BIO 190- Ch #12 Gene Regulation

gene regulation

the ability of cells to control the expression of their genes

"turn genes on or off"

constitutive gene

genes that are always on, their promotors are always open

how do many proteins regulate gene expression

through binding DNA

How must RNA pol be guided to gene promotors

by transcription factors that say "come here"

what happens if a promotor is hidden

then RNA pol can not attach/ find the promotor

how do some transcription factors reveal gene promotors

by changing nucleosome spacing

what do some transcription factors attach to histone proteins to loosen the hold on DNA to reveal promotors

attach functional groups to histones

how do genomes and proteomes differ

all cells have the same genome, but different proteomes

what is cell differentiation

the process by which cells become specialized into particular types by expressing specific genes at specific times

what does hemoglobin do embryonic vs post natal

embryonic: picks up oxygen from uterine environmental/ maternal blood

post natal: picks up blood in lungs

describe the different quaternary composition of hemoglobin in embryonic, fetal, and post natal

embryonic: 2 sigma and 2 zeta (oxygen affinity highest)

Fetal: 2 alpha and 2 zeta (high oxygen affinity)

post natal: 2 alpha and 2 beta (moderate oxygen affinity)

what do most promoters include

a core promoter (essential for the start of transcription)

and regulatory elements (modulate how much, when, and where a gene is transcribed)

what does the core promoter contain

TATA box and transcription start site

the core promotor alone results in what

a low level basal transcription

The core promoter is enough to start transcription, but only at a very low level. This low level is called basal transcription — it’s the minimum amount of transcription that happens even without help from additional regulatory elements (like enhancers).

what does the +1 mean on the core promotor

refers to the transcription start site (TSS) — the exact spot on the DNA where RNA polymerase II begins transcribing the gene into RNA

+1 site = First nucleotide of the RNA transcript.

transcription factors bind to ______

gene regulatory elements

what are the two types of gene regulatory elements

enhancers and silencers

enhancers vs silencers

enhancers: enhances RNA pol ability to find and bind to promotors

silencers: inhibits RNA pol ability to find/bind to a promotor

what does RNA polymerase II do

transcribes genes that encode proteins

what does TF2D bind to

the TATA box and is a common target for activators and repressors

how do activators and repressors commonly exert their regulation of transcription

through affecting the function of general transcription factors

what does it mean by most eukaryotic genes are under combinatorial control

that most expression is regulated by the combination of many factors

what are activators

stimulate RNA polymerase to initiate transcription

what are repressors

inhibit RNA polymerase from initiating transcription

what are modulation

small effector molecules, protein- protein interactions and covalent modifications can modulate activators and repressors

what is chromatin structure

activator proteins promote loosening up the region in the chromosome where a gene is located, making it easier for RNA polymerase to transcribe the gene

push nucleosomes apart so promotor is visible

what is DNA methylation

usually inhibits transcription either by blocking an activator protein or by recruiting proteins that inhibit transcription

if eukaryotes do not have operons how do they turn on (express) multiple genes at one time

Multiple RNA polymerase II enzymes can transcribe multiple genes across the genome at the same time.

can a chromosome have both open and closed regions

yes

describe closed conformation in chromatin structure and an example

a region that is difficult or impossible to transcribe; transcription requires changes in chromatin structure. "constitutive heterochromatin"

ex: when you are awake the sleeping gene is closed in chromatin

describe open conformation in chromatin structure and an example

is accessible to general transcriptional factors and RNA pol II and can therefore be transcribed

facultative heterochromatin

ex: awake gene is open when you are awake

what are chromatin remodeling complexes

protein machines that use the energy of ATP hydrolysis to change the position of the DNA wrapped around nucleosomes

they can move nucleosomes around

describe how nucleosomes reposition

DNA is in a closed conformation --> activator binds to enhancer --> chromatin remodeling --> nucleosome reposition

what are the 2 types of chromatin remodeling (how chromatin structure open up chromatin)

