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FTM_09 Flashcards

1
Q

Describe the flow of genetic information:

A

DNA contains the info (genes) used to transcribe RNA, which is then translated into proteins built up of amino acids. (Central Dogma)

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2
Q

What are the three main components of Nucleotides:

A
  1. Sugar 2. Triphosphate 3. Base (A,C,T,G)
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3
Q

What is the importance of the 3’ hydroxyl group?

A

It is necessary for the formation of new phosphodiester bonds between nucleotides in a strand of DNA, by binding with the 5’ phosphate groups of new nucleotide triphosphates.

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4
Q

What is a nucleosome?

A

A complex of 8 histones around which DNA is wrapped twice to yield “quaternary structure”.

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5
Q

What are the 3 basic levels of Eukaryotic packaging smaller than chromosomes:

A
  1. Nucleosomes 2. Loops-of-Fibers 3. 30 nm Fibers
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6
Q

What is another name for the 30 nm fiber?

A

Solenoid Structure

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7
Q

What is DNA wrapped around in the Nucleosome?

A

Histone Octamers

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8
Q

Each histone core has _______ base pairs of DNA wrapped around it to form a nucleosome.

A

146

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9
Q

How many BP’s of DNA does each linker region contain?

A

54

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10
Q

What is H1?

A

The histone protein that holds the core particle down to secure the DNA wrapped around the octamer.

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11
Q

Solenoid structures are also called:

A

Chromatin Fibers

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12
Q

What is the main difference between euk. and prok. DNA?

A

Euk is linear Prok. is circular

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13
Q

Describe the 2 steps that prokaryotes use to compress DNA:

A
  1. Negative Supercoiling: Opening up the closed DNA loop to allow negative supercoiling of the DNA. 2. Use of HU protein core to loop the negatively supercoiled DNA around it.
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14
Q

How many ORI’s does prokaryotic DNA contain?

A

1

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15
Q

Prokaryotic replication continues towards the ________ until completion, when the _________.

A
  1. Replication Forks 2. Termini signal is received.
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16
Q

What are two things about eukaryotic rep. that are not true about prok. rep.?

A
  1. Many ORI’s 2. No Termini Signal
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17
Q

What are the 2 important sequences of the OriC in E. Coli?

A
  1. Consensus Sequence: 3 tandem-arrayed 13-Nucleotide Sequences. 2. An additional FOUR 9-nucleotide sequences.
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18
Q

What do the 9-nucleotide sequences do?

A

Serve as high affinity binding sites for the protein dnaA

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19
Q

What is the function of dnaA? How does it achieve this function?

A

To help open up the parental double stranded DNA. It does so by breaking hydrogen bonds between base pairs.

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20
Q

How does the opening of closed prokaryotic DNA begin?

A

When enough dnaA proteins bind the 9-nucleotide sequences, they use ATP to begin opening the parental strands.

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21
Q

What is DnaB and what does it do?

A

Helicase: 2 are needed and one associates with each replication fork to open up the double HELIX. Hence the name.

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22
Q

What is DnaC and what does it do?

A

DnaC is a transport protein that complexes with DnaB proteins to deliver them to the replication forks, with the use of ATP, to allow them to separate the double helix.

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23
Q

Where does strand separation begin in prokaryotic DNA?

A

At the consensus sequence, once enough DnaA proteins form a barrel that is activated by ATP.

24
Q

What is another name for DnaC?

A

Helicase Inhibitor

25
Q

Helicase acts by binding to _______ and then _______.

A
  1. SINGLE strands of parental DNA 2. Unwinding it in opposite directions away from the origin.
26
Q

DnaB binds to ______ at the replication forks to form ______.

A
  1. Primase 2. Primosome Protein complex
27
Q

What are ssb’s and what do they do?

A

Single-Stranded-Binding Proteins: They bind to the opened single strands of DNA near the primosome in order to stabilize the DNA and prevent the reforming of secondary structure (the re-binding of the 2 parental strands.

28
Q

Where do DnaA, DnaB, and DnaC bind to respectively?

A
  1. 9-Nucleotide sequences at the OriC 2. The left and right replication forks 3. Binds to DnaB and delivers it
29
Q

What is the function of DNA Polymerase?

A

To use the parental strand of DNA to synthesize a new daughter strand.

30
Q

How does DNA Polymerase 3 work and in which type of cells does it work?

A

Prokaryotic Cells. It uses the parental strand as a template and forms phosphodiester bonds between the free -OH groups on the 3’ end of the PRIMER strand and the phosphate groups of incoming nucleotide triphosphates.

