HRR: transcription II

Question 1

Specify the major components of the lac operon model is prokaryotes and describe their corresponding functions in controlling transcription

Answer 1

Regulator gene: codes for repressor or activator protein; trans regulator

Operator: cis element; regulatory sequence of the operon

Operon: polycistronic message, set of coordinately regulated target genes

Inducer: lactose

Question 2

Explain how cAMP positively regulates transcription in the operon model

Answer 2

1] Low glucose causes activation of the enzyme Adenylyl cyclase, which increase cAMP levels.
[2] cAMP binds to a protein called Catabolite Activator Protein (CAP).
[3] CAP*cAMP binds to a consensus sequence near the promoter region of the lac operon.
[4] CAP facilitates binding of RNA Polymerase holoenzyme to the promoter of the lac operon to initiate transcription

Question 3

Describe negative regulation of lac operon

Answer 3

In the absence of lactose, a repressor protein is bound to operator, making the transcription of lac operon repressed due to blocking the binding of RNA polymerase. In the presence of lactose, lactose is the inducer that causes a conformational change in the repressor protein rendering it inactive and keeping it from binding to an operator. This process makes it so the genes involved in lactose metabolsim (lac operon) will only be transcribed when lactose is present.

Question 4

explain glucose repression of the lac operon

Answer 4

transcription of the lac operon does not occur if glucose is still present. This is termed catabolite or glucose repression. Although the repressor has been inactivated by addition of lactose, RNA Polymerase does not bind to the promoter. High glucose inhibits the expression of enzymes involved in breakdown of alternative sugars such as lactose by lowering cAMP.

Question 5

describe cis-acting regulatory elements in eukaryotes

Answer 5

Core promoter: minimal stretch of DNA that is sufficient to direct accurate initiation of transcription by RNA polymerase II. Contains tata box, bre, mte, dpe.

Proximal promoter elements: close to the transcription start site of the gene. They have binding sites for specific transcription factors (activators or repressors)

Enhancers: serve as binding sites for specific transcription factors (activators). Their proximity to the transcription start site does not matter…they can be anywhere. They can be upstream or downstream from the start site. They can be flipped experimentally and still function.

Silencers: serve as binding sites for repressors. Similar to enhancers, the proximity to the transcription start site does not matter. They can be flipped experimentally and still function.

Question 6

true or false: cis acting elements are different for every gene

Answer 6

true!

Question 7

describe the types of trans-acting factors in eukaryotes

Answer 7

General: they regulate assembly of PIC; needed for all genes!

Specific: gene-specific, and depends on the cis elements present in the gene. Activators or repressors bind directly to the sequence. They can then recruit co-regulators, which do not bind to the DNA sequence directly.

Co-regulators do not bind to the DNA directly, but can modify chromatin structure to regulate PIC formation.

Question 8

Describe co-regulators and how they function in transcriptional regulation.

Question 9

Describe the subunits in specific transcription factors bind directly to target genes and explain how they function as either an activator or repressor

Answer 9

They have common subunits, but the function they carry out is different

1.DNA binding domain: recognizes a consensus DNA sequence

2.Transactivation/transrepression domain: binds to co-regulator proteins with HAT or HDAC activity (co-activator or co-repressor) and interacts with the mediator complex and other pic components to activate transcription

3.Dimerization domain: dimer that binds to DNA sequence in both strands.

Question 10

describe 3 mechanisms by which a repressor can inhibit transcription of a target gene

Answer 10

Block access to enhancer element: binds directly to a cis acting element, blocking DNA binding to the enhancer and activator protein access, preventing promotion of the assembly of PIC

Direct inhibition of activator protein: This type of repressor protein binds directly to an activator,
which inhibits protein interactions with co-regulator(s) that
promote the assembly of pre-initiation complexes

transrepressor specific transcription factors!

Question 11

Define the concept of combinatorial regulation by transcription factors

Answer 11

The looping of DNA means different transcription factors at different points on the strand can interact and communicate with each other. This method of regulation is one reason why species with similar genomes can be so different- its all about how we regulate!

Question 12

describe bZIP

Answer 12

a specific transcription factor in eukaryotes that binds into the major grooves and recognizes specific sequences. The leucine zipper holds together the dimer

Question 13

describe zinc fingers

Answer 13

a specific transcription factor in eukaryotes composed of an alpha helix + 2 antiparallel beta sheets. A dimerized structure. The zinc finger binds into a major groove in DNA. They bind to a specific consensus sequence in the enhancer of a target gene called the hormone response element. They then recruit co-regulators. Big example are steroid hormone receptors

ZINC FINGER BINDS TO DNA

Question 14

describe bHLH

Answer 14

specific transcription factors in eukaryotes composed of 2 bHLH transcription factors form a dimer. One helic has a binding domain, one helix has a dimerization domain.

Question 15

Define the concept of epigenetics and name three main methods

Answer 15

epigenetics is all about modifying chromatin

1. DNA methylation
2. Covalent modifications of histones (acetylation/deacetylation)
3. chromatin remodeling

Question 16

Define the concept of DNA methylation in eukaryotes

Answer 16

epigenetic modification; when CpG appears within DNA, the C can be methylated; this typically occurs in CpG rich regions known as CG islands. methylation tends to decrease or silence transcription of a gene, due to prevention of activator binding or recruiting proteins that condense or compact chromatin.

Question 17

what is genetic imprinting

Answer 17

mechanism by which expression of a gene is dependent on whether it is inherited from paternal or maternal chromosome

Question 18

describe acetylation of histones in eukaryotes

Answer 18

epigenetic modification; lysine gets acetylated by HATs in the terminal tails of histone to neutralize the positive charge. this relaxes the histones and allows for better access for the transcription factors

increased acetylation = increased gene activation

Question 19

describe deacetylation of histones in eukaryotes

Answer 19

HDACs deacetylate the lysine in histones, causing them to compact and be less available to transcription factors. HDACs are often recruited upon a repressor binding to a silencer.

increased deacetylation = transcriptional repression

Question 20

describe the remodeling process

Answer 20

noncovalent epigenetic modification; Breaking and reforming of histone-DNA interactions that alter the positioning, shape or number of nucleosomes, thereby affecting accessibility of regulatory elements in genes to transcription factors.

Question 21

describe chromatin remodeling complex

Answer 21

noncovalent epigenetic remodeling; Diverse group of non-histone chromatin proteins that use ATP for energy to unwind DNA from the nucleosome core. They are often recruited to the promoter of genes by specific transcription factors to remodel chromatin

Question 22

name the types of chromatin remodeling complex

Answer 22

• Sliding of histone octamers to increase/decrease relative spacing between nucleosomes
• Changing conformation of nucleosomes to alter protein interactions
• Removal or reassembly of individual nucleosomes

Question 23

Explain the functional significance of chromatin sites that are hypersensitive to DNase I

Answer 23

Regions of transcriptionally active euchromatin can be detected by increased sensitivity to DNase I digestion, which produces DNA fragments that are smaller in size than ~ 200 bp protected by nucleosomes in inactive chromatin. Hypersensitive sites result from chromatin remodeling of genes by epigenetic mechanisms that extend chromatin structure

Question 24

Describe how initiation of transcription is regulated through changes in the amount and/or activity of transcription factors

Answer 24

Can bind and regulate transcription; they can have a sequence similar to the DNA and sequester the transcription factor so it doesn’t bind to the DNA.

Question 25

Describe how lncRNAs regulate transcription of target genes

Answer 25

Can bind and regulate transcription; they can have a sequence similar to the DNA and sequester the transcription factor so it doesn’t bind to the DNA.