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Molecular Genetics Module 3

Terms in this set (82)

Two formal terms used to describe categories of mutational nucleotide substitutions in DNA are called
transversions and transitions
What term refers to a contiguous genetic complex that is under coordinate control?
operon
When referring to attenuation in regulation of the tryptophan operon, it would be safe to say that when there are high levels of tryptophan available to the organism,
transcription termination is likely
Under the system of genetic control of the tryptophan operon
when there is no tryptophan in the medium, transcription of the trp operon occurs at high levels.
What term would be applied to a regulatory condition that occurs when protein greatly reduces transcription when associated with a particular section of DNA?
negative control
DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to
addition of methyl groups to the cytosine of CG doublets.
Name two mutagens that would be classified as base analogs.
5-bromouracil and 2-aminopurine
Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two?
transcriptional regulation
The role of tautomerism in causing mutations relates to the fact that the process ultimately affects the:
hydrogen bonding affinities of nitrogenous bases
In the absence of glucose and in the presence of galactose, several genes are activated to enable yeast utilize galactose. The key regulator(s) of the yeast GAL system is/are the _______ protein(s).
All of the above: Gal80, Gal4, Gal3
Riboswitches were first discovered in 2002 and have been found in...
In all of the listed organisms: fungi, archaea, bacteria, plants
A leading hypothesis regarding the source of some transposable elements is the integration into the genome of a virus. What evidence supports this hypothesis.
The conservation of some gene sequences between transposable elements and extant viral genes. These include sequences such as "pol."
Name three consensus sequences or modular DNA sequences that exist upstream from the coding regions of some eukaryotic genes.
CAAT, TATA, GC sequence
When transcription factors interact with DNA, is the resulting genetic control typically positive or negative?
Positive control
The human condition _____________ is caused by unrepaired UV-induced lesions.
xerodurma pigmentosa
A mutation that occurs naturally, without exposure to a known mutagen, is called a ________.
spontaneous mutation
One type of mutation involves the replacement of a purine with a purine. What general term is associated with this mutational phenomena?
transition
Proteins that affect chromatin structure without altering histone chemical structure are called _______________.
chromatin remodeling complexes
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 DNA contribute significantly to the genome complexity of other organisms?
LTR retrotransposons, LINES, SINES
The region of a protein that is capable of holding on to a particular nucleotide sequence in order to affect proper gene regulation.
DNA binding domain
We discussed cis regulatory elements (CRMs) in transcripitonal networks. What are CRMs and how the are involved in gene regulation?
CRMs are parts of the DNA sequence that are involved in transcriptional regulation. They are cis-acting, meaning they are directly next to the DNA sequence being regulated. This is in contrast to trans-acting elements, which are not near the gene being regulated but operate via diffusable entities (ie. repressor proteins). Examples of CRMs include the promoter and the operator of an operon.

CRMs are involved in gene regulation by either inhibiting or enhancing transcription of a specific gene or set of genes. They can do this in many ways, such as binding repressor proteins that prevent RNA polymerase from binding, binding activator proteins that enhance RNA polymerase binding, binding RNA polymerase etc.
Describe alternative splicing. What is the result of the alternative splicing mechanism?
Alternative splicing refers to the fact that a single pre-mRNA transcript can be spliced in several ways. This would result in different exons coming togeter to form different mRNA transcripts, and therefore result in different proteins.

Thus, several possible protein products can come from the same pre-RNA molecule. The result of alternative splicing is a proteome that is much larger than the genome, as the same sequence of nucleotides can code for many proteins.Changes in splicing patterns can have many different effects on the translated protein. Even small changes can alter the protein's enzymatic activity, receptor-binding capacity, or protein localization in the cell. Thus, humans can produce several hundred thousand different proteins (or perhaps more) from the approximately 25,000 genes in the haploid genome.
How are miRNAs produced? How do miRNAs function to affect production of proteins? Provide sufficient detail in your answer for full credit.
1. Transcription through an inverted repeat in the DNA
2. produces an RNA molecule that folds to produce double stranded RNA
3. double stranded RNA is cleaved by the enzyme dicer
4. produces MiRNA
5. one strand of the miRNA combines with proteins to form an RNA induced silencing complex (RISC)
6. RISC pairs with an mRNA and inhibits translation, thus inhibits protein production
miRNAs come from single-stranded RNAs that are transcribed within the nucleus from the cell's own genome and that contain a double-stranded stem-loop structure. Nuclease enzymes within the nucleus recognize these stem-loop structures and cleave them from the longer single-stranded RNA. The stem-loop RNA fragments are exported from the nucleus into the cytoplasm where they are further processed by the Dicer complex into short, linear, double-stranded miRNAs. these noncoding miRNAs work to negatively regulate gene expression. miRNAs can also repress the transcription of specific genes and larger regions of the genome. They do this by associating with a different complex— the RNA-induced initiation of transcription silencing complex (RITS). The antisense RNA strand within the RITS targets the RITS complex to specific gene promoters or larger regions of chromatin. RITS then recruits chromatin remodeling enzymes to these regions. These enzymes methylate histones and DNA, resulting in heterochromatin formation and subsequent transcriptional silencing.
Describe 3 pieces of evidence that supports the hypothesis that DNA methylation is important factor in gene regulation.
1- adegree of methylation is inversely proportional to the degree of expression . Large transcriptionally inert regions of the genome, such as the inactivated X chromosome in mammalian female cells, are often heavily methylated
2. Methylation patterns are tissue specific and heritable for all cells in that tissue
3. Incorporation of 5-azacytyine, which is not able to be methylated, can cause changes in the pattern of gene expression.
P-element transposons provide a powerful tool for the study of Drosophila genetics. What are P elements, and why are they so useful?
-are 31-bp inverted terminal repeats
-produce two proteins: transposase and repressor proteins
-are useful due to their ability to be injected into a gene and cause a mutation
-p-elements are mutagenic
-transposon specific to Drosophila
-probably arose from horizontal transfer
-can be used to manipulate Drosophila genome and create genetically modified flies for research:

