control of gene expression: topic 4

what are some reasons why a cell needs to be able too regulate how much of each gene it should translate and transcribe into protein

1. proteins are energetically costly to make

2. cells need to be able to adjust to changing conditions

3. making the wrong protein in the wrong cell can be problematic

4. during development from a single cell to trillions of cells, different proteins are needed at different times

what are the three levels of control for prokaryotes

1. transcription: how fast you can make RNA

2. translation: how fast you can make protein

3. post translation: adding phosphate groups

which of the 3 control levels for prokaryotes will be the most efficient in terms oe energy which will allow the fastest response

most efficient: transcriptional
fastest: post translational because all you do is add phosphate group (least efficient w energy)

change in frequency of transcription initiation can involve:

negative control and positive control

what is negative control

use regulatory protein called repressor to bind to DNA, stop transctiption

what is positive control

regulatory protein called activator binds to DNA and triggers transcription (starts it)

bacteria can coordinate control via

operons

what are operons

set of genes located next to one another and transcribed together as a single mRNA, share single promoter

what is a lac operon

a collection of genes that are important in coding for enzymes that metabolize lactose

what are 2 main proteins needed for lactose metabolism

galactoside permease

b-galactosidase

lac operon is coded for by

lacY and lacZ

lac operon is transcribed as

single polycistronic mRNA

what does galactoside permease do

transports lactose into the cell

what does b-galactose do

breaks down lactose inside the cell

a repressor is always

transcribed or translated

immediately after the promoter is the

operator

if no lactose

repressor binds to operator
operon is “off” -no transcription, - no enzymes made

if a repressor binds to dna

transcription is blocked

if lactose is present

lactose itself will bind to repressor protein, so it changes shape

lactose binds to repressore protein

releasing from operator

lactose follows an

allosteric regulation process

what would happen if loss of function mutation in repressor gene

transcription would increase, there is no control

no way to stop proteins from being made

trp operon is used

to build tryptophan and allows oppresor to bond to repressor

tryptophan is

corepressor - negative feedback

when trypotphan is present,

transcription is blocked

when tryptophan is absetn

transcription occurs

what is a regulon

more than one operon under the control of a single regulatory protein

cells need to be able to regulate gene expression for a variety of reasons

1. proteins are costly

2. responding to the environment

3. making the right proteins in each cell type

4. turning on genes at the right time in development

bacteria/prokaryotes can control gene expression at several levels with varying speed and energy efficiency using

transcriptional control (most energy efficient)

translational control or post-translational control (fastest)

transcriptional control can be negatively controlled by a

repressor that shuts down transcription

transcriptional control be positively controlled by a

activator that increases transcription

operons are sets

of genes that are controlled together by the same regulatory proteins/promoters and transcribed as a single mRNA

lac operon has multiple genes important for breakdown of lactose
it has a __ that binds to an operator sequence

repressor

what does the repressor do

binds to an operator sequence between the promoter and the genes if lactose is absent, blocking transcription

if lactose is present, lactose will bind to

the repressor, altering its shape so that the repressor no longer binds to the operator, transcription can now occur

trp operon contains multiple genes important in

tryptophan synthesis

when tryptophan is common in the cell it acts as a

corepressor, keeping the repressor bound to the operator

when tryptophan is absent, the repressor

can no longer bind and the tryptophan synthesis genes can be transcribed

regulons regulate many genes and or operons for coordinated responses by using

regulatory proteins and the same regulatory sequences

what is chromatin

the complex DNA and proteins that make up eukayotic chromosomes

what is a histone protein

helps organize DNA

DNA is tight wrapped around

histone proteins

what charge does DNA have

negative

what charge do histone proteins have

positive

histones are highly

attracted to negatively charged DNA because of their positive charge

default of chromatin is

tightly wrapped

how does having tightly wrapped chromatin affect transcription

how is this diifferent from prokaryotes

the default is to not transcribe that gene

• don’t have that default of not transcribing DNA

different phenotypes are due to

genetics or environment or due to the effects of the environment on gene expression

what is epigenetics

gene expression altered by factors other than the cell’s underlying DNA sequence

the switching on and off of genes based on environmental cues

epi means

on top

epigenetics is the layer control on top of genetics itself

unlike a mutation epigenetics is

easily reversible and doesn’t affect gene nucleotide sequence, just whether it can be transcribed or not

