Learn: BIOL 3333 Exam 2 -- Fall 2024

The pre-initiation complex (PIC) contains several proteins. What would be the direct consequence be if PIC failed to form?

Transcription would not be initiated

In regards to mRNA stability, what is the effect of decapping enzymes?

The m7G cap of mRNAs is removed causing mRNAs to be degraded from the 5' end.

Which of the following would be an example of a cis acting eukaryotic gene regulatory element?

enhancer

A regulatory sequence of DNA that is 10,000 base pairs away from the gene it regulates is mutated. The result is that the gene being regulated is now expressed at a higher rate compared to when this regulatory sequence was not mutated. What would the wild-type sequence be called (before it was mutated)?

silencer

What is one cause for the 21,000 protein encoding sequences in the human genome producing between 200,000 and 1 million different proteins?

alternative splicing

The human genome contains many genes that encode antioxidant proteins. The transcription of these genes is upregulated using antioxidant response elements (AREs) when damaging oxidants flood the cell. Isothiocyanates (ITCs) are found in broccoli and other leafy green vegetables. It is known that when ITCs are added to cells grown in culture, the amount of antioxidant proteins increases in the cells.

As a nutrition scientist, you are interested in learning the mechanism behind ITCs. You hypothesize ITCs activate a protein which then binds to the ARE. You engineer (clone) a reporter construct using an ARE and luciferase and transfect the construct into HEK293 cells. What is the best prediction?

Adding ITC to the system will increase relative fluorescence units (RFU).

Which of the following statements about transcriptional regulation is false?

A response element binds to an enhancer

What is the result of a short polyA tail on an mRNA?

Translation of the mRNA is inhibited

What is the general name of enzymes that add phosphate groups to protein targets?

kinases

Which protein modification is most closely linked to protein degradation?

ubiquitination

Which of the following is the most common place to find DNA methylation?

on cytosines when adjacent to guanines

The sum of histone modifications and their interactions is called the ________.

histone code

All of the following are epigenetic mechanisms, EXCEPT ________.

changing gene expression by changing the nucleotide sequence through mutation

Which of the following statements about alternative splicing is true?

Exons can be spliced out of a transcript along with introns.

Which of the following is an example of genetic imprinting in humans?

In some allele pairs, only the paternal sourced allele is expressed, and for other allele pairs, only the maternal sourced allele is expressed.

What type of DNA sequence would a repressor protein bind to?

silencer

If a promoter region is mutated in such a way that it can no longer be methylated, what would the most likely effect be?

The gene linked to the promoter would be expressed at regular levels

The recessive disease Friedreich's ataxia is caused by a trinucleotide repeat in intron 1 of the FXN gene. Studies have shown the expansion causes decreased FXN expression, leading to the disease phenotype. Scientists have proposed several models of how the mutant locus might silenced. Which of the following is the most likely to cause silencing of the mutant FXN locus?

CpG methylation

What does HDAC do?

Deacetylates histone tails

Which protein in RISC cleaves the mRNA?

Argonaute

Which of the following categories of mutations is not possible to pass to offspring?

Somatic

What is alternative splicing?

One gene can encode more than one protein because different combinations of exons can be spliced together

What are housekeeping genes?

the genes that are constitutively expressed (always transcribed and translated), whose products are used for essential cell processes

Which of the following is a potential effect of transposons in the genome?

All of the above

What is the interchromosomal domain?

the space in between chromosomes where transcriptional machinery is located

XRN1 (exonuclease)

degrades mRNA from 5' end

Deadenylase

removes the polyA tail on the 3' end

Exosome (exonuclease)

degrades mRNA from 3' end

Decapping enzyme

removes cap on the 5' end

What makes up the Pre Initiation Complex?

General Transcription Factors and RNA polymerase

Which of the following is NOT a method used by chromatin remodeling complex to make genes more accessible to transcriptional machinery?

histone acetylation → CRC uses ATP to add acetyl groups to the histone core

Polymorphisms

cause genetic variation in a population

___ adds a phosphate group, ___ removes a phosphate group

Kinase, Phosephatase

Queen Victoria's family has an X-linked blood clotting disorder. What sort of mutation does her family have?

germ-line mutation

Mrs. Phillips knows she is a carrier for the autosomal recessive disease hemochromatosis. Mr. Phillips is affected with the disorder. The couple discovers that they are both carriers for cystic fibrosis, also an autosomal recessive disorder. What are the chances of them having a child with both disorders, assuming independent assortment of those genes?

1/8

What are conditionally expressed genes?

the genes that are expressed in response to the needs of the cell; they are only transcribed & translated circumstantially

Of the following, which is an example of epigenetic changes?

All are examples of epigenetic changes

This graph shows the effect of X-ray dose on number of mutations induced. What can you conclude from it?

That any exposure to X-rays will cause mutations

What are chromosome territories?

the defined regions of the nucleus where chromosomes segregate

Damage by which of the following is the most likely to result in frameshift mutations?

Intercalating agent, which inserts in between the base pairs

Mutations

are a change in the DNA sequence

What is the probability that two parents who are heterozygous for the recessive trait of albinism will have two albino offspring?

1/16

Which of the following can trigger the RNAi pathway?

siRNA and miRNA

A(n) ___ has all the machinery/genes within its sequence to transpose on its own

Autonomous element

Why does somatic mutation happen after conception?

Non-sex cells are divided by mitosis and are not passed to next generations

In a cross between two individuals BbGG X Bbgg, what ratio of phenotypes would be expected in the offspring if the two genes show independent assortment?

