Lecture 8: Chromosomes and Genomes

Question 1

Introns vs. exons

Answer 1

Introns are non-coding, exons are coding (eventually translated into proteins)

Question 2

How many nucleotide pairs in one DNA molecule of a mitotic chromosome?

Answer 2

48 x 10^6

Question 3

What 3 sequences must each chromosome contain?

Answer 3

Centromere, two telomeres, origin(s) of replication

Question 4

Composition of chromatin

Answer 4

1/3 DNA, 1/3 histone, 1/3 non-histone proteins

Question 5

Components of nucleosome

Answer 5

Core histones, DNA wrapped around histone (147 nucleotide pairs), and linker DNA

Question 6

Core histones and how many per nucleosome

Answer 6

H2A (2), H2B (2), H3 (2), H4 (2)

Question 7

Which dinucleotides are preferred on the side of the DNA touching the histone core?

Answer 7

AA, TT, and TA (in minor groove)

Question 8

Which dinucleotides are preferred on the outside of the DNA wrapped around the histone core?

Answer 8

GC (minor groove outside)

Question 9

What catalyzes nucleosome sliding for ATP-dependent chromatin remodeling complexes?

Answer 9

ATP hydrolysis

Question 10

Function of histone chaperones

Answer 10

Help the ATP-dependent chromatin remodeling complex remove the histone octamer, replace it, etc.

Question 11

How wide is a usual chromatin fiber?

Answer 11

30 nm

Question 12

Function of linker histone H1

Answer 12

Binds to the nucleosome, changing DNA’s path as it leaves the nucleosome, helps compact chromatin

Question 13

Position effect variegation

Answer 13

Spreading of heterochromatin affects cells (of the same type) in different ways, leading to a “mixed” phenotype

Question 14

Where are core histones covalently modified?

Answer 14

N-terminal “histone tails” that stick out of the histone core (modifications on AA side chain)

Question 15

3 common covalent modifications on histones

Answer 15

Lysine acetylation and methylation, and serine phosphorylation

Question 16

Effect of trimethylated K9 (lysine 9) on histone H3

Answer 16

Heterochromatin formation and gene silencing

Question 17

Effect of trimethylated K4 and acetylated K9 on histone H3

Answer 17

Gene expression

Question 18

Effect of trimethylated K27 on histone H3

Answer 18

Gene silencing (Polycomb repressive complex)

Question 19

Function of histone variant H3.3

Answer 19

Transcriptional activation

Question 20

Function of histone variant CENP-A

Answer 20

Centromere function and kinetochore assembly

Question 21

Function of histone variant H2AX

Answer 21

DNA repair and recombination

Question 22

Function of histone variant H2AZ

Answer 22

Gene expression, chromosome segregation

Question 23

Function of histone variant macroH2A

Answer 23

Transcriptional repression, X-chromosome inactivation

Question 24

Function of reader complex

Answer 24

Recognize specific combo of histone modifications and recruit appropriate molecules (which will then catalyze biological function like gene expression or silencing)

Question 25

What do barrier DNA sequences do?

Answer 25

Block spread of reader-writer complexes and separate neighboring chromatin domains

Question 26

How do barrier DNA sequences block spread of reader-writer complexes?

Answer 26

(1) Form physical barrier to block heterochromatin spread, (2) bind to nucleosomes and prevent their modification, (3) get rid of marks that trigger heterochromatin spread

Question 27

How can chromatin structures be inherited?

Answer 27

After DNA replication, or epigenetically

Question 28

What phase of interphase is DNA replication?

Answer 28

S phase

Question 29

Significance of genes in the loops of lampbrush chromosomes

Answer 29

Being actively expressed

Question 30

Summary of chromosome conformation capture (3C) method

Answer 30

Add DNA-binding proteins, which bind at loop --> fix with formaldehyde --> cut DNA that isn't crosslinked with restriction nuclease --> ligate the strands --> remove cross-links --> use PCR to find joined segments (marks where loops were)

Question 31

How many nucleotides in a chromosome loop?

Answer 31

50k-200k

Question 32

Composition of polytene chromosome DNA

Answer 32

95% in bands (3700 bands), 5% in interbands (3700 interbands)

Question 33

Significance of polytene chromosome puffs

Answer 33

RNA synthesis occurring (puffs caused by decondensing of chromatin loops as genes in that area are expressed

Question 34

Heterochromatic regions associate where in nucleus?

Answer 34

Near the nuclear lamina

Question 35

Conformation that most regions of chromosomes are folded into

Answer 35

Fractal globule (dense but retains ability to fold and unfold)

Question 36

Function of nuclear subcompartments

Answer 36

Form set of distinct biochemical environments inside nucleus

Question 37

Composition of nuclear subcompartments

Answer 37

networks of proteins and RNA

Question 38

Each DNA molecule in a chromosome is _____ times shorter than its full length

Answer 38

10,000