GN 311 Exam 3

Which type of point mutation alters a stop codon into a codon that codes for an amino acid, leading to a protein that is longer than the wild-type?

Readthrough mutation

A readthrough mutation is specifically defined as a point mutation where a stop codon is changed to a codon that codes for an amino acid. This results in the ribosome continuing translation past the normal termination point, leading to a longer protein than the wild-type.

Missense (nonsynonymous) point mutation:

Changes the amino acid (may alter protein function or protein is nonfunctional).

• Neutral: a missense mutation that doesn’t affect protein function

Nonsense point mutation

• Changes codon so that it becomes a stop codon.

• E.g. GAG mutates to UAG.

Slient (synonymjous) point mutation 

• Codes for the same amino acid.

• E.g. AGG mutates to CGG (both code for Arginine).

When an individual is heterozygous for a paracentric inversion, crossing over within the inversion loop during meiosis I often leads to inviable recombinant gametes. What specific chromosomal structures are formed during this crossing over that contribute to the inviability of gametes?

Dicentric bridges and acentric fragments are formed, which lead to unbalanced and often inviable gametes.

In a heterozygote for a paracentric inversion (where the inverted segment does not include the centromere), a characteristic inversion loop forms during synapsis in meiosis I (anaphase). If crossing over occurs within this loop, it generates recombinant chromatids that contain two centromeres (a dicentric bridge) and a segment with no centromere (an acentric fragment). The dicentric bridge often breaks irregularly during anaphase I, and the acentric fragment is typically lost, resulting in gametes that are missing or have duplicated segments of DNA, rendering them largely inviable.

Which of the following common causes of spontaneous frameshift mutations involves the mispairing of complementary bases during DNA replication, especially in regions with repetitive sequences?

Strand or template slippage

Template slippage, also known as strand slippage, is a common cause of spontaneous frameshift mutations, especially in repetitive DNA sequences. During replication, one of the DNA strands (either the template or the newly synthesized strand) can "slip" relative to the other, leading to either an insertion or a deletion of nucleotides. This often occurs due to the formation of hairpin structures within repeat regions.

A change in the DNA from a GC base pair to a CG base pair is called a ___ mutation.

Frameshift or point

point mutation

Point mutations result in the substitution of one base for another.

This specific point mutaiton is a tranversion

Which repair mechanism(s) involve(s) the removal of a single nucleotide? 

Base Excision Repair (BER): removed modified bases

Proofreading Repair (during replication): euk and pro, DNA polymersase repairs mistakes. exonucleus from DNA pol removes incorrect nucleotide and DNA pol inserts correct nucleotide

Paracentric vs Pericentric inversion

Inversions have a segment of a chromosome that is removed,

turned 180 degrees, and reinserted back into the chromosome.

Paracentric Inversion

• Inverted area does not include centromere.

Pericentric Inversion

• Inverted area does include centromere.

An organism described as 2n=4 has the chromosomes below with genes indicated by letters and centromeres indicated by periods. Select the BEST description of the chromosome aberration present in this organism.

ABC.EGGEH          ABC.EGH          RT.VXZ          RT.VXZ

Tandem duplication 

• extra copy of part of chromosome is reversed 

Which of the following statements accurately compares loss-of-function and gain-of-function mutations?

a. Both types of mutations are typically recessive and require two mutated alleles for phenotypic expression.

b. Gain-of-function mutations lead to a less severe phenotype than loss-of-function mutations.

c. Loss-of-function mutations always involve deletions, whereas gain-of-function mutations always involve insertions.

d. Loss-of-function mutations result in a complete or partial absence of protein function and are typically recessive, while gain-of-function mutations cause the production of a new or abnormally active protein, usually acting as dominant.

Loss-of-function mutations lead to a reduction or complete elimination of a protein's normal activity and are generally recessive, meaning both alleles must be mutated for the phenotype to appear. Gain-of-function mutations result in a protein with an abnormal activity, a new function, or expression at an incorrect time or location, and these mutations are usually dominant because the presence of one mutated allele is sufficient to cause the phenotype.

Depurination is a common spontaneous event where the glycosidic bond of a purine base (Adenine or Guanine) is removed, creating an apurinic (AP) site in the DNA. How can this type of damage lead to a point mutation after replication?

