Exam 1 For Practice

*During which sub-stage of Prophase I does the synaptonemal complex form?

Zygotene

Which sub-stage of Prophase I does the DNA condense from chromosomes?

Leptotene

Which sub-stage does crossing over occur?

Pacytene

Which sub-stage of Prophase I does the synaptonemal complex degrade, but chromosomes remain together through cohesion?

Which sub-stage of Prophase I results in the preparation for metaphase with the chromosomes approaching the middle?

Diakinesis

*Gene "A" in a triploid organism controls poison production. In a population, 9 different alleles for this genes have been identified. Of these 8, how many alleles might any one individual have?

3

*Gene "A" in a tetraploid organism controls poison production. In a population, 9 different alleles for this gene have been identified. Of these 9, how many alleles might any one individual have?

4

*At which stage of meiosis does ALL cohesion become degraded?

Anaphase II as sister chromatids separate

What phase do chromesomes line up and kinetocore microtubles attach to sister chromesomes?

Metaphase II

Which phase of meiosis is responsible for independent assortment?

Metaphase I

If non-disjunction occured in the male gamete during meosis I and fused with a properly generated female gamete, which zygote would be possible?

XXY; because 2 X's make a female and the Y is a male chromesome

Which phase of meiosis does a nuclear envelope reform with 4 genetically different haploid cells?

Telophase II

Which phase of meiosis prepares for metaphase and deals with crossing over?

Prophase I

Which phase of meiosis do homologous chromosomes separate with sister chromatids remaining attached?

Anaphase I

OY

nonviable zygotes

XY

male sex chromosomes

XXX

triple X syndrome that only affects females

XYY

Jacobs syndrome

XO

Turner syndrome

Using binomial expansion, what is the probability of a couple having 2 girls and 1 boy, assuming the probability of a boy is p= 1/2 and the probability of a girl is q= 1/2 (p^3 + 3p^2q + 3pq^2 + q^3 =1)?

3/8

Using binomial expansion, what is the probability of a couple having 2 girls and 1 boy, assuming the probability of a boy is p= 1/2 and the probability of a girl is q= 1/2? (p^4 + 4p^3q + 6p^2q^2 + 4pq^3 + q^4 =1)

1/4

Mitochondrial Inheritance Pattern

passed by female only, passed to all offspring of affected female

Autosomal dominant

passed down when only one copy of a mutated gene is needed for the condition to manifest

Autosomal recessive

occurs when an individual inherits two copies of a mutated gene, one from each parent, on a non-sex chromosome

X-linked dominant

no M-to-M transmission; affected M passes trait to all daughters, every generation; affected F passes trait to both sons and daughters; a single mutant allele can produce the disease.

X-linked recessive

carried by females and affects males

*You perform a dihybrid cross of two dogs with black fur and droopy ears. What is the probability of a pup also being black furred with droopy ears if the ear gene is only 55% penetrant?

31%

*You perform a dihybrid cross of two dogs with black fur and droopy ears. What is the probability of a pup being black furred with non-droopy ears if the recessive, non-droopy ear gene is only 20% penetrant?

3.8%

*Genes A produces an enzyme that converts a colorless compound into a yellow pigment. Gene B produces an enzyme that uses that previous yellow pigment as a substrate to create a red pigment. Assume recessive, null mutations exist for both of these genes. Which of the following would best describe the effects of these mutations?

Genotype aa produces the same recessive phenotype regardless of the genotype for gene B

*How would you describe the genetic interaction between genes A and B in the previous question?

A is epistatic to B

*Beards in goats is a sex-influenced trait. A bearded male goat with genotype B1B2 is crossed with a beardless female goat with genotype B1B2. If B2 promotes beard growth, what is the probability of having bearded offspring?

50%

*Beards in goats is a sex-influenced trait, such that a heterozygous male grows a beard while a heterozygous female will not. A bearded male goat with genotype B1B2 is crossed with a beardless female goat with genotype B1B1. If B2 promotes beard growth, what is the probability of having bearded offspring?

