Week 3

Question 1

1KB

Answer 1

1000 base pairs

Question 2

cross-talk

Answer 2

over time, some genes from mitochondrial and chloroplast sequences have migrated to the nucleus

Question 3

why do organisms across the tree of life have such noticeable differences in size?

Answer 3

as complexity increases, there seems to be a trend toward larger genomes

Question 4

what is included in the DNA that we have?

Answer 4

• 50% of the genome is made up of repetitive DNA
• 50% is unique sequences
• less than 1% of your genome encodes proteins

Question 5

label a diagram for the percentage of the human genome and their functions

Question 6

describe the necessity of packaging of DNA in the cell in prokaryotes

Answer 6

• in a non-packaged state, even the small prokaryotic genome would occupy a considerable portion of the cell volume
• DNA is condensed through folding and twisting and is complexed with proteins
• this forms the prokaryotic nucleioid

Question 7

the chromosome solution

Answer 7

method of getting eukaryotic genome packed into cell

Question 8

fluorescence in situ hybridisation (FISH)

Answer 8

• heat up chromosomes
• DNA helix will loosen a bit
• mix in a probe (short sequence of DNA) that is complementary to some of the sequence on the chromosome
• fluorescent dye is stuck onto the probe
• some of the strands will find their complementary sequence and bind there

Question 9

describe the constitution of a chromosome

Answer 9

• each chromosome contains a single, long, linear DNA molecule and associated proteins called chromatin
• chromatin is tightly packaged, but dynamic as the DNA must remain accessible for transcription, replication and repair

Question 10

draw interphase chromatin

Question 11

draw M phase chromatin

Question 12

centromere and sequencing

Answer 12

difficult area to sequence as it is very compact

Question 13

telomeres and sequencing

Answer 13

compact so hard to sequence

Question 14

levels of organisation of chromatin

Answer 14

• short region of DNA double helix
• ‘beads on a ring’ form of chromatin (double wrapped around nucleosome with some linker DNA)
• chromatin fibre of packed nucleosomes (30nm fibre)
• chromatin fiber folded into loops
• entire mitotic chromosome

Question 15

describe the types and arrangement of histone proteins

Answer 15

• small proteins - rich in lysine and arginine
• positive charge neutralizes negative charge of DNA
• four core histone proteins (H2A, H2B, H3 & H4)
• pair of each in octamer core
• one linker histone (H1)
• H2A and H2B form a dimer, H3 & H4 form a dimer
• each core histone protein has a tail that can be covalently modified (reversibly) to be methylated, phosphorylated, acetylated; this is important for regulation of nucleosomes and how compact the DNA is

Question 16

H1

Answer 16

acts as a paper clip and changes the trajectory of the linker DNA so it is bent and compacted better

Question 17

how are chromatin loops made

Answer 17

sequence-specific clamp proteins and cohesions are involved in forming chromatin loops

Question 18

how are chromatin loops altered during mitosis?

Answer 18

as cells enter mitosis, condensins replace
most cohesins to form double loops of
chromatin to generate compact chromosome

Question 19

each DNA molecule has been packaged into a mitotic chromosome that is ——- times shorter than its extended length

Answer 19

10,000

Question 20

function of chromatin re-modeling complexes an histone modifying enzymes

Answer 20

proteins that work together to make changes in chromatin structure and alter access to DNA for replication or transcription, so that the DNA is in a state where the cell can actually use it.

Question 21

heterochromatin

Answer 21

highly condensed chromatin
- meiotic and mitotic chromosomes
- centromeres and telomeres
- time spent highly condensed varies (constitutive vs facultative)

Question 22

heterochromatic regions of interphase chromosomes are areas where gene expression is

Answer 22

suppressed

Question 23

euchromatin

Answer 23

relatively non-condensed chromatin
- degree of condensation varies
- level of activity varies (ie quiescent vs active)

Question 24

active euchromatic regions of interphase chromosomes are areas where genes tend to be

Answer 24

expressed

Question 25

constitutive heterochromatin

Answer 25

highly condensed pretty much all the time (eg centromeres/telomeres)

Question 26

facultative heterochromatin

Answer 26

easier to decondense; genes that may need attention sometimes, like regulatory sequences

Question 27

quiescent euchromatin

Answer 27

a level of condensation that is not as loose as active euchromatin but not as tight as heterochromatin

Question 28

active euchromatin

Answer 28

genes are being expressed (transcribed)

Question 29

heterochromatic vs euchromatic

Answer 29

a continuum that is dynamic

Question 30

what is the degree of chromatin condensation controlled by?

Answer 30

localised covalent modification of histones, the presence of chromatin remodelling complexes, and RNA polymerase (transcription) complexes model the reversible switching from euchromatic to heterochromatic regions along chromosomes

Question 31

how are interphase chromosomes arranged in the nucleus?

Answer 31

- discrete regions - these regions can vary from cell to cell

Question 32

gene off -> gene on

Answer 32

- homologous chromosomes detected by hybridisation techniques - part of the chromosome is loosened so specially marked gene is moved to loosely compacted area of chromosome

Question 33

is DNA replication conservative or semi-conservative? describe both

Answer 33

conservative: daughter cells have both parental DNA strands in one daughter cell and both of the newly synthesised strands in the other cell semi-conservative: two daughter cells each have one parental DNA strand and one newly synthesised strand

Question 34

why is conservative DNA replication problematic?

Answer 34

- if there is a mistake in the newly synthesised strands, there is no other strand to rectify this

Question 35

what is the direction of DNA replication?

Answer 35

there are three main models that occur in nature, but we will focus on bidirectional growth from one starting point - DNA is growing in two directions from every point of origin. Bacteria and eukaryotes use this methods

Question 36

describe the start of DNA replication

Answer 36

- double helix is opened with the aid of initiator proteins at the replication origin - single stranded DNA templates are thus ready for DNA synthesis

Question 37

where does DNA replication start?

Answer 37

always starts from the same location on DNA

Question 38

What are some of the characteristics of the sequences at replication origins?

Answer 38

Easy to open, A-T rich Recognized by initiator proteins that bind to the DNA

Question 39

how many origins of replications do origins have?

Answer 39

bacteria have a single one, eukaryotes have multiple (DNA is a lot bigger, so this is more effective)

Question 40

Rolling Circle Replication

Answer 40

bidirectional; only applies to circular genomes

Question 41

what happens at DNA replication forks?

Answer 41

5' to 3' direction (rule of DNA polymerase) growth in DNA. Okazaki fragments are formed in the lagging strand. The replication fork is asymmetrical - leading strand (5' to 3') replicated continuously, lagging (3' to 5') replicated discontinuously