Genetics Exam 2

UARK 2025 Spring Don Shepard

Without looking at the genetic code, which of the following point mutations would be most likely to affect protein function?

TAA to TAC

CAA to TAA

AGG to AGA

CTT to CTC

CAA to TAA

Which of the following is correct about the lac and trp operons?

A) Both operons respond to glucose availability. B) The lacI and trpR repressor genes both encode trans-acting factors.

C) Binding of a regulatory protein is prevented in the presence of an inducer.

D) Both operons are regulated by catabolite repression.

E) The trp operon is inducible and the lac operon is repressible

B) The lacI and trpR repressor genes both encode trans-acting factors.

3. Assume that in an organism under study the DNA polymerase has an error rate of 1 error in every 106 bases copied. However, the overall mutation rate is much lower. This is most likely because:

The repair mechanisms correct errors made by the polymerase

A defect in an aminoacyl-trna synthetase would directly lead to an _________ trna

An uncharged trna

Through the course of evolution, a mutation arose in the guinea pig genome that negatively affects the ability to produce ascorbic acid (vitamin C). The mutation maps to a gene encoding an enzyme in the biosynthetic pathway that produces ascorbic acid. Would this be a neutral or loss of function mutation?

Loss of function mutation

In the lac and trp operons, repressor proteins are said to be allosteric because they undergo conformational changes in their ___ -_______ _______ when they bind their respective effector molecules

DNA-binding domains

Except for Met-tRNA used in translation initiation, all tRNAs pass through the three sites of the ribosome in a specific order. What is that order?

A to P to E sites

DNA methylation can be a significant mode of gene regulation in some eukaryotes. In this context, methylation refers to the ________ of methyl groups to the _________ of CpG islands

addition; cytosines

What is the primary determinant of protein structure? (NOT TO BE CONFUSED WITH THE DETERMINANT OF AN AMINO ACID) structure meaning: secondary, tertiary, quatenary, etc.

AA sequence

Regions of DNA sequence that are bound by regulatory proteins contain what kind of elements and are they located near/far from where RNA polymerase binds?

They contain cis-acting elements that can be located quite far from where RNA polymerase binds

An observable change in phenotype may arise from a change in: which if not all of the following:

The AA sequence of a protein

The regulation of gene expression

The number of gene copies

All of the following

What happens at the trp operon in the absence of tryptophan?

The repressor is inactive and does not bind to the operator. Transcription occurs.

In eukaryotes, association of DNA with histones to form chromatin affects transcription by which if not all of the following:

decreasing transcription rates

requiring histone modifications

requiring chromatin remodeling complexes

all of the following

14. What types of mutations are responsible for the change in meaning of the wild-type sentence below? Wild type: THE CAT SAW THE DOG Mutation

A: THE CAT WAS THE DOG Mutation

B: THE CAT SAW THE HOG Mutation

C: THE CAS AWT HED OG Mutation

D: THE CAT SAT WTH EDO G

A: Inversion

B: Substitution

C: Deletion

D: Insertion

For E. coli with lac operon genotype IS P+ O+ Z+ Y+ A+ , the repressor protein has a mutation resulting in it being unable to bind allolactose. The expression of β-galactosidase will be repressed or induced?

repressed

The role of tautomerism in causing mutations relates to the fact that the process ultimately

affects the ______.

Hydrogen bonding affinities of nitrogenous bases on opposite strands

In eukaryotes, the association of RNA polymerase 2 to a specific region of DNA is positively affected by what factors (there are three)

promoters, enhances, and TF’s

Assume that a new antidepressant medication is developed. The chemical structure is novel

and the medication is tested using the Ames test for mutagenicity. The following results are

obtained. What conclusion is most consistent with these data?

Sample Number of his+ revertant colonies

distilled water 2

distilled water + rat liver enzymes. 3

antidepressant 3

antidepressant + rat liver enzymes 65

The drug is not mutagenic, but can break down into strong mutagens

True or false, if the CAP site is nonfunctional, would it lead to a reduction in the total amount of Beta-galactosidase produced by a bacterial cell?

True

During translation termination in both bacteria and eukaryotes:

A release factor binds to a stop codon at the A site

True or false: A frameshift mutation could be cause by a transition, transversion, or a deletion of 3 base-pairs.

