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Biochem BLOCK 3 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

Central dogma of molecular biology

A
  • DNA stores info which is transcribed to make RNA
  • RNA is modified and used as a template and translated to make a protein

Replication–DNA–transcription–RNA–translation–protein

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2
Q

Building blocks of DNA and RNA

A

5 carbon sugars

  • ribose
  • deoxyribose
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3
Q

What are the nitrogenous bases?

A

Purines

Pyrimidines

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4
Q

Purines

A

Adenine and guanine

-2 rings

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5
Q

Pyrimidines

A

Cytosine, thymine, and uracil

-1 ring

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6
Q

DNA contains what nitrogenous bases?

A

Adenine, guanine, cytosine, and thymine

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7
Q

RNA contains what nitrogenous bases?

A

Adenine, guanine, cytosine, and uracil

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8
Q

Nucleotide di- and triphosphates (such as ADP and ATP)

A

Are high energy compounds due to the energy associated with anhydride bonds

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9
Q

Where does the energy necessary for nucleus acid synthesis come from?

A

The high energy bonds in nucleotide triphsophates (NTPs)

ATP and GTP are also used as a source of energy for many reactions

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10
Q

Carbon 1 (1’) on the sugar residue

A

Covalently linked to a base (glycosidic bond)

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11
Q

Carbon 2 (2’) on the sugar residue

A
  • Hydroxyl group in RNA

- no oxygen in DNA (deoxy-)

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12
Q

Carbon 3 (3’) on the sugar residue

A

OH group in both DNA and RNA, REQUIRED for polymerization of nucleic acids, joined to the 5’ carbon through a phosphodiester bond

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13
Q

Carbon 5 (5’) of the sugar residue

A

Linked to one or more phosphates, joined to carbon 3 of an adjacent nucleotide through a phosphodiester bond

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14
Q

Is DNA polar or non polar?

A

Polar

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15
Q

At what end of DNA is the free phosphate group

A

5’

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16
Q

At what end of the DNA molecule is the free OH group?

A

3’

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17
Q

What are the nucleotides joined together by in DNA?

A

Phosphodiester bonds

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18
Q

What are the bases linked together by?

A

Glycosidic bonds

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19
Q

DNA is always assumed to be written…

A

5’-3’

Can be written 5’-TACG-3’ or just TACG
Or 3’-GCAT-5’

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20
Q

Ways DNA can be written

A
  • Sometimes written with the location of the phosphate groups PTpApCpG
  • sometimes type of nuclei acid is indicated dTdAdCdG (DNA)
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21
Q

DNA structure

A

Antiparallel and complimentary

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22
Q

Antiparallel

A

The two strands are opposite in direction

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23
Q

Complementary

A

A always pairs with T
G always base pics with C
Via H bonding

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24
Q

How many H bonds does A::T have?

A

2H bonds

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25
Q

How many H bonds does G::C have?

A

3 H bonds

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26
Q

How do you indicate the complementary strand

A

You have to indicate that it is 3’ to 5’

Sometimes it will be reversed to 5’ to 3’ too

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27
Q

Chargaffs Rule

A
  • A=T
  • G=C
  • A+T+G+C=100%
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28
Q

Using Chargaff’s rule, what percentage of T is in a sample of DNA with 10% G?

A
  • G=C, so G=10% and C=10%
  • G+C=20%
  • 100-20=80%
  • A+T=80%
  • T=80%/2
  • T=40%
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29
Q

What feature of DNA is important for regulatory proteins (gene expression)?

A

The major and minor grooves formed by the double helix

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30
Q

What is on the outside of the helix and contains a negative charge?

A

Hydrophilic sugar-phosphate backbone

-can interact with water

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31
Q

What forms the “stairs” of the helix, perpendicular to the axis of symmetry?

A

Hydrophobic hydrogen-bonded base pairs

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32
Q

Is DNA hydrophobic, hydrophilic, or amphipathic?

A

Amphipathic

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33
Q

What is the normal DNA structure?

A

Right handed or Watson and Crick DNA or B-DNA

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34
Q

Rare form of DNA

A

Contains higher GC content and a left handed helix, possibly important for gene regulation
-mammals don’t normally have this

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35
Q

Melting

A

Desaturation

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36
Q

Why is desaturation and repatriation important?

A
  • important for regulation and transcription

- important for molecular biology techniques

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37
Q

What can “melt” dsDNA?

A

Heat
Alkali
Certain chemicals

38
Q

How does desaturation work

A

Hydrogen bonds between base pairs are broken but phosphodiester bonds linking the nucleotides are not broken

  • maintains integrity of the two strands
  • results in a single stranded DNA (ssDNA)
39
Q

Tm

A

Temperature required to melt 50% of the DNA in a sample

40
Q

Tm for a high GC content

A

Higher because of triple bonds

41
Q

Tm of high AT content

A

Lower because double bonds

42
Q

Reannealing

A

The DNA is allowed to cool and the hydrogen bonds will reform and the DNA will renature
-temp falls below the Tm

43
Q

How often does DNA associate/dissociate?

A

Until they find proper orientation so the complimentary strand is correct

44
Q

Are genomes of most organisms big or small compared to the size of the cell?