25%

To solve biochemical pathways:

For vertically (letters/words): Least + to Most +

For horizontally (genes/mutants): Most + to Least +

Which of the following would you find in a Sanger sequencing reaction but not in a polymerasechain reaction?

Answer is ddNTPs; terminate sequences which is not used in PCR since PCR aims to copy full DNA

-dNTPs; amplify DNA in PCR without termination

-DNA template; need to start either of the processes

-DNA polymerase; builds new DNA strand by adding new nucleotides to both sequences

-DNA primer; it gives DNA polymerase a place to start sequencing

You wish to create a mutation that prevents access of RNA polymerase to the gene. Which region of a gene would you mutate?

The answer is promoter Sequence: Is the specific DNA sequence upstream that RNA polymerase binds to to start translation, so a mutation would prevent RNA polymerase from binding and would not transcribe.

-Coding Sequence: is the part that contains the instructions, so mutating that changes the entire protein.

-Start codon: signals where translation begins, the mutation would prevent the ribosome from starting translation, but RNA polymerase would still bind.

-Terminator sequence: Is the sequence that tells RNA polymerase to stop, so if it mutates, it may transcribe too long. -Stop Codon: signals end of translation and mutation would affect protein synthesis and not transcription

You wish to create a mutation that produces an abnormally long protein, but the size of the mRNA appears to be the same. Which region of a gene was likely mutated?

stop codon because there was signal to stop the coding of the mRNA and therefore, the protein grows

terminator sequence?

coding sequence?

promoter sequence?

would cause the size of mRNA to get longer

contains instructions to make the protein, so the protein structure would have changed instead

it would not get transcribed period

Translate the following mRNA: 5' cap CAGUGGCAUGGACUGCUGA

Met-Asp-Cys

Translate the following mRNA: 5' cap CAGUGGCAUGGAGUGG

Met-Glu-Trp

In producing an E. coli plasmid to be an expression vector, an experimenter includes genes for selectable markers and a promoter for the expression of the introduced genes. She uses a cDNA sequence to ensure the insert contains no introns. The gene inserted is transcribed, but not translated. What sequence did she omit from the plasmid?

Answer is Shine-Dalgarno Sequence, it initiates translations in prokaryotes; it is a ribosome binding site upstream from the start codon and guides it there to start translation.

RNA polymerase II occurs in

transcription

What is a eukaryotic transcription factor that bringd RNA Polymerase II to the ribosome?

TFIID

What is the TATA box and what binds to it?

The TATA box is a place for eukaryotic RNA to bind DNA

The gene encoding sigma factor 32 has been deleted. Which of the following would likely be the consequence of this?

Transcription will fail to initiate at a subset of prokaryotic genes

The gene encoding sigma factor 32 has been deleted. Which of the following would likely be a consequence of this?

Transcription will fail to initiate at a subset of prokaryotic genes since sigma is needed to bring RNA Pol II

A chemical that inhibits Poly-A polymerase is added to a eukaryotic cell. What effect might you expect?

a global reduction of MRNA half-lives

A tRNA synthase (the enzymes that charge tRNAs) has been mutated so that instead of binding tryptophan, it binds to histidine. How much would this affect the cell?

The tryptophan of all proteins will be replaced with histidine

Secondary structures of proteins is determined by what?

H-bonds between the backbones of amino acids

What is true regarding post-translational modifications of a protein?

Answer is Poly-ubiquitination tags proteins for degradation by the proteasome. If you delete the sites where ubiquitin normally attaches, the protein may not get recognized for degradation, and therefore last longer in the cell.

-Phosphorylation can either activate or deactivate a protein, depending on the protein and context.

-Splicing happens at the RNA level (pre-mRNA splicing), before translation

-Phosphatases remove phosphate groups, and this can either activate or deactivate a protein.