During DNA replication, the base opposite the apurinic site is not specified, leading DNA polymerase to often insert an improper base, which can result in transitions or transversions in subsequent replication rounds.

A reciprocal translocation is a type of chromosomal aberration where there is no net gain or loss of DNA. What is the defining characteristic of a reciprocal translocation?

Two nonhomologous chromosomes exchange arms (or parts of arms).

A reciprocal translocation is characterized by the exchange of segments between two nonhomologous chromosomes. This results in a rearrangement of genetic material, but typically no net gain or loss of DNA. Familial Down Syndrome can be caused by a Robertsonian translocation, which is a specific type of non-reciprocal translocation.

An alteration in the DNA from an AT base pair to a TA base pair is called a ___.

Transversion (point mutation)

An insertion of a single base pair in the DNA strand is called a ___ mutation.

frameshift 

Which repair mechanism(s) involve(s) the removal of several nucleotides? 

Nucleotide excision repair (NER)

• removes bulky lesions

• Strands of DNA are separated and held apart by SSB

• Enzyme cleaves sugar phosphate bonds on both sides of lesion removing several nucleotides including the defective area

Mismatch repair (MMR)

• Mismatch repair proteins recognize abnormal helical structure and identify the incorrect base.

• Exonucleases remove an area of the new strand from the methylated sequence to the mismatch.

• DNA polymerase fills in the gap and ligase seals the nick.

• Does not remove lesions (damaged DNA)

An organism described as 2n=4 has the chromosomes below with genes indicated by letters and centromeres indicated by periods. Select the BEST description of the chromosome aberration present in this organism.

EGHI.LNP          EI.LNP          QT.VWZ          QT.VWZ

Interstitial Deletion

• requires 2 breaks 

Barbara McClintock was awarded the Nobel Prize in 1983 for her discovery of "jumping genes." What are these genetic elements formally known as, and how do they generally cause mutations?

They are called transposable genetic elements (transposons), and they cause mutations by moving from one site to another, disrupting genes or regulatory areas.

Unequal crossing over between homologous chromosomes during meiosis can lead to frameshift mutations. How does this process result in insertions or deletions in the genetic material?

Misalignment of homologous chromosomes during crossing over leads to one chromatid receiving an insertion and the other receiving a deletion of genetic material.

Which type of chromosomal aberration involves a segment of a chromosome being lost?

Deletion

A deletion is a chromosomal aberration where a part of a chromosome is missing. A terminal deletion, specifically, results in an acentric fragment (a segment without a centromere) that is lost during cell division, leading to genetic imbalance. Cri du Chat syndrome is an example of a human disorder caused by a deletion.

An alteration in the DNA from an AT base pair to a CG base pair is called a ___.

Transversion

An organism described as 2n=4 has the chromosomes below with genes indicated by letters and centromeres indicated by periods. Select the BEST description of the chromosome aberration present in this organism.

HJM.PRTZ          M.PRTZ          DF.GJH          DF.G

Nonreciprocal Translocation

Part of one chromosome is moved to a non-homologous

chromosome.

Types of aberrations? (deletions and duplications)

Deletions: missing part of chormosome

• Terminal deletion. Produces acentric fragment which is lost during cell division. Gap in Chromosome

• Interstitial Deletion: requires 2 breaks. loop structure.

Duplications

• tandem duplication:

• reverse tandem

• displaced same arm (homobrachial)

• displached different arm (heterobrachial)

What is the difference between an autopolyploid and an allopolyploid?

Autopolyploids have extra sets of chromosomes identical to the normal chromosome set, originating from the same species, while allopolyploids have combined sets of chromosomes from different species.

*Polyploidy - more than 2 copies of haploid genome.

What is an example of DNA modification contributing to epigenetic inheritance?

Imprinting of genes conveyed by parent to offspring, where only one copy of a gene is expressed.

Which of the following regulatory DNA sequences is required for transcription of nearly all RNA Pol II genes?

