Ls3-Ch07 Chromatin

Front 1

01: Why is it ideal to put DNA into chromosomes? (4)

Back 1

-Compact
-Protection
-Better to send to daughter cells
-organization for expression

Front 2

02: What is a NUCLEOSOME? Who has them?

Back 2

Wrap DNA around them.

only EUKARYOTES have them

Front 3

03: What is a CHROMOSOME

Back 3

DNA w/ associated proteins

Front 4

04: How long are chromosomes?

Back 4

10^6 base pairs long

Front 5

05: What is at the center of a chromosome?

Back 5

CENTROMERE: where we build KINETOCHORE-to attach to microtubules and spindle

Front 6

06: Does a chromosome have one or many replication origins? Why?

Back 6

MANY replication origins. Since it takes a while to replicate the entire x-some, this will speed it up

Front 7

07: What are on the ends of x-somes?

Back 7

TELOMERES: repeating segments

Front 8

08: What is GENE DENSITY? Who has more of it?

Back 8

amount of useful DNA vs filler.

E. Coli and other simple organisms have high gene density

Front 9

09: What are regions of DNA that have nothing to do with genes? How do we get rid of them?

Back 9

INTRONS: don't encode for protein

RNA SPLICING: removes introns by making primary RNA, then introns taken out.

Front 10

10: Of our whole genome, how much is for genes?

Back 10

3.2 billion BP total

2 billion INTERGENIC

1.2 billion for genes overall

Front 11

11: Of the DNA for genes, how much encodes for the actual gene vs related items?

Back 11

1.2 billion BP overall for genes

48 million BP encode genes specifically

1.15 billion BP related

Front 12

12: regions of DNA related to genes (3 types)

Back 12

INTRONS

GENE FRAGMENTS

PSEUDOGENES: reverse transcriptase makes DNA from RNA, but not expressed due to lack of regulatory sequences

Front 13

13: What are HOMOLOGOUS x-somes?

Back 13

copies of the same x-some, carrying same trait

one from each parent.

Front 14

14: What can be a cause of down's syndrome?

Back 14

POLYPLOID: too much protein made, will mess up body

Front 15

15: What about REPETITIVE DNA?

Back 15

higher % of repetitive DNA in more complex organisms

Front 16

16: What are short, repeated DNA sequences?

Back 16

MICROSATELLITE DNA

Front 17

17: What are genes that move around?

Back 17

TRANSPOSABLE ELEMENTS: sequences that move from one place in genome to another, making COPIES as they go

Front 18

18: What are two key x-some parts with repeated sequences?

Back 18

TELOMERES (often single stranded)

CENTROMERES

Front 19

19: Stages of the cell cycle (4)

Back 19

G1: growth (interphase 1)
S: replication (synthesis)
G2: more growth (interphase 2)
M: Mitosis (or meiosis)

Front 20

20: In which phase of the cell cycle do we see sister chromatids?

Back 20

G2: were made in S phase

Front 21

21: stages of MITOSIS

Back 21

PROPHASE: x-somes condense

PROMETAPHASE:

METAPHASE

ANAPHASE: sister chromatids separate

TELOPHASE/Cytokinesis

Front 22

22: What is a protein re. DNA active in PROPHASE?

Back 22

COHESIN: holds sister chromatids together like rubber bands.

they will be cut in ANAPHASE, and sister chromatids will drift apart

Front 23

23: What is a protein re. DNA active in METAPHASE?

Back 23

CONDENSIN: helps x-somes condense. stabilizes loops, brings them closer together

cut in TELOPHASE

Front 24

24: What are the forms of condensed/noncondensed DNA called?

Back 24

10nm FIBER: normal condition

30nm FIBER: due to loops

Front 25

25: What is the structure of 10nm fiber analogous to?

Back 25

BEADS ON A STRING

Front 26

26: What is the term for DNA in between nucleosomes? ON nucleosomes?

Back 26

LINKER DNA: in between

CORE DNA: around nucleosome

Front 27

27: How much DNA is wrapped around a nucleosome? How much is in between?

Back 27

146bp around nucleosome

20-60bp in between

Front 28

28: are histones neutral?

Back 28

NO: they are positively charged, so interact well w/ DNA backbone

Front 29

29: How do we know the length of core/linker DNA?

