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Advanced Molecular > Chromosomes and DNA > Flashcards

Chromosomes and DNA Flashcards

1
Q

What is a karyotype, how is it observed and what does this method allow?

A
  • An organisms complete set of chromosomes
  • Chromosomes spread out on a slide and are spread during metaphase
  • You can observe crossing over, differences in sizes, view duplications
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2
Q

What happens during interphase?

A
  • Under the electron microscope the chromatin resembles ‘beads on a string’
  • The chromatin becomes supercoiled (30nm fibre)
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3
Q

What is the double helix wrapped around?

A

Histones to form nucleosomes

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4
Q

Describe what nucleosomes are

A
  • Structural unit consisting of a histone protein core in which DNA is wound
  • The core of nucleosomes is histone proteins
  • The N-terminal tails of the 8 core histone subunits project out from the nucleosome core and are free to interact with other proteins, facilitating regulation of chromosome structure and function
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5
Q

What is heterochromatin?

A

Tightly packed form of DNA or condensed DNA

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6
Q

What helps facilitate the establishment of transcriptionally silent heterochromatin?

A

H1 strap DNA onto histone octamers and limit movement of DNA relevant to the histone octamer

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7
Q

How is it ensured that DNA is flexible for regions that need to be accessed and replicated?

A

Specific proteins come and ‘open up’ the helix to allow proteins to bind

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8
Q

What is a fractal globule?

A
  • A way to describe the structure of the chromatin in interphase
  • Compact polymer
  • Can reversible condense and decondense without becoming knotted
    -Visualised as highly organised
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9
Q

What are telomeres?

A
  • Protect chromosome against loss of genetic information
  • 3’ overhang
  • Allows telomerase to bind and synthesise the end of the sequence (replicate it)
  • Can be several hundred nucleotides long
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10
Q

What are centromeres?

A
  • The platform for which kinetochores form which are important for segregation during proliferation as it binds to the mitotic spindle
  • Allows separation of the two daughter cells
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11
Q

What is the structure of the centromere?

A
  • Made up of repeated sequences called the alpha satellite DNA repeat
    -Has an inner and outer plate
  • Inner plate proteins bind to chromatin containing alpha satellite DNA
  • The outer plate binds to protein components of mitotic spindle
    i.e. microtubules
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12
Q

How is the kinetochore different in yeast?

A
  • The kinetochore is a basket that links a single nucleosome of centromeric chromatin to a single microtubule
  • The centromere specificity comes from histone H3
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13
Q

What comes with increasing biological complexity?

A
  • increasing numbers of protein-coding genes
    AND
    increasing amounts of non-protein-coding DNA
    for regulating transcription and organising access to protein-coding genes.
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14
Q

What percentage of the DNA sequence of eukaryotic genomes encodes information for making cellular proteins?

A

1.5%

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15
Q

What percentage of DNA is made up of repeated sequences

A

50%

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16
Q

What are transposons and what are the three different types?

A

Transposons are mobile genetic elements that jump around
the genome – also called “transposable elements”, they are repeated sequences

  1. DNA Transposons
  2. Retroviral retrotransposons
  3. Non-retroviral polyA retrotransposons
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17
Q

How do DNA transposons work?

A
  • Move by cut and paste mechanism without self duplication so it requires the enzyme transposase
  • Transposase cuts DNA and reintergrates itself at a different target sequence
  • Leaves a break in the DNA which gets rejoined but at the expense of genetic information loss
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18
Q

What do retroviraltransposons do?

A

Replicate via RNA intermediates, producing new DNA copies that integrate at new genomic locations used self-encoded Reverse transcriptase

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19
Q

What do non-retroviral, PolyA retrotransposons do?

A
  • Abundant in vertebrate genomes
  • Reverse transptiase with endonuclease activity - binds to POlyA
  • Nicks DNA activity
  • Reverse transcribes itself which then gets incorporated into the DNA strand
  • Can introduce mutations into the DNA i assume because ur nicking the DNA again
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20
Q

Why is DNA replication referred to as semi-conservative?

A

Made up of 1 old conserved strand of DNA and one new one

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21
Q

Give a brief recap of DNA replication (first yr stuff)

A
  • Creation of replication fork created by DNA helicase (breaks hydrogen bonds). Strands are separated
  • DNA synthesis occurs on leading strand (from 5’-3’ left to right)
  • Lagging strand replication occurs from 5’-3’ from right to left using okazaki fragments
  • Leading strand is continuous and lagging strand is discontinuous
  • Synthesis occurs between the gaps between the okazaki fragments
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22
Q

Explain the role of DNA polymerase

A
  • Responsible for synthesising DNA chain
  • Get added on to 3’ hydroxyl end
  • Cannot add nucleotides without a template, must be a pre-existing sequence for it to bind to
    aka a primer
  • Primer is RNA and it binds to DNA creating a RNA-DNA hybrid
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23
Q

How is a primer made?