Core (Basal) Promoter

Which of the following eukaryotic gene regulatory mechanisms acts after transcription has occurred?

differential splicing of RNA transcript

The enzyme histone deacetylase _____________ the association between DNA and histones.

tightens

*acetylation refers to loosening DNA 

DNA ______________________  the histones before transcription occurs.

unwinds from

*allow the DNA bound to the nucleosome to be more exposed and more able to bind transcriptional activators.

High concentrations of the ___ protein stimulate the development of anterior structures in D. melanogaster.

Bicoid

Bicoid mRNA is anchored at anterior end.

• represses caudal 

• stimulates hunchback

Nanos mRNA is anchored at posterior end.

• inhibits 

A plant species is described as 2n=32.

 

How many chromosomes present in a triploid cell from this plant?

48

A plant species is described as 2n=32.

 

How many chromosomes present in a monosomic cell from this plant?

31

A plant species is described as 2n=32.

 

How many chromosomes present in a double trisomic cell from this plant?

34

A plant species is described as 2n=32.

 

How many chromosomes present in a nullisomic cell from this plant?

30

In which type of regulation is transcription normally off and turned on when a small molecule binds to a regulatory protein?

Inducible control

Which characteristic best describes a riboswitch?

An RNA sequence within mRNA that affects its own translation.

Riboswitches are specific RNA sequences located within the messenger RNA (mRNA) itself. These sequences can fold into different secondary structures in response to binding small molecules, and these structural changes directly influence whether the mRNA is translated into protein.

What happens to the cAMP-CAP complex and Lac operon activation when glucose is present?

cAMP levels are low, and the cAMP-CAP complex does not effectively activate the Lac operon.

Glucose presence inhibits cAMP formation, leading to low cAMP concentrations. As a result, the cAMP-CAP complex does not form or binds inefficiently to the DNA, thus preventing the positive activation of the lac operon. This mechanism, known as catabolite repression, ensures that the cell preferentially uses glucose when available.

Select the type(s) of prokaryotic regulation that fit(s) the description below:

Transcription occurs with high levels of the small molecule (effector).

Positive Inducible, Negative Inducible

Why is regulation by attenuation primarily restricted to prokaryotes?

Prokaryotes lack a nucleus, allowing transcription and translation to be coupled.

Attenuation relies on the coupling of transcription and translation. In prokaryotes, both processes occur simultaneously in the cytoplasm, allowing the ribosome's progress on the mRNA to directly influence the secondary structure of the nascent mRNA, which in turn affects RNA polymerase's ability to continue transcription. Eukaryotic cells separate transcription (nucleus) and translation (cytoplasm), making this coupled regulation impossible.

What is the effect of attenuation in the Trp operon when tryptophan levels are high?

It leads to premature termination of transcription.

When tryptophan is abundant, the ribosome translates the leader sequence quickly. This allows region 2 to be covered by the ribosome, enabling regions 3 and 4 to pair. The pairing of regions 3 and 4 forms a hairpin structure that acts as a transcriptional termination signal, leading to the premature termination of transcription.

What is the primary function of the Trp operon?

To synthesize tryptophan.

The Trp operon is an anabolic operon, meaning it is responsible for the biosynthesis of tryptophan. It contains genes (trpE, trpD, trpc, trpB, trpA) that encode enzymes necessary for tryptophan synthesis.

A mutation occurs in an operon that prevents the transcription factor from binding to its recognition site on the DNA. In which type(s) of gene regulation would this mutation result in constitutive expression of the structural gene?

negative repressible, negative inducible

In this mutant, preventing the transcription factor from binding to DNA results in constitutive expression. For a mutation in the regulatory protein or its binding site to result in constitutive expression, the protein must be a repressor, and the operon must thus be under negative control. 

What are the main categories of gene expression regulation in eukaryotes?

Changes in chromatin, initiation of transcription, RNA processing and stability, and protein modification

These four categories represent the major levels at which gene expression is regulated in eukaryotes

Why are Bicoid and Nanos considered "maternal-effect" genes in Drosophila?

Because their mRNAs are deposited into the egg by the mother during oogenesis, and their translation after fertilization dictates the embryo's anterior-posterior axis

What is the primary function of homeotic genes in Drosophila development?

To determine the identity of each segment, ensuring that appropriate structures develop in the correct body region.

