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Biochem > RNA/DNA > Flashcards

RNA/DNA Flashcards

1
Q

What is DNA?

A

Deoxyribonucleic acid. The information necessary to sustain and perpetuate life is found within a molecule. This is the genetic material that is passed from one generation to the next, a blueprint for building living organisms.

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2
Q

In 1928, what was Fred Griffith’s experiment?

A
  1. He injected mice with a cell free extract of a lethal strain of pneumococcus and they all lived.
  2. Took the cell free extract and mixed it with a nonlethal strain of mutant pneumococcus and infected a batch of mice with it, the mice died.
  3. The mutant pneumococcus were now converted to the lethal strain, transformation.
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3
Q

In 1944, what did Avery, Macleod, and McCarty’s experiment do?

A

They fractionated the cell free extract into different fractions. The transforming fraction contained nucleic acid, which up unto that point proteins were thought to be involved in the passing of genetic information.

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4
Q

DNA has a limited library of only ____ monomers, these are called __________.

A

4, nucleotides or bases

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5
Q

What are the three parts of monomeric nucleotides?

A

a) sugar molocule (ribose or deoxyribose)
b) nitrogen containing base molecule
c) one or more phosphates

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6
Q

Ribose Carbon #1

A

Determines the anomeric form of the sugar (hemiacetal).
Alpha: OH group down with respect to carbon 5
Beta: OH group up, same side of ring as carbon 5, this is found only in DNA and RNA.

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7
Q

Ribose Carbon #2

A

Determines whether the sugar is ribose or deoxyribose. When the OH group is missing, it is called deoxyribose.

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8
Q

Ribose Carbon #3

A

Called the 3’ position. This OH group covalently links the next nucleotide unit via the phosphates to form RNA or DNA polymers.

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9
Q

Ribose Carbon #4

A

Determines the absolute configuration of L or D

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10
Q

Ribose Carbon #5

A

Called the 5’ position. This OH group binds the phosphates in the nucleotide structure. This position is also involved in the polymer formation.

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11
Q

What is a base?

A

Nitrogen containing molecules that are grouped into two sets.

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12
Q

What are Purines?

A

Large, two ring structures. Adenine and Guanine.

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13
Q

What are Pyrimidines?

A

Single six membered rings. Thymine (DNA), Cytosine, and Uracil (RNA).

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14
Q

What is a phosphoester bond?

A

Linkage of phosphate with OH group.

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15
Q

What is a phosphoanhydride bond?

A

Triphosphate and diphosphate.

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16
Q

Base + Ribose.

Nucleoside and Abbreviation for Adenine.

A

Adenosine, A

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17
Q

Base + Ribose.

Nucleoside and Abbreviation for Guanine.

A

Guanosine, G

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18
Q

Base + Ribose.

Nucleoside and Abbreviation for Thymine.

A

Thymidine, T

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19
Q

Base + Ribose.

Nucleoside and Abbreviation for Cytosine.

A

Cytidine, C

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20
Q

Base + Ribose.

Nucleoside and Abbreviation for Uracil.

A

Uridine, U

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21
Q

What is polymer formation?

A

Ester formation between the 3’ OH group of one nucleotide with the 5’ phosphate on another.

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22
Q

List three things about polymer formation.

A
  1. 3’ OH from the one ribose is the nucleophile. The leaving group is a diphosphate group on the 5’ end of second nucleotide.
  2. Bond formed is called 3’-5’ phosphodiester backbone structure of DNA
  3. 5’ end is considered the start and 3’ OH is considered the end.
23
Q

T or F DNA base sequence is always written in the 3’ end to 5’ end.

A

False. Its read from 5’ to 3’ direction.

24
Q

In 1953, who discovered the 3D structure of DNA? In what paper was if presented in?

A

Watson and Crick. Nature.

25
Q

Double Helix Structure of DNA…

A

DNA always has a second or complimentary strand associated with the first strand. The second strand always found lying opposite direction.