A
  1. Short RNA primer is synthesised using template and NTPs (nucleotide triphosphates) by DNA primase
  2. Once the RNA primer is in place, DNA polymerase ‘extends it’
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24
Q

How is the lagging strand synthesised?

A
  • DNA primase makes these primers at different points upstream on the DNA strand
  • RNA primers moved using ribonuclease
  • DNA polymerase extends across the gap
  • DNA ligase seals the nick
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25
Q

How does DNA helicase create the replication fork?

A

2 DNA helicase bind to certain points on the strand and break the hydrogen bonds pulling apart the helix and unwinding it

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26
Q

What are is Werner Syndrome and what causes it?

A
  • Mutation in gene coding DNA helicase
  • Causes Premature ageing
  • Autosomal recessive disease
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27
Q

What is blood syndrome and what causes it?

A
  • A rare cancer syndrome caused by mutations in Rec-Q family DNA helicase which maintains genome integrity
  • Causes replication collapse and inaccurate replication
28
Q

What is processivity?

A

Enzymes ability to catalyse consecutive reactions without releasing a substrate

29
Q

What increases the processivity of DNA polymerases?

A

Sliding clamp will bind to primer template junctions and load the polymerase onto the DNA causing displacement of clamp loader so that the polymerase binds to the sliding clamp

  • Keeps it in place and moves it along the DNA so it can accurately and rapidly synthesise the strands of DNA
30
Q

What is a problem that can arise through DNA helicase?

A

Exposing single strands of DNA through DNA helicase can cause ‘hairpin’ structures where pairs complementary to each other on the single strand bind to eachother

31
Q

What do topoisomerases do?

A
  • Prevent DNA from becoming tangled during DNA replication and enhance processivity of DNA polymerase
32
Q

What is the difference between Topoisomerase I and Topoisomerase II?

A
  • Topoisomerase I nick and reseal one of the 2 strands no ATP required, relaxing the tension in the supercoil
  • Topoisomerase II cuts both strand of double stranded DNA and removes two twists at a time, requiring ATP
33
Q

What do specific sequences recruit during the origin of replication?

A
  • Initiator proteins
  • Sequences thought to be near genes which initiate the cell cycle
34
Q

Explain why initiation of DNA replication in yeast is biphasic (has two phases)

A
  • There are two parts:
  1. Replicator selection occurs in G1 phase
    (formation of pre-replicative complex)
  2. Origin activation occurs in S phase
    (unwinding of DNA and recruitment of DNA polymerase)
35
Q

What is the benefit of biphasic initiation?

A

Temporal separation between these 2 events ensures that each origin is only used once and chromosomes are only replicated once

36
Q

How does replicator selection occur in G1?

A
  • Origin receptor complex (ORC) binds to receptor sewuence
  • Helicase loading proteins called cdc6 and cdt1 bind to ORC
  • Helicase mcm2-7 binds to complete formation of pre-replicative complex which is loaded on to the DNA and stays inactive until S phase
37
Q

Why does the pre-replicative complex stay inactive until S phase?

A
  • Cdk activity low in G1
  • Cdk activity increases in S phase signalling to the pre-replicative complex to become activated which initiates the helicases to activate and start the whole process

ANOTHER WAY HOW IT IS IMPORTANT THAT CHROMOSOMES ARE ONLY REPLICATED ONCE IN THE CELL CYCLE

38
Q

How does replication stop?

A
  • Primers at end (from okazaki fragments)removed by ribonuclease H
  • Leaves an overhang
  • To sort this out telomerase extends the DNA sequence in the form of repeated DNA sequences (telomeres) which allows a new primer to be formed and an okazaki fragment so synthesis can occur in the usual way, we dont care about not getting this new end bit because its just repeated stuff
39
Q

What are the consequences of DNA damage?

A
  • Mutations get passed onto daughter cells if not repaired which gives rise to cancer (proliferative cells) or ageing (non-proliferative cells)
40
Q

What are endogenous sources?

A

Reactions with other molecules within the cell e.g. hydrolysis, by-products of metabolism

41
Q

What are Exogenous sources?

A

Reactions with molecules outside of the cells e.g. UVs, X-rays

42
Q

Name some types of Endogenous and Exogenous DNA damage?

A

Endogenous (effecting nucleotide base)
- Depurination
- Deamination
- Methylation
- Replication errors

Exogenous:
- Single strand breaks
- Pyrimidine dimers
- Double strand breaks
- Interstrand crosslinks

43
Q

What is deamination (endogenous)?

A
  • Removal of the amino group by hydrolysis in changes to the DNA bases
  • Transition and Transversion mutations
44
Q

What is the most common type of deamination?

