Topic 2 - Section 1

Question 1

describe the viral genome and how it is packed

Answer 1

nucleic acid contained within a capsid

Question 2

how does + and - ssRNA viral genome differ in using host machinery

Answer 2

+ = replicates straight away single step
- = has to make a strand template before translating into protein

Question 3

describe the t7 bacteriophage lifecycle

Answer 3

lytic and lysogenic life cycle

Question 4

describe the structure of eukaryotic nucleus

Answer 4

chromosomes condensed chromatin, chromatin condenses into chromosomes

Question 5

describe the bacterial genome organisation

Answer 5

• supercoiled nuclei
• large number of loops of duplex DNA forming independent structural domains

Question 6

describe the replicating origin of bacteria

Answer 6

one origin where replication begins resulting in 2 circular daughter DNA molecules

Question 7

describe the eukaryotic cell cycle

Answer 7

g1 - interphase
s - DNA replication
g2 - checking for errors
m - mitosis

Question 8

what are the 2 purposes of compaction of chromatin in mitotic state

Answer 8

• sister chromatids disentangle from eachother lying side by side
• protects fragile DNA molecules from broken during separation

Question 9

difference between replication time of heterochromatin and euchromatin

Answer 9

euchromatin = early heterochromatin = late

Question 10

what is a karyotype

Answer 10

number and appearance of chromosomes in the nucleus, stop mitosis in metaphase

Question 11

how are chromosomes visualised?

Answer 11

cytogenetics arrange and analyse into ideogram. various dyes used for banding

Question 12

what is SKY?

Answer 12

spectral karyotyping: molecular cytogenetic technique for simultaneously visualising all the pairs of chromosomes in different colours.

Question 13

define the p arm and the q arm in chromosomes

Answer 13

p arm = petite
q arm = longer

Question 14

Chr12q13

Answer 14

chromosome 12, 13 on the q arm

Question 15

what is the HGP

Answer 15

map of all human chromosomes at single nucleotide resolution

Question 16

heterochromatin vs euchromatin

Answer 16

euchromatin - relaxed regions, early replicating and GC rich, participates in active transcription

heterochromatin - tightly coiled condensed regions, less transcribed , compact chromatin, rich in AT base pairs, late replicating

Question 17

what does “positional effects” mean?

Answer 17

gene expression in euchromatin segments experimentally moved to heterochromatin sites

Question 18

constitutive vs facultative heterochromatin

Answer 18

Constitutive heterochromatin
 Present at identical positions on all chromosomes in all cell types of an organism
 Any genes contained within will be poorly expressed
 Human chromosomes 1, 9, 16, and the Y chromosome contain large regions
 In most organisms, constitutive heterochromatin occurs around centromere and near telomeres

Facultative heterochromatin
 Varies with the cell type. Condensed (heavily stained) chromatin in only certain differentiated somatic cells in the same organism.
e.g., X-chromosome inactivation in female mammals: one X chromosome is packaged in facultative heterochromatin & silenced, while the other X chromosome is packaged in euchromatin and expressed.

Question 19

how do chromosome anomalies occur and what r the 2 types

Answer 19

occurs when there is an error in cell division during meiosis or mitosis

• extra = numerical
• wrong w banding = strucutral

Question 20

what is aneuploidy?

Answer 20

an abnormal number of chromosomes

• missing 1 chromosome from a pair = monosomy
• has more than 2 chromosomes of a pair = trisomy, tetrasomy etc

Question 21

chromosome global structure

Answer 21

• one section of chromosome = made up of chromosome fibres
• fibres unwound = nucleosomes packed
• next level = chromatin = DNA wrapped around histone

Question 22

land brush loop tucked in vs out

Answer 22

in = ess accessible so less transcription

Question 23

interior of nucleus

Answer 23

• intra-nuclear structures act as anchor points for chromosomes to hold onto
• patches of region → is dynamic, constant flotation and movements
  
  • dark - chromatin domain - contains chromosomes
  • light - other areas without chromatin (interchromatin)
  • dark but not membrane bound (nucleolus)

Question 24

how are chromosomes organised in the nucleus and what experiment demonstrated this?

