Chapter 4: The Structure of DNA Flashcards
1
Q
He studied proteins and isolated DNA. May have been the first.
A
Friedrich Miescher
2
Q
He proposed the tetra-nucleotide hypothesis
A
Phoebus Levene
3
Q
The tetra-nucleotide hypothesis suggests that …
A
Bases were in equimolar quantities in chromosomes
4
Q
Fredrick Griffith
A
Discovered transformation while studying pneumonia
5
Q
He showed DNA was the genetic material via transformation
A
Oswald Avery
6
Q
He discovered A=T and G=C.
A
Erwin Chargaff
7
Q
Worked with bacteriophage
A
Alfred Hershey and Martha Chase
8
Q
Disproved the tetra-nucleotide hypothesis
A
Erwin Chargafff
9
Q
He developed the idea of alpha-helix and beta sheet. Worked with keratin.
A
William Astbury
10
Q
This is composed of a base, a sugar, and a phosphate
A
Nucleotide
11
Q
How many hydrogen bonds are between adenine to thymine?
A
2 hydrogen bonds
12
Q
How many hydrogen bonds are between guanine to cytosine?
A
3 hydrogen bonds
13
Q
He discovered the alpha helix structure, inspired by Atsbury. He wrongly proposed a three chain model of DNA.
A
Linus Pauling
14
Q
Antiparallel structures
A
Looks the same right-side up or upside down.
15
Q
Franklin’s Photo 51 was used to show that …
A
DNA is antiparallel in nature
16
Q
Which DNA bases identifies as a purine
A
Adenine and guanine
17
Q
Which DNA bases identifies as a pyrimidine
A
Cytosine and thymine
18
Q
True or False:
Purine bases has 1 ring
A
FALSE
Purine bases have 2 rings
19
Q
Base + sugar is called a …
A
Nucleoside
20
Q
Bases are formed with a …
A
3’5’ phosphodiester linkage
21
Q
DNA bases are found in the …
A
amino/keto conformation
22
Q
The purpose of the mica experiment was to …
A
determine the periodicity of DNA helix
23
Q
What is DNA’s periodicity?
A
34 A and 10.5 bp/turn
24
Q
The mica experiment involved …
A
binding DNA to mica and digesting with an enzyme to determine the periodicity of DNA helix
25
DNA is antiparallel. What does this mean?
One strand goes in the 5'-->3' direction. The other strand goes in the 3'->5' direction
26
In what direction does DNA polymerase synthesize?
5' -> 3' direction
27
In what direction is the DNA polymerase read?
3' -> 5' direction
28
Ribonuclease is converted into deoxyribonuclease by ...
Reductase
29
Rare circumstances where mispairing can occurs
Thymine-guanine wobble
Cytosine-adenine protonated wobble
30
Most enzymes interact in the major or minor groove?
Major groove
31
zinc fingers interact in the major or minor groove?
Major groove. Can sometimes cross into the minor groove
32
True or False:
| Proteins can always distinguish major groove interactions
True
33
Proteins cannot distinguish _______ in the minor groove
AT/TA
34
What strong bonds does DNA have?
B-S-P and 3'5' phosphodiester linkage
35
The two DNA strands are held together via ____
H bonds between complementary base pairs: purine::pyrimidine
36
True or False:
| Purine/pyrimidine base stacking which are van der waals that creates hydrophobic interactions
True
37
AT is _____ stable the GC and are _____ likely to break
less, more
38
Heating DNA, RNA, or proteins will not break _____
disulfide bridges because they are covalent
39
Tautomerization
Tautomers are in imino/enol bases should be in the amino/keto conformation.
40
In typical DNA, Cytosine and Adenine are found in the amino or keto conformation?
Amino conformation
41
In typical DNA, Guanine and Thymine are found in the amino or keto conformation?
Keto conformation
42
Why are tautomers an issue?
Tautomers cannot be detected
43
What is essential and limits proper base pairing to C:G and A:T?
Hydrogen bonding between bases
44
Sugar/phosphate backbone has a negative or positive charge?
Negative charge
45
What is the width of DNA?
2 nm
46
Is double helix left handed or right handed?
Right handed
47
What is the width of the minor groove?
12 A
48
What is the width of the major groove
22 A
49
Why does DNA have both a major and minor groove, and not two equal grooves?