Genetically engineered P elements can be injected into eggs, which enables the P-element bearing gene to be inserted into the embryo's DNA. With proper markers, the flies bearing the modified element can be recognized and transformed and mosaic flies may pass the element in the germ cells. P-elements can also be used to generate mutations by inserting into genes, thus disrupting their function.
The following table lists several genotypes associated with the lac operon in E. coli. For each, indicate with a "+" or a "—" whether β-galactosidase would be expected to be produced at induced levels. (Assume that glucose is not present in the medium.)
Genotype No lactose With lactose
a. I + O+ Z+/ F' I + O+ Z+ ____-_____ ____+____
b. I - Oc Z -/ F' I - Oc Z- ____-_____ _____+___
c. I - Oc Z +/ F' I - O+ Z+ ____+_____ ____+___
d. I s Oc Z -/ F' I s O+ Z+ _____-_____ _____-__
List at least two different types of DNA repair and briefly explain how each is carried out.
1. Nucleotide Exicision Repair--In this type of DNA repair, the damage is detected and the nucleotide is removed. Then, the segment of DNA is excised, replaced, and ligated through the coordiation of a variety of enzymes (including DNA ligase and polymerase).
2. Repair of damaged DNA through photolyase--This type of DNA repair occurs prior to DNA replication. Dimerization of adjacent thymine residues, a hallmark of UV damage, is reversed via the enzyme photolyase.
3. Base-excision repair: a repair enzyme detects any abnormalities with the base pairing and excises any mistakes, then replaces the entire nucleotide.
4. DNA mismatch repair: corrects errors, such as base substitutions and insertions or deletions, made by DNA polymerase during DNA replication
Fill in the blanks in the "level of transcription" column of this table with: + for high levels of transcription, and - for minimal levels of transcription of the lac operon. Consider regulation by both the lac repressor and CAP (catabolite activator protein). The strain is wild type, with no partial diploidy. Please label your answer with numbers 1-4 based on the chart below.
1 high glucose, no lactose