Answer 24

chromosome territoris /discrete regions bc when damage was induced locally, only a subset of chromosomes was damaged

Question 25

what is the consistency of nucleus and chromosome dynamic

Answer 25

- atomic force microscopy to test how thick/fluid is the nuclear properties - slow → inside nucleus there are high concentrations of content, very thick and crowded

Question 25

where are the protein coding genes ALU in interphase

Answer 25

- where are protein coding genes? - green = sequences with Alu (protein coding genes reside here) - red = alu poor (non-protein coding genes)

Question 26

how are DNA and histone in nucleosomes separated

Answer 26

- salt is able to be used to separate becasue the DNA and histone is joined by electrostatic forces and not covalent bonds

Question 27

how many hydrogen bonds between DNA and histone core in each nucleosome?

Answer 27

142

Question 28

describe the assembly of a histone octamer/dna complex

Answer 28

- assemby is mediated by histone chaperone proteins - groove that faces outwards = mostly C and G - vest way to wrap histones is A and T touching histone

Question 29

3 ways of epigenetic

Answer 29

methylation, histone modification, RNAi

Question 30

how are histone modifications inherited?

Answer 30

- involve reader writer remodelling complex

Question 31

what are CpG islands and where are they found

Answer 31

lots of C-G dinucleotides, frequently found in promotor regions. active transcribing genes has unmethylated CpG sequences

Question 32

centromeres where is it found? what does it contain?

Answer 32

- found in a stretch of centric heterochromatin - contains centromeric specific variant of H3 histone, contain short repeated DNA squences

Question 33

describe the end replication problem and telomeres

Answer 33

- final rna primer made on lagging strand template cannot be replaced by DNA as there is no 3OH available for repair polymerase - regular replication machinery cant fully elongate the end of a linear chromosome - bacteria deal with this by having circular DNA - telomere = heterochromatic tandem repeats

Question 34

how does telomerase function

Answer 34

has reverse transcriptase and carries its own RNA molecules it recognises existing telomeric DNA repeats and elongates in 5’-3’ using RNA template

Question 35

what is a T loop

Answer 35

structure at the end of telomere to protect it, regulated by sheltering

Question 36

compare the telomere activity in embryonic stem cells, cancer cells and mature differentiated cell types

Answer 36

- high in Es/cancer cells, low in differentiated mature cell typed

Question 37

describe the nucleolus change in appearance during cell cycle

Answer 37

- interphase - DNA loops formed in nucleolus - M phase - nucleolus disappears - telophase - nucleolus reforms

Question 38

function of nucleolus

Answer 38

makes rRNA and ribosomes

Question 39

what is endosymbiosis

Answer 39

mitochondria developed from aerobic bacterium entering a eukaryotic cell

Question 40

describe the mitochondrial genome

Answer 40

- very packed, nearly every nucloeotide forms a part of coding sequence - little space for regulatory sequences - less complex repair systems hence 100x higher deletions and pooint mutation

Question 41

descrfibe the variant genetic code in mitochondria

Answer 41

- only 22 tRNA required for protein synthesis bc wobble at 3rd position so less tRNA needed

Question 42

What are Meganucleases and what challenges are associated with them?

Answer 42

Naturally occurring endonucleases Recognize long DNA sequences (14–40 bp) Very specific, low off-target effects Hard to re-engineer for new targets Limited number of natural recognition sites

Question 43

What are ZFNs and what are their limitations?

Answer 43

Fusion of Zinc Finger Proteins (ZFPs) + FokI nuclease Each zinc finger binds 3 DNA bases Can target longer sequences by linking fingers Designing ZFPs is complex Not all DNA sequences can be targeted Limited binding site options

Question 44

What makes TALENs easier and more specific than ZFNs?

Answer 44

Derived from Xanthomonas bacteria Each repeat recognizes one nucleotide Recognition depends on 12th & 13th amino acids (RVDs) Easy and fast to design More specific and less toxic than ZFNs TAL proteins wrap around DNA with spacers

Question 45

How does CRISPR/Cas9 work and what are its components?

Answer 45

Based on bacterial immune defense system Uses crRNA + tracrRNA to guide Cas9 nuclease Requires PAM sequence for binding Steps: Transcription → Processing → Complexing → Editing Simplified to Cas9 + single guide RNA (sgRNA) Nobel Prize 2020: Doudna & Charpentier