A

Cysteine deamination to uracil (CG-TA)

45
Q

What is a Transition mutation?

A

When a purine changes to another purine or a pyrimidine changes to another pyrimadine e.g. cysteine deamination to uracil
Purine = Adenine and Guanine
Pyrimidine = Cytosine and Thymine

46
Q

What is a transversion mutation?

A

A transversion is a type of point mutation in which a purine is replaced by a pyrimidine or vice versa.

47
Q

What is Depurination (endogenous)

A
  • Base removed from the DNA by water
  • Bond between the base and backbone (N-glycosidic bond) is a substrate for hydrolysis
  • Most frequent at purine bases
  • Results in a frameshift mutation
48
Q

How many reading frames does DNA have?

A

3

49
Q

What is a missense protein?

A
  • Dont code for anything
  • Generated by frameshift mutation
50
Q

What is a pyrimidine dimer? (exogenous)

A
  • Creates an extra bond between two pyrimidine bases on the same strand to distort the DNA rather than change composition
  • UV light is an e.g.
51
Q

What is an interstrand link? (exogenous)

A
  • Links between the bases
  • Block replication and transcription
  • Can also be caused by UV
52
Q

What is a single/double strand break?

A
  • Damage that effects the phosphate backbone
  • Caused by X-rays, radiation etc.
53
Q

What is base excision repair?

A
  • Repairs base-damage were there is a deaminated C base
  • Damaged base gets flipped out by Uracil DNA glycosylase
  • The missing base is solved by causing a single strand break in the backbone by AP endonuclease, and adding a new nucleotide with DNA polymerase and DNA ligase sealing the nick
54
Q

What nucleotide excision repair?

A
  • Repairs where pyrimidine dimers have formed
  • Effected bases are removed by excision of short patches of single stranded DNA
  • Excision nuclease carries this out
  • DNA helicase removes the DNA
  • DNA polymerase and DNA ligase sorts the remaining bit out in the same way as base excision repair
55
Q

What is translesion synthesis?

A
  • When sliding clamp encounters DNA damage causing polymerase to dissociate from it
  • Means DNA replication can continue by skipping bases but can also cause mutations if big bits aren’t replicated
  • Used to repair/move past interstrand links
56
Q

What are the two ways to repair double-stranded breaks?

A
  1. Non-homologous end joining
  2. Homologous recombination
57
Q

How does nonhomologous end-joining work?

A
  • G1 phase of cycle
  • MRN detects break
  • Ku protein binds to break and DNA protien kinase binds to that, forming a synaptic complex pulling the DNA together to be in close proximity
  • DNA ligase seals gap
  • Error-prone as it can seal gaps even when there is an insertion/deletion mutation
58
Q

How does homologous recombination work?

A
  • S phase, uses newly synthesised DNA as template
  • Alligns two same sequences
  • MRN creates 3’ overhang
  • RPA and Rad51 coat overhang to initiate strand invasion (activating other proteins)
  • Strand crossed over into new sister chromatid and invades
  • The crossover is called the holiday junction
  • Once crossed over synthesis occurs using the strand as a template
  • DNA rejoins its own double helix to form a double holiday junction
  • Two double helices separate and accurate repair has occured
59
Q

What are the three stages of mitosis where DNA damage is detected?

A
  1. G1
  2. Entry to S-phase
  3. Entry to mitosis
    no repair= apoptosis
60
Q

How is DNA damage detected?

A
  • ATM/ATR activated +associates with DNA damage site
  • P53 established and activates p21
  • p21 renders cell cycle and effects cdk levels so cell cant enter S phase
  • Stops cell cycle and allows DNA repair
61
Q

How does BRCA1/2 link to homologous recombination?

A
  • BRCA1/2 involved in homologous recombination
  • Defects in BRCA1/2 present in breast cancer patient
  • Means repair cant occur and tumours form
62
Q

Why do we treat cells with BRCA1/2 mutations with ionising radiation?

A
  • The cancer cells don’t have the means to repair because they cant do homologous recombination so they die
  • Healthy cells can repair themselves from the ionising radiation
63
Q

What is synthetic lethality?

A

The simultaneous loss or inactivation of two or more genes results in a lethal or nonviable phenotype
e.g. cancer cells deficient in homologous recombination rely on other pathways so if the genes responsible for them are knocked out then the cancer cell dies

64
Q

Name 3 ways we can study DNA damage?

A
  • DNA damage markers
  • Common assay
  • Western blot
65
Q

How do a common assay and a western blot work?

A

Common assay= cells treated with drug, electrophoresis, cell damage leaks out and u can see how much is released
Western blot = Different proteins expressed at different levels in different repair pathways

Advanced Molecular (13 decks)

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