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Flashcards in ALL THE THINGS Deck (81)
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1

What is the central dogma of molecular biology?

DNA --> RNA --> Protein

2

What does a nucleotide consist of?

nitrogenous base, pentose sugar, 1 to 3 phosphates

3

What do nucleosides lack?

phosphates

4

What are the purines?

Adenine and guanine

5

How can you distinguish between the two purines?

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

Adenine has an amino group at C-6 only

6

What are the pyrimidines?

cytosine, thymine, uracil (RNA ONLY)

7

How can you distinguish between the pyrimidines?

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

8

Structurally, how are purines and pyrimidines different?

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

9

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

-sine for Purines(Ex. Adenosine)

-dine for Pyrimidines (Ex. Cytidine)

10

For a deoxyribose what prefix will you use?

deoxy-

11

How are the phosphate groups indicated when naming nucleotides?

5' mono-, di-, tri- phosphates

12

What kind of bond is formed to join nucleotides together?

3'-5' phosphodiester bond

13

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

3' hydroxyl
5' phosphate

14

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

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

15

In a basic solution, is DNA degraded?

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

16

What are the 2 methylated bases seen in DNA?

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

17

Which methylated base is only present in Eukaryotes?

methylcytosine

18

What methylated bases are found in bacteria?

methylcytosine and methyladenosine

19

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

C's followed by G's

20

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

GATC

21

What are the two methylase enzymes that produce methylated bases?

Bacteria: DAM (deoxyadenosine methylase)

Eukaryotes: DNMT (DNA methyltransferase)

22

What is special about the recognition sites for methylase enzymes?

they are palindromic

23

Functions of methylation in Bacteria

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

24

Functions of methylation in Eukaryotes

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

25

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

2 antiparallel strands

backbone is hydrophilic

bases are hydrophobic

26

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

~10 base-pairs

27

How many H-bonds between A-T?

2

28

How may H-bonds between G-C?

3; 50% stronger, more difficult to dissociate

29

What are Chargaff's Rules?

A = T ; C = G

(A + G) = (C + T)

30

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

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

31

Describe G-Quadruplex DNA

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

32

Where is G-Quadruplex DNA found physiologically?

Telomeres

33

What kinds of grooves are present in DNA?

Major (wide) and Minor grooves (narrow)

34

What binds in the grooves?

DNA-binding proteins usually bind the major grooves

35

What are Inverted repeats?

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

36

Is GACCAG a DNA palindrome?

NO!
5'-GACCAG-3
3'-CTGGTC-5

37

Is GACGTC a DNA palindrome?

YES!
5'-GACGTC-3'
3'-CTGCAG-5'

38

Palindromic DNA sequences are important for what?

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

39

Are palindromes interrupted in order to bind restriction enzymes?

NO

40

Are palindromes interrupted for transcription factors?

YES, by a few bases

41

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

hairpin or stem loop structures

42

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

triple stranded or Hoogsteen (H) DNA

43

What kind of mirror repeat forms H-DNA?

Repeat of a poly-puridine:polypyrimidine tract

44

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

Major groove

Hoogsteen base-pairing

45

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

structural chromosomal abnormalities

46

By what mechanism do tandem and inverted repeats cause abnormalities?

unequal crossing over in meiosis

47

What changes are associated with Tandem (direct) repeats?

deletions and duplications

48

Inverted repeats are associated with what changes?

inversions

49

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

trinucleotide repeat expansion

50

What is DNA denaturation?

H-bonds broken causing strand separation

51

How can DNA be denatured?

applying high heat or high pH

52

What is DNA renaturation?

separated strands can reassociate or reanneal, reforming H-bonds

53

How can the progress of denaturation and renaturation be followed?

by UV spectrometry

54

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

NO! ssDNA absorbs at 260 nm more strongly than dsDNA

55

When does UV absorbance increase?

during denaturation

56

What is the melting temperature (Tm) of DNA?

temperature at which dsDNA is 50% denatured

57

What is DNA hybridization?

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

58

Is 100% complementarity required for hybridization?

NO! mismatches can be controlled by us in the lab

59

What is Deamination?

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

60

What are some examples of common DNA deaminations?

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

What enhances DNA deamination reactions?

Nitrous acid (HNO2)

62

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

5'-CG-3'

(MUTATION HOTSPOT)

63

What is depurination?

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

64

What is generated as a result of depurination?

apurinic sites (AP)

10,000 purines lost per cell, per 24 hrs

65

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

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

66

What happens when you expose DNA to alkylating agents?

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

67

What bulky group commonly causes induced DNA damage?

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

68

What are intercalating agents?

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

69

What kinds of structural abnormalities are caused by intercalating agents?

insertions, deletions, and frameshift mutations

70

Name some common intercalating agents?

ethidium bromide, proflavin, acridine orange

71

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

X ray and UV exposure

72

What happens when DNA is exposed to X-rays?

free radicals generate that cause double stranded breaks

73

What happens when DNA is exposed to UV radiation?

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

74

What cause oxidative damage to DNA?

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

75

How is DNA damaged from reactive oxygen species?

bases are oxidized; single or double stranded breaks occur

76

How is RNA different from DNA?

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

What are the unusual bases in RNA?

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

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

hairpin or stem loop

79

Complex RNA structures are generated by what?

H-bonds and base stacking

80

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

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

81

Describe the structure of tRNA

ssRNA with secondary structure; has 3 loops