Genetics Exam 2

Let's suppose a mutation in the glucocorticoid receptor does not prevent the binding of the glucocorticoid hormone to the protein but prevents the ability of the receptor to activate transcription. Make a list of all the possible defects that may explain why transcription cannot be activated.

1. It could be in the DNA-binding domain, so that the receptor would not recognize a GRE. 2. It could be in the HSP90 domain, so that HSP90 would not be released when the hormone binds. 3. It could be in the dimerization domain, so that the receptor would not dimerize. 4. It could be in the nuclear localization domain, so that the receptor would not travel into the nucleus. 5. It could be in the domain that activates RNA polymerase, so that the receptor would not activate transcription, even though it could bind to GREs.

2 types of RNA that promote interference

1. MicroRNA 2. Small-interfering RNA's

What are the common points of control in eukaryotic gene regulation.

1. Transcription. This includes regulatory transcription factors; DNA methylation (the attachment of methyl groups, which usually inhibits transcription); and changes in the arrangements and composition of histones and nucleosomes. 2. RNA level. This includes RNA processing, regulation of alternative splicing via SR proteins; RNA stability, regulation of RNA half-life and RNA translation via RNA binding proteins; regulation via miRNA and siRNA. 3. Protein level. This includes feedback inhibition, small molecules that modulate enzyme activity; and posttranslational modification-covalent changes to protein structure that affect protein activity.

3 phases of CRISPR-Cas system

1. adaption 2.expression 3.interference

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

As described in Chapter 15, enzymes known as aminoacyl-tRNA synthetases are responsible for attaching amino acids to tRNAs. Let's suppose that tryptophanyl-tRNA synthetase was partially defective at attaching tryptophan to tRNA; its activity was only 10% of that found in a normal bacterium. How would that affect attenuation of the trp operon? Would it be more or less likely to be attenuated? Explain your answer.

A defective tryptophanyl-tRNA synthetase would make attenuation less likely. This is because the bacterial cell would have a lower amount of charged tRNATrp. Therefore, it would be more likely for the ribosome to stall at the tryptophan codons found within the trpL gene, even if the concentration of tryptophan amino acids in the cell was high. When the ribosome stalls at these tryptophan codons, this prevents attenuation.

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

Would a mutation that inactivated the lac repressor and prevented it from binding to the lac operator site result in the constitutive expression of the lac operon under all conditions? Explain. What is the disadvantage to the bacterium of having a constitutive lac operon?

A mutation that prevented the lac repressor from binding to the operator would make the lac operon constitutive only in the absence of glucose. However, this mutation would not be entirely constitutive because transcription would be inhibited in the presence of glucose. The disadvantage of constitutive expression of the lac operon is that the bacterial cell would waste a lot of energy transcribing the genes and translating the mRNA when lactose was not present.

conditional mutation

A mutation that results in a characteristic phenotype only under certain environmental conditions. Something can survive in 33-38°C temps but not 40-42°C temp.

Operator site

A nontranscribable region of DNA that is capable of binding a repressor protein

transversion mutation

A point mutation in which a pyrimidine is substitued for a purine, or vice versa.

Repressor

A protein that suppresses the transcription of a gene.

miRNA low expression

Alzheimer's and Multiple Sclerosis

genetic mosaic

An individual with somatic regions that are genetically different from each other

What is antisense RNA? How does it affect the translation of a complementary mRNA?

Antisense RNA is RNA that is complementary to a functional RNA such as mRNA. The binding of antisense RNA to mRNA inhibits translation.

somatic cells

Any cells in the body other than reproductive cells

What is meant by the term attenuation? Is it an example of gene regulation at the level of transcription or translation? Explain your answer.

Attenuation means that transcription is ended before it has reached the end of an operon. Because it causes an end to transcription, it is a form of transcriptional regulation even though the translation of the trpL region plays a key role in the attenuation mechanism.

