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BIOC3021 > Nucleic Acids and Structure > Flashcards

Nucleic Acids and Structure Flashcards

1
Q

____ structure is the sequences of bases along DNA or RNA

A

primary

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2
Q

___ structure is the formation of a double helix via specific base pairing

A

secondary

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3
Q

___ structure is the supercoiling of circular DNA or organizing of DNA into chromosomes

A

tertiary

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4
Q

What are the 3 components needed for DNA sequencing?

A

primer, DNA polymerase (enzyme), dNTPs, and fluorescent labeled ddNTPs

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5
Q

What enzyme is used in DNA sequencing?

A

DNA polymerase

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6
Q

What is the role of the primer in DNA synthesis?

A

starting the process

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7
Q

DNA polymerase extends the primer by adding ______ that ____ _____ with the template strand

A

nucleotides, base pair

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8
Q

Incorporation of a ddNTP _____ polymerization

A

terminates

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9
Q

The newly synthesized DNA chains differ by _ _______

A

1 nucleotide

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10
Q

The terminating bases of all of the newly synthesized DNA strands make-up the _____

A

unknown sequence

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11
Q

In DNA synthesis, the terminating base pair (ddNTP) is _____ -______

A

color-coded

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12
Q

ddNTPS differ from DNA in that they lack _____

A

a 3’ OH group

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13
Q

Instead of a 3’OH ground, ddNTPS have____

A

H

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14
Q

ddNTPS cannot form a ______ bond with the next incoming nucleotide in a DNA synthesizing reaction because they lack a 3’OH group

A

3’-5’ phosphodiester bond

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15
Q

The H bond of ddNTPs is ______ reactive

A

non

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16
Q

B DNA is another term for what type of DNA?

A

traditional

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17
Q

What are the two types of DNA grooves?

A

minor and major

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18
Q

The _____ groove of DNA is narrow

A

minor

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19
Q

The ____ groove of DNA is wide

A

major

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20
Q

DNA major and minor grooves are formed by _____ _____

A

backbone strands (of DNA)

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21
Q

What type of bond is a covalent bond that involves a carbohydrate (such as deoxyribose) and is involved in the creation of major and minor grooves

A

glycosidic bond

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22
Q

The glycosidic bonds not being directly across from each other help cause the ______

A

major and minor grooves

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23
Q

B-DNA has a width of ____ A

A

20

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24
Q

B-DNA has a pitch of ____ A

A

34

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25
Q

B-DNA has _____ base pairs per turn of the double helix

A

10

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26
Q

B-DNA strands run in what type of direction to each other?

A

opposite

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27
Q

B-DNA has what type of turn of the helix?

A

right-handed

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28
Q

What are the 3 types of DNA?

A

A,B,Z

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29
Q

____ DNA is made when B-DNA is isolated and dried out (looses H2O molecules from the cell)?

A

A

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30
Q

___ DNA has a similar structure to that of the double helix of RNA and DNA/RNA hybrids

A

A

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31
Q

____ DNA is formed by synthetic oligonucleotides with an alternating purine-pyrimidine sequence

A

Z

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32
Q

____ DNA is short and broad, has right-handed turns, and has roughly 11 bp per double helix turn

A

A

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33
Q

_____ DNA is longer and thinner, has right-handed turns, and has roughly 10 bp per double helix turn

A

B

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34
Q

_____ DNA is elongated and slim, has left-handed turns, and has roughly 12 bp per double helix turn

A

Z

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35
Q

A DNA has ____ glocsyl bond conformation

A

anti (bases are projected away from dexoy. ring)

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36
Q

B DNA has ____ glocysl bond conformation

A

anti (bases are projected away from dexoy. ring)

37
Q

Z DNA has _____ glocysl bond comformation

A

anti at C (bases are projected away from dexoy. ring), syn at G (bases are projected towards dexoy. ring)

38
Q

______ glycosyl bond conformation has the bases projected away from the deoxy. ring

A

anti

39
Q

______ glycosyl bond conformation has the bases projected towards the deoxy. ring

A

syn

40
Q

The DNA melting curve plots ___ vs _____

A

temperature, relative absorbance

41
Q

What type of light is used on the DNA melting curve?

A

UV

42
Q

Tm is ______ of DNA

A

melting temp

43
Q

at low temperatures, bases do not absorb as much light because ______

A

bases are hidden away in the double helix

44
Q

At high temperatures, bases absorb more light because ______

A

the base pair bonds (H) are broken and the base pairs are exposed to light

45
Q

Do all DNA have the same Tm (melting point value)?

