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LS 3 Midterm 2 > Lecture 8: Chromosomes and Genomes > Flashcards

Lecture 8: Chromosomes and Genomes Flashcards

1
Q

Introns vs. exons

A

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

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2
Q

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

A

48 x 10^6

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3
Q

What 3 sequences must each chromosome contain?

A

Centromere, two telomeres, origin(s) of replication

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4
Q

Composition of chromatin

A

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

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5
Q

Components of nucleosome

A

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

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6
Q

Core histones and how many per nucleosome

A

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

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7
Q

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

A

AA, TT, and TA (in minor groove)

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8
Q

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

A

GC (minor groove outside)

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9
Q

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

A

ATP hydrolysis

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10
Q

Function of histone chaperones

A

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

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11
Q

How wide is a usual chromatin fiber?

A

30 nm

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12
Q

Function of linker histone H1

A

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

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13
Q

Position effect variegation

A

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

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14
Q

Where are core histones covalently modified?

A

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

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15
Q

3 common covalent modifications on histones

A

Lysine acetylation and methylation, and serine phosphorylation

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16
Q

Effect of trimethylated K9 (lysine 9) on histone H3

A

Heterochromatin formation and gene silencing

17
Q

Effect of trimethylated K4 and acetylated K9 on histone H3

A

Gene expression

18
Q

Effect of trimethylated K27 on histone H3

A

Gene silencing (Polycomb repressive complex)

19
Q

Function of histone variant H3.3

A

Transcriptional activation

20
Q

Function of histone variant CENP-A

A

Centromere function and kinetochore assembly

21
Q

Function of histone variant H2AX

A

DNA repair and recombination

22
Q

Function of histone variant H2AZ

A

Gene expression, chromosome segregation

23
Q

Function of histone variant macroH2A

A

Transcriptional repression, X-chromosome inactivation

24
Q

Function of reader complex

A

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

25
Q

What do barrier DNA sequences do?

A

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

26
Q

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

A

(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

27
Q

How can chromatin structures be inherited?

A

After DNA replication, or epigenetically

28
Q

What phase of interphase is DNA replication?

A

S phase

29
Q

Significance of genes in the loops of lampbrush chromosomes

A

Being actively expressed

30
Q

Summary of chromosome conformation capture (3C) method

A

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)

31
Q

How many nucleotides in a chromosome loop?

A

50k-200k

32
Q

Composition of polytene chromosome DNA

A

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

33
Q

Significance of polytene chromosome puffs

A

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

34
Q

Heterochromatic regions associate where in nucleus?

A

Near the nuclear lamina

35
Q

Conformation that most regions of chromosomes are folded into

A

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

36
Q

Function of nuclear subcompartments

A

Form set of distinct biochemical environments inside nucleus

37
Q

Composition of nuclear subcompartments

A

networks of proteins and RNA

38
Q

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

A

10,000

LS 3 Midterm 2 (4 decks)

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