CRISPR-Cas System

Clustered Regulated Interspred Short Palindromic Repeats defends agains foreign invaders effective against bacteriophages and prokaryotes also plasmid and transposons most archeal and 1/2 of bacterial contain this

Most common types of molecular change

DNA methylation Chromatin remodeling Covalent histone modification localization of histone variants feedback loops

Factors that promote epigenetic change

Genomic imprinting X-chromosome inactivation cell differentiation temperature

If a gene is repressible and under positive control, describe what kind of effector molecule and regulatory protein are involved. Explain how the binding of the effector molecule affects the regulatory protein.

In this case, an inhibitor molecule and an activator protein are involved. The binding of the inhibitor molecule to the activator protein would prevent it from binding to the DNA and thereby inhibit its ability to activate transcription.

With regard to cellular efficiency, why do you think the cell has several mechanisms to regulate gene expression at the level of translation?

It takes a lot of cellular energy to translate mRNA into a protein. A cell wastes less energy if it prevents the initiation of translation rather than a later stage such as elongation or termination. C19. C20.

If an abnormal repressor protein could still bind allolactose, but the binding of allolactose did not alter the conformation of the repressor protein, how would this affect the expression of the lac operon?

It would be impossible to turn the lac operon on even in the presence of lactose because the repressor protein would remain bound to the operator site.

snoRNA low expression

Lung cancer

A species of bacteria can synthesize the amino acid histidine so it does not require histidine in its growth medium. A key enzyme, which we will call histidine synthetase, is necessary for histidine biosynthesis. When these bacteria are given histidine in their growth medium, they stop synthesizing histidine intracellularly. Based on this observation alone, propose three different regulatory mechanisms to explain why histidine biosynthesis ceases when histidine is in the growth medium. To explore this phenomenon further, you measure the amount of intracellular histidine synthetase protein when cells are grown in the presence and absence of histidine. In both conditions, the amount of this protein is identical. Which mechanism of regulation would be consistent with this observation?

One mechanism is that histidine could act as corepressor that shuts down the transcription of the histidine synthetase gene. A second mechanism would be that histidine could act as an inhibitor via feedback inhibition. A third possibility is that histidine inhibits the ability of the mRNA encoding histidine synthetase to be translated. Perhaps it induces a gene that encodes an antisense RNA. If the amount of histidine synthetase protein was identical in the presence and absence of extracellular histidine, a feedback inhibition mechanism is favored, because this affects only the activity of the histidine synthetase enzyme, not the amount of the enzyme. The other two mechanisms would diminish the amount of this protein

Attenuator

Region of the trp operon where transcription often terminates

Discuss the structure and function of regulatory elements. Where are they located relative to the core promoter?

Regulatory elements are relatively short genetic sequences that are recognized by regulatory transcription factors. After the regulatory transcription factor has bound to the regulatory element, it will affect the rate of transcription, either activating it or repressing it, depending on the action of the regulatory protein. Regulatory elements are typically located in the upstream region near the promoter, but they can be located almost anywhere (i.e., upstream and downstream) and even quite far from the promoter

In what ways are the actions of the lac repressor and trp repressor similar and how are they different with regard to their binding to operator sites, their effects on transcription, and the influences of small effector molecules?

The two proteins are similar in that both bind to a segment of DNA and repress transcription. They are different in three ways. (1) They recognize different effector molecules (i.e., the lac repressor recognizes allolactose, and the trp repressor recognizes tryptophan. (2) Allolactose causes the lac repressor to release from the operator, whereas tryptophan causes the trp repressor to bind to its operator. (3) The sequences of the operator sites that these two proteins recognize are different from each other. Otherwise, the lac repressor could bind to the trp operator, and the trp repressor could bind to the lac operator.

What are the functions of transcriptional activator proteins and repressor proteins? Explain how they work at the molecular level.