26
Q

In a double helix structure, the bases are found _____ the helix and the deoxyribose and phosphates form the candy stripe on the ________ (_______).

A

Inside, outside (backbone)

27
Q

In a double helix structure, the _______ are found inside the helix and the ________ and _________ form the candy stripe on the outside (Backbone).

A

Bases, deoxyribose and phosphates

28
Q

In a double helix, the two strands are held together by what?

A

h-bonds formed among the bases

29
Q

In a double helix, what binds with what?

A

Purines H-bond with pyrimidines.
G bonds with C: 3 H-bonds formed (stronger)
A bonds with T: 2 H-bonds formed (weaker)

30
Q

One full twist of a double helix is….

A

10 bases with a rise of 3.4A. Just multiply the nucleotide by 3.4.

31
Q

Semiconservative replication

A

Refers to the conservation of one original strand for the parent organism or cell and one newly synthesized strand. So the daughter cell receives one original strand and on newly synthesized strand.

32
Q

Who provided evidence to semiconservatice replication?

A

Messelson and Stahl

33
Q

What is Melting DNA?

A

The separation of the two strands in the double helix by heating the sample.

34
Q

The melting temperature of DNA depends on what two things?

A
  1. The length or total number of bases in the duplex structure.
  2. The G-C ratio within the duplex.
35
Q

Humans are diploid. What does this mean?

A

They contain two copies of the same chromosome, one from the mother and one from the father.

36
Q

All cells (except for reproductive cells) contain a duplicate set of ____ chromosomes and ____ sex chromosomes, which totals to be ___ chromosomes.

A

22, 2, 46

37
Q

RNA in most organisms is ________ stranded.

A

single

38
Q

T or F There cannot be a duplex RNA.

A

False, RNA can form this structure though it is not as common.

39
Q

What is a DNA polymerase?

A

Protein enzymes found in the nucleus which copy a strand of DNA by laying down new bases on an existing strand. Use existing strands of DNA to synthesize copies.

40
Q

DNA replication occurs on the ____________ strands of DNA in only the __’ to __’ direction.

A

complimentary strand, 5’ to 3’

41
Q

T or F DNA polymerases have proof-reading capability by going back and repairing incorrect base pairings.

A

True.

42
Q

Name some requirements for DNA polymerase:

A
  1. Requires dNTP’s
  2. Divalent cation such as Mg or Mn
  3. A ssDNA template strand
  4. A small ssDNA or ssRNA bound to template strand which serves as a primer.
43
Q

T or F There are just a couple of starting sites in which replication can begin.

A

False. There are estimated about 30,000 starting sites in the human genome.

44
Q

What is a helicase and what is the replication site called?

A

an enzyme which functions like a zipper and separates the duplex DNA. The site is called the replication bubble.

45
Q

What does Topoisomerase I do?

A

It runs out ahead of the replication and prevents supercoiling of the DNA as the two strands separate.

46
Q

What attaches to the separated strands to prevent the bases from H-bonding back together during replication?

A

ssDNA binding proteins

47
Q

What does DNA polymerase III do?

A

Its the main enzyme which starts laying down bases like bricks in row, continuously moving in one direction.

48
Q

What is the leading strand?

A

The template strand of DNA that is replicated by the Polymerase III continuously and happens to lie in a 3’ to 5’ direction but is copied 5’ to 3’.

49
Q

What is the lagging strand?

A

Replicated by polymerase III at the same time as leading strand. Is more in fragements.

50
Q

Segments in the Lagging strand are called…

A

Okazaki fragments

51
Q

_______ fill in the gaps between Okazaki fragments and the last joint is filled by an enzyme called ______.

A

Other DNA polymerase, DNA ligase

52
Q

Histones pack together in another layer of twisting called….

A

Nucleosome

53
Q

DNA duplex is a twisted double helix. The Helical structure tends to coil on proteins with lots of positive charges called…

A

Histones

54
Q

Chromatin are….

A

An entire DNA duplex nicely packaged into a small structure.

Biochem (6 decks)

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