Microbio Ch 14 and 16

Transposons

(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material

characteristics of transcriptional regulatory proteins

- Bind to DNA - Bind to palindromic DNA sequences

Characteristics of regulatory proteins

- Binds to palindromic sequences on DNA - Individual subunits associate to form dimers - Responsible for processes such as induction and repression

Transcription of the trp operon is controlled by

- Premature termination through attenuation - Repressor protein inhibits initiation

DNA-bound repressor proteins inhibit the initiation of transcription by either ___ or ___.

- Preventing the movement of RNA polymerase - Blocking the binding of RNA polymerase

Attenuator terminator loop

- Similar to factor-independent transcription terminators - Formed by the pairing of regions 3 and 4 - Immediately followed by a poly-U region

Attenuator pause loop

- Slows down RNA polymerase - Formed by the pairing of regions 1 and 2

Which two of the following statements about the inhibition of transcription by the lac repressor protein are true? - The lac repressor binds to the O2 and O3 lac operator sites. - The lac repressor binds and inhibits RNA polymerase. - The lac repressor degrades the polycistronic message. - The lac repressor binds to O1 and one additional lac operator site. - The lac repressor bends the DNA in the promoter region.

- The lac repressor binds to O1 and one additional lac operator site. - The lac repressor bends the DNA in the promoter region.

Under normal growth conditions, the rate of naturally-occurring mutant cells is one mutant cell out of approximately ___ cells.

10^7 to 10^11

Forward mutation

A mutation that causes the wild type strain to become a mutant strain.

conditional mutation

A mutation that results in a characteristic phenotype only under certain environmental conditions. Phenotype is only affected at high temperatures

transversion mutation

A point mutation in which a pyrimidine is substitued for a purine, or vice versa.

transition mutation

A point mutation in which a pyrimidine is susbstituted for a pyrimidine, or a purine is substituted for a purine.

Missense mutation

A point mutation that involves a single base substitution and results in a change to the amino acid encoded by that codon

Which three types of mutations are classified as reversion mutations? A second frameshift mutation that restores an original reading frame. A second mutation that restores the original wild-type sequence. A second mutation that creates a different codon that codes for the wild type amino acid. A mutation that causes the wild type strain to become a mutant strain. A second mutation creates a codon that replaces the wild type amino acid with a similar amino acid.

A second mutation that restores the original wild-type sequence. A second mutation that creates a different codon that codes for the wild type amino acid. A second mutation creates a codon that replaces the wild type amino acid with a similar amino acid.

A DNA-binding protein that promotes transcription initiation is termed a(n) ________ protein

Activator

When _______ proteins bind to their transcriptional regulatory sites they facilitate the binding of RNA polymerase.

Activator

A repressor protein synthesized in its inactive form is referred to as a(n) ____.

Aporepressor

Transcription of the trp operon is regulated at the level of initiation by the trp repressor, and at the level of elongation by a process called

Attenuation

In E.coli regulatory pathways, which molecule functions to ensure that glucose is used as the preferred carbon and energy source?

CAP

Base analogues, DNA-modifying agents, and intercalating agents are three types of ________ mutagens

Chemical

Which two of the following are characteristics of the lac repressor protein? Has an arabinose binding site Composed of two identical subunits Composed of four identical subunits Each monomer has a helix-turn-helix domain

Composed of four identical subunits Each monomer has a helix-turn-helix domain

A mutant strain of E. coli that grows normally at 30°C, but dies at 40°C, is a(n)_________ mutant. nonsense prototrophic conditional silent

Conditional

Which three of these statements about nonsense mutations are correct? Effects range from mild to complete loss of normal gene function. They involve a single base substitution that changes a codon for one amino acid to a codon for a different amino acid. They cause the early termination of translation. They are typically not as severe when they occur near the beginning of a gene. By definition, they always produce stop codons.

Effects range from mild to complete loss of normal gene function. They cause the early termination of translation. By definition, they always produce stop codons.

T/F The Ames test can determine whether a particular substance is carcinogenic.

False The Ames test determines mutagenicity. Although many mutagens are carcinogens, carcinogenicity can only be determined by testing in animals.