Transcriptional activation occurs when a regulatory transcription factor binds to a regulatory element and activates transcription. Such proteins, called activators, may interact with TFIID and/or mediator to promote the assembly of RNA polymerase and general transcription factors at the promoter region. They also could alter the structure of chromatin so that RNA polymerase and transcription factors are able to gain access to the promoter. Transcriptional inhibition occurs when a regulatory transcription factor inhibits transcription. Such repressors may interact with TFIID and/or mediator to inhibit RNA polymerase.

imprinting control region (ICR)

a DNA region that is differentially methylated and plays a role in genomic imprinting

spontaneous mutation

a change in DNA structure that results from random abnormalities in biological processes

tautomeric shift

a change in chemical structure, such as an alternation between the keto and enol forms of the bases that are found in DNA

position effect

a change in phenotype that occurs when the position of a gene changes from one chromosomal site to a different location

housekeeping genes

a gene that encodes a protein required in most cells of a multicellular organism

tissue-specific genes

a gene that is highly regulated and is expressed in a particular cell type -may be silenced by methylation of CpG island

Inducer

a molecule that initiates gene expression

Inhibitor

a molecule that slows down a chemical reaction

down promoter mutation

a mutation in a promoter that inhibits the rate of transcription

germ-line mutation

a mutation occurring in gametes; passed on to offspring

neutral mutation

a mutation that has no effect on survival or reproduction

X-chromosome inactivation (XCI)

a process in which mammals equalize the expression of X-linked genes by randomly turning off one X chromosome in the somatic cells of females. -becomes Barr body

Activator

a protein that binds to DNA and stimulates transcription of a gene

methyl-CpG-binding proteins

a protein that binds to a CpG island when it is methylated -inhibits transcription

mutant allele

a rare allele in the same population

Corepressor

a small molecule that cooperates with a repressor protein to switch an operon off

trinucleotide repeat expansion (TNRE)

a type of mutation that involves an increase in the number of tandemly repeated trinucleotide sequences

1. Mutations may have an effect on the expression of the lac operon and the trp operon. Would the following mutations have a cis- or trans-effect on the expression of the protein-encoding genes in the operon? a. A mutation in the operator site that prevents the lac repressor from binding to it b. A mutation in the lacI gene that prevents the lac repressor from binding to DNA c. A mutation in trpL that prevents attenuation

a. A mutation in the operator site that prevents the lac repressor from binding to it: Cis-effect. It would affect only the genes that are in the adjacent operon b. A mutation in the lacI gene that prevents the lac repressor from binding to DNA: Trans-effect. This is a mutation that affects a protein that can move throughout the cell. c. A mutation in trpL that prevents attenuation: Cis-effect. It would affect only the genes that are in the adjacent operon.

Are the following statements true or false? a. An enhancer is a type of regulatory element. b. A core promoter is a type of regulatory element. c. Regulatory transcription factors bind to regulatory elements. d. An enhancer may cause the down regulation of transcription.

a. An enhancer is a type of regulatory element. True b. A core promoter is a type of regulatory element. False c. Regulatory transcription factors bind to regulatory elements. True d. An enhancer may cause the down regulation of transcription. False, it causes up regulation.

1. Transcriptional regulation often involves a regulatory protein that binds to a segment of DNA and a small effector molecule that binds to the regulatory protein. Do the following terms apply to a regulatory protein, a segment of DNA, or a small effector molecule? a. Repressor b. Inducer c. Operator site d. Corepressor e. Activator f. Attenuator g. Inhibitor

a. Regulatory protein b. Effector molecule c. DNA segment d. Effector molecule e. Regulatory protein f. DNA segment g.Effector molecule

1. Transcriptional repressor proteins (e.g., lac repressor), antisense RNA, and feedback inhibition are three different mechanisms that turn off the expression of genes and gene products. Which of these three mechanisms would be most effective in each of the following situations? a. Shutting down the synthesis of a polypeptide b. Shutting down the synthesis of mRNA c. Shutting off the function of a protein

a. Shutting down the synthesis of a polypeptide Antisense RNA or a translational repressor would shut down protein synthesis the fastest. A transcriptional repressor would also shut down the synthesis of mRNA, so it would eventually shut down protein synthesis once all of the preexisting mRNA had been degraded. Feedback inhibition would have no effect on protein synthesis. b. Shutting down the synthesis of mRNA Only a transcriptional repressor protein would shut down the synthesis of mRNA. c. Shutting off the function of a protein Feedback inhibition is the fastest way to shut down the function of a protein. Antisense RNA and transcriptional repressors eventually prevent protein function once all of the pre-existing mRNA and proteins have been degraded.

