Chapter 12 Part One: Regulation Transcription in Eukaryotes

in eukaryotes what regulates transcirption

Tfs

the human genome encodes how many protein encoding genes

20,000

there are many noncoding genes which encode functional ______ that do not get translated into proteins

RNA

what is an example of a protein that is abundant in specialized cells in which they function and cannot be detected elsewhere 

hemoglobin can only be detected in red blood cells. 

what are the 2 components of a cell that allows it to determine which genes will be trasncribed

1. short stretches of DNA of defined sequence

2. gene regulatory proteins recognize and bind to these shrot segments

what are the two components of eukaryotic gene regulation

1. transcriptional gene regulator

2. post trasncriptional gene regulation including miRNAs, lncRNAs, and siRNAs

what is the ground state of transcriptional regulation in bacteria vs eukayotes

in bacteria the ground state is always on and represesed state is always off.

In eukaryotes the ground state is always off and the active state is always on

what is the 3 main differences between transcription with bacteria vs eukaryotic orgnaisms 

1. in bacteria all genes get transcribed into RNA by 1 RNA polymerase while in eukayotes ir 3 RNA polymerases

2. RNA transcripts in eukaryotes must be processed meaning that the 5’ to 3’ ends are modified and introns are spliced out

3. RNA polymerase II is much lager and complex in Eukaryotes 

what does RNA pol II do in Eukaryotes

trasncribes mRNA

what is trans acting and what is cis acting in eukaryotes

regulatory proteins can diffuse and are trans acting

regulatory DNA sequences are on the SAME DNA molecule as the gene making it cis acting

access to transcription regulatory seqeunces tends to be restricted in DNA because

DNA is packaged with proteins in the nucleus

what are enhancers 

enhancers are regulatory proteins that can bind directly to DNA with the help of trasncription factors 

what are proximal enhancers and what are distal enhancers

proximal: close to core promoter

distal: further away from core promoter

general transcription factors can do what

they can directly bind DNA regulatory sequence within core pomroters

what are the names of regulatory proteins that DO NOT bind directly to DNA

coregulators

what are two types of coregualtors 

1. coactivators

2. corepressors

what are coactivators (coregulators)

what are corepressors (coregualtors)

coactivaters increase the rate of gene transcription, and are recruited by activtor transcription factors.

corepressors: decrease the rate of gene trasncirption and are recruited by repressor transcription factors

what is TFIID and what does it do

TFIID is a coactivator that interacts with transcirption factors and recruits RNA pol II to gene transcription start site

25% of promoters in yeast and humans contain what ?

the TATA box.

point mutations throughout the proximal enhancer and core prooter regions of B globin gene does what to transcribption?

reduces it

what is the galactose-ultilization pathway in yeast

Gal 1, Gal 2, Gal 7 and Gal 10 encodes enzymes that catalyze steps in a biochemical pathway to convert galactose into glucose.

Gal 3 Gal 4 and Gal80 encodes what

they encode proteins that regulate the expression of enzyme genes

which is the key regulator of the GAL gene expression?

Gal 4 protein because it is a sequence specific DNA binding protein

Gal4 transcription factor binds to ____ elements in yeast

UAS: upstream activating sequences

what are the 2 domains of the Gal4 dimer

Activation Domain

DNA binding Domain

if the Gal 4 does not have the activation domain what happens

LacZ is off

If LexA does not have the activation domian what happpens?

what about when it does have the activation domain?

does not= OFF

does= On

If Gal80 protein is binded to Gal4 what happens

inhibits the Gal 4 activity and the Gal 1 gene is off 

what happens when Gal 3 is added with galactose?

Gal 3 is a sensor and inducer, it will bind to galactose and change the conformation of Gal 80 protein, which causes the Gal80 to release Gal 4, and RNA pol II will activate trasncription turning the gene on

Gal 80, Gal 3 and Gal 4 are all part of a switch state that is determiend by

presence or absense of galactose

the activity of eukaryotic transcriptional regualtory proteins is often controlled by interactions with

other proteins

does Gal4 work in most eukaryotes?

yes it has worked w insects, humans and other species. 

what is the first step of transcription initiation in eukaryotes?

eukaryotic promoters are first recongized by general tasncription factors.

what is the function of these GTFs

there role is to attract the core RNA pol II to the so it can begin RNA synthesis at transcription stat sie.

the preinitiation complex also known as the PIC is made up of what

general transcription factors and RNA poll II

the assembly of the PIC complex begins with what 

TFIID. this leads to the recurimtent of RNA pol II and other GTFs

why is TFIIH important

it is required to open the transcription bubble and phosphorylate the carboxy terminal domain known as CTD

what does Gal 4 protein bind to in order to recruit RNA pol II to gene promoters. Is this a direct or indirect interaction.

Gal 4 protein must bind to multiple protein complexes, including the TFIID and mediator compleces.

This is indirect

what is the MCM1 Transcription factor

it is expressed in all three cell types, but its function is changed with interactions of alpha1 and alpha2

compare transcriptional regulation with bacteria vs eukaroyes 

there are diff ground states in bacteria its on in euakryotes its off. There are more regulatory proteins in eukaryotes. RNA Pol II is larger than Pol I. Compared with eukaryotes, DNA is naked in bacteria.Eukaryotes chromatin strcutrue impacts gene expression. 

what makes up chromatin

11nm nucelosomes that fold upon one another into a chromatin fber

a nucelosome contains a protein core made up of _ ______ molecules the core histones

8 histone 

Histone H1 is a ______ histone because it binds the DNA that links adjacent nucelosomes

linker

a histone octamer forms a protein_____ around which the double stranded DNA is wound

core

Nucelosomes and chromatin are composed of DNA around _______ histones. The octamer of the histone is made up of two copies of each of the 4 core histones

8

H2A, H2B, H3 and H4)

nucelosomes are spaced at intervals about _____ nucleotide pairs, and they are usually packed together with the aid of histone_____ molecules to form a 30-nm chromatin fiber. 