Riboswitches

Folded RNAs that act as switches that can turn protein synthesis on or off in response to certain environmental conditions based upon the binding of an effector molecule to the mRNA.

characteristics of the attenuator antiterminator loop

Formed by the pairing of regions 2 and 3 Prevents the generation of the terminator loop Located in the leader region Prevents the generation of the pause loop

Silent, missense, nonsense, and frameshift are all common types of ________ mutations.

Forward

Mutations that arise from the insertion or deletion of 1 or 2 base pairs within the coding region of a gene are called _________ mutations

Frameshift

inducible genes

Genes whose expression is turned on by the presence of some substance. Regulate catabolic pathways.

The catabolite activator protein (CAP) functions in a regulatory network that allows E. coli to preferentially use ________, over all other carbon and energy sources.

Glucose

The first processes that regulate gene expression to be understood in detail were

Induction and repression

What conditions must exist to fully induce the lac operon?

Lack of preferred carbon and energy source Lactose present in the medium

Point mutations in a single base that result in a change to the amino acid encoded are called _______ mutations

Missense

missense mutations

Most common type of mutation, a base pair mutation in which the new codon makes sense in that it still codes for an amino acid. - They are a single base substitution that changes a codon for one amino acid into a codon for a different amino acid. - Effects range from no change to complete loss of normal gene function

resistance mutations

Mutant is not affected by a particular pathogen, antibiotic, or chemical

Suppressor mutation

Mutation that hides or suppresses the effect of another mutation at a site that is distinct from the site of the original mutation. ex: A second frameshift mutation that restores an original reading frame.

When transcription initiation is inhibited by a repressor protein binding to DNA, it is termed ___________ transcriptional control

Negative

describe the lac operon in E. coli

Negative transcriptional control of inducible genes (i.e., turned "off" until turned "on")

A missense mutation that has little to no effect on the activity of a gene product is called a(n) ________ mutation

Neutral

Point mutations that create a stop codon within a reading frame are called ______ mutations

Nonsense

The lac operon is considered a negative control system because it is considered to be turned ___ until lactose is present.

OFF

In bacteria, repressor proteins bind to a specific DNA sequence called the ____.

Operator

MutS

Recognizes single base mismatches

Which example of a missense mutation in a protein-encoding gene would most likely be a neutral mutation?

Replacement of a polar amino acid with another polar amino acid at the protein's surface Even though the amino acids are similar, changes inside a protein's interior are more likely to affect functions than changes to the protein's outer surface.

A DNA-binding protein that inhibits transcription initiation by binding to an operator is termed a(n) _______

Repressor

Point mutations that change the nucleotide sequence of a codon but do not change the amino acid encoded by that codon are called _________ mutations

Silent

Which term is used to describe genes that encode the non-regulatory proteins (enzymes) in an operon? Multiple choice question.

Structural genes

T/F Lethal mutants can be recovered only if they are conditional mutants.

T because a microbe cannot be studied unless it is able to grow under certain conditions.

Ames test

Test in which special strains of bacteria are used to evaluate the potential of chemicals to cause cancer.

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.

Mutation

The general term for heritable changes in DNA sequence

recombinational repair

The repair of damaged DNA by recombination with an undamaged homologous DNA molecule

Why are transversion mutations more rare than transition mutations?

There are steric problems with pairing purines with purines.

prototroph

They are chemoorganotrophs able to grow on a minimal medium containing only salts and a carbon source.

Which two of these statements are correct about frameshift mutations? They are typically not as severe when they occur near the beginning of a gene. They usually result in the synthesis of nonfunctional proteins. They usually yield mutant phenotypes. By definition, they always produce stop codons. They involve a single base substitution that changes a codon for one amino acid into another.

They usually result in the synthesis of nonfunctional proteins. They usually yield mutant phenotypes.

Which two of the following are components or regulatory sequences for the lac operon?

Three structural genes lacI

T/F The ara operon is an example of both a positive and negative control system.

True The AraC protein can act as both a repressor and activator.

T/F A mutation can prevent a gene from being expressed, even if the coding sequence is completely unchanged.