False

Eukaryotic gene expression can be repressed by __________ changes caused by deacetylation of histone tails

chromatin

ribosomes are composed of

rRNA and protein

The _____ _______ of the ribosome is important in translation initiation because it scans eukaryotic mRNA for the first start codon AUG and binds the Shine-Dalgarno sequence in bacterial mRNAs

small subunit

True or false: mismatch repairing, base excision repairing, and nucleotide excision repairing would require DNA polymerase

true

_________ (______): are excised by the endonuclease dicer, associate with cellular proteins, bind to mRNAs and block their translation, and are a mechanism of post-transcriptional regulation of gene expression

microRNAs (miRNAs)

The codon ACU specifies the AA Threonine. A mutation that changes the codon to AAU, specifying Asparagine, is an example of what kind of mutation?

Transversion and a non-synonymous substitution

True or false: you CAN predict when and where a mutation will occur

false

This level of structure of a protein refers to the 3-d folded state of a protein

the tertiary structure

The trp operon in E. coli is regulated by trpR, and has the following features:

1) When you delete the trpR gene, the operon is constitutively ON

2) When tryptophan binds to the trpR protein, it causes a conformational change allowing

trpR to bind to its DNA-binding site in the trp operator.

From this, you can conclude that the trp operon is under:

negative-repressible control

During the peptidyl transferase reaction, the polypeptide attached to the tRNA in the

______becomes bound via ______to the amino acid attached to a tRNA in the ______.

P site, a peptide bond, A site

A mutation that renders the trp repressor unable to bind _________ will result in the following: constitutive expression of the trp operon, the repressor not being able to undergo an allosteric change

tryptophan

The ___ ________ is capable of: undergoing an allosteric change, binding to the operator, and binding to the inducer

lac repressor

When bacterial cells are exposed to low glucose and high lactose, the lac operon:

will be transcribed at high levels

Which type of DNA repair removes pyrimidine dimers?

nucleotide excision repair

Acetylation of histones, removal of N-terminus AA, addition of phosphate groups and polypeptide cleavage are all examples of what kind of modification?

post-translational modification

true or false: DNA methylation is considered to be a post-translational modifcation

false

Base excision repair requires DNA glycosylases and AP endonuclease to replace an altered __________,

Nucleotide

What primarily determines the unique chemical character of a particular AA?

The R group

Which of the following is a fundamental difference between gene regulation in bacteria

compared to eukaryotes?

A) In bacteria, but not eukaryotes, there is a specific sequence that specifies where RNA

polymerase binds and initiates transcription.

B) In eukaryotes, but not bacteria, transcription can be influenced by how the DNA sequence

of a promoter region interacts with histones.

C) Transcription regulation is the most common form of control of gene expression in

bacteria but not in eukaryotes.

D) Gene regulation is readily reversible in eukaryotes but not bacteria.

E) DNA looping at promoter regions only occurs in bacterial transcription.

B) In eukaryotes, but not bacteria, transcription can be influenced by how the DNA sequence

of a promoter region interacts with histones.

True or false: two or more different codons specifying the same AA explains the existence of silent mutations

true

_____________ is the synthesis of a SS RNA molecule (transcript) from a DNA template (gene). This mRNA specifies the AA of a polypeptide (protein)

Transcription

___________ is the process of synthesizing a polypeptide using the mRNA template

translation

The boundaries of translation are defined by a _____ _____ that corresponds to the N-terminus of the protein and a ____ _____ that corresponds to the C-terminus

start codon; stop codon

During translation, _____ act as adaptor molecules that interpret and act on information in mRNA , they have __________ that are complementary and antiparallel to mRNA codons

tRNAs; anticodons

tRNAs used during translation are called _______ tRNAs, whereas tRNAs lacking AA attached are _________

charged;uncharged

An enzyme called _________-____ __________ catalyze the addition of the correct AA to tRNAs, there are 20 of these enzymes per 20 AA

aminoacyl-tRNA synthetases

What organelle is responsible for assembly of AA, turning them into strings of polypeptides? They also bind mRNA and identify the start codon, and they facilitate comp. base pairing of mRNA codons and the corresponding tRNA anticodons

ribosomes

Ribosomes are composed of what two subunits

large subunit and small subunit

The _ ____ binds the tRNA containing the next AA to be added to the growing polypeptide chain

A site

The _ ____ holds the tRNA to which the polypeptide is attached

P site

The _ ____ provides an avenue for the tRNA to exit after its AA has been added to the polypeptide chain