adding methyl groups to DNA does what

triggers chromatin condensation, making genes attached inaccessible

adding acetyl groups to histones does what

neutralizes histone positive charge which makes chromatin decondense

when we add acetyl groups this makes DNA more

accessible because the DNA is less tightly wound to the histone proteins

chromatin becomes more condensed

tags can be ___ in DNA replication

preserved

what does epigenetics effect

cancer addiction and learning

which would increase cancer risk if epigenetic made them more accessible

proto oncogenes

tumor supressor genes

mutator genes

which would increase cancer risk if they were less accessible

proto onco genes because they would increase cell division, this would lead to out of control cell division if made more accessible

the other two options could be problematic if they were inaccessible

how do eukaryotes control gene expression

epigenome/epigenetics

one type of epigenetic change is

chromatin remodeling which involves chemical additions to DNA and histones

these changes make a gene more or less accessible to be transcribed

the complex of DNA and protein is

chromatin

chromatin is often relatively ___ by default

condensed

the DNA of a specific gene must be __ in order for it to be transcribed as RNA or protein

decondensed

some tags added to DNA and histones lead to __ of chromatin. for example

condensing

methyl groups

what groups help open up the chromatin

acetyl groups

epigenetics is different from mutations because it does not

permanently alter the nucleotide sequence, it only adds/subtracts tags that control whether a certain gene is decondensed or condensed

when a gene is decondensed it

is available for transcription

when a gene is condensed it

is unable to be transcribed

what is condensed DNA

condensed DNA, also known as chromosomes, is the tightly packed form of DNA that appears during cell division, allowing for easy segregation and distribution of genetic material to daughter cells.

what is decondensed DNA

decondensed DNA, or chromatin, is the loose, accessible form that allows gene expression and replication during other stages of the cell cycle

epigenetic changes are often preserved in rounds of

DNA replication

most epigenetic markers are

wiped clean with each new generation but some can be preserved

what are transcrpiton factors

regulatory proteins that bind to specific DNA sequenes

post transcriptional control starts with

RNA processing

what is RNA interference

targets specific mRNAs for destruction

why is RNA interference more needed in eukayites than in prokaryotes

eukaryotes have more stable RNA

what is miRNA

single stranded miRNA (microRNA) are small, highly conserved non coding RNA molecules inolved in the regulation of gene expression by degrading their target mRNAs and/or inhibiting their translation

miRNA and the RISC protein complex

recognizes specific mRNAs through base pairing

chopss up or stops translation

in both eukaryotes and prokaryotes, the primary mechanism to regulate gene expression is at the

level of transcriptional regulation

transcription must also be __ once the chromatin is decondensed

initiated

regulatory sequences can be close to the promoter or

can be upstream/downstream/part of intron

promoter proximal is

when the regulator sequence is close to the promoter

ehancers or silencers are found

upstream downstream part of intron

transcription factors are proteins. what do they bind to that regulate transcription

bind to the regulatory sequences

RNA interference prevents the

translation of mRNA

a single stranded miRNA binds to

then, mRNA is

complementary mRNA

destroyed or prevented from translating

proteins can also be targeted for destruction by

the addition of ubiquitin tag and subsequent destruction by a proteasome

different cell types have different gene expression for several reasons including different

patterns of epigenetic tags

types of transcription factors

proteins involved in alternative splciing

what is differentiation

the process by which a cell changes to become specialized for its job

after a certain point, the cell is

locked into a specific path

once an animal cell is determined

usually cant go back (not as true of plant cells)

what is a determined cell

one that has irreversibly committed to a specific developmental pathway, meaning it is destined to become a particular type of cell

what are master regulators

gene products that unleash a series of events to produce specialized cells

cell differentiation is important because

it is important for organismal development

what is apoptosis

programmed cell death

differential gene expression over the course of development determines

which cells end up where in an individual organism

cells in a developing embryo gradually commit to a specific cell fate by being

promoted by a series of signals

eventually they are locked into becoming a specific cell type (determined)

each step in commitment and determination are regulated by

transcription factors including master regulators

what are several processes that occur during development

cell differentiation

apoptosis