True This would be false if the mutation affects a regulatory gene

The most prevalent form of a gene, and its associated phenotype, is called the _______ type

Wild

A suppressor mutation, which returns a mutant back to its wild-type phenotype, occurs at ____________ the first mutation.

a different site from

mutations in regulatory sequences

a mutation in the lac operator so the lac repressor cannot bind a mutation in a promoter so that RNA polymerase cannot bind

lac operon inducer

allolactose

tautomeric forms

alternate chemical forms of nucleotides that allow pairing with non complementary bases

In the trp operon attenuator, the formation of the __________ loop prevents the formation of both the 1:2 pause and 3:4 terminator loops.

anti terminator

The trpL operon encodes the leader peptide and ___________ sequences

attenuator

The lac repressor protein inhibits transcription by ____.

bending DNA in the promoter region

induced mutations

caused by environmental agents (physical and chemical)

morphological mutation

change in DNA sequence that alters a structural feature of the cell Affects the appearance of colonies.

reverse mutation

changes a mutant phenotype back to the wild-type phenotype

Aporepressors are synthesized in an inactive form and are activated by the binding of small effector molecules called _________

corepressor

excision repair

corrects damage that causes distortions in double helix - nucleotide excision repair - base excision repair

Riboswitches are regulatory mRNAs that can fold into different patterns based upon ____.

direct binding of an effector molecule to mRNA

DNA proofreading occurs

during DNA replication, before the next nucleotide is added

trpL

encodes a short peptide called the leader peptide which functions in attenuation

MutH

endonuclease, nicks DNA near damaged base

Direct DNA repair

enzymatic removal of damage such as thymine dimers and alkylated bases

A suppressor mutation that occurs in a different gene from the first mutation is called a(n) ______ suppressor mutation.

extragenic

point mutation

gene mutation in which a single base pair in DNA has been changed

constitutive genes

housekeeping genes that are expressed continuously by the cell

Positive transcriptional control

indicates that the binding of an activator protein to DNA promotes transcription initiation

The lac operon is expressed at high levels when the sugar ________ is available and a preferred source of carbon and energy is lacking.

lactose

Photoreactivation

light repair Enzyme uses energy from light Breaks covalent bonds of thymine dimer Only found in bacteria Direct dna repair

auxotroph mutation

mutant cannot synthesize an essential molecule such as an amino acid They are unable to grow on medium lacking a particular molecule, where the wild-type strain could grow. They have a conditional phenotype.

The trp operon is best described as an example of the ______.

negative transcriptional control of repressible genes

A tautomeric form is an isomer of a nucleotide in which the _____ is changed.

nitrogenous base

extragenic suppressor mutation types

nonesense suppresor physiological suppressor

catabolite activator protein (CAP)

protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available

global regulatory systems

regulatory systems that affect many genes, operons, and pathways simultaneously

Which two of these missense mutations would be predicted to have the most severe effects on the function of the protein encoded by the mutated gene? replacement of a hydrophobic amino acid with a different hydrophobic amino acid replacement of a nonpolar amino acid with a polar amino acid substitution of an amino acid located at the active site of an enzyme replacement of an amino acid located in a surface loop of an enzyme

replacement of a nonpolar amino acid with a polar amino acid substitution of an amino acid located at the active site of an enzyme

Proteins that inhibit transcription initiation by binding to operator DNA are called ___.

repressor proteins

The bacterium Deinococcus radiodurans is best known for its ability to

resist damage by radiation

Possible causes of spontaneous mutation include Multiple select question.

spontaneous lesions in DNA transposons errors in DNA replication

The attenuator pause loop of the trp operon slows down RNA polymerase by forming what structure in the newly formed mRNA?

stem loop

intragenic suppressor mutation

suppresses the effect of an earlier mutation within the same gene

Spontaneous mutations can occur when a nitrogenous base shifts to a different isomer, also called a(n)

tautomeric form

attenuation of trp operon

termination of transcription occurs with higher levels of Trp-tRNA Termination of transcription elongation before RNA polymerase enters the first structural gene of an operon

trp operon

tryptophan binds to the repressor protein and enables it to repress gene transcription. Repressible operon

Which three of these factors contribute to the extreme radiation resistance of Deinococcus radiodurans? two homologous chromosomes thick cell wall blocks radiation radiation-resistant proteins complex, atypical electron transport chain proteins that quickly repair damage to genome several unique DNA repair mechanisms

two homologous chromosomes radiation-resistant proteins proteins that quickly repair damage to genome