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MBB 222 > Final > Flashcards

Final Flashcards

1
Q

Three theories for DNA replication

A

Conservative:One daughter molecule is all new
Disperse: Each daughter molecule contains a mixture of old and new
Semi conservative:Each daughter DNA molecule contains one new strand and one old strand

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2
Q

Meselson-Stahl experiment

A

Using the 14 and 15 isotope of nitrogen to determine that DNA conservation is semi conservative

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3
Q

DNTP

A

deoxynucleotide triphosphate contains three phostphates, two of which will break off to extend the growing DNA chain

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4
Q

What bonds are formed in DNA polymerizing?

A

Phosphodiester bonds between the 3’OH and the 5’ Phosphate group

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5
Q

Direction of DNA replication

A

5’->3’

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6
Q

5 ingredients for DNA synthesis

A

1)Template strand
2)Primer to provide first OH
3)DNA polymerase
4)dNTP
5)Mg2+ ions

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7
Q

Phosphodiester Bond making process

A

1)DNA polymerase adds a DNTP to the 3’ end of the DNA chian
2)Mg2+ ions stabalize the DNA charge and steal a proton from the 3’ OH
3)3’ Oxygen now performs a nuclophillic attack on the first phosphate in the DNTP breaking the other 2 phosphates releasing energy
4) Phosphate and oxygen link up and the strand has been extended by one

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8
Q

How does DNA polymerase ensure the correct Watson and Crick base pairings?

A

When pairs that aren’t Watson and Crick pairs enter the active site the steric clash of these pairings forces DNA Poly 3 to spit the bond back out

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9
Q

DNA Poly 1

A

Proof reading strands of DNA, primer removal and repair. It’s secret is that it can move 5’ to 3’ or reverse the regular direction. Medium sized, 10 nucleotide reading speed and 10-20 posecivity

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10
Q

DNA Poly 2

A

Repair DNA molecules, reads 3’->5’, slow and small

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11
Q

DNA Poly 3

A

Polymerizes DNA, 3’->5’ large and fast with unlimited possession ability

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12
Q

Endonuclease

A

Cleave DNA backbones such as topoisomerase

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13
Q

Exonuclease

A

Catalyze the removal of a single nucleotide from the end of a strand such as DNA poly 1 and Pol3

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14
Q

How is DNA poly 3 able to read both strands of DNA simultaneously?

A

By looping the lagging strand around inside of the molecule it can be read backwards

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15
Q

Diffrence between the origin of replication for Eukaryotic and Prokaryotic cells

A

Eukaryotes cells have multiple origins of replication that bridge together but fro Prokaryotic they only need one origin

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16
Q

Helicase

A

Unwind DNA for replication

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17
Q

Primase

A

Lay down RNA primers to signify where DNA poly 3 will bind to

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18
Q

Ligase

A

Protien that uses ATP to reseal the fragments of DNA together after DNA pol 1 has removed the primers

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19
Q

Label the following and explain their roles

A

A)DNA polycore, Synthesises the DNA strand
B)Beta clamp, links the replication complex to DNA
C)Tau protien- Loads the DNA into the beta clamp

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20
Q

nick translation

A

Adds deoxyribonucleotides to the 3’ end of the adjacent Okazaki fragment (lagging strand),
due to its 5’-> 3’ polymerase activity (recall that polymerization always occurs 5’ ® 3’)

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21
Q

How does DNA poly 1 proof read DNA strands?

A

When a mistake is read on the 3’ end of an ozaki fragment it causes the DNA poly 1 to stall in place, this segment will then melt and because the polymerase cannot hold onto the mismatched base it is expelled through the exonuclease site

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22
Q

What process is being depicted in this picture?