A

Huge

45
Q

What is the length of the DNA in a single human cell?

A

2m

46
Q

How long is all the DNA end to end?

A

Would reach to the sun and back

47
Q

What kind of DNA has lots of supercoiling

A

Prokaryotes and mitochondria

48
Q

What is DNA gyrase (topoisomerase II) inhibited by?

A

Quinolones (norfloxacin/ciprofloxacin)

49
Q

Why are quinolones toxic in high dosages?

A

Because it can target the mitochondrial DNA in humans

50
Q

nucleosomes

A

DNA in the nucleus of eukaryotes associates with histones and nonhistone proteins forming these
-DNA wraps around his tones

51
Q

Chromatin

A

Nucleosomes are packaged tightly to form this

52
Q

Nucleosome packaging

A
  • want the DNA accessible to do translation/transcription

- they are packed for protection, but leave parts exposed to do transcription/translation

53
Q

What are histones rich in?

A

Lysin and arginine (+ charged basic AA)

54
Q

What do histones bind tightly too?

A

Negatively charged DNA

55
Q

How many types of histones are there?

A

4 (H2A, H2B, H3, and H4)

-there are two units to each his tone forming an octamer

56
Q

What is the DNA tightly wound around to form nucleosome?

A

Histone octamer

57
Q

histone sensitive to nuclease degradation

A

A group of fire nucleosomes (without H1) called “beads on a string”
-necessary for gene expression

58
Q

Histone H1

A

Associates with the DNA between the nucleosomes to further condense the DNA into a thick 30nm fiber called a nucleofilament

59
Q

Why is condensation important?

A

For cell division

-reverse-can see gene expression

60
Q

What does further condensation of nucleosomes form?

A

Chromatin and chromosomes

61
Q

What sugar does DNA contain

A

Deoxyribose

62
Q

What sugar does RNA contain

A

Ribose

63
Q

What base does DNA contain that RNA does not

A

Thymine

64
Q

What base does RNA contain that DNA does not

A

Uracil

65
Q

Can DNA or RNA base pair back on itself?

A

RNA (tRNA)

66
Q

Which is smaller, DNA or RNA?

A

RNA

67
Q

Why is RNA smaller than DNA?

A

DNA contains many units of information, RNA contains individual units of information

68
Q

What does DNA store?

A

Genetic information (storage molecules)

69
Q

What is RNA used for?

A

To express genetic information (transient expression molecules)

70
Q

What are the 3 major types of RNA?

A

mRNA, rRNA, tRNA

71
Q

What do the three major RNA types do?

A

Act n conjunction with proteins to allow the information contained in DNA to be translated into protein

72
Q

mRNA

A

Processed in a way so that they can get in the cytosol. Recognized by molecules that use them

73
Q

rRNA

A

Associate with proteins. From large molecules, ribosomes to make protein
-mostly structural

74
Q

tRNA

A

No enzymatic activity but transfers AA to proper place

75
Q

Size of mRNA

A

Very heterogenous in size, depending on the size of the proteins encoded

76
Q

What does the 5’ terminus contain on the mRNA?

A

m7G-cap structure

-ribosome recognition

77
Q

What does the 3’ terminus contain on the mRNA?

A

Poly A tail

  • 50-200 adenine residues that are not part of the genomic sequence
  • helps release from ribosomes
78
Q

Do prokaryotic mRNAs contain the cap and poly A tail?

A

No

79
Q

All mRNA’s contain:

A
  • 5’ untranslated region
  • 3’ untranslated region
  • coding region
80
Q

Eukaryotic ribosome size

A

80s ribosome

  • 60S (large) subunit
  • 40S (small) subunit
81
Q

Prokaryotic ribosome size

A

70S ribosomes

  • 50S (large) subunit
  • 30S (small) subunit
82
Q

What is the unit if size for ribosome?

A

S (svedberg)

  • unit of sedimentation value
  • how it passes through a medium such as a gel
83
Q

How many nucleotides in tRNA

A

About 80

84
Q

What is tRNA linked to?

A
  • Covalently linked to a specific AA

- At least one specific tRNA for each of the 20 AA

85
Q

What is specific for each of the AA?

A

At least one specific tRNA

86
Q

Where is the AA attachment site on tRNA

A

CCA-3’ terminus

87
Q

Structure of tRNA

A
  • Cloverleaf like structure-extensive intrachain base pairing (similar to dsDNA)
  • unusual bases , many modified bases, primarily methylated bases
88
Q

What is the only RNA that contains thymine?

A

tRNA

89
Q

Anticodon loop

A

On tRNA

Determines AA specifically by base pairing with mRNA during translation

90
Q

hnRNA

A

Heterogenous nuclear RNA, also called pre-mRNA-represents mRNA in various stages of processing in the nucleus of eukaryotes

91
Q

snRNAs

A

Small nuclear RNAs, only in the nucleus of eukaryotes, combines with certain proteins to form snRNPs, used for splicing hnRNA to form mRNA

92
Q

Robozymes

A

RNAs that act as enzymes

Biochem BLOCK 3 (12 decks)

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