Module 4 final

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mod 4 final

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

Alteration of structure, transcription, mRNA processing, RNA stability, translation, Post-translational modification

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.

Medium conditions
1 high glucose, no lactose


2 no glucose, high lactose


3 high glucose, high lactose


4 no glucose, no lactose

Level of transcription
1. off
2 high
3 off
4 off

List at least three different types of DNA repair and briefly explain how each is carried out.

Direct repair - changes altered nucleotides back into their original (correct) structures.

Base-excision repair - a modified base is first excised and then the entire nucleotide is replaced.

Nucleotide-excision repair - removes bulky DNA lesions (like pyrimidine dimmers) that distort the double helix.

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 - O+ Z- __________ _________
c I s Oc Z +/ F' I + O+ Z+ __________ _________
d I - O+ Z +/ F' I - O+ Z+ __________ _________

I + = wild-type repressor

I - = mutant repressor (unable to bind to the operator)

I s = mutant repressor (insensitive to lactose)

O+ = wild-type operator

Oc = constitutive operator (insensitive to repressor)

a -,+
b -,+
c +,+
d-,-

Under certain circumstances, one can make use of expression libraries to identify and clone a gene of interest. Describe an expression library and how one could be used to clone a gene.

In many cases a vector can be designed so that the cDNA will be expressed, frequently as a fusion protein. In this case the cDNA has been incorporated into a vector in a position where it is within a coding sequence of another protein. The vector also incorporates promoter sequences that allows the protein to be expressed (both transcribed and translated). When such a vector is used to make a library it is called an expression library*. Expression libraries have the advantage and disadvantage that the protein is present. In some cases this may mean that there may be selective pressure against the expression a cDNA of interest, but in many cases this expression allows for a novel screening approaches. The most straight forward of these is the use of antibodies to screen a library.

What is the general scheme for generating a transgenic mouse strain?

the gene of interest is injected into fertilized oocytes to be subsequently transferred into pseudo-pregnant recipient mothers. Pups are then screened for integration of the transgene.

One type of mutationinvolves the replacement of a pyrimidine with a purine. What general term is associated with this mutationalphenomena?

transversion

An insulator is also known as a(n) __________________ .

boundary element

Parts of chromosomes that are not methylated for inactivation, but rather are less dense-staining and are likely active in transcription in the cell.

euchromatin

mRNAs are degraded by enzymes called ____________

Ribonucleases

Regions of chromosomes that are inactivated through methylation are termed this.

silent chromatins

What are the approximate positions of consensus sequences (modular elements) at the 5' end of eukaryotic genes?

GC box (-110), CAAT box (-70), TATA box (-30)

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 binds at more distant regions (enhancers).

Explain how one would use epistasis analysis to determine order of gene action in genetic networks?

The order of action of genes in a regulatory hierarchy that is governed by a signal can often be determined by the method of epistasis analysis, in which the phenotype of a double mutant is compared with that of single mutants. The epistatic mutation may be in either the upstream or the downstream gene, depending on the nature of the two mutations and the type of regulation. Nevertheless, when the regulatory hierarchy satisfies certain conditions, simple rules allow the position of the epistatic locus in the pathway to be determined without detailed knowledge of the nature of the mutations, the pathway, or the molecular mechanism of regulation.

The process of error correction of mismatched bases carried out by DNA polymerases is called

proof reading

Which term describes a mutation that restores function to a loss-of-function mutant?
a) Suppressor
b) Balancer
c) Conditional
d) Enhancer

a) Suppressor

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

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?
Question options:

lacI+ lacP+ lacO+ lacZ- lacY+ lacA+

lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

lacI- lacP+ lacO+ lacZ- lacY+ lacA+

lacI+ lacP- lacO+ lacZ+ lacY+ lacA+

lacI+ lacP+ lacOc lacZ+ lacY+ lacA+

Nutritional mutations can be defined as
Question options:
a) all strains which are not auxotrophic.
b) those mutations which do not allow an organism to grow on minimal medium, but do allow the organism to grow on complete medium.
c) those mutations caused by site-specific mutagenesis
d) those mutations which change the composition of the medium.
e) those mutations which change the composition of the medium.

b) those mutations which do not allow an organism to grow on minimal medium, but do allow the organism to grow on complete medium.

(I = lac repressor gene; Z, Y, A = lac operon structural genes; P = lac promoter; O = lac operator)
Reference: Ref 16-2
I----P-O--Z---Y--A
Which parts of the DNA region shown in the diagram encode proteins?
Question options:

P

I, Z, Y, A

P, O, Z, Y, A

I, P, O, Z, Y, A

I, Z, Y, A

Within the control region of the tryptophan operon is a section of DNA that is sensitive to levels of tryptophan in the system. What is the name of this region?

operator??

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?
Question options:
a) By forming covalent bonds with DNA bases
b) By forming hydrogen bonds with DNA bases
c) By forming covalent bonds with DNA sugars
d) None of the above.
e) a) and c)

b) By forming hydrogen bonds with DNA bases

Which of the following terms best characterizes catabolite repression associated with the lactose operon in E. coli?
Question options:
a) constitutive
b) positive control
c) repressible system
d) inducible system
e) negative control

b) positive control

An example of a gene product encoded by a regulatory gene is

repressor protein.

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.
Question options:

positive inducible

positive repressible

negative inducible

negative repressible

negative inducible

Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation?
Question options:

cis-acting, vairable position, fixed orientation

cis-acting, variable orientation, variable position

trans-acting, fixed position, fixed orientation

trans- and cis-acting, variable position

cis-acting, fixed position, fixed orientation

cis-acting, variable orientation, variable position

In general, a "model organism" used in genetics studies is one in which there is a large body of genetic knowledge that has been compiled over decades of genetic research. In addition, model organisms have available their DNA sequences and collections of ________ that make detailed genetic analysis possible and efficient.
Question options:


epigenetic developmental system


museum specimen


complete metamorphic system


strains with specific mutations


incomplete metamorphic system

strains with specific mutations

The role of tautomerism in causing mutations relates to the fact that the process ultimately affects the:
Question options:
a) deoxiribose sugar
b) ability of DNA to replicate at all
c) covalent bonding affinities of nitrogenous bases
d) hydrogen bonding affinities of nitrogenous bases

d) hydrogen bonding affinities of nitrogenous bases

Under certain conditions, the rate of mutation of a particular gene may be determined in humans. What properties of the mutation would favor the most direct determination of mutation rate in humans?

Select all that apply:

fully expressed


100% penetrant


recessive


dominant


single locus

single locus
dominant

What term refers to a contiguous genetic complex that is under coordinate control?

operon

Mutations that arise in nature, from no particular artificial agent, are called

spontaneous mutations

In general, a "model organism" used in genetics studies is one in which there is a large body of genetic knowledge that has been compiled over decades of genetic research. In addition, model organisms have available their DNA sequences and collections of ________ that make detailed genetic analysis possible and efficient.
Question options:


epigenetic developmental systems


incomplete metamorphic systems


museum specimens


complete metamorphic systems


strains with specific mutations

strains with specific mutations

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?
Question options:


polyadenylation of the 3' end of the mRNAs


intron processing


capping


exon processing


transcriptional

transcriptional

Name two mutagens that would be classified as base analogs.
Question options:


ethylmethane sulfonate and ethylmethylketone peroxide


hydroxyurea and peroxidase


ultraviolet light and cosmic radiation


5-bromouracil and 2-aminopurine


acridine orange and proflavin

5-bromouracil and 2-aminopurine

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