Module 4

siRNAs and miRNAs are produced by the cleavage of RISCs by endonucleases the cleavage of functional mRNA within the cytoplasm the cleavage of pre-mRNA in the nucleus the cutting and processing of double-stranded RNA by Dicer enzymes the cutting and processing of double-stranded RNA by Slicer enzymes

the cutting and processing of double-stranded RNA by Dicer enzymes

Which of the following is TRUE for both prokaryotic and eukaryotic gene expression? Alter transcription: a 3' poly A tail and 5' cap are added to mRNA RNA polymerase binds to the promoter region to begin transcription mRNA is synthesized in the 3' à 5' direction the mRNA is the exact complement of the gene from which it was copied

RNA polymerase binds to the promoter region to begin transcription

How does the availability of glucose in the environment affect the regulation of the lac operon? What is the term describing this regulation, and how is it accomplished? (short outline)

The availability of glucose is inversely proportional to the expression of the lac operon. When glucose is present, the lac operon is repressed and transcription does not occur. In the absence of glucose and the availability of lactose, the lac operon becomes operational and is expressed, and translation occurs. This regulation is called catabolite repression, where glucose is the favored source of energy. In the presence of glucose, adenyl cyclase does not form cAMP. But in the absence of glucose, cAMP is formed, and binds with CAP to bind to the CAP binding site on DNA. This binding allows for RNA polymerase to bind to the DNA also, and initiate transcription

A condition in which gene or group of genes is expressed all the time

constitutive

Mutations in the lacI and lacO genes in the lactose system often lead to full production of the three structural genes related to the lac operon even with no lactose available to the organism. Such mutations would be called ______

constitutive

This process moves a nucleosome from the TATA box of a gene's promoter so that transcription can occur

Chromatin remodeling

This term describes genetic elements that affect other elements only when they are located adjacent to them.

Cis-Acting

ranscriptional repression by methylation of DNA is most common in sequences called ____ islands.

CpG

The molecular nature of transposable elements was first understood in E. coli due to the simplicity of the E. coli genome. Which of the following types of transposable elements contribute significantly to the genome complexity of eukaryotic organisms. LINEs SINEs IS elements Genes LTR retrotransposons Rhines

LINEs SINEs LTR retrotransposons

List four levels at which gene control can take place in eukaryotes.

Transcription, RNA processing (splicing, transport, stability), Translation, protein modification, protein stability

Regarding eukaryotic and prokaryotic genetic regulation what process is most similar between the two? Transcriptional regulation RNA splicing regulation Intron/exon shuffling 5' capping regulation poly A addition

Transcriptional regulation

What modification neutralizes the changes on histones that promote ionic interaction with DNA? phosphorylation demethylation acetylation polyadenylation

acetylation

A recombination event involving a chromosome with an inversion will not result in a deletion and duplication product? A double cross-over event takes place within the inversion loop If a single cross-over event takes place within the inversion loop If four cross-over events take place within the inversion loop If three cross-over events take place within the inversion loop If one cross-over event takes place within and one cross-over takes place adjacent to the inversion loop If all cross-over events take place outside the inversion loop

A double cross-over event takes place within the inversion loop If four cross-over events take place within the inversion loop If all cross-over events take place outside the inversion loop

DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to Altering RNA polymerase activity by methylation Changes in DNA-DNA hydrogen binding Altering translational activity especially of highly methylated tRNAs Alteration of DNA polymerases activity by addition of methyl groups to glycine residues Addition of methyl groups to the cytosine of CG doublets

Addition of methyl groups to the cytosine of CG doublets

Describe alternative splicing. What is the ultimate result of the alternative splicing process? Provide an example.

Alternative splicing is the differential combination of exons during mRNA processing. The ultimate result is the mature mRNA which leaves the nucleus to be transcribed. Because the exons can be arranged in many different ways during splicing, many different protein products can arise from a single gene. The result of alternative splicing is a mRNA product that has a differently arranged set of exons from how it was originally transcribed

Regulatory proteins that bind DNA have common motifs that interact with sequences of DNA. How do AA in DNA binding proteins interact with DNA? By forming covalent bonds, with DNA bases By forming hydrogen bonds with DNA bases By forming covalent bonds with DNA sugars None of the above A and C

By forming covalent bonds, with DNA bases

What are Cis Regulatory Elements and how are they involved in gene regulation?

CRE are elements that have effects on the genes that are adjacent to the element, which are genes that are close in location. An example of CRE is promoters. The promoters act to help regulate the transcription of the genes depending on the elements that are being bound. As well, CRE's have effects on one side of the gene/chromosome while in turn trans elements have effect on the entire gene/chromosome.

What is catabolic repression? How does it allow a bacterial cell to use glucose in preference to other sugars?

Catabolic repression is when the presence of a catabolite inhibits a pathway. When glucose is present in the cells, other pathways that use other sugars are inhibited. This is evident with the lac operon that utilizes lactose, whose catabolites are glucose and galactose. When glucose is present, cAMP levels are low. cAMP is necessary to bind to the CAP to activate the operon, but in low levels of cAMP the pathway will not proceed.

Transcription factors are proteins with at least two functional _____

Domains

The process by which excessive numbers of a sex chromosome are corrected, often by methylating the X chromosome to form a Barr body.