A

no

46
Q

The more GC bonds, the _____ the melting temp.

A

higher

47
Q

The more AT bonds, the ____ the melting temp.

A

lower

48
Q

Why do GC bonds melt at higher temps?

A

GC base pairs need 3 H bonds to pair (so higher energy needed to break) and GC bp have stronger staking interactions

49
Q

If you heat and then cool DNA too rapidly, _____ base pairing occurs

A

improper

50
Q

an improper base pairing be reverse?

A

yes (called renaturation)

51
Q

Improper base pairing involves base pairs connecting in a _____ fashion

A

random

52
Q

DNA melting and renaturation is ______ reverse

A

readily

53
Q

What are the two types of DNA that can form supercoils?

A

circular and linear

54
Q

What is supercoiling?

A

two strands of the double helix being underwound or overwound

55
Q

Supercoiling puts _____ on the DNA double helix

A

strain

56
Q

Compacted DNA via supercoiling _____ the volume of the DNA within the cell

A

decreases

57
Q

A DNA loop has a _____ base

A

fixed

58
Q

_______ supercoiling is the theoretic method that circles an imaginary circle

A

toroidal

59
Q

______ supercoiling is found in prokaryotes

A

interwound

60
Q

_____ supercoiling is a combo of toroidal spirals and interwound supercoils and occurs in ______

A

interwound and toroidal supercoiling, eukaryotes

61
Q

_____ is the enzyme used in bacteria supercoiling of circular DNA

A

Topoisomerase 2 (bacterial DNA gyrase)

62
Q

Another name for bacterial DNA gyrase is ______

A

topoisomerase 2

63
Q

Topoisomerase 2 is composed of ______ protein subunits

A

4 (2A, 2B)

64
Q

Topoisomerase _____ the DNA strand in 2 spots and then ____ the DNA back together as a supercoil

A

cuts, links

65
Q

_____ enzyme cuts one DNA strand

A

Type 1 topoisomerases

66
Q

Formation of a _______ structure comes from a palindrome sequence in eukaryotes

A

cruciform

67
Q

Formation of a cruciform structure comes from a ______ sequence in eukaryotes

A

palindrome

68
Q

A _____ _______ is able to repeat itself when inverted

A

palindrome sequence

69
Q

Creation of a cruciform structure from a palindrome sequence allows for the formation of a ____ ____ _____

A

stem loop structure

70
Q

What would be the function of the formation of stem loop structures in eukaryotes if they exist?

A

regulation of gene expression (i.e. binding of RNA polymerase to the correct location)

71
Q

If it were real, the function of Z DNA would be what?

A

to regulate gene expression (i.e. binding of RNA polymerase to the correct location

72
Q

In higher cells (eukaryotes), ___ binds to the DNA negative charge to create “beads on a string” nucleosome filaments

A

histones

73
Q

How many histones are in each “bead” on the string?

A

8

74
Q

How many times is the helix wrapped around the histone in chromatin fiber?

A

twice

75
Q

Beads on a string nucleosome filaments are _____ nm

A

11

76
Q

Chromatin fibers are _____ nm

A

30

77
Q

Eukaryotic loops are _____ nm

A

.25

78
Q

_____ RNA does not have a tertiary structure

A

M

79
Q

mRNA does not have a tertiary structure for what reason?

A

they remain linear without folds in order to not interfere with ribosome bonding and free movement

80
Q

The _____ structure of tRNA is folded into a _____ structure

A

cover-leaf, L-shaped

81
Q

What two types of RNA have tertiary structures?

A

tRNA, rRNA

82
Q

The ____ and _____ sides of the tRNA clover-leaf structure ______ _____ on the verticle part and are bent in the middle to create the L-shape

A

Left, right, fold back

83
Q

rRNA molecules interact with _____ _____ to form small and large ribosomal subunits

A

ribosomal proteins

84
Q

The lower the melting temperature, the higher the _____ bp concentration

A

AT

85
Q

The higher the melting temperature, the higher the ______ bp concetration

A

GC

86
Q

What enzyme is used to synthesize cDNA strands?

A

reverse transcriptase

87
Q

dideoxyonulecotides (ddNTPS) lack a _____ ____ group and a ____ _____ group

A

3’ OH, 2’ OH

88
Q

ddNTPS cannot form what type of bond?

A

3’-5’ phosphodiester

89
Q

The supercoiling of DNA is facilitated by what enzyme?

A

DNA gyrase (topoisomerase 2)

BIOC3021 (25 decks)

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