intact and cleaves x-gal b. that the lac Z sequence was distrupted by an insert, and didn't form a functional enzyme c. no insert is present in the vector d. the bacteria do not have plasmid

b. that the lac Z sequence was distrupted by an insert, and didn't form a functional enzyme

A piece of unknown DNA is cloned into an exon trapping vector. When this vector is transcribed and translated, new sequence is observed between exon 1 and exon 2. This means: a. yeast sequences contaminated the experiment b. that there was an exon in the unknown DNA c. shotgun sequencing needs to be done d. Only junk DNA was in the piece of unknown DNA

b. that there was an exon in the unknown DNA

Plasmids are incompatible and will not exist in the same cell after multiple rounds of division when a. they are transferable b. they have similar DNA sequences in the replication genes c. they produce toxins d. they carry genes for antibiotic resistance

b. they have similar DNA sequences in the replication genes

How is the copy number of a plasmid maintained? a. by limiting the amount of nucleotides in a cell b. through RNA I and RNA II interactions that block the formation of a primer for DNA synthesis c. Via plasmid incompatibility d. By providing a nutrient that stimulates growth of the plasmid

b. through RNA I and RNA II interactions that block the formation of a primer for DNA synthesis

When separating proteins by SDS-PAGE why do we use SDS? a. to make the sample bubbly, bc bubbles are great b. to denature the protein and give it the net negative charge proportional to its size c. to refold the protein and restore activity d. to remove cell fragments that may be attached to the proteins

b. to denature the protein and give it the net negative charge proportional to its size

How many H-bonds form between G and C? a. 1 b. 2 c. 3 4. 0

c. 3

How is chain termination sequencing difference from PCR? a. RNA polymerase is used in PCR b. Chain termination sequencing requires multiple templates c. Chain termination sequencing uses one primer, PCR uses two primers d. Chain termination sequencing only used ddNTPs.

c. Chain termination sequencing uses one primer, PCR uses two primers

In___, interacting protein and DNAs are cross linked and pulled down with an antibody against the protein. The final result? Identify protein and DNA a. SAGE b. Gel shift assay c. Chromatin immunoprecipitation d. DNA microarray

c. Chromatin immunoprecipitation

What information does MALDI-TOF or electrospray mass spectroscopy give us about a protein? a. it identifies sites for protein-protein interaction b. it identifies the precise nucleotide sequence for protein DNA interactions c. Its tells us an exact molecular weights, from which we can determine the proteins identity d. it calculates the overall charge for the protein

c. Its tells us an exact molecular weights, from which we can determine the proteins identity

You want to find out how many copies of a particular mRNA are in a cell - which technique would you use? a. RNA-Seq b. Chromatin immunoprecipitation c. Quatitative PCR d. Footprint analysis

c. Quatitative PCR

All of the following statements about replication are true, except: a. sythesis of the leading strand occurs continuously in the 5-3 direction b. Dna polymerase uses an RNA primer c. Replication does not need single strands of DNA as templates and occurs ahead of the replication fork. d. prokaryotic chromosomes have a single origin of replication that is AT rich

c. Replication does not need single strands of DNA as templates and occurs ahead of the replication fork.

Which of the following is an example of negative regulation? a. a gene is switched on in the presence of an activator b. a gene is de-repressed (the repressor is removed) c. a gene is switched off by a repressor protein d. a gene is induced

c. a gene is switched off by a repressor protein

The antibiotic resistance gene for ampicillin encodes a. A transferase that adds acetyl groups onto the antibiotic b. a channel that pumps ampicillin out of the cell c. an enzyme that destroys ampicillin structure d. a kinase that phosphorylates the antibiotic

c. an enzyme that destroys ampicillin structure

In chain termination sequencing, when DNA polymerase adds a deoxy nucleotide to the 3' end of the nucleic acid strand, a. energy is produced for and used in a second reaction b. chain elongation is terminated c. and chain elongation continues until a dideoxynucelotide is added d. a primer is formed for the next round of sequencing

c. and chain elongation continues until a dideoxynucelotide is added

Which of the following is true for an activator? a. it blocks the binding of RNA polymerase b. the signal molecule causes it to come off of the DNA c. binding of the signal molecule to the activator causes the activator to bind to DNA d. it binds to the operator sequence in the promotor

c. binding of the signal molecule to the activator causes the activator to bind to DNA