E site

Translation can be divided into what 3 phases:

initiation, elongation, termination

Initiator tRNA carries the first AA of the polypeptide and binds to the start codon, then the large ribosomal subunit joins the small subunit to form a ribosome, these proteins aid in the process of ribosomal formation and the binding of the initiator tRNA _________ ______ proteins

Initiation factor proteins

In bacterial translational initiation, the pre-intiation complex forms when the 16s rRNA of the 30s ribosomal subunit pairs with the _____-________ ________ on the mRNA

Shine-Dalgarno sequence

The AA on the initiator tRNA is a modified AA, N-formylmethionin (fMet), the initiator tRNA during the second step of initiation binds to the _____ _____ where the P site will be once the ribosome is fully assembled.

start codon

In the last step of initiation, the two subunits join to form the intact ribosome which is driven by the hydrolysis of ___ ( the energy used to fuel the initiation mechanism) into GDP.

GTP

In the final steps of eukaryotic initiation, the start codon (AUG) can be located because it is embedded in a consensus sequence called the _____ ________

Kozak Sequence

Polypeptide Elongation beings with recruitment of __ ________ that use energy from GTP.

EF proteins

________ ___________ catalyzes formation of peptide bonds between AA at the P and A sites in Bacteria

Peptidyl Transferase

The ribosome is translocated along the mRNA to the next codon, where they polypeptide beings to move with the ribosome while moving towards the _ ____

P Site

Elongation cycle continues until one of the 3 ____ ______ (UAA, UAG, UGA) enters the A site of the ribosome and release factors bind to it.

stop codons

In eukaryotic cells, ribosomes are produced in the nucleus and then exported to the _________ for translation, but are concentrated on rough er. In bacteria they are located in _______

cytoplasm;cytosol

Bacteria lack a ______ meaning they must go through other means to produce ribosomes

nucleus

Each polypeptide-producing gene in eukaryotes produces _____________ ____: this directs synthesis of a SINGLE polypeptide

monocistronic mRNA

Groups of bacterial genes (not eukaryotic genes) called operons share a single promoter and produce _____________ _____ which have MULTIPLE polypeptide producing segments and direct synthesis of several different polypeptides, genes of operons are regulated as a unit and proteins function in the same metabolic pathway

polycistronic mRNAs

In _______________, kinases attach phosphate groups to hydroxyl groups, phosphatases remove them—- changes charge and thus shape of protein, which is an example of a post-translational modification.

phosphorylation

Protein sorting uses ______ _________ to direct proteins to their cellular destinations

signal sequences

For protein sorting, in the golgi apparatus, _____________ (addition of carb side chains) of proteins determines their ultimate locations based on which receptors recognize the modified polypeptide. Receptor binding causes particular proteins to be included in vesicles that bud off from the golgi, the vesicbles then move to their cellular destinations

glycosylation

Four levels of protein structure;

1. _______ structure: the sequence of AA comprising the polypeptide

2. _________ structure: polypeptide chain folds into localized, repeating shapes based on bonds formed between nearby AA

3. ________ structure: short regions of secondary structure fold into 3-d shape determined by hydrophobic and ionic interactions (r groups) as well as Hydrogen bonds and dispersion forces *this is the final conformation of proteins composed of a single polypeptide

4. __________ structure: two or more polypeptides associate with one another (weak bonds) to make a functional protein

primary, secondary, tertiary, quantenary

Within the ER, incorrectly folded proteins are bound by other proteins called __________ that help them fold correctly

chaperones

_____ diseases are due to mis-folded proteins

prion

What are heritable changes in the DNA sequence of the genome? They generate alleles and provide phenotype variation on which natural selection can act.

mutations

In ____-____ cells, they can be passed on to offspring via gametes, whereas _______ cells have patches of cells with mutation

germ-line; somatic

In haploid organisms ________ _________ is measured as the number of times mutation alters a particular gene

mutation frequency

True or false, mutation frequencies vary among genes within a single species

true

Regions with elevated mutation frequencies are called ________ ________ and are often associated with large gene sizes

mutation hotspots

Replacement of one nucleotide base pair by another is ____-____ ____________ _________

it has two categories of mutations:

