Genetics 3 from lecture

What is the primary function of a promoter in eukaryotic transcription?

Promoters serve as recognition sites for transcription machinery and are critical for the initiation of transcription.

What is the difference between a core promoter and proximal-promoter elements?

The core promoter determines the accurate initiation of transcription, while proximal-promoter elements modulate the efficiency of basal transcription levels.

How do focused promoters differ from dispersed promoters?

Focused promoters initiate transcription at a specific start site, whereas dispersed promoters initiate transcription from several weak start sites.

What are the common DNA sequence elements found within a eukaryotic promoter?

Common elements include the Initiator (Inr), TATA box, TFIIB recognition element (BRE), Downstream promoter element (DPE), and Motif ten element (MTE).

What is the consensus sequence of the Initiator (Inr) element?

The consensus sequence is YYANA/TYY, where Y represents any pyrimidine.

What is the function of proximal-promoter elements like CAAT and GC boxes?

They are located upstream of the TATA/BRE motifs and serve to enhance the levels of basal transcription.

How do enhancers and silencers differ in their effect on transcription?

Enhancers increase transcription to maximum levels, while silencers repress the level of transcription initiation.

What are cis-acting transcription regulatory elements?

These are DNA sequences, such as promoters, enhancers, and silencers, that regulate the expression of genes on the same chromosome.

What are the two primary functional domains of transcription factor proteins?

The DNA-binding domain, which binds to specific regulatory DNA sequences, and the trans-activating domain, which interacts with other transcription factors or RNA polymerase.

What are three common DNA-binding protein motifs found in transcription factors?

The Zinc Finger, the Helix-Loop-Helix, and the Leucine Zipper.

What is the Pre-Initiation Complex (PIC)?

It is an assembly of general transcription factors and RNA Polymerase II at the promoter that provides a platform for transcription initiation.

What components make up Transcription Factor IID (TFIID)?

TFIID consists of 14 proteins, including the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs).

What is the role of DNA looping in eukaryotic transcription?

DNA looping allows activators, repressors, and general transcription factors bound at distant sites to come into the vicinity of the promoter.

What is an enhanceosome?

An enhanceosome is a complex formed by coactivators that enables activators to make contact with promoter-bound factors to stimulate transcription.

How do repressor proteins at silencer elements function?

They decrease the rate of PIC assembly and inhibit RNA Polymerase II release.

What are structural genes in the context of the GAL system?

Structural genes code for the enzymes required to transport and metabolize galactose.

What is the role of the UASG in the yeast GAL system?

UASG (Upstream Activating Sequence of GAL genes) acts as a central control region that positively regulates the transcription of GAL genes.

How does the presence of galactose affect GAL gene transcription?

The GAL genes are inducible; in the absence of galactose, they are not transcribed, but transcription begins immediately upon the addition of galactose.

What is the function of the hMTIIA protein product?

It binds to heavy metals to protect cells from toxic effects and oxidative stress.

What is the relationship between 'proximal' and 'distal' elements?

These are relative terms; proximal elements are located closer to the promoter than distal elements.

What happens when mutations occur in promoter regions?

Mutations in promoter regions can significantly alter the amount of mRNA produced.

What is the specific role of the trans-activating domain of a transcription factor?

It activates or represses transcription by interacting with other proteins, such as RNA polymerase or other transcription factors.

What is the function of the TATA box?

It is a key promoter element located approximately -30 base pairs upstream of the transcription start site that helps position the transcription machinery.

What is the primary difference between activators and repressors?

Activators increase the rate of transcription initiation, while repressors decrease it.

Why is the hMTIIA gene considered a model for transcriptional regulation?

It demonstrates the complex interplay between promoters, enhancer elements, and specific transcription factors in response to environmental stimuli like heavy metals.

What is the function of the MRE (Metal Response Element)?

The MRE is a regulatory DNA sequence that binds specific transcription factors to regulate gene expression in response to heavy metal exposure.

What is the primary function of GAL3 in yeast?

GAL3 interacts with galactose to produce a metabolite that activates the GAL genes.

Where does GAL80 bind to regulate GAL4?

GAL80 binds to a specific part of the GAL4 protein to inhibit its activity.

Define the genome vs. the proteome.

The genome is the complete sequence of an organism's genetic material, while the proteome is the complete set of proteins an organism can produce.

Why is the number of proteins in the human proteome significantly higher than the number of protein-coding genes?

This is primarily due to alternative splicing of mRNA transcripts.

What are snRNPs and what is their role?

Small Nuclear Ribonucleoprotein Particles; they bind to the ends of introns to facilitate their removal and the splicing of exons.

What are two potential evolutionary or functional advantages of introns?