31
Q

What is the by-product of adding a new nucleotide triphosphate to the primer strand?

A

Pyro-phosphate: The two remaining phosphates from the incoming nucleotide triphosphate.

32
Q

How can base mispairing occur?

A

A tautomer of one of the bases can form, possessing a different configuration that resembles another base.

33
Q

How does DNAPOL3 recognize and remove mispaired bases?

A

When the tautomeric configuration changes back from an Imine to an Amine, the 3’ -OH group will be in the wrong position to form new phosphodiester bonds. So DNAPOL3 has 3’ to 5’ Proofreading Exonuclease activity to cleave off bases with improper orientation of the 3’ -OH group.

34
Q

In terms of DNAPOL3 activity, explain the difference between the “P” and “E” sites.

A

The “P” site is the active site of DNAPOL3 when it is polymerizing, or synthesizing new DNA in the 5’ to 3’ direction. The “E” site is the active site of DNAPOL3 when it is editing mispaired bases in the 3’ to 5’ direction.

35
Q

What is DNA Primase?

A

A polymerase required for DNAPOL to begin elongation of daughter strands.

36
Q

What is DNAPOL3?

A

A multi-subunit protein used for elongation, and the synthesis of DNA leading and lagging strands.

37
Q

What does DNAPOL1 do?

A

It removes the original RNA primer laid down by DNA Primase, and replaces it with DNA.

38
Q

What does DNA Ligase do?

A

It joins Okazaki fragments together

39
Q

What do Helicases do?

A

Untwist the double helix at replication forks.

40
Q

What does Topoisomerase do?

A

It corrects overwinding ahead of the replication fork by breaking, swiveling, and rejoining DNA strands in order to relieve the tension caused by supercoiling.

41
Q

How does DNA Primase function?

A

It uses the template strand to synthesize a short segment of complimentary RNA bases, leaving a free 3’ -OH, for DNAPOL3 to use as a substrate to begin elongation (continue replication).

42
Q

DnaA ______ in double stranded parental DNA, while DnaB _____ in the double stranded parental DNA.

A
  1. Breaks Hydrogen bonds between base pairs 2. Untwists the double helix at the replication fork
43
Q

As each molecule of _____ joins the DNA strand via DNAPOL3 activity, it loses _____.

A
  1. dNTP 2. Pyrophosphate
44
Q

Describe Lagging Strand Synthesis:

A

The lagging parental strand is synthesized by DNAPOL3 in the 5’ to 3’ direction AWAY from the replication fork, resulting in the formation of many okazaki fragments as DNA Primase must continually lay down more RNA primers for elongation to continue as the replication bubble opens wider towards the 3’ end of the parental lagging strand template. The primers of these fragments are then removed by DNAPOL1 and replaced with DNA nucleotides, and the fragments are then joined by DNA Ligase which REESTABLISHES the backbone with phosphodiester bonds.

45
Q

Azidothymidine Zidovudine is an

A

-HIV medication

46
Q

What is Didanosine

A

HIV medication

47
Q

What is Acyclovir

A

Herpes and Varicell Zoster (chickenpox) medication

48
Q

What is Tenofovir

A

HIV drug

49
Q

How do the viral drugs mentioned in lecture function

A

Cause DNA synthesis to be terminated b/c once they are incorportated they lack a 3’ OH

50
Q

What is araC. How does it function

A

Drug used for people with leukemia.

Drug has a misplaced OH group that terminates DNA replication

51
Q

What proteins hold DNA POLY3 down to the DNA template

A

-Clamp Proteins

52
Q

During replication, what enzyme rectifies positive supercoiling

A

DNA gyrase (Topoisomerase-ll).

-rectifies by introducing negative supercoiling

53
Q

What is Ciprofloxacin

A
  • drug that inhibits bacterial DNA gyrase
  • can be used to treat tract infection and anthrax
54
Q

What polymerases are found on eurkaryotic DNA

A

Polymerase-alpha:

•Synthesizes RNA primer on leading and lagging strand

Polymerase-d(delta):

•Synthesizes DNA from leading and lagging strands

55
Q

What is Camptothecin

A

-Anticancer drug that inhibits Topoisomerase-l

56
Q

What is Etoposide

A

anticancer drug, inhibits the activity of topisomerase II

57
Q

What is Dactinomyosin/ Actinomyosin-D

A
  • anticancer drug
  • inhibits the ability for the DNA to undergo strand seperation
  • Intercalates b/w GC bases

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