Which structural element of a eukaryotic chromosome is matched with its correct description? a. replication origins: where replication of circular DNA begins b. telomeres: used to separate homologous chromosomes c. centromeres: point of attachment for microtubules during mitosis

c. centromeres: point of attachment for microtubules during mitosis

In PCR, when (in which step) is a new strand of DNA formed/extended? a. denaturation b. annealing c. elongation d. transcription

c. elongation

Some DNA polymerases have 3'-5' proofreading ability and will remove a mismatched nucleotide from the 3' end. This is an example of the enzyme acting as a. ligase b. endonuclease c. exonuclease d. modification enzyme

c. exonuclease

Bacteria can transcribe and translate the same mRNA; why can this NOT happen in eukaryotes? a. This happens all the time in eukaryotes b. mRNA is in the nucleus which ribosomes are in the nucleous c. mRNAs are transcribed and processed in the nucleus, while translation only occurs in the cytoplasm d. eukaryotic RNA polymerases and ribosomes are too big to be on the same piece of mRNA at the same time.

c. mRNAs are transcribed and processed in the nucleus, while translation only occurs in the cytoplasm

All prokaryotic and eukaryotic living cells have a. nucleus b. chloroplasts c. phospholipid outer membrane d. ER

c. phospholipid outer membrane

The RNA polymerase binds to the ___on the DNA to initiate transcription a. enhancer b. origin c. promoter d. 5' UTR

c. promoter

Often seen in the processing of RNA that will become tRNA, trimming a. removes introns and splices together exon b. adds extra bases c. removes nucleotides from the ends of the transcript d. changes one base into another

c. removes nucleotides from the ends of the transcript

______uitlizes mRNA, tRNA, and a ribosome to make a protein a. transcription b. replication c. translation d. duplication

c. translation

DNA polymerase a. denature double stranded DNA into single strands b. remove the strain created by supercoiling c. use a DNA template to make a complementary strand of DNA d. create polymers of amino acids during translation

c. use a DNA template to make a complementary strand of DNA

Each of the following groups are found in both DNA and RNA nucleotides, except: a. phosphate group b. 5-carbon sugar c. nitrogenous base d. 2' (OH) group

d. 2' (OH) group

Which sequence would have the highest melting temp? a. TATATATA b. ATATATAT c. CTCTCTCT d. GTGTGTGT

d. GTGTGTGT

The specificity of an enzyme for its substrate is determined by all of the following, except: a. size of active site b. shape of the active site c. presence or absence of charge within active site pocket d. all of these determine how specific an enzyme for its substrate

d. all of these determine how specific an enzyme for its substrate

All of the following are examples of eukaryotes or eukaryotic cells, except: a. plants b. animals c. neurons d. bacteria

d. bacteria

Which of the following is NOT a characteristic of a bacterial chromosome? a. circular, double-stranded DNA b. little intergenic sequence c. contains replication origin where DNA replication begins d. contains a centromere and telomeric ends

d. contains a centromere and telomeric ends

Transcription occurs in the ___of prokaryotes and the ___of eukaryotes: a. nucleus; nucleus b. cytosol; cytosol c. nucleus; cytosol d. cytosol; nucleus

d. cytosol; nucleus

All of the following statements are false, except: a. prokaryotic mRNA are processed in the nucleus b. mRNA are stable and cannot be degraded by exonucleases c. eukaryotic mRNAs have no introns d. eukaryotic mRNAs are monocistronic

d. eukaryotic mRNAs are monocistronic

The regions of transcript that contain protein coding sequences are called___ a. inteins b. exteins c. introns d. exons

