lec 6

Question 1

Are different parts of the chromosome packed differently

Answer 1

Yes, some are packed tighter than others

Why? Sometimes if u have alleles, u dont want to express both so u want to switch off some, so to swithc off certain genes, u have to make it so tightly bound that the transcription factors cant bind

Question 2

Euchromation vs Heterocrhomatin

Answer 2

Euchromatin: trancriptionally active dna, sucesptible to DNase digestion

Heterochromatin: less suceptible to dnase digestion and tracriptionally inactive

Question 3

What are the two types of heterochromatin

Answer 3

1) constitutive: highly condensed inactive chromatin: more or less permenantly wound up, repetivive dna , few genes
essentially always turned off bc we dont want anything to be transcribed
ex: centroemere: spind fiberes attach here, we want it to be tightly wound up so that it is a more solid anchor
Telomere: end of chromosomes, enzymes of our body love open ended dna, thats why bacteria have circular dna to protect it from enzymes, these telomeres make it harder for these enzymes to eat, these are repetitive units and each time we replicate we lose one so eventually we could have some with no dna

2)faculative: not actine in particular tissue, forms under specifc contidions or certain tissues to silence gene expression
ex: x chromosome inactivation (in women, one x gene must be switched off in cell or else can cause issues
or imprinting: have two alleles and silence one of the alleles

Question 4

What is an example of faculative heterchromatin

Answer 4

x chromosome inactiviation

need to make sure in women that one x gene is switched off cuz double x gene is lethal, called bar body formation in men we only have one so its not a problem

Question 5

Why do normal cells lose telemeres

Answer 5

they lose them every time they divide, these are heterchromtin structures that are tightly wound, once we lose all telemere area, cell is killed off giving it a finite lifetime since these cells are more suceptible to mutations and erors

Question 6

What are locus control regions

Answer 6

-upstream from gene cluster
-shared control regions
-control chromatin condensation
-essntially a region of dna that controls multiple genes

Question 7

What are the three chromatin elements

Answer 7

1) Locus control regions
2) matrix and scaffold regions
3) insulators

Question 8

What are matrix and scaffold associated regions

Answer 8

mostly AT rich dna whcih anchors dna to nuclear matrix

chromosmes have fixed positions in cells, to be kept in there fixed positions these areas anchor them

Question 9

What are insulators

Answer 9

-spaces that seperate genes freom one another
-regulatory domains of dna, if we have two different genes that express different things, we need an insulator to ensure that both genes are not expressed togehter

Question 10

Centromeres and proteins

Answer 10

usually dont have much proteins binded to the centromenere

BUT during mitrosis and miosis, proteins bind, making a kinetochore (centromere with proteins) so that spindle fibers can attach to them

Question 11

Telomeres

Answer 11

-specialized regions of dna at the end of chromosomes
-repititve
-protect chromosomes from shortening during replication and from degrading (by nucleases)
-it is the looping of the 3’ overhang, makes a triple strand structure that protects ends of dna from being degraded

Question 12

Non histone proteins

Answer 12

types:
1) proteins are important for attaching chromosome
- ex: matrix attachment regions proteins and/or scaffold attachment regions proteins (MAR AND SAR)
-chromosme hs to be attached yo one particular area of the cell wall, mars and sars proteins help to attach it to cytoskeleton

2) Structural maintenece of chromosome proteins (SMC)
-responsible for scaffolding

3) dna replication proteins

4) Transcriptional factors

Question 13

Histone proteins

Answer 13

-highly conserved proteins esp h4,
-5 types: H3, H4, H2a, H2b, H1
H3 and H4 are the most conserved, H2a and H2b are the middle conserved, H1 is least conserved
h1 is less conserved, because how much packing u do is dependent on the species

Question 14

What are h3 and h4 responsible for

Answer 14

intially binding the histone to the dna

2a and 2b comes in after,

h1 comes in and binds the two units together (the h3 and h4 unit 1 to h3 and h4 unit 2, same with the othe

look at pic on video tbh

Question 15

What do fish , amphibians , reptiles, and birds have that the others dont for histone proteins

Answer 15

h5, lysine rich histone, variant of h1

Question 16

When do u need to disassmble nucleosome binding

Answer 16

during transcription
nucleosomes have to come off to allow polymerase to bind to it

Question 17

When replication occurs, more dna is formed, so that means in regards to nucleosomes

Answer 17

new nuclesomes are needed because we dont want to have an under tughtened dna (than normal)

old and new histones are present on daughter cell so new histones can be on parent cell too, not necessarily the same ones go back to the same strand it was on before, it is random

chaperone proteins help the nucleosomes bind again

Question 18

Will the nuclesomes bind to new sequences

Answer 18

NO it will bind to the same sequence as before (ie ATCG) but it can be on either strand daughter or parent