The signal sequence of a secreted protein has been mutated. What is a likely effect of this?

The answer is the protein will localize in the cytoplasm instead of the extracellular matrix; Without a functional signal sequence, the ribosome will not dock at the ER, and the protein will just stay in the cytoplasm, never reaching the extracellular space.

-Protein Structure will be altered; A mutation in the signal sequence doesn't necessarily change the protein's folding or 3D structure

-The protein will aggregate in the extracellular matrix; If the signal sequence is mutated, the protein won't even get to the extracellular matrix.

-The protein will always be in an activated state; the mutation affects localization, not necessarily the protein's activity

What assists DNaA to achieve its function?

AT-rich DNA sequences in the orgins

What removes primers?

DNA polymerase I

What is processivity and what increases processivity?

processivity is about how many nucleotides an enzyme can add without falling off the DNA. This is aided by the sliding clamp, not exonuclease activity.

What relieves torsional strain of supercoiling?

topoisomerase

What is the function of DNA polymerase III exonuclease activity?

reduce mutation rate; because DNA pol III is responsible for proofreading and removing matches

Why the other answers are wrong for this question: Which of the following assists/allows DnaA to achieve its function? A. AT-rich DNA sequences in the origin B. DnaC recruiting DnaA to chromatin C. Synthesis of RNA primers at the replication fork D. Topoisomerase relieving supercoiling upstream of the replication fork

B. DnaC recruiting DnaA to chromatin❌ Wrong — DnaC doesn't recruit DnaA.

DnaC helps load DnaB (the helicase) onto DNA after DnaA has already opened the origin.

DnaA acts first — DnaC works later in the process.

C. Synthesis of RNA primers at the replication fork❌ Wrong — RNA primers are made later, after helicase has unwound the DNA and DNA polymerase needs a starting point.

This has nothing to do with DnaA's initial function of opening the origin.

D. Topoisomerase relieving supercoiling upstream of the replication fork❌ Wrong — Topoisomerase (like DNA gyrase) acts after the DNA is unwound to relieve tension ahead of the fork.

It's important for replication overall but doesn't assist DnaA specifically.

A strain of bacteria has been made in which the shine-dalgarno sequence of the lac repressor gene is deleted. Which of the following scenarios would be true regarding transcription of the lac operon in this mutant?

High transcription in all media types: Since there is no functional repressor, the lac operon is transcribed all the time, regardless of glucose or lactose levels.

Which type of mutation is possible due to the redundant nature of the genetic code?

Silent because the code does not change

Which type of mutation is possible due to a change in one amino acid?

Missense

Which type of mutation is possible due to an addition of a stop codon?

Nonsense

Which type of mutation is possible due to a change in the reading frame?

Frameshift

Splice site mutations

Alters a site where an intron is normally removed from mRNA

Which of the following is able to cause a change in a reading frame?

Deletion because most frameshift mutations are caused from indel mutations

Which of the following is able to cause a change with purines to pyridines?

tranversion

Which of the following is able to cause a change with purines to another purine or pyridine to another pyridine?

transitions

Transposons can integrate into the promoters of genes, what is the most likely outcome of such event?

altered gene expression

Transposons can integrate into the coding sequences of genes, what is the most likely outcome of such event?

frame shift

Transposons can cause base substitutions of genes, what is the most likely outcome of such event?

point mutation

How would you interpret an Ames test in which his- bacteria are able to form colonies on histidine-deficient media after exposure to either a test compound OR a test compound mixed with S9 extract but cannot form any colonies when exposed to a control substance mixed with S9 extract

The test compound is mutagenic in isolation AND when metabolized by an animal

Transposons can cause base modifications of genes, what is the most likely outcome of such event?

deamination

You are doing a screen, and you have found a mutation in Mdm2, which you remember from genetics class is important for degrading p53. However, now that the gene has been mutated (loss of function mutation), what might you expect to happen in this cell?

p53 would trigger apoptosis even in the absence of DNA double strand breaks

nucleotide excision repair

removes bulky lesions like thymine dimers. Not dependent on methylation

translesion synthesis

a bypass mechanism to replicate across damaged DNA, not directly related to methylation

NHEJ

repairs double-strand breaks; again, not methylation dependent.

