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Trends in MB and BT > Nucleic Acids: Chemistry, Structure, Organization & Replication > Flashcards

Nucleic Acids: Chemistry, Structure, Organization & Replication Flashcards

1
Q

DnaA

A

Binds to OriC (DnaA binding site), initiates replication in bacteria

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2
Q

DnaB

A

Hexamer of these creates DNA helicase (ATP driven unwinding of DNA in DNA replication in bacteria). Binds to primases which makes the RNA primers.

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3
Q

DnaC

A

Helicase loader in DNA replication in bacteria

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4
Q

Primase

A

Makes the RNA primers for leading and lagging strand

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5
Q

Topoisomerase

A

Type I - adds twist, increases Lk by 1. Relaxes neg. supercoiling.
Type II - cuts dsDNA, writhe decreases by 2. Lk changes by 2. Requires ATP. Can either relieve or introduce supercoiling.

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6
Q

DNA Pol III holoenzyme

A

Three cores, flexible linkers that link cores to sliding clamp loader + sliding clamp

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7
Q

Sliding Clamp Loader

A

Loads sliding clamps onto DNA at primer:template junctions

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8
Q

Sliding clamp

A

Big enough space in the middle for dsDNA -> unstable for ssDNA or RNA. Increases the processivity of DNA pol + holds it in the right position

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9
Q

DNA polymerase regions

A

Palm - catalytic site for adding base, proofreading site and exonuclease site
Finger - changes conformation when right base is in catalytic site so no more bases can come in until it is added. Stabilize beta,gamma P
Thumb - Responsible for placement of primer:template junction, proofreading activity?

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10
Q

Mechanism of topo-I

A

Tyrosine (-OH) in active site attacks phosphodiester bond -> generates break. Topo joined to 5’ end phosphatase. 3’ end with free -OH group. tyrosine - pi linkage provides high energy bond needed for nucleophilic attack.

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11
Q

DNA ligase mechanism

A

Ligase creates a high
energy bond by fusing AMP
to the 5’-Phosphate.
Then 3’OH of the next
Okazaki fragment attacks
this bond, thereby forming
a phosphodiester bond
between the two. AMP is
released in the reaction.

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12
Q

DNA pol I function

A

5’ exonuclease activity. DNA repair and RNA primer excision.

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13
Q

DNA pol II function

A

DNA repair probs

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14
Q

DNA pol III function

A

Main DNA synthase

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15
Q

Alpha polymerase function

A

Initial extension of DNA, RNA primers

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16
Q

Polymerase Beta function

A

DNA repair (Base Excision Repair)

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17
Q

Polymerase Delta function

A

Lagging strand synthesis; DNA repair (both NER and BER)

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18
Q

Polymerase epsilon function

A

Leading strand syntheses; DNA repair (NER & BER)

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19
Q

Which amino acids are positively charged/basic at physiological pH and what does this mean?

A

Arginine, Histidine, Lysine. Wants to bind H

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20
Q

Which amino acids are negatively charged/acidic at physiological pH and what does this mean?

A

aspartic acid (Asp) and glutamic acid (Glu). Looses H at ph=7

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21
Q

Polar, uncharged amino acids

A

serine (Ser), threonine (Thr), cysteine (Cys), asparagine (Asn), and glutamine (Gln)

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22
Q

Nonpolar, hydrophobic amino acids

A

glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), methionine (Met), and phenylalanine (Phe).

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23
Q

Phosphodiester linkage

A

The Pi between 3’ OH one one nucleotide and the 5’ CH2 on another. Is what links together polynucleotide chains

24
Q

Chemistry of phosphodiester linkage

A

3’ -OH group does a nucleophilic attack on the alpha-phosphate, causing pyrophosphate to fall off.

25
Q

Pyrophosphatase

A

Breaks down pyrophosphate into organic phosphate. Important to prevent the backward reaction of the phosphodiester linkage

26
Q

Glycosidic bond

A

The link between the base and the 1’ ribose of the DNA/RNA. Can be broken by addition to water, which yields an AP site

27
Q

Minor groove

A

No information of which base is on which strand. Always symmetrical. Will either be ADA (if G-C) or AHA (if A-T) -> cant tell which strand they are on. Can be used correctly base paired DNA?