d. exons

In prokaryotic replication,____is responsible for relieving strain on the DNA caused by opening up and unwinding the DNA ahead of the replication form. a. helicase b. Dna polymerase c. primase d. gyrase

d. gyrase

Where does transcription occur in eukaryotes? a. On methylated CG islands b. in the cytoplasm c. on ribosomes d. in the nucleus

d. in the nucleus

Which of the following features are primarily found on eukaryotic chromosomes and not bacterial chromosomes? a. regulatory regions b. genes c. replication regions d. introns

d. introns

What does a tRNA synthetase do? a. it releases amino acids from tRNAs b. it links an amino acid to the anicodon of its cognate tRNA c. it links an amino acid to the codon of its mRNA d. it charges a tRNA by adding an amino acid to the tRNA's acceptor stem

d. it charges a tRNA by adding an amino acid to the tRNA's acceptor stem

Telomerase a. removes RNA primers in prokaryotes and eukaryotes b. relieves twist in the circular chromosomes of bacteria c. keeps the single strands separated d. maintains the ends of linear chromosomes in eukaryotes

d. maintains the ends of linear chromosomes in eukaryotes

The biggest difference between prokaryotes and eukaryotes is a. only eukaryotes replicate DNA and divide b. viruses only infect prokaryotes c. eukaryotic chromosomes are free in the cytoplasm d. prokaryotes do not have a nucleus

d. prokaryotes do not have a nucleus

All of the following are examples of where the cell regulate at the transcriptional level EXCEPT a. controlling recognition of promotor regions through sigma factors b. using anti-termination proteins to transcribe downstream sequences c. regulating access to DNA d. regulating activation of the protein

d. regulating activation of the protein

x-activation ______ a. only occurs in males b. is the deactivation of both X-chromosomes in all females c. occurs by the action of histone acetylation d. shuts off genes on one of the two chromosomes in females

d. shuts off genes on one of the two chromosomes in females

Gel mobility shift assays can be used to determine a. the ability of a protein to bind to an rRNA sequence b. the ability of DNA to bind to an RNA sequence c. the ability of RNA to bind to another RNA sequence d. the ability of a protein to bind to a DNA sequence

d. the ability of a protein to bind to a DNA sequence

A signaling molecule binds to an activator, and then the activator then binds to the promotor of a gene. What happens next? a. the gene can be replicated into a DNA copy b. transcription of the gene is shut off c. the promotor becomes hypermethylated and permanently shut off d. the gene can be transcribed

d. the gene can be transcribed

How does a hairpin loop and UUUUU termination sequence work together to stop transcription? a. the hairpin loop cuts at the UUUUU sequence to release the transcript from the polymerase b. the UUUUU sequence binds to the AAAA sequences in the polymerase, and the loop blocks the elongation tunnel. c. these structures tag the polymerase for degradation d. the loop destabilizes the RNA-RNA polymerase interaction; the weak A=U bonds are easily broken

d. the loop destabilizes the RNA-RNA polymerase interaction; the weak A=U bonds are easily broken

A snoRNA base pairs with a region of rRNA-what is likely to happen next? a. a 5'cap and a 3'polyA tail are added to the rRNA so it can be translated into protein b. the rRNA sequence is degraded c. a charged amino acid is added to the rRNA's acceptor stem d. the snoring acts as a guide for enzymes that will modify bases in the rRNA

d. the snoring acts as a guide for enzymes that will modify bases in the rRNA

Sequence tagged sites (STS) are a. contain highly repetitive sequences of DNA b. found multiple times on each chromosomes c. never expressed regions in the genome d. unique sequences that can be mapped to specific locations in the genome

d. unique sequences that can be mapped to specific locations in the genome

A method that uses an antibody to detect a specific protein is called a. phage display b. mass spectrometry c. yeast two hybrid system d. western blot

d. western blot

All prokaryotic and eukaryotic living cells have a. nucleus b. chloroplasts c. ribosomes d. ER

ribosomes