Transition mutations: one purine replaces another purine, or one pyrimidine replaces another pyrimidine

example: G mutating to A or T mutating to C

Transversion mutations: a pyrimidine is replaced by a purine

example: A mutating to C, or G mutating to T

base-pair substitution mutations

A consequence of base-pair substitution: ______ ________ is a base-pair change that does not alter the resulting AA sequence due to the redundancy of the genetic code (synonymous substitution)

silent mutation

A consequence of base-pair substitution: ______ ________a base-pair change that results in an AA change in the protein (non-synonymous substitution)

missense mutation

A consequence of base-pair substitution: ______ ________a base-pair change that creates a stop codon in place of a codon specifying an AA

nonsense mutation

A __________ ________, which either inserts or deletes on or more base pairs, deleting/adding mRNA molecules and ultimately altering the reading frame.

frameshift mutations

mutations that alter the amount of protein product produced by a gene via altering gene expression, they are referred to as __________ _________ affecting regions such as promoters, enhancers, silencers, etc.

regulatory mutations

________ _________ mutations that alter consensus sequence of nucleotides in promotors ultimately interfering with initiation of transcription

promoter mutations

________ ________ mutations that effect the removal of introns from mRNA, can result in splicing error and the prod. of mutant proteins

splicing mutations

in a ___-__-________ mutation, the function of gene product is reduced or lost, when it is completely it is called a null mutation. However, in a ____ -__-________ mutation, the gene product is enhanced or has a new function

loss-of-function; gain-of-function

A _______ ________: change converts a wild-type allele to a mutant allele. Whereas, a _______ _________/__________: change converts mutant alleles to wild-type or near wild-type

forward mutation; reverse mutations/reversions

True or false: When heterozygous with the mutant allele B^A/B^S survive and reproduce better than those that are homozygous for the B^A or B^S genotype for sickle cell and malaria

true

____ ______ _______ (___) consist of a short sequence motif repeated many times consecutively

Short Tandem Repeats (STRs)

Alterations in number of DNA repeats occur via _______ _________ which is when DNA polymerase temporarily dissociates from the template and a portion of the newly replicated DNA forms a hairpin structure, as the polymerase attempts to continue replication this causes “re-replication” of some of the areas that have already been repeated through the slip up and so on and so forth

strand slippage

DNA nucleotides can occasionally convert to alternative structures called _________ with slight differences in bonding and placement of hydrogens, ___________ ______ can lead to base pair mismatches and incorporation of incorrect bases during replication

tautomers; tautomeric shifts

Agents that cause DNA damage leading to mutations are called ________

mutagens

What are mutations that are produced by interactions between DNA and physical, chemical or biological agents that generate mutations referred to as?

Induced mutations

The ____ ____ mimics what happens when animals are exposed to chemicals, and tests chemicals and their breakdown products for mutagenic potential

ames test

__________ ______ are produced by the formation of one or two additional covalent bonds between adjacent pyrimidine nucleotides

pyrimidine dimers

Errors after proofreading by the DNA polymerase can be fixed by the ________ ______ _________ which involes: an endonuclease nicking the strand with an error, an exonuclease removing the bases of the nicked strand, DNA polymerase synthesizing and filling the gap, DNA ligase seals the gap

mismatch repair mechanism

Pyrimidine dimers due to UV exposure can be repaired via _________________ ______ in bacteria, single-celled eukaryotes, plants, and some animals (but not humans) the enzyme __________ uses energy from visible light to break the bonds between pyrimidine dimers

photoreactivation repair; photolyase

____ ________ _______ corrects mispairings due to chemical modification of bases

Base Excision Repair

___ _____________ recognize and remove mis-paired nucleotides by cleaving the modified based from the sugar, leaving an apurinic or apyrmidnic (AP) site __ _____________ then removes the remainder of the nucleotide DNA polymerase and DNA ligase fill and seal the gap with the appropriate nucleotide

DNA glyclosylases; AP endonuclease

If UV-induced damage cannot be directly repaired, it can be excised and replaced, protein binds the DNA strand opposite the damage, then proteins dissociate, and another protein joins and cleaves the phosphodiester bonds on the damaged DNA strand on both sides of damage- about 12-13 nucleotides apart. Lastly, a helicase unwinds DNA to release damaged segment, DNA polymerase synthesizes the missing nucleotides, finally DNA ligase fills the gap. This is all apart of the ___________ ________ ______.

Nucleotide Excision Repair