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NUCLEOTIDES & NUCLEIC ACIDS > ALL THE THINGS > Flashcards

ALL THE THINGS Flashcards

1
Q

What is the central dogma of molecular biology?

A

DNA –> RNA –> Protein

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2
Q

What does a nucleotide consist of?

A

nitrogenous base, pentose sugar, 1 to 3 phosphates

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3
Q

What do nucleosides lack?

A

phosphates

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4
Q

What are the purines?

A

Adenine and guanine

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5
Q

How can you distinguish between the two purines?

A

Guanine has a carbonyl at C-6 and an amino group at C-2

Adenine has an amino group at C-6 only

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6
Q

What are the pyrimidines?

A

cytosine, thymine, uracil (RNA ONLY)

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7
Q

How can you distinguish between the pyrimidines?

A

Cytosine has a one carbonyl and one amino group attached to the ring

Thymine has 2 carbonyl groups and a methyl group attached to the ring

Uracil has 2 carbonyl groups attached to the ring

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8
Q

Structurally, how are purines and pyrimidines different?

A

Purines form a double ring structure, while pyrimidines are just one aromatic ring

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9
Q

When naming a nucleoside, what suffix is added to the nitrogenous base?

A
  • sine for Purines(Ex. Adenosine)

- dine for Pyrimidines (Ex. Cytidine)

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10
Q

For a deoxyribose what prefix will you use?

A

deoxy-

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11
Q

How are the phosphate groups indicated when naming nucleotides?

A

5’ mono-, di-, tri- phosphates

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12
Q

What kind of bond is formed to join nucleotides together?

A

3’-5’ phosphodiester bond

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13
Q

What is the 3’ end called and what is the 5’ end of the phosphodiester bond called?

A

3’ hydroxyl

5’ phosphate

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14
Q

By what reaction is RNA degraded in a basic, alkaline solution?

A

hydrolysis; degraded to individual nucleotides (mix of 2’ and 3’ monophosphates)

The overall reaction is attack of the 3’-5’ phosphodiester bond that leads to full breakdown of the phosphate backbone

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15
Q

In a basic solution, is DNA degraded?

A

No, it is stable since it lacks the 2’ OH that is the target of hydrolysis

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16
Q

What are the 2 methylated bases seen in DNA?

A

5-methylcytosine and N6-methyladenosine (Methyl attached to the amino group at C-6)

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17
Q

Which methylated base is only present in Eukaryotes?

A

methylcytosine

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18
Q

What methylated bases are found in bacteria?

A

methylcytosine and methyladenosine

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19
Q

Which cytosine groups are methylated? What base must follow the cytosine in the sequence?

A

C’s followed by G’s

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20
Q

Only A’s part of what sequence can be methylated?

A

GATC

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21
Q

What are the two methylase enzymes that produce methylated bases?

A

Bacteria: DAM (deoxyadenosine methylase)

Eukaryotes: DNMT (DNA methyltransferase)

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22
Q

What is special about the recognition sites for methylase enzymes?

A

they are palindromic

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23
Q

Functions of methylation in Bacteria

A

control initiation of replication; discrimination of self DNA (methylated) from foreign DNA (non-methylated; discriminate old and new stands in mismatch repair; regulation of gene expression

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24
Q

Functions of methylation in Eukaryotes

A

regulation of chromatin structure and gene expression; can lead to gene splicing

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25
Q

Describe the orientation of DNA strands and explain why the sugar phosphate backbone faces outward while the bases are stacked in the interior

A

2 antiparallel strands

backbone is hydrophilic

bases are hydrophobic

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26
Q

Approx. how many base pairs per turn in a DNA double helix?

A

~10 base-pairs

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27
Q

How many H-bonds between A-T?

A

2

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28
Q

How may H-bonds between G-C?

A

3; 50% stronger, more difficult to dissociate

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29
Q

What are Chargaff’s Rules?

A

A = T ; C = G

A + G) = (C + T

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30
Q

Watson & Crick DNA is B-Form DNA. What are the other alternative structures?

A

A-DNA, Z-DNA, G-Quadruplex DNA

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31
Q

Describe G-Quadruplex DNA

A

has guanine tetrads (4 G’s in a plane connected by H-Bonding); stabilized by cation; stacks of 2 or more tetrads

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32
Q

Where is G-Quadruplex DNA found physiologically?

A

Telomeres

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33
Q

What kinds of grooves are present in DNA?

A

Major (wide) and Minor grooves (narrow)

34
Q

What binds in the grooves?

A

DNA-binding proteins usually bind the major grooves

35
Q

What are Inverted repeats?

A

Palindromic repeats; DNA sequences read the same 5’ - 3’ on complimentary strands

36
Q

Is GACCAG a DNA palindrome?

A

NO!
5’-GACCAG-3
3’-CTGGTC-5

37
Q

Is GACGTC a DNA palindrome?

A

YES!
5’-GACGTC-3’
3’-CTGCAG-5’

38
Q

Palindromic DNA sequences are important for what?

A

they are important recognition sequences for restriction endonucleases and some transcription factors

39
Q

Are palindromes interrupted in order to bind restriction enzymes?

A

NO

40
Q

Are palindromes interrupted for transcription factors?

A

YES, by a few bases

41
Q

Inverted repeates, when single-stranded, may form what?

A

hairpin or stem loop structures

42
Q

Mirror repeats are important for the formation what kind of DNA?