Back 29

Use a restriction enzyme to cut DNA right to one side of nucelosome.

run on gel, will see bands every 200bp.

if use enzyme that digests linker, will see bands of length 146 bp.

THEREFORE linker DNA is 38-53 bp.

Front 30

30: How are histones charged?

Back 30

20-25% positively charged (to balance DNA backbone)

Front 31

31: What is the H1 histone?

Back 31

LINKER HISTONE: binds to linker DNA to bring it closer, thus bringing more DNA into contact w/ nucleosome

Front 32

32: What is a domain found in all core histones?

Back 32

HISTONE FOLD DOMAIN: 3 helices+2 loops.

Front 33

33: What is a key variation of the core histones?

Back 33

N-TERMINAL TAILS: stick out of cores. vary in length.

Front 34

34: What are the core histones? How many of each? What do they form together?

Back 34

H2A-H2B DIMER: two of these

H3-H4 TETRAMER: One of these (contains 2 of each histone).

together form OCTAMER CORE

Front 35

35: What would you say a nucleosome looks like?

Back 35

two discs in opposite directions.

Front 36

36: How do the histone tails work?

Back 36

"fingers" that reach into DNA grooves and direct it to wrap around the histone like a nut/bolt/screw.

higher charge causes CONDENSING

Front 37

37: What are two forms of 30nm fiber?

Back 37

SOLENOID: keeps curling around. linker DNA in corners of center.

ZIG ZAG: coils like drawing a six-pointed star, w/ linker DNA in center.

Front 38

38: What is an overall shape 30nm fiber can form...what can control it?

Back 38

LARGER LOOPS: around x-some scaffold.

TOPOISOMERASE II: controls how much DNA is wound by breaking strands, twisting it around twice, relieving loops

Front 39

39: What can specialized histones do?

Back 39

form KINETOCHORE by interacting w/ kinetochore protein.

Front 40

40: what forms do active/inactive DNA take? Are they stagnant?

Back 40

CONDENSATION: 30nm, inactive

ELONGATION: 10nm, free to be transcribed

it is DYNAMIC: constantly changing except histones at CENTROMERE and TELOMERE are always condensed.

Front 41

41: Where do proteins regulating gene expression bind?

Back 41

LINKER DNA, rarely binds to DNA on nucleosome

Front 42

42: What kinds of proteins regulate gene expression?

Back 42

CHROMATIN REMODELING PROTEINS (aka remodeling complexes). slide or transfer histone around to expose DNA.

DNA BINDING PROTEINS: bind to DNA and protein to create POSITIONED NUCLEOSOMES: stuck out of the way.

Front 43

43: What kind of DNA likes to bind to nucleosomes?

Back 43

A-T rich DNA, often in minor groove

Front 44

44: Ways to modify histones

Back 44

attach groups to TAILS:

METHYLATION: repression of a gene

ACETYLATION: activation, reduces positive charge so tails don't bind to P backbone of DNA.

Front 45

45: how does histone acetylation/methylation work?

Back 45

ACETYLATION: tails cannot stick w/ other histones, interact w/ BROMO domain proteins, recruits ACETYL TRANSFERASE, acetylates histones around it...DNA gradually unwinds.

METHYLATION: interacts w/ CHROMO domain proteins...etc

Front 46

46: What happens to nucleosomes during DNA replication?

Back 46

original nucleosome is removed.

H2A, H2B pop out and drift away (tails are not as important)

H3-H4 tetramer pop out but are held closely by polymerase, then put back into one of the daughter strands, alternating so every other strand gets old H3-H4, so then DNA can condense or relax depending on H3-H4 methlyation/acetylation.

histone ACETYLTRANSFERASE/METHYLTRANSFERASE modifies new H-3 H-4.

Front 47

47 What helps nucleosomes get put back together after replication?

Back 47

HISTONE CHAPERONES

Front 48

48: How do we know if histones are positioned or disorganized?

Back 48

use an enzyme to cut at certain points on linker DNA.

remove protein, then cut DNA w/ EcoR1, then run on gel. Add a probe that will recognize the end of the sequence.

Ordered histones will show up in regular, defined bands. others will be lots of different sizes.