Introns may facilitate the production of proteins with different domains and may aid in genetic recombination.

How does the calcitonin gene demonstrate alternative splicing?

It produces two different polypeptides (calcitonin and CGRP) by splicing different combinations of exons depending on the tissue type (thyroid vs. neurons).

What is the significance of the Dscam gene in Drosophila?

It can produce over 38,000 unique protein isoforms through alternative splicing, which are essential for guiding axon connections.

What is a spliceopathy?

A genetic disorder caused by mutations that affect the regulation of splicing, such as myotonic dystrophy.

What determines the steady-state level of mRNA in a cell?

It is determined by the balance between the rate of transcription and the rate of mRNA degradation.

What are the three primary pathways of mRNA degradation?

Shortening of the poly-A tail, removal of the 7-methylguanine cap (decapping), and internal cleavage by endonucleases.

What is the role of the proteasome?

It is a cylindrical structure that recycles proteins into amino acids.

What is the function of ubiquitin?

Ubiquitin acts as a tag that marks proteins for degradation by the proteasome.

How is p53 protein regulated in a normal cell?

p53 has a very short half-life and is rapidly degraded by the proteasome after being tagged with ubiquitin by the Mdm2 ligase.

What happens to p53 levels when a cell experiences DNA damage?

DNA damage activates kinases like Chk2, ATM, and ATR, which phosphorylate p53, preventing Mdm2 from binding and thus stabilizing p53.

What is the relationship between p53 and Mdm2?

p53 is a transcription factor that induces the expression of Mdm2, which in turn tags p53 for degradation, creating a feedback loop.

What are 'cassette exons' in alternative splicing?

Exons that may be excluded from the mature mRNA by joining the upstream exon directly to the downstream exon; this is the most common form of alternative splicing in animals.

What occurs during intron retention?

Noncoding introns are included in the mature mRNA, often leading to degradation or negative regulation of gene expression.

What are mutually exclusive exons?

A mechanism where the inclusion of one exon in a cluster necessitates the exclusion of others, allowing for the swapping of protein domains.

How do alternative promoters affect gene expression?

They provide different initiation sites for transcription, resulting in pre-mRNAs with different 5' exons.

What is alternative polyadenylation?

The process where different 3' ends are produced by skipping an exon containing a polyadenylation signal, thereby utilizing a downstream signal.

What is the role of SR proteins in splicing?

They bind to splicing enhancers and recruit spliceosome components to activate splicing.

What is the role of hnRNPs in splicing?

They bind to splicing silencers and inhibit the splicing process.

What is the Dscam gene's function in humans?

It codes for a transmembrane protein that promotes cell-cell interactions and is expressed at high levels in fetal tissue.

Why is the half-life of mRNA important for cellular regulation?

It allows the cell to adjust the amount of protein produced in response to changing environmental needs or metabolic signals.

What is the primary effect of Mdm2 binding to p53?

Mdm2 adds ubiquitin to p53, which targets it for degradation by the proteasome.

Why are double-strand breaks (DSBs) considered extremely dangerous to a cell?

They can result in chromosomal rearrangements, cancer, and cell death.

What are the two primary pathways for repairing double-strand breaks?

Homologous recombination repair and nonhomologous end joining.

During which cell cycle phases does homologous recombination repair typically occur?

Late S or early G2 phase.

What is the key mechanism of homologous recombination repair?

It recognizes the break, digests the 5' end to leave a 3' overhang, and aligns the 3' end with a complementary sequence on the sister chromatid.

When is the nonhomologous end joining (NHEJ) pathway typically activated?

In G1 phase, prior to DNA replication.

How does nonhomologous end joining repair a double-strand break?

A complex of proteins (which may include kinases and BRCA1) binds to the free ends of the DNA and ligates them back together.

What are transposable elements (TEs)?

Genetic sequences, often called 'jumping genes,' that can move within and between chromosomes.

What are insertion sequences (IS elements) in bacteria?

Simple bacterial transposons that can move to new locations and cause mutations if they insert into a gene or regulatory region.

What is the significance of larger bacterial transposons compared to IS elements?

They can carry multiple drug resistance genes and spread this resistance between bacterial strains by moving from plasmids to chromosomes.

What is the Ac-Ds system in maize?

A system of mobile genetic elements where the movement of the Dissociation (Ds) element is dependent on the Activator (Ac) element.

What is the difference between autonomous and nonautonomous transposable elements?

Autonomous elements can transpose by themselves, while nonautonomous elements require the assistance of an autonomous element to provide necessary gene products.

How can a transposable element cause a null mutation?

By inserting itself into a protein-coding region, thereby disrupting the protein's sequence.

What is the effect of a transposable element inserting into a gene promoter?