200

H1

which is more compacted euchromatin or heterochromatin

heterchromatin is more compacted

compare euchromatin

heterochromatin

constituitve chromatin

euchromatin: least compact

hetero: most compacted, coated w proteins

consittiutive” remains heterochromatic throughtout cell cycel concentrated at telomeres and centromere

what is the chromatin structure

insulator, enhancer, promoter

nucelosomes cover most regions but are excluded from _____ and ________ of active genes to create ________ _______ _______

enhancer and promoter

nucleosome free regions 

in chromosomes, group of genes are kept apart by _______ formed by interaction of insulator binding proteins such as CTCF

TADS— topologically associating domains

what happens with chromsoones with tads

enhancers bound by TFs are positioned to act on GTS at particular promoters

what do insulators do?

divide chromosomes into precisely defined loops that determine which enhancer promoter interactions are allowed and which are not

when there is packaging of eukaryotic DNA into chromatin what does that mean

much of the DNA is not readily accessible to trasncription machinery 

eukaryotic genes that are generally inaccessible are

silent unless activated

the modifictiion of chromatin structure is important in (3)

1. gene regulation

2. DNA replication

3. DNA repair

in chromatin modification what happens

enzymes alter te chemical structure of

amino acids in histones OR
nucleotides in DNA

what are the most conserved proteins ? meaning they are near dientical in all eukaryotic organsimss 

histones 

definiton of nucelosoems

DNA wrapped around 8 hisotones octamer

H2A

H2B

H3

H4

histone tails are subject to what

many different types of post trasnaltional covalent modifications that control aspects of chromatin structure and function

histone proteins with amino terminyl ends make an ________ contact with the phosphate backbone of the DNA

electrostatic

when do covalent modification occur with histone tails 

after the histone protein has been translared, and incorporated into the nucelosome 

the ________ side chain of the lysine amino acid residues in histones.

how is it neutalzid?

+

it is neutralized with post translational addition of an acetyl group.

what is an acetyl group

CH3-C=O

histone acetylytransferases (HATs) is what ?

histone deacetylases (HDACs) is what?

catalyzation acetylation (the use of acetyl-coA as a donor of the acetyl group ) ADDITIOn

HDACs is the catalyze removal of the acetyl group

Acetlyatio leads to more _____ chromatin by loosening interactins between histones and DNA

open

what happens with Acetylation?

it nuetrlaizes the + charge of the lysine and decreases teh affinity of te lysine for the negatvie charge of the phosphate group of the DNA and reduces the electrostatic interactions between the adjacent nucleosones.

deacetylation _______ chromation compaction and promotes transcription _______.

Acetylation ____ chromation compaction and ______ accessibility of machinery to DNA which promotes trasncription _________

increases

repression

reduces

increases

activation

how does histone acetylation alter chromatin structure and facilitate changes in gene expression?

not only does it decrease chromatin comapction, but with other histone modifications, it influences binding of regulatory proteins to DNA.

can histone deacetylation turn off or on gene transcription?

off

in the presence of glucose, GAl1 transcription _____ by MIG1 protein.

repressed

what does the MIg 1 protein recruit

recruits the TUP 1 repressing complex, which recruits the histone deacetylaase, which turns gene transcirption off.

TUP Complex s a ______ meaning that it faciltiates gene repression but is not itself a DNA binding repressor

corepressor

+ charged amino acid can be covalently modified w the addition of 

acetyl groups

methyl groups

How many times can lysine be methylated?

How many times can arginine be methylated?

1,2,3 times

1 , 2 times in symmetric or assymetric config

what are some diff types of histone methylation

lysine

monomethylysine (one methyl group)

dimethylysine (two methyl groups)

trimethyllttsine three methyl groups

name these three molecules

left is onomethylarginine

middle is assymetric dimethylarginine

right is symmetricdimethylarginine

does the methlyation of lysine residues effect charge?

no but it creates binding sites for other proteins that can either actviate or repress gene expression

Methylation of H3 Lysine Residue for H3K4me3 is associated with ______ of gene expression and is enriched in nucleosomes near start of transcirption

activation

what is post translational modificatiojs and where does it aminly ocur

histone protein tails

what is DNA modification:

additio of methyl groups to DNA resdiues after replication

in verterbrates 85%. of CpGs are methylated. Many of the unmethylated CpGs, are clusted into 200-4000 bp regios called

CpG islands

majority of gene promtoers are asosciated with what

CpG isalnds of unmethylated CpGs

Unmethylated CpG islands at promtoers are generally correlated with _____ chromatin and _____ transcirption.

Methylated CpG are assocaited with ______ chromatin and _______ transcirption

open. active

clossed, repressed

what effects the trasncription of dna

proteins that bind unmethylated or methylated CpGs

what are CpGs

specific sequence of DNA strands where Cytosine nucleotide is immediatly followed by a Guanine nucleotide in the 5’ → 3’ direction. the phosphate group is what links the two nucleotides togehter. 

what are the two major mechanisms that operate in eukaryotic cells to enable access of trasncription amchinery to DNA

1. chromation modificaiton

2. chromatin remodeling