1. Modify histone tails

2. demethylate cytosines in DNA

how does modifying histone tails open up chromatin

Histone acetylation

adds on a acetylation which “loosens” DNA, making genes neutralized and easier to turn on

how does demethylate cytosines in DNA open up chromatin

think of the methyl group as an oil droplet that drags nucleosomes close to each other through hydrophobic attraction which closes the chromatin

demethylation removes that methyl group/ oil droplet groups so the nucleosomes spread and open chromatin

what is a nucleosome free region (NFR)

used for genes we need quickly, they are found at the begging and end of the gene (they don't need to put nucleosomes at promotors) short stretch of DNA that is not wrapped around nucleosomes, meaning it’s free of histones

what happens to nucleosomes during transcription elongation

During transcription elongation, nucleosomes are temporarily loosened or rearranged so RNA polymerase II can pass, and then they are reassembled behind it.

does removal of acetyl groups from histone tails decrease or increase gene expression

Removal of acetyl groups from histone tails → decreases gene expression

Acetyl groups neutralize the positive charges on histone tails.

This loosens the interaction between histones and negatively charged DNA, making the DNA more accessible to transcription.

So, when acetyl groups are removed (a process called deacetylation): Histones become more positively charged.

DNA binds more tightly to histones. Chromatin becomes more condensed (heterochromatin) and Transcription factors and RNA polymerase can’t access the DNA as easily.

Removing acetyl groups (histone deacetylation) tightens chromatin and reduces gene expression.

does removal of histones from a region decrease or increase gene expression

Removing histones from DNA increases gene expression by making the DNA more accessible for transcription

Histones package and wrap DNA into nucleosomes, which makes the DNA less accessible to transcription factors and RNA polymerase. Removing histones (even temporarily) from a DNA region: Opens up the chromatin structure

does aceytlation of histone tails decrease or increase gene expression

Histone acetylation opens up chromatin and increases gene expression.

Histone tails have positive charges, and DNA is negatively charged. When acetyl groups are added (acetylation), the positive charges on the histones are neutralized.

This causes histones to bind DNA less tightly, leading to:

Looser chromatin structure (called euchromatin).

Greater access for RNA polymerase and transcription factors.

More transcription of genes in that region.

does a decrease in compaction of histones decrease or increase gene expression

increases gene expression.

Less compacted chromatin (called euchromatin) means:

DNA is more exposed.

RNA polymerase and transcription factors can access promoter and enhancer regions more easily.

This leads to higher levels of transcription.

does an increase in compaction of histones decrease or increase gene expression

decreases gene expression.

When histones compact the DNA more tightly (heterochromatin):

The DNA becomes less accessible to transcription factors and RNA polymerase.

Promoters and enhancers are hidden, preventing gene activation.

As a result, transcription is reduced or silenced.

DNA is associated with proteins to form

chromatin

a ______ is composed of DNA wrapped around an octamer of histone proteins

nucleosome

An activator can increase transcription by attracting a _____ to the region.

histone acetyltransferase

removal of acetyl groups from histones result in a _________ in gene expression

decrease

addition of -COCH3 groups to histones amino terminal tails results in a _______ gene expression

increase

regulation of transcription is efficient however ..

it requires a fair amount of time to drive effects of cell function

what is alternative splicing and when does it occur

occurs during post translational action

allows an organism to use the same gene to make different proteins at different stages of development

Alternative splicing is a process in eukaryotic gene expression where a single pre-mRNA can be spliced in different ways to produce multiple different mRNA transcripts, and therefore different proteins, from the same gene.

faster regulation can be achieved at the stages of pre-mRNA _______ & ________

splicing and translation

what is ferritin

storage form of iron (iron ion sponges)

how are ferritin levels controlled

by holding its mRNA in standby until needed

what does the active iron regulatory protein do

stops ferritin when iron levels are low you don't want a lot of it (inhibits translation)

what happens when iron levels are high

iron regulatory protein binds to iron causing a conformational change that releases it from the iron regulatory element and translation proceeds.

