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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
what stabilizes the DNA double helix
-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
26
what mechanism determines the nucleotide sequence of each newly synthesized strand
base pairing
27
non coding segments of DNA/RNA
introns
28
coding segments of DNA/RNA
exons
29
eukaryotic transcription and translation
introns (non coding regions) are removed via splicing so that exons (coding regions) can be joined
30
what is rRNA?
found in the ribosome scaffold for ribosomal proteins
31
what is mRNA?
transcription product of the gene
32
what are tRNA
carriers of specific amino acids
33
composition of ribosomes
2/3 RNA, 1/3 protein
34
how are different species of rRNA are referred to?
based on their sedimentation coefficients
35
modified nucleotides that rRNAs typically contain
pseudouridine and ribothymidilic acid
36
genetic function of ribosomes
translates the genetic information in the nucleotide sequence of mRNA into the amino acid of a polypeptide chain
37
what makes the structure of rRNA and tRNA complex?
the number of intrastrand H bonds
38
characteristics of transfer RNA
-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
the 3’ terminal sequence is always ____ . the amino acid is attached in _____ to the 3’ OH.
CCA-3’-OH ester linkage
40
substrates of protein synthesis
aminoacyl tRNA
41
what distinguishes of DNA from RNA
DNA contains 2-deoxyribose and contains thymine instead of uracil
42
why does DNA contain thymine?
-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
what makes RNA more susceptible to degradation?
-because of the vicinal -OH groups in the 2’ and 3’ position, making it more susceptible to hydrolysis
44
what makes DNA more stable than RNA?
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
characteristics of DNA replication
1. semiconservative 2. bidirectional 3. semi-discontinuous/semicontinuous
46
explain DNA replication comprehensively
explanation…
47
continuously synthesized in DNA replication
leading strand
48
this strand is synthesized in fragments called ____
lagging strand; Okazaki fragments
49
enzyme that unwinds DNA helix
helicase
50
enzyme that relieves the supercoiling of DNA
topoisomerase, DNA gyrase
51
enzymes that replicate DNA
DNA polymerases
52
DNA polymerases cannot synthesize out of nowhere. Thus, _____
it requires a primer oligonucleotide with a free 3’ OH to build upon
53
direction of elongation
5’ to 3’
54
responsible for the synthesis of RNA primer
DnaG (primase)
55
undwinding of 5’ to 3’ DNA is catalyzed by
DnaB (helicase)
56
what happens if DnaG is bound to DnaB
formation of new RNA primers on the kagging strand
57
coats all the single stranded regions of DNA
SSB primers (single stranded DNA binding protein)
58
direction of the template of the leading strand of the lagging strand?
3’ to 5’ (leading strand template) otherwise, 5’ to 3’
59
enzyme that excises the RNA primer on the lagging strand as it replaces it with DNA
DNA pol I
60
enzyme that seals the nicks between Okazaki fragments
DNA ligase
61
RNA that direct protein synthesis
mRNA
62
Nucleotide Triphosphates (NTPs) like ATP, GTP, CTP, UTP are linked by _____ via base pairing with DNA template
RNA polymerases
63
direction of the polymerase along the DNA strand
3’ to 5’
64
RNA chain grows in what direction
5’ to 3’ direction
65
cleaves phosphodiester bonds
pyrophosphatases
66
four stages of transcription
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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