lecture 4- chromosomes

Question 1

what is the largest micromolecule in the cell

Answer 1

chromosomes

Question 2

which chromosome is the smallest

Answer 2

21

(1-22)

Question 3

describe the chromosomes of viruses

Answer 3

can be circular or linear and can be single or double stranded (DNA viruses)

Question 4

describe the chromosomes of bacteria

Answer 4

only circular chromosomes

Question 5

describe chromosomes in eukaryotic cells

Answer 5

chromosomes inside nucleus, nuclear membrane separating from other organelles

Question 6

DNA in mitochondria = ___

Answer 6

circular

Question 7

describe DNA supercoiling

Answer 7

• the first level of compaction of DNA in bacteria (coiled coil)
• DNA double helix coiled on itself- forms a new superhelix, called a supercoil
• add 2 turns — over-rotate— positive supercoil
• remove 2 turns — under-rotate — negative supercoil

Question 8

DNA unwinding and relaxation are catalyzed by ___

Answer 8

DNA topoisomerases

Question 9

describe the packaging of bacterial chromosomes

Answer 9

• DNA gyrase (a type II topoisomerase) introduces negative supercoils to bacterial chromosomes
• nucleoid: region in bacteria where chromosomes are arranged (not separated from other organelles, but localized)
• a “typical” bacterial chromosomes contains about 50 giant loops of supercoiled DNA arranged around a protein scaffold (proteins in scaffold are positively charged because DNA is negative)

Question 10

describe eukaryotic chromosome compaction

Answer 10

• length of each chromosome may be more than 2000 times the size of nucleus
• chromatin: made of 50% DNA and 50% proteins
  . basic unit of chromatin is nucleosome
  . nucleosomes= the basic units of DNA condensation (beads on a string,
  nucleosomes made of DNA and histones)
• next level of compaction is the 30 nm chromatin fibre of packaged nucleosomes
• chromosomes are in most condensed form and duplicated right before cell division

Question 11

when they isolated proteins bound to DNA and run on a gel, they found…

Answer 11

4 histone proteins in equimolar amounts- H2A, H2B, H3, H4 (also found H1 but in smaller amounts)
- small, highly conserved positively charged proteins
- about 25% of each histone is made of lysine and arginine

Question 12

describe histone protein structure

Answer 12

• all have N terminal tails that are important for the regulation of chromatin structure
• histone-fold domain has 3 alpha helices
• N terminal tails are unstructured domains
• C terminus

Histone fold motif (domain): 3 alpha helices — supersecondary structure

Question 13

histone octamers organize _____

Answer 13

DNA into repeating units

Question 14

describe the histone proteins when DNA is not present and is present

Answer 14

not present: H2A & H2B form a dimer ; H3 & H4 form a tetramer

DNA present: they come together and form a histone octamer

Question 15

describe histone octamers

Answer 15

• core of nucleosome formed by two of each core histone: H2A, H2B, H3, H4
• left-handed supercoil of 146 bp winds 1.67 times around the histone octamer (compacts DNA 6-7x)
• N terminus tails of histone stretch out of nucleosome
• histone folds are responsible for protein-protein interactions between core histones as well as binding DNA to form nucleosomes

Question 16

interactions of DNA and histones are through ___

Answer 16

hydrogen bonds

Question 17

name 2 ways to regulate chromosome structure

Answer 17

1- chromatin remodeling complexes

2- histone modifications by enzymes

Question 18

describe chromatin remodeling complexes

Answer 18

nucleosomes can be rearranged by ATP-driven chromatin remodeling complexes
- these complexes change the association between the histone cores with the DNA wrapped around
- the most well-known chromatin remodeling complex is SWI/SNF in humans

Question 19

name 3 examples of how variant histone subunits locally alter chromatin structure and function

Answer 19

1- replacing H3 with H3.3 — maintains a transcriptionally active open state

2- replacing H3 with CENPA — maintains kinetochore attachment to spindle fibers

3- replacing H2A with H2AX — H2AX is phosphorylated and attracts DNA repair proteins to seal DNA Break

Question 20

describe histone modifying enzymes

Answer 20

modifications of histone tails alter chromatin structure
- histone modifying enzymes attach chemical groups to amino acids of nucleosome subunits

• if the outcome is the direct result of a modification — cis
• if the modification attracts another protein that performs the histone-modifying function — trans
• the modifications to tails with either affect clamping together nucleosomes closer or pushing them farther away, altering DNA accessibility

Question 21

name a few examples of histone tail modifications

Answer 21

• acetylation of histone tails in lysine residues decreases positivity and enhances DNA accessibility (because looser)- acetylation done by enzymes called HAT- histone acetyltransferase
• tails comprise 25-30% of the mass of histones, tails are rich in:
  lysine: acetylation, methylation, ubiquitination
  serine: phosphorylation
  arginine: methylation

Question 22

can histone tail modifications be passed down?

Answer 22

yes, histone modifications are inheritable
- inheritance of genetic properties that are not coded in DNA sequence = epigentic

Question 23

describe H1

Answer 23

H1 is the “linker histone,” packs adjacent nucleosomes
- H1 helps nucleosomes condense into a higher level of packaging – 30 nm filament
- the 30 nm fiber is maintained by interactions between tails of the adjacent nucleosomes as well as compaction by H1

Question 24

euchromatin vs. heterochromatin

Answer 24

eu- undergoes condensation and decondensation- becomes active (relaxed and accessible)

hetero- stays more condensed