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KEMBIO1: Biochemistry 1 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

common component of DNA and RNA

A

phosphate group

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2
Q

4 DNA bases

A

AGCT

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3
Q

4 RNA bases

A

AGCU

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4
Q

sugar of DNA

A

2-deoxyribose

reduced OH group on the 2’ position

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5
Q

sugar of RNA

A

ribose

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6
Q

structure of pyrimidine

A

one ring
2 N atoms labeled as 1 and 3
double bonds located 2,4,6

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7
Q

structure of purine

A

2 ring system (one pyrimidine-like and one imidazole-like)
4 nitrogen atoms at positions 1,3,7,9
double bonds at 1,4,6,8

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8
Q

pyrimidine bases

A

CUT

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9
Q

purine bases

A

AG

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10
Q

difference of nucleoside and nucleotide

A

base + sugar = nucleoside (base linked to a sugar via glycosidic bonds)
base + sugar + phosphate = nucleotide

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11
Q

nomenclature of nucleosides

A

-idine suffix if the base is pyrimidine
-osine suffix if the base is purine

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12
Q

nucleotides are what type of acids?

A

polyprotic

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13
Q

what are nucleic acids?

A

linear polymers of nucleotides linked 3’ to 5’ by phosphodiester bridges

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14
Q

3’,5’-phosphodiester bridges link nucleotides togethre to form polynucleotide chains.

orientation of 5’ and 3’ ends

A

5’ ends are on top
3’ ends on bottom

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15
Q

what are ribosomal RNA (rRNA)

A

-synthesized by ribosomes
-the basis of structure and function of ribosomes

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16
Q

what are mRNA?

A

carries the message for protein synthesis

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17
Q

what are transfer RNAs (tRNA)

A

carries amino acids for protein synthesis

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18
Q

explain the structure of DNA

A

-antiparallel in nature
-have opposite orientations (5’ to 3’ and 3’ to 5’)

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19
Q

the person who has first seen the image of DNA through X-ray fiber diffraction

A

Rosalind Franklin

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20
Q

scientist who has shown that DNA was a helix

A

Francis Crick

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21
Q

scientist who figured out H bonds

A

James Watson

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22
Q

difference between the two base pairs (AT and GC)

A

the number of H bonds
AT pair has 2 H bonds
GC pair has 3 H bonds

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23
Q

structure of DNA

A

-antiparallel double helix
-1.6 million nm length (E.coli)
-compact and folded (E. coli cell is only 2000 nm long)
-eukaryotic DNA wrapped around histone proteins to form nucleosomes
-Base pairs: AT GC

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24
Q

explain the structure of DNA

A

length of one turn: 3.4 nm
2 strands are antiparallel

contains major and minor groove
major groove: 2.2 nm
minor groove: 1.2 nm

diameter: 2 nm

right handed twist

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25
Q

what stabilizes the DNA double helix

A

-H bonds between base pairs
-electrostatic repulsions: mutual repulsion of phosphate groups which makes them most stable on the helix interior
-base pair packing interior
-right twist closes the gaps between base pairs to 3.4 A

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26
Q

what mechanism determines the nucleotide sequence of each newly synthesized strand

A

base pairing

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27
Q

non coding segments of DNA/RNA

A

introns

28
Q

coding segments of DNA/RNA

A

exons

29
Q

eukaryotic transcription and translation

A

introns (non coding regions) are removed via splicing so that exons (coding regions) can be joined

30
Q

what is rRNA?

A

found in the ribosome
scaffold for ribosomal proteins

31
Q

what is mRNA?

A

transcription product of the gene

32
Q

what are tRNA

A

carriers of specific amino acids

33
Q

composition of ribosomes

A

2/3 RNA, 1/3 protein

34
Q

how are different species of rRNA are referred to?

A

based on their sedimentation coefficients

35
Q

modified nucleotides that rRNAs typically contain

A

pseudouridine and ribothymidilic acid

36
Q

genetic function of ribosomes

A

translates the genetic information in the nucleotide sequence of mRNA into the amino acid of a polypeptide chain

37
Q

what makes the structure of rRNA and tRNA complex?

A

the number of intrastrand H bonds

38
Q

characteristics of transfer RNA

A

-small polynucleotide chains with 73 to 94 residues
-several bases usually methylated
-each aa has at least one unique tRNA which carries the amino acid to the ribosome

39
Q

the 3’ terminal sequence is always ____ . the amino acid is attached in _____ to the 3’ OH.

A

CCA-3’-OH
ester linkage

40
Q

substrates of protein synthesis

A

aminoacyl tRNA

41
Q

what distinguishes of DNA from RNA

A

DNA contains 2-deoxyribose and contains thymine instead of uracil

42
Q

why does DNA contain thymine?

A

-cytosine spontaneously deaminates to form uracil
-repair enzymes recognize these “mutations. and replace Us with Cs
-the repair enzymes are able to distinguish natural U from mutant U by using thimine or 5-methyl U in place of uracil

43
Q

what makes RNA more susceptible to degradation?

A

-because of the vicinal -OH groups in the 2’ and 3’ position, making it more susceptible to hydrolysis

44
Q

what makes DNA more stable than RNA?

A

because it lacks the OH in the 2’ position. note that in the structure of ribose, the two OHs in the 2’ and 3’ position are vicinal, which makes them more susceptible to hydrolysis

45
Q

characteristics of DNA replication

A
  1. semiconservative
  2. bidirectional
  3. semi-discontinuous/semicontinuous
46
Q

explain DNA replication comprehensively

A

explanation…

47
Q

continuously synthesized in DNA replication

A

leading strand

48
Q

this strand is synthesized in fragments called ____

A

lagging strand; Okazaki fragments

49
Q

enzyme that unwinds DNA helix

A

helicase

50
Q

enzyme that relieves the supercoiling of DNA

A

topoisomerase, DNA gyrase

51
Q

enzymes that replicate DNA

A

DNA polymerases

52
Q

DNA polymerases cannot synthesize out of nowhere. Thus, _____

A

it requires a primer oligonucleotide with a free 3’ OH to build upon

53
Q

direction of elongation

A

5’ to 3’

54
Q

responsible for the synthesis of RNA primer

A

DnaG (primase)

55
Q

undwinding of 5’ to 3’ DNA is catalyzed by

A

DnaB (helicase)

56
Q

what happens if DnaG is bound to DnaB

A

formation of new RNA primers on the kagging strand

57
Q

coats all the single stranded regions of DNA

A

SSB primers (single stranded DNA binding protein)

58
Q

direction of the template of the leading strand

of the lagging strand?

A

3’ to 5’ (leading strand template)

otherwise, 5’ to 3’

59
Q

enzyme that excises the RNA primer on the lagging strand as it replaces it with DNA

A

DNA pol I

60
Q

enzyme that seals the nicks between Okazaki fragments

A

DNA ligase

61
Q

RNA that direct protein synthesis

A

mRNA

62
Q

Nucleotide Triphosphates (NTPs) like ATP, GTP, CTP, UTP are linked by _____ via base pairing with DNA template

A

RNA polymerases

63
Q

direction of the polymerase along the DNA strand

A

3’ to 5’

64
Q

RNA chain grows in what direction

A

5’ to 3’ direction

65
Q

cleaves phosphodiester bonds

A

pyrophosphatases

66
Q

four stages of transcription

A
  1. binding of RNA polymerase holoenzyme to template DNA at promoter sites
  2. initiation of polymerization
  3. chain elongation
  4. chain termination

KEMBIO1: Biochemistry 1 (4 decks)

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