It can prevent the gene from being expressed or, if the TE contains its own promoter, cause the gene to be expressed inappropriately.

Who discovered mobile genetic elements in maize and received a Nobel Prize for it?

Barbara McClintock.

In the context of McClintock's maize research, what causes the speckled appearance of kernels?

The excision of a Ds element from the C gene during development, which reverts the gene to its functional state and allows pigment deposition in specific cells.

What is the role of the Ac element in the Ac-Ds system?

It is an autonomous element that produces the enzyme transposase, which allows both Ac and Ds to move.

What are retrotransposons?

Transposable elements that amplify and move within the genome using an RNA intermediate.

What are the two main proteins produced during the retrotransposition process?

Reverse transcriptase and integrase.

What is the function of reverse transcriptase in retrotransposition?

It transforms the RNA transcript of the retrotransposon back into double-stranded DNA.

What are Copia elements in Drosophila?

A class of DNA elements that are transcribed into copious amounts of RNA and are dispersed throughout the Drosophila genome.

What is hybrid dysgenesis in Drosophila?

A condition of high mutation rates and sterility caused by the rapid transposition of P elements in the germ line.

Why does crossing a P-strain male with an M-strain female result in hybrid dysgenesis?

The M-strain egg cytoplasm lacks the suppressor protein found in P-strain eggs, allowing P elements to transpose uncontrollably.

Why are crosses between P-strain females and M-strain males typically viable?

P-strain females produce a suppressor protein that prevents the transposition of P elements in the offspring.

How do geneticists utilize P elements in research?

They use them as tools for genetic analysis, specifically as vectors.

How are P elements utilized in Drosophila research?

They are used to produce transgenic organisms by injecting plasmids containing P elements and a specific gene into an egg, which then inserts the gene into the host cell's germ line.

What percentage of the human genome is composed of transposable elements?

Approximately half of the human genome.

What are the two main types of human transposable elements mentioned?

LINEs (Long interspersed elements) and SINEs (Short interspersed elements).

How do transposable elements contribute to evolution?

They contribute to genetic variability, which serves as the underlying basis for evolution.

What is a primary difference in transcriptional control between prokaryotes and eukaryotes?

Prokaryotic transcriptional control is generally limited to 'on/off' or simple levels, whereas eukaryotes have more complex processing that allows for finer control of gene expression.

What are the two structural features that distinguish eukaryotic genes from prokaryotic genes?

Eukaryotic genes are situated on chromosomes in distinct locations, and eukaryotic DNA is combined with histones and nonhistone proteins to form chromatin.

What is a 'chromosome territory'?

A discrete domain within the interphase nucleus where each chromosome stays separate from others.

What are interchromosomal domains?

Channels between chromosome territories that contain little or no DNA.

What are transcription factories?

Dynamic nuclear sites containing active RNA polymerase and regulatory molecules where transcription occurs.

How does histone acetylation affect transcription?

It decreases the positive charge of histones, reducing their affinity for DNA and increasing transcription.

Which enzymes catalyze histone acetylation?

Histone acetyltransferase enzymes (HATs).

What is the primary function of chromatin remodeling?

It involves repositioning or removing nucleosomes to make chromosome regions accessible to transcription regulatory proteins and RNA polymerase II.

What is the function of the SWI/SNF complex?

It loosens the attachment between histones and DNA and reorganizes internal nucleosome components to facilitate transcription.

What is a nucleosome?

The combination of DNA wrapped around a protein octamer called a histone.

What is the difference between heterochromatin and euchromatin?

Heterochromatin is highly condensed even during interphase and often contains inactivated DNA, while euchromatin is less condensed.

What is the effect of DNA methylation on gene expression?

It suppresses transcription by recruiting proteins that remove acetyl groups and block transcription factors from binding to promoters.

What is genetic imprinting?

A phenomenon where only one of the two inherited gene copies is expressed, based on the sex of the parent.

What are the essential components of a eukaryotic gene?

A coding region, a promoter, a polyadenylation site, and a terminal (stop) region.

What is the difference between exons and introns?

Exons are the coding regions of a gene that are translated, while introns are intervening sequences that are not translated.

Define 'cis-acting' in the context of gene regulation.

Refers to regulatory sequences located on the same chromosome as the gene they regulate.

Define 'trans-acting' in the context of gene regulation.

Refers to regulatory factors that are located on one chromosome but can regulate gene expression on a different (non-homologous) chromosome.

What are three examples of cis-acting sequences?

Promoters, enhancers, and silencers.

What is the role of a promoter in a gene?

It acts as the 'on/off' switch for transcription.

How does the addition of methyl groups to histones affect gene expression?

It generally suppresses transcription.