Regarding eukaryotic and prokaryotic regulation, which process seems to be the most similar between the two?

Transcriptional Regulation

High levels of methylation of the base ____ are associated with low levels of gene activity.

Cytosine

A(n) _____ in acetylation of histones is associated with an increase in transcription.

increase

If there are no mutations in the flower development genes of Arabidopsis thaliana, then determine the structures present in each whorl, beginning with the outermost whorl and ending with the inner most whorl. If a whorl does not contain the normal structure for that whorl as found in a normal flower, then choose the word "mutant".

Whorl #1 (outermost)	sepals
Whorl #2	petals
Whorl #3	stamens
Whorl #4 (innermost)	carpals

In D. melanogaster, the Gap genes ....

Are regulated by the gradients established by the bicoid and nanos proteins.

Regulate the expression of pair-rule genes.

A plant species is described as 2n=40.

 

How many chromosomes present in a nullisomic cell from this plant?

38

(n-2)

A plant species is described as 2n=40.

 

How many chromosomes present in a double trisomic cell from this plant?

(n+2) 

42

A plant species is described as 2n=40.

 

How many chromosomes present in a monosomic cell from this plant?

39

A plant species is described as 2n=40.

 

How many chromosomes present in a triploid cell from this plant?

60

have 3 copies of every chromosome

(40/2 sets of chromosomes) = 20 chromosomes

20× 3 copies = 60

• In mutants lacking B, transcription of M does occur

• In mutants lacking H, transcription of M does not occur.

• In double mutants lacking B and H, transcription of M does occur.            

H —|  B —| M 

How are homeotic genes organized in Drosophila?

They are organized into two major gene clusters (Antennapedia and Bithorax complexes) on the same chromosome, and their order on the chromosome often corresponds to the anterior-to-posterior body regions they affect.

What is the primary effect of histone deacetylation on gene expression?

It tightens the association between histones and DNA, typically repressing transcription.

Histone Deacetylases (HDACs) remove acetyl groups, making histones more positively charged, which increases their affinity for DNA and tightens chromatin, generally reducing gene expression.

What are the typical pairing possibilities for chromosomes during meiosis in an autotetraploid (AAAA)?

Two bivalents, one quadrivalent, or a univalent and a trivalent.

In eukaryotes, repressors can function by:

binding to the regulatory promoter

Repressors are proteins that inhibit gene expression by preventing RNA polymerase from accessing the promoter region of a gene, thus blocking transcription.

Histone modifications during chromatin remodeling can include additions of all of the following except ____.

Acetyl groups

Phosphate groups

Methyl groups

Amino groups

Amino groups

Transcriptionally acive DNA is _______ tightly coiled than DNA that is not being transcribed.

less

Which class of genes is most likely to be mutated in a D. melanogaster organism that has antennae where its front legs should be?

Homeotic Genes

High concentrations of the ___ protein stimulate the development of anterior structures in D. melanogaster.

Bicoid

DNA ______________________  the histones before transcription occurs.

unwinds from

The enzyme histone deacetylase _____________ the association between DNA and histones.

tightens

Which of the following eukaryotic gene regulatory mechanisms acts after transcription has occurred?

differential splicing of RNA transcript

Which of the following regulatory DNA sequences is required for transcription of nearly all RNA Pol II genes?

Core (Basal) Promoter

What is an example of DNA modification contributing to epigenetic inheritance?

Imprinting of genes conveyed by parent to offspring, where only one copy of a gene is expressed.

What is the difference between an autopolyploid and an allopolyploid?

Autopolyploids have extra sets of chromosomes identical to the normal chromosome set, originating from the same species, while allopolyploids have combined sets of chromosomes from different species.

Below is the final functional kappa light-chain protein produced from germline DNA for the kappa light-chain in humans in a mature B-cell.

V2

J3

C

Mature B-cell DNA

pre-mRNA

mRNA

V1, V2, V3, V4, V5

J1, J2, J3, J4, J5

C

Mature B-cell DNA: V1, V2, J2, J4, J5, C

pre-mRNA: V2. J2, J4, J5, C

mRNA: V2, J3, C

Why is it that mutations in bicoid and nanos exhibit genetic maternal effect in Drosophila (a

mutation in the maternal parent produces a phenotype that shows up in the offspring), but

mutations in gap genes and pair rule genes do not?

