Genetics Exam #2

Why is gene regulation necessary?

To ensure expression of genes in an accurate pattern during the different stages of the life cycle

True or False: Some genes are only expressed during embryonic stages, and other are only expressed in adults

True

Gene regulation is necessary to ensure differences among _____________.

Distinct cell types

Why do nerve and muscle cells look different?

Because of gene regulation

Transcription factors

Proteins that influence the ability of RNA polymerase to transcribe a given gene

What are the two types of transcription factors?

General and regulatory

What are the general transcription factors?

TFIIB, TFIID, TFIIE, TFIIF, TFIIH

What are the regulatory transcription factors?

Activators and repressors

What are general transcription factors required for?

The binding of the RNA pol to the core promoter and its progression to the elongation stage

Why are general transcription factors necessary?

Basal transcription

What do regulatory transcription factors do?

Serve to regulate the rate of transcription of target genes

How do regulatory transcription factors influence RNA?

They influence the ability of RNA pol to begin transcription of a particular gene

How much of human genes encode transcription factors?

2-3%

What is a gene activator?

A regulatory protein that increases the rate of transcription

What is the DNA sequence that a gene activator binds to called?

A gene enhancer

What is the DNA sequence that a gene repressor binds to called?

A gene silencer

What is a gene repressor?

A regulatory protein that decreases the rate of transcription

What can regulatory protein possibly alter?

Nucleosomes near the promoter

What does DNA methylation do?

Prevent binding of an activator protein and recruit proteins that compact the chromatin

Various combinations of ___________ factors can contribute to the regulation of a single gene.

Methylated DNA, unmethylated DNA, and chromatin

Up-regulation

The increase in rate of transcription

Down-regulation

The decrease in rate of transcription

What is the effect of activator/coactivator transcription factors of TFIID?

TFIID will be recruited to the core promoter, it will be activated, and transcription will be enhanced

What is the effect of repressor transcription factors of TFIID?

TFIID will be inhibited from binding to the core promoter and transcription will be silenced

What are ways that the function of regulatory transcription factors can be modulated?

Binding of a small effector molecule (ex: hormone), protein-protein interactions, and covalent modification (ex: phosphorylation)

What does the glucocorticoid hormone do?

It binds to the glucocorticoid receptor and the receptor releases a protein HSP90

What does the protein HSP90 do?

It exposes a nuclear localization signal (NLS)

What does the NLS do?

Form a homodimer that binds to a glucocorticoid response element (GRE) with two glucocorticoid receptors in order to activate the transcription of an adjacent target gene

What does the activation of the CREB protein do?

It causes a signaling molecule to bind to a receptor in the plasma membrane

What occurs after the activation of the CREB protein?

The G protein is activated, which activates adenylyl cyclase and cAMP is synthesized

What does cAMP bind to?

protein kinase A (activates kinase)

What does the protein kinase do after cAMP binds to it?

It enters the nucleus and phosphorylates CREB protein

What does the phosphorylated CREB protein do?

It acts as a transcriptional activator by promoting the binding of CBP (coactivator)

What do ATP-dependent chromatin remodeling complexes do?

It causes changes in chromatin structure via ATP hydrolysis

What two conformations can chromatin alternate between?

Closed and open conformation

What is closed conformation also called?

Heterochromatin

What is open conformation also called?

Euchromatin

What are the features of closed conformation?

Tightly packed chromatin that makes transcription more difficult

What are the features of open conformation?

Accessible chromatin that makes transcription possible

What is a key role of some transciptional activators?

To orchestrate changes in chromatin structure

How does ATP-dependent chromatin remodeling orchestrate changes in chromatin structure?

Energy from ATP hydrolysis drives change in location or composition of nucleosomes and makes DNA more/less amenable to transcription

What are the possible remodels due to ATP-dependent chromatin remodeling?

Change in nucleosome position, replacement of nucleosomes with histone variants, and histone eviction

What is histone eviction?

The creation of a gap with no nucleosomes due to ATP-dependent chromatin remodeling

What are the possible modifications of histone tails?

Acetylation, methylation, and phosphorylation

What do modifications of histone tails affect?

The level of transcription and the interactions between nucleosomes

What is the histone code?

The patterns of histone modification that are recognized by proteins

What does acetylation do?

Result in more open chromatin using the enzyme HATs

What is HATs?

Histone acetyltransferase

What enzyme reverses acetylation of histones?

HDACs

What is HDACs?

Histone deactylase

Where are nucleosome-free regions (NFR) found?

At the beginning and end of many genes

What is the process of transcriptional activation?

Binding of activators, chromatin remodelling and histone modification, formation of preinitiation complex, and elongation

What happens during the binding of activators in transcriptional activation?

The activation protein binds enhancer sequences

What happens during chromatin remodeling and histone modification in transcriptional activation?

