Lecture 18

The centra dogma

tRANSCRIPTION (RNA sythesis), translation (protein sythesis), protein

gene expression

process by which the information encoded in a DNA sequence is translated into a product that has some effect on a cell or organism

differential gene expression theory

1. genome is same in all cells

2. only a portion of the genome in any cell type is expressed

3. different cell types have different groups of genes that make unique cellular characteristics

4. unused genes aren’t destroyed or mutated bc they can be expressed later

gene expression can be what at many levels

controlled

Proteins have to be regulated because

you dont wnat to make what you dont use

transcriptional control

slow, most energy efficient, most common control point for long term regulation like in development

two ways that gene expression can be regulated

molecular switches (GTPase) (protein reg) and protein degradation (M cyclin degradation)

regulation of transcription is what

slow but more energy efficent (turning off gene before investing energy to transcribe RNA and translate a protein)

posttranscriptional controls

fast acting and more readily reservable, more energy intensive

Prokaryotic transcription #1

RNA polymerase binds to the promoter with the help of transcriptional factors and sigma factor

promoter

stretch of DNA containing certain sequences, upstream from transcription start site, tells RNA polymerase to start

Prokaryotic transcription #2

promoter defines where RNA polymerase starts to synthesize RNA

Prokaryotic transcription #3

RNA polymerase synthesizes RNA in the 5’-3’ directions using template strand of DNA

Prokaryotic transcription #4

RNA polymerase stops at the terminator (specific DNA sequences), falls off from the DNA and releases the completed RNA

Prokaryotes are blank model systems to understand blank of gene expression

useful, regulation

Terminators

dna sequences, included in the RNA transcript, downstream

promotors can vary in what

strength of binding to RNA polymerase, dependent on sequences of DNA

if a RNA polymerase binds tightly then

more RNA, enhances by transcriptional regulator

if a RNA polymerase binds weakly then

less RNA, inhibited by transcriptional regulator

activators and repressors can act in what to provide highly sensitive transcriptional regulation

concert

transcriptional regulators

proteins that have DNA binding domains for specific DNA sequences. They can be activators or repressors

DNA binding domain of a transcription factor

bind a stretch of unique DNA sequences, allowing for specificity

The tightness of the transcriptional regulator depends on

DNA sequences, bind tight, loos or not at all

transcriptional regulators bind with the

alpha helix, H+ bond interacts with bases of DNA

do prokaryotes and eukaryotes use transcriptional regulators

yes

Housekeeping genes

strong promotors and are expressed at stable levels

sigma factor gets released when

transcription begins

operon

within promotor, reg by single operator (DNA sequence that is recognized by one or more transcriptional regulators)

operator acts as a what for transcription of the genes in the operon

master switch

Lac operon only is expressed when

glucose is absent AND lactose is present, has genes to metabolize lactose

Lac repressor inhibits transcription when

lactose is not present (on the operator)

is the Lac promotor weak or strong

weak, so it’s not sufficient to allow transcription

allolactose

metabolite of lactose, takes away the repressor when lactose is present

CAP activates

transcription when glucose is not present

When glucose levels are low these levels go up

cAMP, stress response

CAP activator recruits

RNA polymerase to the promoter

Eukaryotic cells have 3 RNA polymerases

RNA Pol I,RNA Pol II,RNA Pol III

RNA Pol I

transcribes rRNA to make ribosomes

RNA Pol II

transcribes all mRNA, transcripts RNA makes proteins

RNA Pol III

transcribes tRNA for translation

promoters have a TATA box

which helps recuirt general transcription factors

TATA Box

are proteins that help RNA polymerase bind to DNA not enough to strart transcription more of a req to bind to DNA

RNA Pol II opens

DNA double helix to prepare for transcription, not enough to strat

Enhancers

regulatory DNA sequence bound by transcriptional regulators which usually bind activators

in development enhancer allow transcription of a given gene in specific cell type or developmental stage

located either close to or far away from transcription start site

Enhancers regulate

gene expression

proteins bound to enhancers act from a

distance

Mediator

24-subunit complex that serves as an intermediary between transcription regulator and RNA polymerase

enhancer bind to

transcriptional regulators (activator)

DNA looping

brings enhancer bound transcription regulator to mediator protein that will integrate information from transcription regulator to control whether RNA polymerase should transcribe the gene

enhances do what for development

allow for specific regions of gene expression during development

expression of Shh is controlled by

limb specific enhancer

what does single base pair change in enhancer of Shh cause

digit duplication, ectopic expression

Move it experiment with Shh

sub mouse enhancer with snake —> no limb mouse, make snake enhancer more like human in mouse —> limbs

Shh is expressed

posterior of the limb bud and works as a morphogen to pattern digits if anterior then more digitis

Snakes have

17 base pair deletion in their limb enhancor for Shh, in mouses then limbs dont develop, why snakes dont have limbs