28
Q

Major groove

A

Rich in chemical information -> if it interacts with a specific sequence, it interacts here. AADH / HDAA for G-C / C- G, ADAM / MADA for A-T / T-A

29
Q

What are the stop codons?

A

UAG, UAA, UGA

30
Q

What is the start(f-Met) codon?

A

AUG

31
Q

DNA helix, basic info

A

Twists in a right handed, 20Å in diameter, 10.5 in one helical turn. Negative charge due to sugar/phosphate backbone

32
Q

cccDNA

A

covalently closed circular DNA

33
Q

Linking number

A

Lk = Tw + Wr. While Tw and Wr can change, Lk can only be changed by topoisomerases

34
Q

Twist

A

Number of helical turns of one strand around the other

35
Q

Writhe

A

How many times the DNA is twisted around itself. Positive number = right handed writhe and vice versa.

36
Q

Supercoiling

A

If the difference between Lk and Lk0 (# base pairs/10.5) =/= 0. Means the DNA is topologically strained. cccDNA is often negatively supercoiled.

37
Q

Why does the cell “want” negative supercoiling?

A

Can be thought of as store of free energy, can be converted into untwisting double helix (ex. Lk=10, 10 = 14 + - 4 -> 10 = 10 + 0, we now have less twists)

38
Q

DNA gyrase

A

Only in bacteria. Form of type II topo, introduces negative supercoiling. Important for initiation of transcription and replication.

39
Q

DNA topoisomers

A

Different forms of the same cccDNA -> same length but different Linking numbers. Greater writhe -> more compact -> can move faster

40
Q

EtBr effect on cccDNA

A

decreases twist > must increase wr. If neg. from beginning, will become relaxed. if relaxed from beginning, will become pos. supercoiled

41
Q

Why are mutations essential?

A

Allows organisms to evolve and adapt

42
Q

Consider a cross between the parental genotypes RRTT and
rrtt in a pea plant. What are the recombinant gametes?

A

Rt and rT (draw chromosomes and place genes)

43
Q

What is the principle of general assortment?

A

Assortment of each pair of traits/genes are independent from one another. Only true if gene is on different chromosome/on opposite sides of chromosomes

44
Q

What are recombinant gametes?

A

A gamete with a combination of allele not present in the gamete of previous generation.

45
Q

Heterochromatin vs euchromatin

A

heterochromatin is more tightly packed and inactive. Telomers and centromere. Euchromatin is less dense and more active.

46
Q

Histones

A

Positively charged proteins that interacts with DNA, winding it around them. Interacts in minor groove.

47
Q

Histone tails

A

N terminal of histones that point outwards. Can be modified to relax/tighten up the winding of the DNA. Also stabilizes DNA wrapping

48
Q

Nucleosome

A

DNA wound around histone in a left handed manner (neg. supercoil)

49
Q

Acetylation of histone tail

A

The DNA will be less tightly bound to histone -> more easy to reach for DNA or RNA pol

50
Q

Phosphorylation of histone tail

A

DNA will be less tightly bound -> easier to start transcription

51
Q

Methylation of histone tail

A

Associate more tightly with DNA -> less easy to start transcription

52
Q

Steps in replication initiation (bacteria)

A
  1. DnaA binds to OriC, DNA helix starts to open
  2. SSB covers ssDNA regions, recruits DnaB and C. DnaC loads Helicase (DnaB)
  3. Primase bind to helicase, makes RNA primers
  4. DNA pol III recruited, binds to RNA primer and “walks” to replication fork.
53
Q

Replication initiation steps (eukaryotes)

A
  1. Cdc6 recognize ORC
  2. Cdt1 loads mcm2-7 helicase
  3. activation of mcm2-7 helicase by phosphorylation (CDK) (only in S, G2, M phase)
  4. pol epsilon binds to helicase monomer, ADD MORE LATER
54
Q

Rnase H

A

Removes RNA primers from DNA, but only when its RNA/DNA hybrid

55
Q

Telomerase

A

Makes telomers by extending the 3’ end of the template of the lagging strand, leading to a 3’ overhang big enough for DNA pol to bind to it. Only works in embryonic condition.

56
Q
A

Trends in MB and BT (5 decks)

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