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Foundation Unit 1 > Lectures 1.6-1.7 > Flashcards

Lectures 1.6-1.7 Flashcards

1
Q

How is DNA compacted to fit in the eukaryotic nucleus?

A

DNA wraps around protein cores called nucleosomes (which is composed of histone octamers). Binding to nucleosomes compacts DNA 7x. The nucleosomes are arranged into tightly spaced structured called 30nm fiber. 30 nm fiber then loop and form a rosetter around a “nuclear scaffold” which then forms coils making up a chromatid.

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2
Q

properties of histones

A
  • small, basic proteins
  • highly conserved in eukaryotes
  • H2A, H2B, H3, and H4 form histone core (nucleosome octamer)
  • post translational modification of histone proteins regulates chromatin structure/function
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3
Q

How do histones interact with DNA?

A

DNA wraps around histones to form chromatin

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4
Q

homologous recombination (general recombination)

A

genetic exchange between homologous DNA sequences:

  • basepairing occurs between sequences
  • DNA is broken and rejoined
  • Holliday junction intermediate
  • forms heteroduplex DNA
  • initiation from double stranded DNA break
  • strand invasion, DNA synthesis and ligation casues formation of joint molecule (Holliday junction)
  • migration and resolution of holliday junction leads to DNA exchange and results
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5
Q

Which histones make up the histone core?

A

H2A, H2b, H3, H4

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6
Q

Nucleosome

A
  • one nucleosome every 200 bp

- N terminal tails extend out from the core and are sites of modification and regulation

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7
Q

homologous recombination (general recombination)

A

genetic exchange between homologous DNA sequences:

  • basepairing occurs between sequences
  • DNA is broken and rejoined
  • Holliday junction intermediate
  • forms heteroduple DNA
  • initiation from dsDNA
  • strand invasion, DNA synthesis and ligation casues formation of joint molecule (Holliday junction)
  • migration and resolution of holliday junction leads to DNA exchange
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8
Q

Holliday junction

A
  • four stranded intermediate which contains two joined DNA duplexes
  • recombinase enzymes catalyze breaking ad rejoining of DNA
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9
Q

What are the classes of products that can be produced when a Holliday junction is resolved?

A
  • Crossover (half new chromatid/ half old chromatid) or non-crossover products (new insertion but chromatid remains the same otherwise)
  • recombined DNA
  • repaired break
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10
Q

site-specific recombination

A
  • occurs in certain cellular processes and viral infections
  • occurs between specific sequences
  • is carried out by recombinases or integrases that act on target sequences
  • causes insertions, deletions or inversions
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11
Q

transposition

A

DNA sequence that can move in the genome by recombination
two types: DNA Transposons and Retrotransposons

  • DNA: mostly in bacteria, recombine into random site on the genome
  • Retrotransposons: found in eukaryotes, related to retroviruses (have RNA intermediate), some produce virus particles (not found outside cell)
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12
Q

transposition

A

DNA sequence that can move in the genome by recombination
two types: DNA Transposons and Retrotransposons

  • DNA: mostly in bacteria, recombine into random site on the genome
  • Retrotransposons: found in eukaryotes, related to retroviruses (have RNA intermediate), some produce virus particles (not found outside cell)
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13
Q

recombination

A

controlled chromosome rearrangements

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14
Q

roles of recombination

A
  • double strand break repair
  • meiosis
  • programmed genetic rearrangements
  • conjugation
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15
Q

types of recombination

A
  • site specific recombination
  • homologous recombination
  • “genome editing”
  • DNA transposition
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16
Q

CNV

A

copy number variant: deletion or duplications of regions of the genome.

  • leads to loss of heterozygosity
  • associated with disease
17
Q

What are the stages of replication?

A
  1. Initiation of replication: process that lead synthesis and assembly of replication fork
  2. Elongation: the process of DNA synthesis. replication forks move through DNA synthesizing new DNA strands.
  3. Termination: when replication stops. usually when replication forks meet.
18
Q

what are the two classes of DNA polymerase ?