The activator protein recruits a chromatin remodeling complex and a histone-modification enzyme that moves nucleosomes and evicts/replaces histones

What happens during the formation of the preinitiation complex in transcriptional activation?

The general transcription factors and RNA pol II bind to the core promoter and form a preinitiation complex

What happens during elongation in transcriptional activation?

Histones ahead of the open complex are acetylated and evicted. Histones behind the open complex are deacetylated and tightly bound to the DNA.

What is DNA methylation?

A change in chromatin structure that silences gene expression

What enzyme performs DNA methylation?

DNA methyltransferase

True or False: DNA methylation is common in all eukaryotic species

False; some

How does DNA methylation silence transcription?

Methylation inhibits the binding of an activator protein

True or False: Eukaryotic gene regulation occurs over long distances but must be limited to one gene

True

What are insulators?

Sequences/segments of DNA that insulate a gene from the regulatory effects of other genes

What happens when insulators act as barriers?

The structure of chromatin changes

What happens when insulators act as blockers?

The effects of a neighboring enhancers are blocked

What is transferrin and what does it do?

It is a protein that is transported into the cytosol by endocytosis and carries iron through the bloodstream

Where is excess iron stored?

In ferritin

Why is the encoding of ferritin and the transferrin receptor by mRNA important?

To regulate iron levels and prevent toxicity

What does the iron regulatory protein (IRP) do?

It affects the translation and degration of the mRNAs that encode for ferritin and the transferrin receptor

What do iron regulatory proteins (IRP’s) bind to?

Regulatory element mRNAs known as the iron response element (IRE)

Is IRE in ferritin mRNA in in 5’ UTR or 3’ UTR?

5’ UTR

Is IRE in transferin mRNA in in 5’ UTR or 3’ UTR?

3’ UTR

When iron is low, how do ferritin mRNA and transferrin mRNA behave?

IRP binds to IRE and prevents the translation of ferritin mRNA. IRE binds to the 3’-UTR of the transferrin receptor mRNA to prevent its degradation and promote iron uptake.

When iron is high, how do ferritin mRNA and transferrin mRNA behave?

Iron binds to the IRP and prevents it from binding to the IRE which means that ferritin mRNA is translated to make more ferritin protein. Iron binds to IRP and IRP dissociates from the IRE causing the mRNA of transferrin and the polyA tail to be cleaved by endonucleases.

What is Rubinstein-Taybi syndrome?

A disorder of histone modifications that is characterized by facial dysmorphisms, broad thumbs and halluces, developmental delays, and short statures

Why is gene regulation important for cell division in prokaryotes?

Because proteins are needed for cell division only when cells are getting ready to divide

Why is gene regulation important for stress response in prokaryotes?

Because proteins are needed when bacteria is confronted with stress. Heat shock/osmotic shock.

At what level does regulation of gene expression occur in bacteria?

Transcription

At what level does regulation of mRNA expression occur in bacteria?

Translation

At what level does regulation of protein expression occur in bacteria?

Posttranslation

In prokayotes, is the inihibition of transcription due to repressor regulatory proteins a negative or positive control transcriptional regulation?

Negative control

In prokayotes, is the increase of transcription due to activator regulatory proteins a negative or positive control transcriptional regulation?

Positive control

What are effector molecules in prokayotes?

Moelcules that bind to regulatory proteins, but NOT to DNA

What do inducers bind to in prokaryotes?

Activators or repressors

What do inducers do in prokaryotes?

Bind to activators and repressors to increase transcription

What is an operon?

A regulatory unit consisting of a few structural genes under the control of one promoter

What does RNA polymerase bind to in prokaryotes?

Promoters

What does the Lac repressor protein bind to in prokaryotes?

Operators

What does Catabolite Activator Protein (CAP) bind to in prokaryotes?

CAP site

True or False: the lacI gene is considered part of the lac operon

False; is not

True or False: the lacI gene has its own promoter, the i promoter

True

True or False: the lacI gene is constitutively (always) expressed at low levels

True

What does the lacI gene encode for?

the lac repressor

True or False: A large amount of the lacI protein is needed to repress the lac operon

False; small

What is the CAP site in the lac operon of the E.coli chromosome?

A sequence recognized by the Catabolite Activator Protein

What is LacP in the lac operon of the E.coli chromosome?

The promoter (RNA polymerase)

What is LacO in the lac operon of the E.coli chromosome?

The operator, the binding site for the repressor protein (lac repressor)

What does lacZ do in the lac operon of the E.coli chromosome?

Encodes for β-galactosidase

What does lacY do in the lac operon of the E.coli chromosome?

Encodes for lactose permease

What does lacA do in the lac operon of the E.coli chromosome?

Encodes for galactoside transacetylase

What is the repressing method of lac operon regulation in prokaryotes?

The inducer, allolactose binds to the lac repressor and inactivates it, allowing transcription to increase