Bicoid and nanos mRNAs are produced during oogenesis by the mother and deposited in the egg. Therefore, the amounts of these mRNAs in the zygote depend only on the mother’s genotype, and these genes exhibit genetic maternal effects. In contrast, Gap and pair rule genes are transcribed after fertilization from the zygote’s own chromosomes. For these latter genes, the zygote’s phenotype depends on its own genotype.

explain how genetic changes can impact biochemical pathways and how phenotypes can result from these changes

if there is a mutation in a gene coding for an enzyme different phenotypes can occur

wildtype: growth mutant: no growth

Somatic vs Germline mutations

somatic mutations occur in nonreproductive cells and are passed to new cells through mitosis, creating a clone of mutant genes

germline mutations occur in cells that give rise to gametes. meiosis and secual reproduction allow germ-line mutation to be passed to approximately half the members of the next generation who will care the mutation in all their cells

Loss of function vs gain of function mutations

loss of function:

• Causes complete or partial absence of protein function.

• Loss of function mutations are recessive acting

gain of function

• Causes the cell to produce a protein that is not normally present.

• Either a new gene product or a gene product in new location or at a new time in development.

• Gain of function mutations are dominant acting (usually).

types of point mutations

Missense (nonsynonymous): Changes the amino acid (may alter protein function or protein is nonfunctional). Neutral: a missense mutation that doesn’t affect protein function

Nonsense: Changes codon so that it becomes a stop codon.

Silent (synonymous): Codes for the same amino acid.

Readthrough: Stop codon is changed to a codon that codes for amino acid resulting in a longer protein.

Spontaneous Point Mutations

Depurination

• Removes the glycosidic bond at either G or A bases.

• Results in an apurinic site (missing purine).

Deamination of Cytosine

• Results in Uracil.

• Causes GC to AT transition.

Wobble Base Pairing

• Mispairing due to flexibility in helix.

• Results in transitions after replication.

common causes for spontaneous frameshift mutations

Strand slippage in replication (new strans loops out resulting in addition of a nucleotide)

unequal crossing over can cause one product to have an insertion and the other to have a deletion

repreat regions that cause hairpins

how can mutagens cause mutations?

X rays

• Chromosome breakage leads to aberrations by breaking phosphodiester bonds.

• X rays can also damage bases and cause point mutations.

UV Light

• Mainly Thymine dimers (pyrimidine dimers)

• Dimers distort the helix and inhibit replication.

Transposons in genes

• Ac (Activator) – complete transposable element with functional transposase and repeats.

• Ds (Dissociation) – lacking functional transposase gene (deletion) so it requires the AC transposase to move.

Types of DNA repair mechanisms

DNA polymerase

• DNA polymerase stalls replication

• Exonuclease from the DNA polymerase removes incorrect nucleotide and DNA pol inserts correct

Mistmatch repair (MMR)

• Mismatch repair proteins recognize abnormal

helical structure and identify the incorrect base.

• Exonucleases remove an area of the new strand

from the methylated sequence to the mismatch.

Nucleotide Excision rapair

• removes bulky lesions (unlike MMR)

Base Excision repair

• removes modified based

Double Strand Break Repair

• homologous recombination and nonhomologous end joining (more dangerous)

Translesion DNA pol

• Specialized polymerases that can bypass lesions on the DNA during replication.

Chromosomal Aberrations : Inversions and Translocations 

Paracentric Inversion: inverted area does not include centromere

Pericentric Inversion: inverted area does include centromere

Transolcations

• Reciprocal Translocations: Two nonhomologous chromosomes exchange arms (or parts of arms).

• Non-reciprocal translocations: A segment from one chromosome is moved to a nonhomologous chromosome.

• Rebertsonian translocations: Two telocentric/nearly telocentric chromosomes combine to make one larger, more metacentric chromosome.

*Assume ½ alternate and ½ adjacent-1. Therefore ½ the gametes are viable.

Robertsonian Translocations

Two smaller chromosomes break near centromere. Small pieces get lost and larger pieces fuse to produce one larger chromosome.

