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Molecules 2 People > Central Dogma > Flashcards

Central Dogma Flashcards

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1
Q

Helicase

A

Unwinds DNA

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2
Q

Topoisomerase (Euk)

A

Cut and Paste

Relieves overwound supercoils, called DNA gyrase in Prok,

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3
Q

Single Strand DNA Binding Protein (SSPB)

A

Binds with single strand DNA to prevent annealing

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4
Q

DNA polymerase alpha (in complex w primase)

A

Synth of RNA-DNA primer

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5
Q

DNA polymerase delta and epsilon

A

Synth new DNA in 5’-3’ direction (DNA Pol III in Prok)

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6
Q

Flap Endonuclease 1 (FEN1)

A

Removes RNA primers (DNA Pol I in Prok)

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7
Q

DNA polymerase delta

A

Fills in gaps (DNA pol I in Prok)

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8
Q

DNA ligase

A

Seals nicks

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9
Q

Carcinogens such as benzopyrene forms

A

Bulky adducts with guanine residue

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10
Q

UV rays excite pyrimidine bases, forming

A

Covalent dimers such as Thymine Dimer

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11
Q

Doxorubicin inhibits which enzyme

A

Topoisomerase II

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12
Q

Cross -linking agents such as nitrogen mustard, cisplatin, mitomycin C, and carmustine are used for what?

A

Forming cross-links between Guanine and comp base strands or same strand, used for antitumor drug, by blocking DNA replication

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13
Q

Alkylating agents

A

Dimethyl sulfate (DMS) and methylmethanesulfonate (MMS) cause cytotoxic methylation.

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14
Q

Exceptions to the dogma:

A

RNA viruses w RNA as genetic material, single or dbl strand, HIV
Prion (Proteinaceous infection) Microscopic particle that multiply by mis-folding of normal protein to prion, causes Creutzafeldt-Jakob disease (CJD)

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15
Q

DNA coils around histones because

A

DNA is neg charge, histones are positive (H2A, H2B, H3, H4)

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16
Q

Each turn of the DNA helix has how many base pairs

A

10

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17
Q

A nucleosome consists of

A

DNA covered octamer of histone proteins (beads on string, 10nm fiber)

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18
Q

What ties one nucleosome to another?

A

H1 histone and linker DNA tie the nucleosomes, which are then further condensed to 30nm

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19
Q

DNA synth occurs by

A

replication, at replication fork

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20
Q

What unwinds the parental strands in Prokaryotes

A

Helicases and topoisomerases

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21
Q

Prok enzyme that copies parental template

A

DNA polymerase

22
Q

Enzyme in prok that initate the synthesis in 5’ to 3’ direction

A

RNA primer (primase)

23
Q

Okazaki fragments form on which strand, joined by what enzyme

A

DNA ligase, on lagging strand

24
Q

Enzyme that synthesizes replication of ends of chromosomes

A

telomerase

25
Q

Which sequence of nucleotides are found in promoter and origins of replication?

A

AT-rich (such has TATA box region)

26
Q

What is the structure of DNA polymerase similar to?

A

A hand, with fingers, thumb, and palm making up the 5’-3’ polymerization domain, the wrist makes the 3’-5’ exonuclease domain

27
Q

Why is a primer required before DNA polymerase can start working?

A

DNA polymerase requires a free -OH group

28
Q

Prok Enzyme that removes sections of RNA primer and replaces w DNA nucleotides at end of DNA synth

A

DNA polymerase I

29
Q

Bacterial enzyme that repairs DNA

A

Polymerase II

30
Q

Bacterial Enzyme that does replication and synth of DNA

A

Polymerase III

31
Q

What are the three stages of DNA strand separation in eukaryotes?

A
  1. Helicase 2. Topoisomerase 3.SSBPs
32
Q

3 stages of Eukaryotic DNA synth/Chain elongation

A
  1. DNA poly alpha and primase
  2. DNA poly delta and epsilon
  3. DNA poly delta and DNA ligases
33
Q

In contrast to bacterial chromosomes, eukaryotic chromosomes have what?

A

Multiple origins at which replication begins, so “bubbles “appear at these points

34
Q

Which amino acids gives histones a positive charge?

A

Lysine and arginine

35
Q

What gives DNA a negative charge?

A

phosphate groups

36
Q

What are the stages of mitosis?

A

G0-stimulus
G1-growth and metabolism
S-DNA replication (DNA and histone synth)

37
Q

What enzyme does Ciproflaxin and Doxorubicin inhibit?

A

Topoisomerase II (DNA gyrase in prok)

38
Q

What does PCNA stand for and what does it do?

A

Proliferating cell nuclear antigen

Enhances processivity of DNA polymerases,; binds to many proteins at rep fork

39
Q

Eukaryotic chromosomes are _____ and the ends are called _____

A

Linear

Telomeres

40
Q

Parts of euk chromosome that consist of possibly thousands of repeating bases: TTAGGG in humans

A

Telomeres

41
Q

Enzyme that maintains length of telomere by replacing them in parent strand

A

telomerase

42
Q

How does DNA repair mechanisms, in general, work in Euk and Prok?

A

Euk- recognized distortion, endo- and exonucleases remove portion, gap filled by DNA poly in 5’-3’, ligase seals nick
Prok- remove thymine dimers via photoactivated enzymes that cleave bonds between bases w light energy (no nucleotides are released)

43
Q

Cyclobutane pyrimidine dimers generated by ____ can be repaired with ____

A 
UV light
DNA photolyase (absorbs at 370nm, activated to catalyze breakage of bonds  in photo-reactivation)
44
Q

MGMT (methyl guanine methyl transferase) does what

A

Manages to transfer methyl group from a guanine to cysteina, reversing mutagenic action by O6-methylguanine (binds to T not C)

45
Q

What are the Steps of Base Excision Repair (BER) in toxic/spontaneous deamination of E. Coli? (Happens throughout cell cycle)

A

Mismatch recognized by DNA glycosylase which removes the base, making an AP site (apyrimidinic/apurinic)
AP endonuclease cuts at AP site, then filled by DNA poly I and ligase.

46
Q

Humans with problems in Nucleotide-Excision Repair (NER) during G1 phase develop what?

A

Xeroderma Pigmentosum, leading to skin cancers after UV exposure.

47
Q

Bulky adducts such as Oxidized Benzo[a]pyrene or mismatched bases are repaired via what process in Eukaryotes?

A

Nucleotide-Excision Repair (NER)

48
Q

Lynch Sydrome (Hereditary nonpolyposis colorectal cancer (HNPCC)) is caused by

A

Defective Mismatch excision repair (MER) mechanism, which replaces a wrong nucleotide inserted in a newly synth’d daughter strand
The MERman had a daughter w colorectal cancer

49
Q

What types of damage are respectively repaired in Direct Repair (enzymatic repair), BER, NER, and MER?

A

Pyrimidine dimers+ O6 methylguanine (ER)

Single-Base mismatches, non-distorting alterations (BER)
Bear doesn’t distort
Chemical Adducts that distort DNA (NER)

Mismatched base in daughter strand (MER)

50
Q

BER Pneumonic

A

GEL PLease

  • Glycosylase
  • ap Endonuclease (cleaves 5’ end)
  • Lyase (cleaves 3’ end)
  • Polymerase (replaces)
  • Ligase (seals)

Molecules 2 People (6 decks)

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