What level of regulation do eukaryotes possess that prokaryotes do not?

transport RNA out of the nucleus

which of the following is not involved in the control of gene expression in eukaryotes

transcription

modification of mRNA

translation

post- translation

replication

replication

is this a valid reason for a cell to regulate gene expression;

made additional cells of the same type in response to demand

true

is this a valid reason for a cell to regulate gene expression;

synthesize enzymes to metabolize a particular nutrient

true

is this a valid reason for a cell to regulate gene expression;

keep a gene product available under all conditions

false, not regulation

is this a valid reason for a cell to regulate gene expression;

execute a specific program of development

true

is this a valid reason for a cell to regulate gene expression;

stop synthesis of a cellular component when there is enough available in the cell

true

is this a valid reason for a cell to regulate gene expression;

synthesize mRNA for every gene in the genome at the same time

false

the most common point of gene regulation in bacteria is

transcription

DNA methylation in many eukaryotic organisms usually cause

decreased transcription levels

what does TF2d do

recruits RNA pol to bind

where does TF2D bind

TATA box

what do activators do

stretch/ move nucleosomes apart in 2 ways

1. acetylate histone tails

2. demythaltate DNA cytosines

for active eukaryotic genes the core promotor is found at a nucleosome free region (NFR) this NFR is needed so that

activators can promote the formation of a pre-initiation complex

is a enhancer a DNA element or protein

DNA element

is a repressor a DNA element or protein

protein

is a silencer a DNA element or protein

dna

is a activator a DNA element or protein

protein

is RNA pol a DNA element or protein

protein

is a promotor a DNA element or protein

DNA element

the iron regulatory protein binds to the iron regulatory element when iron levels are _____ and _____ translation of ferritin mRNA

low and inhibits

when histone tails are unacetylated is chromatin most likely to be open or closed

closed

how do organisms benefit from gene regulation

Gene regulation helps organisms adapt, conserve energy, develop properly, stay healthy, and survive in changing environments.

combinatorial control

the way multiple regulatory factors work together to control the expression of a single gene in eukaryotic cells.

how does alternative splicing increase protein diversity

by allowing a single gene to produce multiple different mRNA transcripts, which are then translated into different proteins.

what are regulatory transcription factors in bacteria

proteins that bind to regulatory sequences in DNA are frequently used to change levels of gene expression

what are the 2 main types of regulatory transcription factors in bacteria

repressors and activators

describe the difference between repressors and activators in bacteria

repressors: transcription factors that exert a negative control and decrease expression

activators: transcription factors that exert a postive control and increase transcription

describe the location in reference to the promotor of repressors vs activators in bacteria

repressors are downstream/ in front of the promotor so they can block RNA pol binding

activators are behind RNA pol and tell it to go

What are operons?

Groups of bacterial genes that share one promoter. allows bacteria to keep genes off until they are needed

eukaryotes do not have operons

what is an example of operons in bacteria

Ecoli have genes that metabolize glucose on all the time but they also have genes that use other fuel sources like lactate to but they only express those when needed

where does the repressor bind to in bacteria

on the operator (lacO)

lacZ

encodes B-galactosidase (part of lac operon )

lacY

encodes lactose permease (part of lac operon )

lacl

encodes the lac repressor

in a bacteria what happens in the absence of lactose

the lac repressor binds the operator and prevents RNA polymerase from transcribing the structural genes (lacZ, lacY, and lacA)

what does the lac repressor do

binds to the operator and blocks in front of RNA pol

what happens when lactose binds to the lac repressor

it changes its shape and function so now RNA pol does not have a road block and can generate mRNA

if lactose is around then the ________ is not bound

repressor

what happens in the presence of lactate

there is a transcription of genes

lac operon is under ___________- control when glucose is low

positive

what is the activator of the lac operon

CAP (catabolite activator operon)

CAP can only bind to a CAP site when bound by ______

cAMP

high cAMP = _____ glucose

Low

When glucose levels are low, cells increase the production of cyclic AMP (cAMP). This is especially important in bacteria like E. coli during the lac operon regulation:

Low glucose → ↑ cAMP

High cAMP binds to CAP (catabolite activator protein)

low glucose = __ ATP and ______ADP

ADP gets converted to _____________ = high ______

low ATP and high ADP

ADP gets converted to cyclic AMP = high cAMP