BLGY2296 Epigenetics

Question 1

What is epigenetics?

Answer 1

The study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself (the concept that the function of a piece of DNA is determined by factors other than its nucleotide sequence alone)

Question 2

Alternation in gene expression can be due to what?

Answer 2

1) Mutation of gene DNA sequence
2) Alteration of methylation status
3) Alteration in underlying chromatin organisation

Question 3

What is chromatin?

Answer 3

A complex of DNA and protein that makes up the chromosomes

Question 4

What does the chromosomal organisation mediate?

Answer 4

• compaction of genetic material
• efficient transmission to daughter cells upon cell division
• protection from DNA damage (because the DNA is wrapped up)
• regulation of DNA accessibility (regulates recombination)
• regulation of gene transcription

Question 5

What does a tetrahymena macronucleus contain?

Answer 5

Thousands of short linear chromosomes (therefore lots of telomeres)

Question 6

Eukaryotes have what shaped chromosomes?

Answer 6

Linear (so need a mechanism to replicate the ends of the DNA)

Question 7

Prokaryotes have what shaped chromosomes?

Answer 7

Circular (so need a mechanism to separate DNA strands)

Question 8

What are chromatids?

Answer 8

A chromatid is one-half of two identical copies of a replicated chromosome

Question 9

Which is the largest human chromosome?

Answer 9

1 (10um)

Question 10

Which is the smallest human chromosome?

Answer 10

21 (2um)

Question 11

How many autosomes do humans have?

Answer 11

22 pairs

Question 12

What is the human chromosome with the lowest density?

Answer 12

4 (8 genes/Mb)

Question 13

What is the human chromosome with the highest density?

Answer 13

19 (27 genes/Mb)

Question 14

In what stage of the cell cycle are chromosomes decondensed?

Answer 14

Interphase

Question 15

What stage of interphase is DNA replicated?

Answer 15

S phase

Question 16

What happens in the M phase of interphase?

Answer 16

Cell division - mitosis

Question 17

What stage of interphase are all the compounds required for DNA synthesis synthesized?

Answer 17

G1 phase

Question 18

What stage of interphase do the cells prepare for mitosis?

Answer 18

G2 phase

Question 19

True of false? Different chromosomes occupy the same territories in the nucleus?

Answer 19

False- they occupy different territories in the nucleus

Question 20

What is a centromere?

Answer 20

The point on a chromosome by which it is attached to a spindle fibre during cell division, it contains highly repetitive DNA

Question 21

What is a kinetochore?

Answer 21

A large protein complex which bones to the centromere and attaches to microtubules (has a role in separating the chromosomes to opposite poles during the metaphase)

Question 22

What is heterochromatin?

Answer 22

Highly repetative DNA that is tightly packed and so not accessible to DNA polymerase. It is found at the centromeres

Question 23

What are telomeres?

Answer 23

Specialized structures at the ends of chromosomes essential for chromosome integrity (the rate at which chromosomes are changed), repetitive DNA, well conserved

Question 24

Which structure prevents chromosomes binding to each other, re-combing or degrading?

Answer 24

Telomeres

Question 25

What is the well conserved sequence of the telomeres?

Answer 25

TTAGGG - form t-loops (bind specific proteins e.g. shelterin)

Question 26

Extraction of nuclei using salt of physiological ionic strength (150um) produces a chromatin fibre of what length?

Answer 26

30nm

Question 27

Extraction of nuclei using lower salt concentrations produces what length of fibre?

Answer 27

10nm (beads on a string)

Question 28

DNA is packaged into what?

Answer 28

Nucleosomes

Question 29

Are histone core proteins highly conserved?

Answer 29

Yes

Question 30

How many times is DNA wrapped around a histone core particle?

Answer 30

Twice

Question 31

How many nucleotides long is a histone core particle?

Answer 31

147 nucleotides

Question 32

Micrococcal nuclease (MNase)cleaves chromatin where?

Answer 32

In the linker between the nucleosome cores

Question 33

What can be used to extract proteins from nucleosome beads?

Answer 33

High salt concentration

Question 34

Each nucleosome contains how many copies of core histones?

Answer 34

Two

Question 35

What are the core histones?

Answer 35

H2A, H2B, H3, H4

Question 36

What is the linker histone?

Answer 36

H1

Question 37

Are histones very acidic or very basic?

Answer 37

Very basic (rich basic tail)

Question 38

What percentage of the mass of core histones are composed of lysine and arginine residues?

Answer 38

20-25%

Question 39

The histone fold domain is made up of what?

Answer 39

Three alpha helices that form a Z shape

Question 40

The interactions between histones mediated by the histone core fold forms which heterodimers?

Answer 40

H2A-H2B (dimer) and H3-H4 (tetramer)

Question 41

Does the H2A-H2B dimer or the H3-H4 tetramer interact with DNA?

Answer 41

H3-H4 tetramer

Question 42

True of false the histone tails protrude from the nucleosome?

Answer 42

True - can be cleaved of by protease (doesn't affect the structure of the nucleosome)

Question 43

Which interaction is the weakest and the first to be disrupted when the nucleosome unfolds in vivo?

Answer 43

H2B-H4

Question 44

Histones form what type of interactions?

Answer 44

Charge interactions (not basic interactions)

Question 45

Where are the AT rich regions found when the nucleosomes bind to DNA?

Answer 45

On the inside