Lesson 2 - DNA and RNA Flashcards
1
Q
- informational molecules of all living organisms
- long, chain-like polymers assembeld from repeating subunits, nucleotides
A
nucleic acids
2
Q
Two types of nucleic acids
A
- Deoxyribonucleic Acid (DNA)
- Ribonucleic Acid (RNA)
3
Q
a unit of only the base and sugar without phosphates
A
nucleoside
4
Q
nucleosides of DNA
A
- deoxyadenosine
- deoxyguanosine
- deoxycytidine
- deoxythymidine
5
Q
nucleosides of RNA
A
- adenosine
- guanosine
- cytidine
- uridine
6
Q
Three components of nucleotides
A
- nitrogenous base
- five-carbon sugar
- phosphate group
7
Q
two types of nitrogenous bases
A
- purine
- pyrimidine
8
Q
six membered ring made up of carbon and nitrogen atoms
A
pyrimidines
9
Q
uracil
A
2,4-dioxypyrimidine
10
Q
thymine
A
- 2,4-dioxy-5-methylpyrimidine or
- 5-methyluracil
11
Q
cytosine
A
2-oxy-4-aminopyrimidine
12
Q
six-membered ring fused to a five-memberd ring
A
purines
13
Q
adenine
A
6-aminopurine
14
Q
guanine
A
2-amino-6-oxypurine
15
Q
- reversible change of one DNA base isomer to another
- shift in the location of H atoms and double bonds
A
tautomeric shift in DNA bases
16
Q
2 forms of the same molecule differing only in the location of a proton and a double bond
A
tautomers
17
Q
in DNA bases, what are the usual forms
A
- amino (NH2)
- keto (C=O)
18
Q
in DNA bases, what are the rare forms
A
- imino (NH)
- enol (C-OH)
19
Q
links covalently to nitrogenous bases
A
five-carbon sugar (pentose)
20
Q
a chain of 1,2, or 3 phosphates linked to the pentose sugar at its 5’ carbon
A
phosphate group
21
Q
where is the phosphate group linked to
A
5’ carbon
22
Q
bonds between base pairs in the interior of the molecule
A
numerous hydrogen bonds
23
Q
- β-N-glycosidic bond (sugar to base)
- phosphodiester bond (nt to nt)
A
covalent bonds
24
Q
sugar to base bond
A
β-N-glycosidic bond
25
phosphate to sugar base bond
phosphodiester bond
26
Primary Structure of DNA
1. linear sequence of nucleotides
2. sugar-phosphate backbone on the outside
27
Secondary Structure of DNA
1. two intertwined antiparellel strands
2. major and minor grooves
3. right-handed helix
4. constant diameter of 20 Å
5. base pases are perpendicular to axis
6. hydrophobic associations form stable non-polar environment
28
essential for binding of proteins
major and minor grooves
29
length between bases
0.34 nm
30
One complete turn of the double helix
- 3.4 nm long
- 10 base pairs
31
what is formed between the hydrophobic associations of base pairs
stable non-polar environment
32
Different DNA conformations
1. A DNA
2. B DNA
3. C DNA
4. D DNA
5. Z DNA
33
Why are there different DNA conformations
adapt to stress
34
most common DNA conformation in nature
B DNA
35
A DNA: overall proportion
short and broad
36
A DNA: helix rotation
right
37
A DNA: bp per turn
11
38
A DNA: conditions of occurrence
- 75% humidity
- K+, Na+, Ca++
39
B DNA: overall proportion
long and thin
40
B DNA: helix rotation
right
41
B DNA: bp per turn
10
42
B DNA: conditions of occurrence
- 92% humidity
- low salt
43
C DNA: overall proportion
long and thin
44
C DNA: helix rotation
right
45
C DNA: bp per turn
9.33
46
C DNA: conditions of occurrence
66% humidity
47
Z DNA: overall proportion
elongated and slim
48
Z DNA: helix rotation
left
49
Z DNA: bp per turn
12
50
A DNA: helix diameter
23 A
51
A DNA: major groove
extremely narrow, very deep
52
A DNA: minor groove
very broad, shallow
53
A DNA: found in
1. dsRNA
2. RNA-DNA duplexes
3. rRNA
4. tRNA
5. viral RNA
6. polypurine strand
54
B DNA: helix diameter
20 A
55
B DNA: major groove
wide, intermed
56
B DNA: minor groove
narrow, intermed
57
B DNA: found in
1. biologically dominant
2. polypyrimidine strand
58
C DNA: helix diameter
20 A
59
C DNA: found in
1. in vitro
2. dehydrated conditions
60
Z DNA: helix diameter
18 A
61
Z DNA: major groove
flattened out on helix surface
62
Z DNA: minor groove
extremely narrow, very deep
63
Z DNA: found in
1. dCGCGCG in vitro
2. in vivo
3. methylated DNA
64
- exists largely as single-stranded chains in living cells
- genetic material of some viruses
ribonucleic acid (RNA)
65
bases in RNA
1. cytosine
2. guanine
3. adenine
4. uracil
66
Segments of RNA molecules may
1. form RNA-DNA hybrid
2. pair temporaily in double-helical form
3. fold back on themselves to set up extensive double-helical regions
67
where can RNA-DNA hybrid repeat be found
during transcription
68
Peculiar NA sequences
1. mirror repeat
2. inverted repeat
69
symmetrical sequence within each strand
mirror repeat
70
two copies of an identical sequence present in the reverse orientation
inverted repeats = palindrome
71
More Secondary Structures of DNA and RNA
1. internal loops
2. bulge loops
3. cruciform
4. hairpin
5. stem-and-loop
6. cloverleaf
72
when there are bases that cannot pair on both sides of the helix
interal loops
73
unpaired bases occur only on one side of the helix
bulge loops
74
- non-B DNA structure characterized by cross-shaped conformations that are observed in inverted repeat sequence features.
- in DNA with a region of dyad symmetry in which the axis of symmetry separates the inverted repeats
cruciform
75
- when it folds back on itself to form a double-helical segment in the region of the sequence
- in ssDNA molecule with an inverted repeat or
- in an RNA molecule copied from a palindromic DNA
hairpin
76
- similar with hairpin structure but occurs when the loop at the end would have many unpaired bases
- plays an important role in attenuation
stem-and-loop structure
77
- characteristic conformation of the tRNA molecule
- made up of three stem-loops
- has four arms
cloverleaf structure
78
four base-paired arms of tRNA
1. Acceptor arm
2. D-arm
3. TΨC arm
4. Anticodon arm
79
- end of a tRNA molecule to which an amino acid becomes bound
- contains both the 5' and 3' ends of the tRNA.
acceptor arm
80
- recognition process is the primary purpose
- serves as a recognition site for the enzyme aminoacyl-tRNA synthetase
- contains the modified nucleotide dihydrouridine.
D-loop
81
specialized region on the tRNA molecule which acts as a special recognition site for the ribosome
TΨC arm
82
- a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule
- complementary to a corresponding codon in a messenger RNA (mRNA) sequence.
anticodon arm
83
Significance of other secondary and tertiary structures of DNA/RNA
1. stabilize genome structure
2. serve as recognition site for initiation and termination
3. important in the function of the nucleic acid made from it
4. form core of catalytic RNA molcules as binding sites for substrates and cofactors
84
catalytic RNA molecules
ribozymes
