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Mcb1 > Nucleotides And Nucleic Acids > Flashcards

Nucleotides And Nucleic Acids Flashcards

1
Q

What is transformation?

A

A transfer of genetic material from one organism to another

E.g. Griffit bacteria mouse experiment

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2
Q

What is a bacteriophage?

A

A virus that infects bacteria

These virus’s transfer genetic material into host, which then replicate the virus

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3
Q

What is transcription?

A

DNA is copied into RNA

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4
Q

What is translation

A

Nucleic acid information is used to synthesize proteins

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5
Q

What do nucleotides play a role in?

A

Building blocks of nucleic acids (DNA/RNA)

Energy currency (ATP/GTP)

Mediator in signaling (GDP/GTP)

Structural component of many enzyme con factors and metabolic intermediates (NAD+. FADH2, UDP-glucose)

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6
Q

Nucleotides consist of:

A

A nitrogenous base (a purine or pyrimidine)

A pentode sugar (ribose or deoxyribose)

1 to 3 phosphates

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7
Q

How do you distinguish a Nucleoside from a nucleotide?

A

They lack phosphates

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8
Q

What are the pyrimidines?

A

Cytosine
Thymine
Uracil

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9
Q

What are the Purines?

A

Adenine and Guanine

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10
Q

How do you know a structure is a purine?

How do you know which is guanine?

A

Two rings

It has a carbonyl and a amino group while the adenine has an amino group where the carbonyl is at

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11
Q

How do you distinguish the pyrimidines?

A

One ring

Cytosine: has an amino group

Thymine: has a methyl group

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12
Q

How do you name the nucleotides?

A
  1. Start with the nucleoside name
  2. If it’s a deoxyribose, use the deoxy prefix
  3. Invite the number of phosphates as 5’ mono-, di- or tri- phosphates
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13
Q

How are nucleotides joined together?

A

A 3’-5’ phosphodiester bond

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14
Q

What are the two distinct ends of a nucleic acid?

A

3’ hydroxyl

5’ phosphate

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15
Q

In which direction are nucleic acids written?

A

In the 5’ to 3’ direction

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16
Q

What happens to RNA and DNA in basic solutions?

A

RNA is degraded to individual nucleotides
-2’ or 3’ monophosphates

DNA is stable since it lacks the 2’ OH

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17
Q

What methylated base do eukaryotes use?

A

Only methylcytosine

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18
Q

What do bacteria use to methylate base?

A

5-methycytosine

N6-metyhadeosine

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19
Q

When are bases methylated?

A

Only C’s followed by G’s can be methylated

Only A’s in the sequence GATC can be methylated

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20
Q

When can a cytosine be methylated?

A

When it is followed by a G

-60-90% of CpG’s are methylated

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21
Q

When can Adenosines be methylated?

A

When in the sequence GATC

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22
Q

What produces methylated bases?

A

Methylase

Bacteria: DAM (deoxyadenosine methylase)

Eukaryote: DNMT (DNA methytransferase )

Recognition site are palindromic!

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23
Q

What does palindromic mean?

A

Sequence is the same forwards no backwards

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24
Q

Why does methylation occur bacteria?

A

Controlling initiation of replication
Discrimination of self DNA (methylated) from foreign DNA (non-methylated)
Discriminate old and new strands in mismatch repair
Regulation of gene expression

-All DNA based

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25
Q

Why do eukaryotes methylate?

A

Regulation of chromatin structure and gene expression

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26
Q

What kind of gene expression does methylation allow?

A

Gene silencing
An epigenetic mechanism

E.g. Imprinting and X-chromosome inactivation

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27
Q

In what order is the DNA double helix stranded?

A

2 antiparallel strands

  • one 5’-3’
    The other 3’-5’
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28
Q

What complementary bases pair in a DNA helix?

A

G pairs with C
A pairs with T

  • Through hydrogen bonds (the number of bonds differs)
  • A purine way pairs with a pyrimidine
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29
Q

In DNA what side is oriented outward and what side is oriented inward?

A

Hydrophilic sugar-phosphate backbone is oriented outward

Hydrophobic bases stacked in the interior

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30
Q

How many bonds do the A-T and G-C complementary bases have?

A

AT:2

GC: 3

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31
Q

About how much stronger is a GC bond than an AT bond?

A

50% stronger

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32
Q

What is base stacking?

A

Interactions between stacked bases above and below through:
Van der walls
Hydrophobic

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33
Q

What does base stacking contribute to?

A

Major contribution to helical stability

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34
Q

What bases have the strongest and weakest base stacking?

A

Stacked GC bases are strongest

Stacked AT bases are weakest

35
Q

What are Chargaff’s Rules?

A

A always = T
C always = G

Pyrimidines nucleotides (T+C) always = total amount of purine nucleotides (A+G)

(A+G)=(C+T)

More AT than GC

36
Q

What is G-quadrupled DNA?

A 
Guanine tetrads: 4 G's in a plane connected by hydrogen bonding 
Stabilized by a cation (k+)
Stacks of 2 or more guanine tetrads
Found physiologically in G-rich region 
E.g. Telomeres
37
Q

Where can you find G-quadruplex DNA?

A

Telomeres

38
Q

What kind of DNA is found physiologically?

A

B-form DNA

39
Q

Which side contains the minor grove?