A

Spliceosome splicing the mRNA precursor

23
Q

Lariat

A

Loop of introns that are removed from the final coding sequence of RNA

24
Q

5 types of DNA repair

A

1)Direct repair:Fixing damaged bases on site O6 Alkyguanaine transferase
2)Base excision:Damaged bases are removed and repaired like deamination
3)Nucleotide Excision:Offending nucleotides are removed and replaced like thymine dimers
4)Mismatch repair:Wrong bases in replication are removed and replaced
5)Homologus recombination:Repair for both strands of DNA

25
Q

Point mutation

A

Substitution of one base for another

26
Q

Indels

A

Insertion of deletion of a base cause by intercalcating agents

27
Q

Transitions

A

substitution of a purine for a diffrent purine or pyrimidine for a pyrimidine

28
Q

Transversion

A

Purine is swapped for pyrimidine or vice versa

29
Q

Deamination

A

Removal of an amine group like Adenine into Hypoxanthane, A-T to G-C

30
Q

Alkylation

A

Addition of methyl groups to a base changing it’s h bond capabilities ex. O6 alkylguanine

31
Q

Intercalcation

A

Flat molecules jam themselves in between base pairs leading to the insertion or deletion of a base as the pairs are unable to bind together

32
Q

UV damage

A

UV light can break the sugar phosphate bone of DNA causing Thymine dimers or 6-4 photoproduct

33
Q

How to fix the following Damage
1)Deamination
2)Methylation
3)UV damage
4)Oxidation Damage

A

1)Base excision
2)Direct repair
3)Direct repair in Prokaryotes and Nucleotide excision in Eukaryotes
4)Base excision

34
Q

Oxidation damage

A

Most common DNA damage caused by reactive oxygen species attacking the DNA backbone and bases leading to strand breakage

35
Q

Base excision

A

1)Identity broken base
2)Remove the base
3)Remove the nucleotide
4) Polymerase fills the gap
5)Ligate

36
Q

Nucleotide Excision

A

1)Find the legion
2)Enzyme cuts the DNA strand
3)DNA polmerase fills the gap
4)Ligase seals the gaps

37
Q

Mismatch repair

A

1) ID mistmatch
2) Mismatch is cut from the DNA
3)DNA polymerase fills the gap
4)Ligate

38
Q

Nucleosomes

A

First level of DNA ornagization which are simply strings of DNA on a histone core aka 11nm fiber

39
Q

Histone core

A

Octometric core that protects DNA from degradation from nuclease, positively charge and held together by the H1 protien clamp

40
Q

Histone fold

A

a special fold that allows the histone subunits to link together

41
Q

Histone core subunits

A

2A, 2B, H3 and H4

42
Q

How does the structure of the histone allow for binding of DNA

A

Using positively charged N terminus of each histone component the tails of the protien stick out and cling to negatively charged DNA

43
Q

30nm fiber

A

second level of DNA organization and is the form taken when DNA is not being replicated but also not being actively transcribed. Regulates which genes are able to be transcribed

44
Q

How is the 30nM fiber unwound?

A

By adding acetyl groups to areas of the histone and by the removal of H1 proteins

45
Q

Condensed chromosome

A

third level of organization of DNA, this only occurs when the cell is undergoing division, formed by a nuclear scafolding holding the 30nm fibers together

46
Q

Chromatin remodelling

A

changing of the organization of DNA using ATP powered proteins to acetylate areas of the DNA

47
Q

What is DNA replication controlled by

A

1)Opening of the replication origin
2)Centromere sequence
3)Telomere sequence

48
Q

Replication Origin

A

Location where DNA duplication begins

49
Q

Centromere

A

Attachment site for the miotic spindle, without it the chromosome cant’ be pulled apart

50
Q

Telomere

A

Ends of the chromosome that protect the DNA from being destroyed during replication. Junk DNA.

51
Q

T-loop

A

a special strucutre at the end of the 3’ end of a telomere that is folded by TRF1 and TRF 2 to protect the start sequence for Telomer growth

52
Q

Diffrence between RNA and DNA

A

1)RNA is Single stranded
2)RNA has an OH at it’s 2’ instead of the H that DNA has
3)RNA uses Uracil as a base instead of thymine

53
Q
A

MBB 222 (2 decks)

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