Question 19

Histone tail

Answer 19

histones in general dont acc look like a circle, its like a jumble of polypeptids
-at the end of it are arginines and lysines (AT THE TAIL)

-histone tails are N TERMINAL TAILS
-act as “ groves pf screw “to direct dna wrapping’

-necessary for the formation and stabilization of 30 nm

Question 20

Why arginine and lysine on the tails

Answer 20

dna neg charge, its positively charged so the pos charge help attach the histones to the dna

Question 21

How do u control whether its euchromatin or heterochromatin

Answer 21

neutralize the aringine and lysines at the end for looser packing

Question 22

Transient modifications of amino acids in tail

Answer 22

1) acetylation of tail: when active gene expression
2
2)ubiquitinylation (lysine) = non destruction modificatio
3)methylation: arginine and lysine: may be associated with active and inactive genes
4)phosphorylation: serine, associatd with active

Question 23

histone code hypothesis:

Answer 23

say we have two alleles, how does cell know to switch off the one we are not expressing? It is more tightly bound by histones, and info is stored in the tails of these histones

SO the theory is:
modifivations of histone tails are landmarks for proteins which read chromatin; the modification either makes the gene more heterochromatic or less heterochromatic depending on whether or not we want the gene to be expressed

-this then creates the open chromatin necessary for transcription, replication etc

SO bc when we are replicating the histones come off the dna, when it is replicated and the new strands exist, the histones pop back on but since it is random, we use the old histones on there in order to make these tails on the new histones express the same traitv(to expressor to not express)

Usefuk explanation:
say we have two alleles, one is expressed one isnot, the histones on the one expressed will have E (a random modication that causes it to be less tightly packed)., the one not expressed has a modification (h causing it to be more tightly packed, typially this would be more pos charges), now when we replicate, the expressed strand (both parent and daughter) will get a random assortment of histones, so we will get the old histones to geive the new histones the E modification so that it will be loosely packed, the same will occur for the non expressed strand

Question 24

What will reduce the positive charge of the protein, making it a modification that causes looser bound dna (euchromatic)

Answer 24

1)methylation and acetylation of Lysine

2)phosphorylation of serine

causes looser dna bc less attraction to the neg charged dna since we are reducing pos charges of the histone tail

Question 25

What are nucleosome free regions

Answer 25

-regions that contain actively transcribed genes, (gene expression in progress) so no tightly bound areas so more suceptible to DNuclease (since the strands are not tightly bound together)

Question 25

Aceylation and Deacetylation of tails facts

Answer 25

enzyme that does this: histone acetylases and deacetylases

-acetlated form is NEGATIVE (H+ is replaced by acetyl group)
-causes chromatins condensation to be loser so more open

IMPORTANT FOR ACTIVATION OF TRANSCRIPTION

ex: acetyl coA + histone –> actyl-histone complex + coenzyme A

Question 26

Dnase 1 Test

Answer 26

DNase 1 cuts between the nuclesomes

what to do for test:
1) isolate nuclei and treat it with dnuclease, sperate protein from dna
use gel electroporesis

NO signal: means that gene was in gene expression, so it was loose meaning that the dnauclease was able to cut it up into really small pieces so not visible

Signal: means that it was not in gene expression so very tightly wound up

Question 27

Prokaryote vs Euk

Answer 27

Pro:
-No membrane bound nucleus
-single circular chromosome
-NO membrane bound organelles
-single celled organism

Euk:
-All have membrane bound nucleus
-linear chromosomes (#varies by species)
-have membrane bound organelles (organelle dna)
-can be single cells or multi cellular organisms

Question 27

What is the purpose of making more cells

Answer 27

for Prokaryote and single cell euk:
CELL DIVISION IS REPRODUCTiON (binary fission) 1 turns to two

For multicellular euk:
division occurs for 3 reasons
1) tissue growth
2) repair of damaged tissues

Reason 1 and 2 are both MITOSIS

3) reproduction (requores specialized cells= germ cells which divide to produce sex cells (gametes)
3 is meisosis

Question 28

What. arethe two main stages of the cell cycle

Answer 28

1) Interphase: normal cell function and prep for mitosis
-G1 (growth occurs, organelles/ proteins double), S (dna replication occurs), and G2 (growth occurs of cytoplasm)
2)mitosis and cytokenesis: nuclear division and final division of parent cell cytoplasm into two daughter cells

Question 29

If a cell doesnt divide so never leaves interphase, what does it go to

Answer 29

G0 (before S)

stem cells can be here until we need them

Question 30

Checkpoints in cell

Answer 30

Specific peoteins (Cyclin dependent kinases and cyclin) STOP the cell cycle to asses everything,
if no problem, evrything continues on
if proble,, try to fx, if it cant fix then cell dies