A

triple stranded or Hoogsteen (H) DNA

43
Q

What kind of mirror repeat forms H-DNA?

A

Repeat of a poly-puridine:polypyrimidine tract

44
Q

The 3rd strand in triple-stranded DNA interacts with which groove? What type of base pairing is seen here?

A

Major groove

Hoogsteen base-pairing

45
Q

Tandem (Direct) and inverted repeats are often involved in what?

A

structural chromosomal abnormalities

46
Q

By what mechanism do tandem and inverted repeats cause abnormalities?

A

unequal crossing over in meiosis

47
Q

What changes are associated with Tandem (direct) repeats?

A

deletions and duplications

48
Q

Inverted repeats are associated with what changes?

A

inversions

49
Q

Tandem (direct) repeats are involved in what kind of expansion seen in disorders like Huntingon’s?

A

trinucleotide repeat expansion

50
Q

What is DNA denaturation?

A

H-bonds broken causing strand separation

51
Q

How can DNA be denatured?

A

applying high heat or high pH

52
Q

What is DNA renaturation?

A

separated strands can reassociate or reanneal, reforming H-bonds

53
Q

How can the progress of denaturation and renaturation be followed?

A

by UV spectrometry

54
Q

Does dsDNA (double stranded) absorb UV at 260 nm more strongly than ssDNA (single stranded)?

A

NO! ssDNA absorbs at 260 nm more strongly than dsDNA

55
Q

When does UV absorbance increase?

A

during denaturation

56
Q

What is the melting temperature (Tm) of DNA?

A

temperature at which dsDNA is 50% denatured

57
Q

What is DNA hybridization?

A

annealing of a single strand of DNA to a complementary strand of a different DNA molecule

58
Q

Is 100% complementarity required for hybridization?

A

NO! mismatches can be controlled by us in the lab

59
Q

What is Deamination?

A

type of spontaneous DNA damage where the amino group on a nucleotide is lost

60
Q

What are some examples of common DNA deaminations?

A

Cytosine’s amino group is changed to a carbonyl and forms Uracil

methylcytosine’s amino group is changed to a carbonyl and forms Thymine

61
Q

What enhances DNA deamination reactions?

A

Nitrous acid (HNO2)

62
Q

Methylcytosine is commonly deaminated to thymine. At what common sequences does this occur?

A

5’-CG-3’

MUTATION HOTSPOT

63
Q

What is depurination?

A

spontaneous DNA damage that leads to the loss of the base from a nucleotide (usually a purine)

64
Q

What is generated as a result of depurination?

A

apurinic sites (AP)

10,000 purines lost per cell, per 24 hrs

65
Q

What are Mutagens and what kind of DNA damage do they cause?

A

physical, chemical, or biological agents that increase the rates of mutations; cause induced DNA damage

66
Q

What happens when you expose DNA to alkylating agents?

A

Induced damage. Alkyl groups are added to bases. The result is mispairing between base-pairs

67
Q

What bulky group commonly causes induced DNA damage?

A

Benzo(a)pyrene; oxidized in cells and binds covalently to guanine, distorting the double helix

68
Q

What are intercalating agents?

A

cause induced damage; flat, planar molecules that slide between the stacked bases of the double helix; distort the double helix increasing base separation

69
Q

What kinds of structural abnormalities are caused by intercalating agents?

A

insertions, deletions, and frameshift mutations

70
Q

Name some common intercalating agents?

A

ethidium bromide, proflavin, acridine orange

71
Q

What are the two causes of radiation-induced DNA damage?

A

X ray and UV exposure

72
Q

What happens when DNA is exposed to X-rays?

A

free radicals generate that cause double stranded breaks

73
Q

What happens when DNA is exposed to UV radiation?

A

pyrimidine dimers are generated (thymidine dimers); covalent bonds between adjacent pyrimidines in the same strand

74
Q

What cause oxidative damage to DNA?

A

ROS (reactive oxygen species) like hydrogen peroxide, hydroxyl radicals, and superoxide radicals; generated by irradiation and from oxidative phosphorylation

75
Q

How is DNA damaged from reactive oxygen species?

A

bases are oxidized; single or double stranded breaks occur

76
Q

How is RNA different from DNA?

A

Ribose (not deoxy)
Uracil (not thymine)

Single stranded with dynamic secondary structure (complimentary to one DNA strand; Chargaff’s rules don’t apply)

Intramolecular base pairing can lead to partially double stranded structures (Watson-Crick or Hoogsteen pairing)

Unstable without protection from proteins

Unusual bases may occur (tRNA)

77
Q

What are the unusual bases in RNA?

A

Inosine (deaminated adenine)
Pseudouridine (Uracil with a ribose attached)
7-methylguanosine (Guanine with a methyl group at C-7)
4-Thiouridine (Uracil has the oxygen at C-4 replaced with sulfur)

78
Q

What structures are formed when inverted repeats are transcribed into RNA?

A

hairpin or stem loop

79
Q

Complex RNA structures are generated by what?

A

H-bonds and base stacking

80
Q

Are the 2D and 3D structures of RNA the same?

A

No. The 2D ones are used to clarify regions of bonding. 3D structures are very different

81
Q

Describe the structure of tRNA

A

ssRNA with secondary structure; has 3 loops

NUCLEOTIDES & NUCLEIC ACIDS (1 decks)

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