1. In the lac operon, how would gene expression be affected if one of the following segments was missing? a. lac operon promoter b. Operator site c. lacA gene

a. lac operon promoter: No transcription would take place. The lac operon could not be expressed. b. Operator site: No regulation would take place. The operon would be continuously turned on. c. lacA gene: The rest of the operon would function normally but none of the transacetylase would be made.

Mutagen

agent that causes alterations in the structure of DNA

Reversion

alteration in DNA that reverses the effects of a prior mutation

trimethylation

attachment of 3 methyl groups to an amino acid such as lysine

mi-200 family low expression

bladder, stomach, colorectal cancer melanoma

induced mutations

caused by environmental agents

When is methylated DNA inherited?

cell division

nonsense mutation

changes a normal codon into a stop codon

oxidative DNA damage

changes in DNA structure that are caused by reactive oxygen species (ROS)

CRISPR locus

contains a series of repeating sequences provides protection against bacteriophage infection contains bacteriophage DNA

mismatch repair system

detects mismatch and removes segment

Non-coding RNA

do not encode polypeptides

base pair mismatch

don't conform to AT/GC rule

RNA interference (RNAi)

double stranded RNA causes the silencing of mRNA -found in mist eukaryotes

regulated gene

expression varies under different conditions In bacteria, the regulation of genes often occurs at the level of transcription by combinations of regulatory proteins and small effector molecules. In addition, gene expression can be regulated at the level of translation or the function of a protein can be regulated after translation is completed.

Photolygase

found in yeast / plants that can repair thymine dimers by splitting them which returns the DNA to its original condition

fully remains ______________ in daughter

full

TrxG

gene activation

point mutation

gene mutation in which a single base pair in DNA has been changed

PcG

gene repression

2 benefits of RNA interference

important to gene regulation (miRNA silences mRNA) provides defense agains viruses (used by plants)

differentially methylated region (DMR)

in imprinting, a site that is methylated during spermatogenesis or oogenesis, but not both

frameshift mutation

involves the insertion or deletion of a nucleotide in the DNA sequence

Drosha low expression

lateral sclerosis

hemimethylation

methylation of cytosine to single strand

wild-type allele

most common allele in a population

cis-effect

mutation affects only the adjacent genes that the genetic regulatory sequence controls.

MicroRNAs (miRNA)

ncRNAs that are transcribed from endogenous eukaryotic genes

Spacer

newly inserted bacteriophage DNA between adjacent repeats derived from past bacteriophage infections passes defense to daughter cell

exogenous

not normally made by cells

small interfering RNA (siRNA)

originate from sources that are exogenous play key role in preventing viral infections

ncRNAs

perform array of cellular functions in bacteria, archaea, and eukaryotes, including important roles in DNA replication, chromatin modification, transcription, translation, and genome defense. -in most cells more abundant that mRNA's -20% mRNA = 80% ncRNA's -can form stem loop structures

maintenance methylation

primary mechanism by which DNA is vertebrates and planet calls are methylated.

Reactive Oxygen Species (ROS)

products of oxygen metabolism in all aerobic organisms that can damage cellular molecules, including DNA, proteins, and lipids

up promoter mutation

promoter mutations that increase transcription

Type II system

provides bacteria w/ defense against bacteriophages

transition mutation

purine to purine (A to G) or pyrimidine to pyrimidine (C to T)

ionization radiation

radiation of short wavelength and high energy

base substitution mutation

simple substitution of one base for another

suppressor mutation

suppresses the effect of an earlier mutation at a different site

piRNA low expression

testicular cancer

mutation rate

the likelihood that a gene will be altered by a new mutation

Breakpoint

the region where two chromosome pieces break and rejoin with other chromosome pieces

Depurination

the removal of a purine base from DNA

Deamination

the removal of an amino group from a molecule. For example, the removal of an amino group from cytosine produces uracil.

Epigenetics

the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself.

thymine dimers

two neighboring thymines attached to one another by covalent bonds

constitutive genes

unregulated, which means that its expression level is relatively constant.

trans-effect

usually in a gene that encodes a genetic regulatory protein.

sources of siRNAs

viruses that infect the cell researchers can make the to study gene function