A

The side with the glycosidic bond

40
Q

Where do DNA binding proteins bind?

A

Bind in the grooves making specific interactions with these atom

-usually the major groove

41
Q

What do the bases in DNA provide for binding proteins?

A

H-bond donors (N-H0
Acceptors (N,O)
Methyl groups for hydrophobic interactions

42
Q

How can you tell if DNA is plindromic DNA?

A

Reads the same 5’ to 3’ on complimentary strands

43
Q

What’s an example of palindromic DNA?t

A

GACGTC

44
Q

Why are DNA palindromes important?

A

They are recognition sequences for restriction endonucleases and some transcription factors

45
Q

What is the difference between DNA palindromes in restriction endonucleases and transcription factors?

A

Restriction: palindrome not interrupted

Transcription: palindrome is often interrupted by a few bases

46
Q

What is the recognition sequence for EcoRI (restriction endonuclease)

A

5’ GAATTC 3’

47
Q

What is the recognition sequence for transcription factors such as Glucocotiocoid receptor binding site?

A

5’AGAACAnnnTGTTCT3’

The nnn is the interruption

48
Q

What are inverted repeats?

A

When single-stranded may form a hairpin or a stem-loop structure

49
Q

What are mirror repeats in DNA?

A

Repeats that are not repeats in the 5’ to 3’ direction

50
Q

Why are mirror repeats important?

A

For the formation of triple stranded DNA

-aka Hoogsteen or H-DNA

51
Q

What repeats facilitates in the H-DNA formation?

A

Repeat of a poly-purine:polypyrimidine tract

52
Q

With what strand does the third strand interact with?

A

Major groove via base-specific hydrogen bonds

53
Q

What are Direct repeats and inverted repeats are often involved in?

A

Structural chromosomal abnormalities

54
Q

What are direct repeats DNA inverted repeats?

A

Direct repeats = deletion and duplications

Inverted repeats= inversions

55
Q

Trinucleotide repeat expansions such are hungtintons Disease are associated with what kind of elemental symmetry?

A

Direct repeats

56
Q

How re direct repeats and inverted repeats formed?

A

Unequal crossing-over in meiosis

57
Q

How can we denature DNA?

A

(Def: bases are broken down)

Heat, high ph

AKA: melting

58
Q

What tool can we use to follow denturation and renaturation of DNA?

A

UV spectrometry

59
Q

What light does ssDNA absorb?

A

260 nm

60
Q

How does the melting temperature of DNA increase?

A

With a higher content of GC

61
Q

Does denaturation cause an increase in absorbance?

A

Yes

62
Q

What is DNA hybridization?

A

Annealing of single-strand of DNA to a complementary strand of different DNA molecule

63
Q

What is demination?

A

Loss of an exocyclic amino group

64
Q

What is usually deaminated? How often does this occur?

A

Cytosine into uracil

1 every 10Mb per 24h

65
Q

What enhance deamination?

A

Nitrous acid (HNO2)

66
Q

What is depurination?

A

Los of the base from a nucleotide (usually a purine)

67
Q

What does depurination lead to?

A

An apurinic site (AP site )

68
Q

What are mutagens?

A

Physical, chemical, or biological agents that increase the rate of mutations

-may be carcinogens or teratogens

69
Q

What are alkylating agents? What do they cause?

A

They add alkyl groups (methyl or ethyl) to bases

Cause mispairing

E.g. O6-methylguanine pairs with T instead of C

70
Q

What are the addition of bulky group do to DNA?

Reword this q….

A

Benzo(a)Pyrenees’s
Found in col tar, tobacco smoke, charred food
Oxidized in cels and binds covalently to guanine, distorting the double helix

71
Q

What are intercalating agents?

A

Flat, planar molecules that slide between the stacked bases of the double helix

72
Q

What do intercalating agents do?

A

Distort double helix and increases separation of bases

  • cause insertions and deletions during DNA replication
  • frameshift mutations
73
Q

What are some examples of radiation-induced DNA damage

A

X rays

UV

74
Q

What do X-rays do to DNA?

A

Generate free radicals that cause DNA double-stranded breaks

75
Q

What does UV generate?

A

Pyrimidine diners (thymidine diners)

-covalent bonds between adjacent pyrimidines in the same strand

76
Q

What is the main example for oxidative damage?

A

Reactive oxygen species (ROS)

-Hydrogen peroxide (H2O2), Hydroxyl radicals (OH*), and superoxide radicals (O2-)

77
Q

How are ROS generated?

A

Irradiation and from oxidative phosphorylation in the mitochondria

78
Q

What are the main differences between RNA and DNA?

A
  1. Ribose
  2. Uracil instead of Thymine
  3. Single-stranded
  4. Intramolecular base-pairing
  5. Unstable
  6. Unusual bases may occur (tRNA)
79
Q

What does intramolecular base pairing create in RNA?

A

Partially double-stranded structures

Either Watson-crick or Hoogsteen base-pairing

80
Q

Wha is Inosine?

A

A deaminated adenosine

81
Q

IS inosine a purine or pyrimidine?

A

Purine

82
Q

What will inverted repeats form in RN?

A

A hairpin or stem-loop

83
Q

How are complex RNA structures generated?

A

H-bonds and base stacking

Mcb1 (13 decks)

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