3:1

Mutations occur more often when a cell needs them

FALSE

Sister chromatids separate in

mitosis and meiosis II

Which of the following describes imprinting?

All of the above

How many different types of gametes can be formed by the genotype AaBbCc?

8

Crossing-over occurs in

meiosis I only

Which of the following statements does NOT accurately complete this statement: An epigenetic trait _________.

is a change in the DNA sequence

Which of the following is explained by Mendel's law of independent assortment?

The traits of eye color (w+/we) and body color (e+/eb) will be found in equal proportions in the offspring

Transcriptionally ___________ genes can show lower levels of adjacent histone acetylation compared with transcriptionally __________ genes.

Inactive, active

Dihybrid cross

Cross of true breeding parents that involve two types of interest

Monohybrid cross

Cross of true breeding parents involving one trait of interest

Reciprocal cross

A pair of crosses in which the phenotypes of females is different from the male and the phenotypes are switched in the second cross

What is chromatin remodeling complex?

a protein aggregation that is recruited by transcriptional machinery to change chromatin structure, so genes are accessible

In terms of somatic mutation, whether the mutant phenotype is visible depends on:

- Where the mutation is in the genome

- How much the mutation affects the gene product's function

- When it happened during development

Induced mutations

Mutagen damages DNA (ex: UV light, ionizing radiation etc.)

Spontaneous mutations

Mistakes during replication or recombination

Transversion mutation

change from a purine to a pyrimidine or a pyrimidine to a purine

Null allele

Gene product completely nonfunctional or absent from the cell

Nonsense mutation

a sense codon is changed to a nonsense (stop) codon

Missense mutation

change in a codon so a different amino acid is added

Frameshift mutation

Shift in reading frame so that a missense or stop results

Silent mutation

codon is altered but still codes for the same amino acid, also known as synonymous mutation

Transition mutation

change from a purine to a different purine or a pyrimidine to a different pyrimidine

Deleterious mutation

Mutation causes death

What makes replicative transposition different from conservative?

replicative is "copy and paste" and a reverse transcriptase

Which of the following about RNAi is true?

gRNA guides RISC to the mRNA through complementary base pairing

What is epigenetics?

Change in phenotype caused by mechanisms other than mutation

What targets a protein for degradation by the proteosome?

Ubiquitin

How is methylation of DNA connected to the acetylation of histones and gene expression? Choose all that are correct.

- When DNA is not methylated but histones are acetylated, it promotes expression of the DNA.

- When DNA is methylated and histones are deacetylated, it represses expression of the DNA.

Homologous chromosomes synapse during

meiosis I only

If a mouse has a dominant phenotype (P-), how would you determine if it is homozygous (PP) or heterozygous (Pp)?

Cross it to a mouse with the recessive trait.

What is the difference between Histone acetyltransferase and Histone deacetylase?

- HAT=acetylates/packing DNA loosens so genes are accessible

- HDAC=removes the acetylation/DNA packed tighter/Genes are silenced

Transcriptionally ___________ genes can show lower levels of DNA methylation compared with transcriptionally __________ genes.

Active, inactive

Repressors bind to

silencers

Activators bind to

enhancers

General transcription factors bind to

core promoter

How is miRNA different from siRNA?

- ssRNA with hairpin structure

- many mRNA targets

- not 100% complementary base pairing

- encoded in the cells genome

What enzyme methylates cytosines of CpG islands?

methyltransferase

While there are several mutations that give rise to cystic fibrosis, a common one results in a missing phenylalanine amino acid at position 508 of the CFTR protein. This is the result of ______.

the deletion of a single codon in the gene

Some animals like C. elegans do not have 5-methylcytosine, but do have methylated adenine. It is not known whether the methylated adenine plays the same role as methylated cytosine. If it does, which of the following would you predict?

That removing the methyl groups from adenines in C. elegans would increase gene expression

Which of the following is the target of the RNAi pathway?

mRNA

Germ-line (GLM) mutation is different from somatic (SM) mutation because

- GLM occurs in the sex cells where as SM happens after conception

- GLM is passed down to the next generation whereas SM is not transmitted to future generations

Why is gene regulation so complex in multicellular eukaryotes?

Controls different genes in different cells

Where does the majority of gene regulation occur in the central dogma, and why?

Transcription, because it's the first step

What is the difference between a housekeeping gene and a conditionally expressed gene? Give one example of each.

Housekeeping genes are always on; condition genes turn on only in specific conditions

Housekeeping gene: GAPDH

Conditionally expressed gene: HSP70

What is a chromosomal territory?

A distinct region in the nucleus where a chromosome resides

What is an interchromosomal domain?

A space between chromosomal territories

How are chromosomal territories and interchromosomal domains related to transcription?

Transcription occurs near interchromosomal domains for easy access to RNA-processing machinery

What is the function of the chromatin remodeling complex? What are the three major mechanisms of this complex?

It changes chromatin structure to regulate gene access.

Three mechanisms:

1. histone sliding

2. histone eviction

3. histone variant exchange

What makes up the pre-initiation complex (PIC)? Where does it assemble?

PIC is made of transcription factors and RNA polymerase; it assembles at the promoter.

What is made of DNA and upregulates transcription?

enhancer

What is made of protein and upregulates transcription?

activator

What is made of DNA and downregulates transcription?

silencer

What is made of protein and downregulates transcription?

repressor

What happens to the PIC when an enhancer is bound?

The PIC is stabilized and enhances transcription initiation