A neuron is a terminally differentiated cell, meaning it typically no longer divides. A neuron was blasted with ionizing radiation, which resulted in a double strand break. Which DNA repair pathway will this cell most likely use?

Non-homologous end joining

SDSA (homologous recombination)

need template strand to rejoin double stranded breaks

A mutation in which of the following will create a frameshift mutation?

Insertion within the coding sequence of an mRNA

Base excision repair

fixes small damaged bases like uracil or oxidized bases. Not dependent on methylation.

A bacteria cell has reduced DNA methylation capabilities meaning that it takes the cell a longer amount of time to methylate its DNA. Which DNA repair mechanism will directly be affected?

Mismatch repair (MMR) uses the methylation mark to tell which strand is the original (correct)

Which of the follow is true for 3rd generation sequencing (Oxford Nanopore)?

Capable of sequencing very long DNA sequences by detecting changes in electrical current

Gene regulation in eukaryotes often involves which of the following, which are not also used by prokaryotes?

histone modification because it deals with eukaryotes and chromatin structure; which changes via histones undergoing HAT or HDAC

Gene regulation in prokaryotes often involves which of the following?

formyl methionine, promoters, transcription factors, and coupled transcription and translation

Which scenario would you expect to have high transcription of the lac operon?

the lac operon is inducible and deals with open transcription leading to more lactose and less glucose, increasing cAMP ; therefore, lac repressor mutant with DNA-binding domain deleted grown in glucose and lactose deficient media

A bacterial cell has an abundance of tryptophan in its culture media. Which of following would result in this scenario?

The ribosome will translate through the first region of the trp operon, but will produce a termination loop in the mRNA, leading to transcriptional termination of the trp operon

Compile the partial sequences below to determine the entire sequence of the circular bacterial chromosome?

Strain 1: QEPTF

Strain 2: IRLAM

Strain 3: TPEQM

Strain 4: RIGFT

TFGIRLAMQEP

Imagine a merozygote that contains one copy of the lac operon containing the super-repressor mutant and one copy of the wild-type lac operon and repressor gene. If this cell is cultured in glucose-deficient and lactose-rich media, how would you describe the transcription of the lac operons?

Neither of the lac operons would be transcribed very highly

Which of the follow is true for 2nd generation sequencing?

Uses reversible terminators to sequence DNA by synthesis, requires fragmentation of DNA samples, requires PCR and bridge amplification of DNA samples

What tumor heterogeneity mean?

Answer: All of above:

- Primary tumors are genetically different from metastatic tumors in the same individual

- Cancer cells within as single tumor are genetically different

- Tumors are genetically different between patients afflicted with the same type of cancer

- Tumors are composed of tumor cells but also many other types of cells

Typically, H3K27me3 of histone tails leads to ______

Answer: Tighter packaging of the chromatin and reduced transcription: H3K27me3 condenses chromatin into a more closed, repressive state, which prevents transcription factors.

- Removal of the protein components of the chromatin from the DNA; H3K27me3 modifies histone proteins but doesn't remove them.

-Relaxed packaging of the chromatin and increased transcription; Methylation at H3K27 tightens chromatin, which decreases transcription, not increases it.

-Increased amounts of euchromatin relative to heterochromatin; Euchromatin = open, transcriptionally active chromatin. Heterochromatin = closed, transcriptionally silent chromatin.

Typically, acetylation of histone tails leads to ________.

relaxed packaging of the chromatin and increased transcription

in negative control, what molecule would you expect to find bound to the operator if there is no transcription?

repressor