Dosage Compensation

What is meant by polycistronic mRNA? Many RNAs but only 1 protein One RNA encoding several different proteins Alternative splicing Many cysteine residues Many cytosine residues

One RNA encoding several different proteins

Define gene regulation. What are 3 ways gene regulation can be controlled in a cell?

Gene Regulation: various systems that control and determine which genes are switched on and off. Transcription, Post-transcriptional, translation, RNA stability, protein modification

Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells? In eukaryotic cells, the 5' end of mRNA is modified with a cap, while is prokaryotic cells there is no cap In eukaryotic cells, the 3' end of mRNA is modified with a poly A tail, while in prokaryotic cells there is no tail In eukaryotic cells mRNA is spliced before translation, while in prokaryotic cells there is no mRNA splicing In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.

In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.

An epigenetic trait is a stable, ____ and _____ heritable phenotype that results from changes in gene expression without alteration in the DNA sequence

Mitotically, meiotically

Match the following terms Paracentric Inversion: centromere not within the inversion Pericentric Inversion: centromere is within the inversion

Paracentric Inversion: centromere not within the inversion Pericentric Inversion: centromere is within the inversion

This is the region of a gene where RNA polymerase binds to initiate transcription

Promoter

__________ is also known as RNA silencing and post-transcriptional gene silencing

RNA interference

Regions of chromosomes that are inactivated through methylation are termed this

Silent chromatin Heterochromatin

Which of the following are Epigenators? Stress Starvation Inflammation All of the above None of the above

Stress Starvation

The _____ box sequence is specific to many (but not all) eukaryotic promoters and often facilitates transcription.

TATA

Insulators can block the effect of enhancers only when They lie between an enhancer and promoter They lie upstream of a promoter They lie adjacent to a promoter They lie within the structural proteins They lie within a consensus sequence

They lie between an enhancer and promoter

When siRNAs or miRNAs are present, the rate of mRNA degradation _____, and the rate of protein production _____.

increases, decreases

The general term for a non-polymerase protein that binds to an operator

repressor

In the lactose operon, the product of structural gene lacZ is capable of nonautonomous replication forming lactose from two glucose molecules replacing hexokinase in the early steps of glycolysis splitting the B-linkage of lactose forming ATP from pyruvate

splitting the B-linkage of lactose

How can inversions of translocation cause a mutant phenotype? Name at least 2 ways and provide a short justification.

1. Inversions cause a breakpoint within a gene, which can cause a mutant phenotype when the gene is disrupted 2. The breakpoint removes regulator region part of gene and places under control of different regulatory region, which can result in change in gene expression. 3. Disruption of a gene: a translocation could introduce a premature stop codon, halting translation and inhibiting normal protein synthesis 4. Mismatch between homologous chromosomes during meiosis: if a portion of a homologous chromosome is inverted it may no longer match with the other chromosome, and when they cross over it could result in a gamete with a disrupted gene

E. coli bacteria are placed in a medium containing glucose and lactose. Which of the genes below do you expect to be turned on? f-galactosidase Lac I Lac P Permease None of the above

None of the above

Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation? cis-acting, variable orientation, variable position trans-acting, fixed position, fixed orientation cis-acting, fixed position, fixed orientation cis-acting, variable position, fixed orientation trans- and cis-acting, variable position

cis-acting, variable orientation, variable position

Since the binding of the _____ to the _____ prevents it from binding to DNA by causing a conformational change in its structure, it is called an _____ protein.

inducer, repressor, allosteric

What is the function of cAMP in regulation of the lac operon? it activates a repressor protein it activates an activator protein in inactivates a repressor protein it inactivates an activator protein

it activates an activator protein

Name at least two mechanisms involved in epigenetic regulation of gene expression

methylation, acetylation, chromatin remodeling

How are miRNAs produced? How do miRNA function to influence production of proteins?

miRNAs are produced when an inverted repeat segment of DNA is transcribed. The RNA folds on itself to form dsRNA, and a dicer cleaves it to make a small single stranded segment of RNA, the miRNA. The miRNA forms a RISC complex that binds to complementary segments of mRNA. inhibiting translation, which means that the end protein product is not able to be produced. The binding and inhibition by the miRNA influences the production of proteins by inhibiting translation and preventing protein production. More miRNA in a system means less proteins will be produced.

A(n) ____ can function at variable distances and in either orientation. However, it differs from an enhancer in that it cannot function downstream of the transcription starting point.

promoter

Alternative splicing is known to be important in the regulation of the production of heat-shock elements the mammalian SV40 virus the lac operon in E. coli. the metallothionein gene

the mammalian SV40 virus

It is possible for a repressor to negatively regulate the expression of an operon because the repressor induces the expression of inducer one of the genes expressed in the operon negatively regulates the repressor the repressor binding site overlaps the promoter site of the operon allowing it to physically block the binding site of RNA polymerase the repressor binding site on the DNA overlaps with the translation start site

the repressor binding site overlaps the promoter site of the operon allowing it to physically block the binding site of RNA polymerase

Match each number with the closest type of DNA: gene-encoding sequence moderately repetitive DNA highly repetitive DNA short interspersed elements long interspersed elements unique-sequence DNA

unique-sequence DNA