2 no glucose, high lactose

3 high glucose, high lactose

4 no glucose, no lactose
1.-
2.+
3.-
4.-
List four levels at which gene control can take place in eukaryotes.
chromatin structure, RNA processing , RNA stability , Posttranslational modification, [5. translation]
In the lactose operon, the product of structural gene lacZ is capable of
splitting the β-linkage of lactose.
Genetic regulation in eukaryotes can take place at a variety of levels from transcriptional to post-translational. At what level is genetic regulation considered most likely in prokaryotes?
transcriptional
DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to
addition of methyl groups to the cytosine of CG doublets.
Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli?
positive control
Which of the following are general categories of mutations? Select all that apply.
Conditional, lethal, behavioral
Which of the following is NOT true regarding the differences in mRNA between prokaryotic cells and eukaryotic cells?
In eukaryotic cells, the transcription to mRNA and the translation from mRNA are coupled, while in prokaryotic cells transcription and translation are not coupled.
Choose the type of control illustrated by each example: E. coli lac operon control by lac I
negative inducible
Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation?
cis-acting, variable orientation, variable position
Transcription factors appear to be important molecules relating to the regulation of gene activity. Regarding eukaryotes, two general classes exist. Briefly describe each.
One class assembles at promoter regions adjacent to the site of transcription. The other class, enhancers, binds at more distant regions.
Constitutive mutations may occur in various components of the lac operon. Name two types of constitutive mutations.
lacI- and lacOc
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
When siRNAs or miRNAs are present, the rate of mRNA degradation_____________ , and the rate of protein production ___________.
increases, decreases
This process moves a nucleosome from the TATA box of a gene's promoter so that transcription can occur.
Chromatin remodeling
The _________ can be used to quickly screen chemicals for their ability to be mutagenic (and hence potentially carcinogenic).
Ames test
Regions of chromosomes that are inactivated through methylation are termed this.
Silent chromatin
How do enhancer elements differ from suppressor mutations?
Enhancers act in the opposite manner from suppressors; they increase the expression of a given phenotype
The _____ box sequence appears to be critical to the ability of many eukaryotic promoters to facilitate transcription.
CAAT
Strand discrimination during the process of _____________ is based on DNA methylation in E. coli.
DNA repair
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.
upstream activator sequence, UAS
A constitutive gene is _______ regulated and is expressed ____________.
not, continuously
Mutations in the promoter region of the b-globin gene indicate that some areas are more sensitive than others. When mutations occur in consensus sequences (modular elements such as GC box, CAAT box, TATA box) transcription ________________.
decreases
_______________ is also known as RNA silencing and posttranscriptional gene silencing.
RNA interference (RNAi)
Degradation of a eukaryotic mRNA is generally preceded by shortening of the _____________.
poly (A) tail
Define gene regulation. What are three ways gene regulation can be controlled in a cell?
Defined as the control of a gene's transcript and its protein product.
1. altering the transcription of the gene
2. altering the translation of the protein from that transcript
3. altering the structure of the DNA such that transcription cannot occur
The following may be caused by mobile genetic elements except
undergo mutation
Choose the type of control illustrated by GAL4 in the control of genes for yeast galactose-metabolizing enzymes.
positive inducible
An example of a gene product encoded by a regulatory gene is
repressor protein
Regulatory proteins that bind DNA have common motifs that interact with sequences of DNA. How do amino acids in DNA-binding proteins interact with DNA?
by forming hydrogen bonds with DNA bases
A _________ mutation changes a codon that specifies an amino acid into one that terminates translation.
nonsense
Frameshift mutations are caused by the __________ or __________ of one or more nucleotides in DNA.
removal, insertion
Transposable elements are also known as:
jumping genes, mobile genetic elements
What is a mutation?
A change in the DNA sequence
What modification neutralizes the charges on histones that promote ionic interaction with DNA?
acetylation
An operon is controlled by a repressor. When the repressor binds to a small molecule, it BINDS TO DNA near the operon. The operon is CONSTITUTIVELY expressed if a mutation prevents the repressor from binding to the small molecule.
Negative repressible
An operon is controlled by a repressor. When the repressor binds to a small molecule, it is RELEASED FROM BINDING to DNA near the operon. The operon is NEVER expressed if a mutation prevents the repressor from binding to the small molecule.
Negative inducible
What is the function of cAMP in regulation of the lac operon?
It activates and activator protein
It is estimated that transposable elements compose approximately what percent of the human genome?
50
Regulation of gene expression using siRNAs is found in
Eukaryotes only
The lac repressor binds to:
lactose and DNA
__________ mutations produce new traits and are usually dominant.
gain of function
A mutation in the gene for the yeast regulatory protein GAL4 causes yeast to grow poorly on galactose. What is the function of GAL4?
It is a transcription activator for the galactose-digesting enzyme gene.
Which of the following is TRUE for both prokaryotic and eukaryotic gene expression?
RNA polymerase binds to the promoter region to begin transcription.
A class of mutations which results in multiple contiguous amino acid changes in proteins is likely to be the following
Frameshift
siRNAs and miRNAs are produced by
the cutting and processing of double-stranded RNA by Dicer enzymes.
Insulators can block the effects of enhancers only when
They lie between an enhancer and a promoter
The lac repressor protein controls expression of the lac operon via ________________
binding to the lac operator site to repress expression
Alternative splicing is known to be important in the regulation of
the mammalian SV40 virus.
What is the function of allolactose in regulation of the lac operon?
inducer
A mutant E. coli strain, grown under conditions that normally induce the lac operon, produces high amounts of ß-galactosidase. What is a possible genotype of the cells?
lacI+ lacP+ lacOc lacZ+ lacY+ lacA+
A mutant E. coli strain, grown under conditions that normally induce the lac operon, does not produce ß-galactosidase. What is a possible genotype of the cells?
lacI+ lacP- lacO+ lacZ+ lacY+ lacA+
Choose the type of control illustrated by GAL4 in the control of genes for yeast galactose-metabolizing enzymes.
positive inducible
What is the common influence of ultraviolet light on DNA? Note that simply stating "mutation" is not an acceptable answer.
Dimer formation
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