A

classical DNA polymerase and Translesion DNA polymerase

19
Q

Classical DNA Polymerase

A

includes replicative and repair polymerases:

  • have 3’ to 5’ exonuclease activity (proofreading)
  • replicative is highly processive (synthesize long stretches of DNA without dissociating from template) and have a high rate of synthesis
  • repair polymerases have low to medium processivity and have lot to high rates of synthesis
20
Q

translesion DNA polymerase

A

involved in DNA repair and DNA synthesis of damaged DNA

21
Q

What are the functions of DNA polymerase accessory factors?

A

to help achieve high processivity by being topologically linked to DNA

  • sliding clamp
  • Clamp loader
22
Q

What are the seven types of protein involved in the replication fork?

A
  1. DNA Polymerase
  2. Primase
  3. DNA helicases
  4. ssDNA binding proteins (SSBs)
  5. DNA nucleases
  6. DNA ligases
  7. Topoisomerases
23
Q

sliding clamp

A

toroid shaped sliding clamp interacts with core polymerase and holds it on the DNA

24
Q

Clamp loader

A

sliding clamps are loaded with double stranded DNA by clamp loading complexes

25
Q

DNA Polymerase

A

enzymes that synthesize DNA

  • synthesize 5’ to 3’ direction
  • require an existing DNA strand to copy (ie.. template)
  • require a primer; add to a 3’ OH
26
Q

Primase

A
  • synthesize sort RNA oligonucleotide primes
  • can initiate synthesis on SSDNA de novo (no 3’=OH needed)
  • most primases start synthesis at random sites
  • usually part of a protein complex at replication fork
27
Q

DNA helicase

A
  • utilize energy of ATP hydrolysis to disrupt the double helix (each strand then becomes a helix)
  • a type of motor protein. Move along ssDNA in one direction disrupting hydrogen bonds. (either move 5’-3’ or 3’-5’)
  • necessary for movement of a replication fork; usually interact with primase.
  • nomenclature: direction of helicase movement is defined on the strand the helicase binds.
28
Q

ssDNA binding proteins

A
  • bind ssDNA
  • prevent formation of secondary structure in ssDNA
  • usually interact with other replication proteins to promote efficient replication
29
Q

DNA Nucleases

A
  • degrade (cleaves the nucleotides off) RNA or DNA from its end (exonucleases) or internally (endonucleases)
  • a 5’ to 3’ exonuclease required in replication to remove RNA primers to give continuous DNA strand
30
Q

DNA Ligase

A
  • form phosphodiester nods that join strands of DNA

- require high energy cofactor (ATP or NAD)

31
Q

Topoisomerases

A
  • parental strands start replication as a single helix but end replication as one strand of each of two separate helices
  • required to release the links between the parental DNA strands
32
Q

What is the problem in replicating linear chromosomes?

A

The DNA at the very end of the chromosome cannot be fully copied in each round of replication, resulting in a slow, gradual shortening of the chromosome. When the replication fork reaches the end of the chromosome, however, there is (in many species, including humans) a short stretch of DNA that does not get covered by an Okazaki fragment—essentially, there’s no way to get the fragment started because the primer would fall beyond the chromosome end

33
Q

steps of enzymatic activity of telomerase

A

The enzyme binds to a special RNA molecule that contains a sequence complementary to the telomeric repeat. It extends (adds nucleotides to) the overhanging strand of the telomere DNA using this complementary RNA as a template. When the overhang is long enough, a matching strand can be made by the normal DNA replication machinery (that is, using an RNA primer and DNA polymerase), producing double-stranded DNA.

34
Q

What is the role of telomerase in the cell?

A

enzyme that extends the telomeres of chromosomes. Telomerase is an RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template.

35
Q

How is replication initiated?

A
  • special complexes form at origin
  • origin is activated causing local unwinding of the DNA helix and loading of DNA helicase.
  • primase binds and synthesizes initial RNA primers
  • DNA polymerase extends primers
  • leading and lagging strand synthesis established
  • primary specificity in DNA replication is initiated

Foundation Unit 1 (6 decks)

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