Familial Down Syndrome can be due to either Robertsonian translocation or isochromosomes.

• Robertsonian translocation by joining chromosomes 14 and 21.

Positive vs Negative control regulation

• Positive Control: Regulatory protein (Activator) binds to DNA to stimulate transcription.

• Negative Control: Regulatory protein (Repressor) binds to DNA to prevent transcription

Inducible vs. Repressible Control

• Inducible Control: Transcription is normally off and is turned on when a small molecule binds the regulatory protein.

• Repressible Control: Transcription is normally on and is turned off when a small molecule binds the regulatory protein.

Cis vs Trans acting mutations of the lac operon 

Cis Acting

• Action of an element affects only the genes adjacent to it.

• E.g. operator and promoter elements

Trans Acting

• Diffusible product is produced. The mutant gene does not have to be adjacent to the other genes to affect them.

• E.g. repressor

Tryp operon

• makes tryptophan

• negative repressible control 

• attenuation: premature termination of transcription when trp is high (3/4 bind)

• when 2/3 bind it does not terminate transcription

the lac operon genes used as an example

positive and negative inducible control

post trancriptional regulation

Anti-sense RNA are small RNA molecules complementary to parts of the mRNA. They base pair to the mRNA and inhibit translation.

Riboswitches also Regulate at the Level of Translation

Levels of Regulation in Eukaryotes

Changes in Chromatin

• Histone modification

• Chromatin remodeling

• DNA methylation

Initiation of Transcription

• Transcription factors (Activators, Repressors)

• Transcription factor binding sites

• Insulators

RNA Processing and Stability

• RNA splicing

• RNA degradation

• RNA interference

• Protein Modification

epigenetics 

Heritable changes in gene expression that occur without changing the DNA sequence.

methylation of histone/DNA

• Histone Methylation can activate or repress expression of a gene (usually repress).

• DNA methylation by DNA methyl transferases tends to cause genes to be turned off (silencing).

• In general, an increase in methylation results in decreased

transcription of DNA.

different types of regulatory DNA sequences that affect the initation of transcription in eukaryotes

Core (basal) promoter

• Basal transcription apparatus binds.

• Includes RNA polymerase and general transcription factors

• Required for transcripti

Regulatory promoter

• Specific transcription factors bind. specific to individual genes. regulate when and how often a gene is transcribes

Transcription factor binding sites

• trancription factors bind (enhancers, silencers, regulatory promoter)

insulators : cis DNA elements that block transcription factors from interacting with the wrong gene.

RNA processing and stability in drosophila

• Sxl (sex lethal) is the master regulator of sex determination in Drosophila.

• Ratio of X chromosomes to autosomes determines whether or not Sxl will produce a protein.

• Processing occurs to make a functional tra protein in females and a nonfunctional tra protein in males.

-Gene product at one locus directs splicing of pre-mRNA at next locus to cause development to go along one path or the other.

RNAi gene regulation in eukaryotes

RNAi in eukaryotes shuts off gene expression using double stranded RNAs

RNA stability in eukaryotic gene expression

• Amount of protein synthesized depends on availability of mRNA for translation.

• Amount of mRNA available depends on rates of synthesis and rates of degradation.

• Ribonucleases

- Poly A tail is shortened by RNAses.

-Once tail is at critical length, 5’ cap is removed.

-RNA is then degraded from the 5’ end.

• RNAi

immune system immunity 

• Humoral Immunity: Antibodies are produced by B cells.

 5 classes depending on type of constant region on heavy chain.

Phagocytosis destroys antibody bound antigens/cells.

• Cellular Immunity: Action of T cell receptors.

immune system somatic recmbination and diversity

somatic recombination in B-cells during B-cell differentiation

• DNA processing to choose constant region, joining region and variable

• region for both the heavy and light chains.

somatic mutations: (up to 2% of sequence is altered in variable area of chains which is the part that binds antigen).

Allopolyploid

• May be able to propagate through mitosis.

• Nondisjunction leads to doubling creating amphidiploid (contains two diploid genomes)

Amphidiploid

An allopolyploid that behaves like a diploid in meiosis.

• Most common natural form of polyploidy in plants since balanced gametes are formed in meiosis.