Due to its geometry. DNA is not a ladder. It is angled, therefore when twisted it gives the major and minor groove. The base pairings are angled. The attachment of the bases and phosphate backbone is asymmetrical results in the grooves. It is not linear
50
True or False:
| There is a lot of information in the minor groove
False
| The Major groove contains a lot if information
51
Which groove contains more “information” and why?
The edges of the base pairs present a more complex environment in the major groove than the minor groove. Many proteins that bind DNA recognize specific sequences, most bind to the floor of the major groove , as it provides more chemical information for recognition than the minor groove
52
In which groove do proteins interact specifically with DNA, and which type of bonds are used?
Proteins interact with DNA in the major groove. Base pairs are easier to distinguish in the major groove.
53
True or False:
| Proteins in the minor groove can distinguish TA and GC. But not AT/TA and GC/CG
```
True
AT
TA
GC
CG
```
54
Zinc finger recognizes ...
Recognizes nucleotides. Need more than 3. Need four or five
55
Proteins specifically recognize a sequence to activate or suppress transcription using ....
Zinc fingers
56
Zinc fingers are ...
Proteins held together by a zinc.
57
How are zinc fingers so specific for a DNA sequence, and what is the zinc finger code?
Zinc finger inserts itself into the major groove and reads code. Zinc finger code dictates sequence specificity.
58
True of False:
| DNA's weak interactions determines the genetic and biochemical function of the molecule
True
59
True or False:
| DNA's weak bonds plays a critical role in determining the secondary and tertiary structures and functions
True
60
True or False:
| DNA is stabilized by H bonds and base stacking
True
61
What is base stacking?
Van der waals interactions that result from the hydrophobic effect, as well as pi bonds overlapping (charge penetration)
62
Which type of base pairs take the most energy to pull apart, and contribute more to Tm?
GC base pairs takes the most energy to pull apart and contributes more to Tm
63
Why would it take longer for more complex DNA to reanneal?
Takes longer for matching as the strands concentrate to one another and slides
64
Tm is the ....
melting temperature
65
Tm increases with ....
1. DNA length
2. GC content
3. Higher salt which stabilize the phosphate backbone
66
The melting temperature of DNA increases as the ionic strength of the solution increases because ...
The cations shield the negatively charged phosphoryl groups which stabilizes the helix
67
DNA is typically _____ -handed (both A and B DNA)
Right handed
68
What is the periodicity of "A form" DNA ?
11 bp/turn
69
What is the periodicity of "B form" DNA?
10 bp/turn
70
What is the periodicity of "Z form" DNA?
12 bp/turn
71
True or False:
| "Z form" DNA is right handed
FALSE
| "Z form" DNA is left handed
72
Which form of DNA is the longest?
"Z form"
73
Which form of DNA is the shortest?
"A form"
74
What is Hoogsteen base pairing, and where would it be found?
Purines can rotate and pair with different H bonds, which changes the shape of DNA. A and T is typically found in the anti position. In hoogsteen base pairing, A becomes/rotates syn and T is anti
75
Quadruple Helix
Found in telomeres. Guanine-rich, parallel and antiparallel conformations
76
I-Motif DNA
Cytosine-rich, found at promoters and telomeres
77
Supercoil
DNA can for supercoils when two dsDNA strands cross over one another
78
Linking Number
The number of times one strnad has to pass over the other to separate completely
79
Twist:
Number of turns of one strand over the other
80
Writhe:
supercoiling
81
If DNA crosses up into the right, it would have a _______ supercoil
negatively supercoil. If wound around nucleosome, it flips
82
If DNA crosses up into the left, it would have a ______ supercoil
positive supercoil. If wound around nucleosome, it flips
83
Negative supercoil
Unwinding, underwinding, subtractive twisting
84
Positive supercoil
Tighter winding, overwinding, restricted access
85
Supercoils are maintained by ________
nucleosomes
86
Topoisomerase
Makes ss/ds beaks, which changes supercoiling
87
Topoisomerase 1
ssDNA cuts, steps of +/-1. Affects the twist.
88
Topoisomerase 2
dsDNA cuts, steps of +/-2. Affects the writhe.
89
True or False:
| Both Topoisomerase 1 and 2 requires ATP
FALSE
| Only topoisomerase 2 for conformational changes (rests enzyme)
90
Tyrosine
attacks the phosphodiester bond in the DNA backbone and forms a covalent intermediate, stabilizing the other end with an OH group.
91
Topoisomerase function is to ...
relieves tension during replication
