11: DNA Structure & Replication Flashcards
Module 2, Lesson 5 (118 cards)
1
Q
The modern model of DNA was proposed by ____ in ____.
A
Watson and Crick ; 1953
2
Q
____ used x-ray diffraction to deduce the 3D structure of DNA in ____.
A
Rosalind Franklin ; 1953
3
Q
DNA is a…
A
Nucleic acid
4
Q
List the three main components of a nucleotide.
A
- 5-carbon pentose sugar
- Nitrogenous base
- Phosphate group
5
Q
In DNA, the chemical group attached to the 2’ carbon is…
A
Deoxyribose
(an H molecule)
6
Q
In RNA, the chemical group attached to the 2’ carbon is…
A
Ribose
(an OH group)
7
Q
Which carbon(s) in the pentose sugar are involved in nucleotide bonding?
A
3’ and 5’
8
Q
What component of a nucleotide is attached the 1’ carbon?
A
Nitrogenous base
9
Q
List the four nitrogenous bases that may be found in DNA.
A
- Adenine
- Thymine
- Cytosine
- Guanine
10
Q
Adenine and guanine are double-ringed structures called…
A
Purines
11
Q
Cytosine and thymine are single-ringed structures called…
A
Pyrimidines
Uracil, found in RNA, is also a pyrimidine.
12
Q
Which component of a nucleotide is attached to the 5’ carbon?
A
The phosphate group
(PO4)
13
Q
Nucleotides are linked together via…
A
Phosphodiester bonds
14
Q
When nucleotides link, bonds form between the ____ end of one and the ____ end of another.
A
5’ (phosphate) and 3’ (hydroxyl)
15
Q
Nucleotides can assemble into long strands using…
A
Dehydration synthesis reactions
16
Q
In a strand of nucleotides, one end will always be a free ____ carbon and the other will always be a free ____ carbon.
A
5’ and 3’
17
Q
True or false:
DNA molecules are nonpolar.
A
False
All DNA molecules have intrinsic polarity.
18
Q
The sequence of nitrogenous bases in a strand of nucleotides is always written…
A
From the 5’ end to the 3’ end
19
Q
Chargaff’s rules state that…
(two)
A
- There is always an equal proportion of purines and pyrimidines in DNA
- The purine:pyrimidine ratio varies between species
20
Q
What can be inferred about nitrogenous bases from Chargaff’s rules?
A
- The amount of adenine equals the amount of thymine
- The amount of cytosine equals the amount of guanine
21
Q
The process of shooting X-rays through a crystal of interest, then analyzing the pattern produced by the rays, is called…
A
X-ray diffraction
22
Q
X-ray diffraction was used to determine…
(three things)
A
- That DNA has a helical shape
- The diameter of the helix
- The distance between helical turns
23
Q
True or false:
In developing their model of DNA, Watson and Crick never performed a single experiment related to DNA.
A
True
24
Q
Each molecule of DNA consists of two strands of nucleotides that twist together to form a…
A
Double helix
25
The "backbone" of each nucleotide strand is composed of...
Sugar and phosphate units
## Footnote
Hence why it is sometimes called the "sugar-phosphate backbone".
26
Nitrogenous bases pair with a base on the opposing strand using...
Hydrogen bonds
27
When cytosine bonds with guanine, they form ____ H-bond(s).
3
28
When adenine bonds with thymine, they form ____ H-bonds.
2
29
The diameter of a DNA molecule is consistently...
2 nm
30
List the two grooves found in the sugar-phosphate backbone.
1. Major groove (larger)
2. Minor groove (smaller)
31
The two strands in a DNA molecule run ____ to each other.
Antiparallel
32
If one strand of DNA has a sequence of 5'-ACCTAG-3', what is the sequence of the other strand?
5'-CTAGGT-3'
## Footnote
*don't memorize this particular sequence, I just made it up to illustrate a point*
33
The Watson-Crick model suggested that the basis of copying genetic information was...
Complementary
34
What does it mean when we say that DNA replication is "complementary"?
The sequence of the parental strand determines the sequence of the daughter strand.
35
List the three proposed models of DNA replication.
1. Conservative
2. Semi-conservative
3. Dispersive
36
Which model of DNA replication did Watson and Crick believe was most likely to be correct?
The semi-conservative model
37
The conservative model suggests that during DNA replication...
Both parent strands stay intact, and the daughter molecule contains all-new material.
38
The semi-conservative model suggested that during DNA replication...
1 parent strand remains intact, and 1 new daughter strand is synthesized
39
The dispersive model suggests that during DNA replication...
Parts of both parental strands are dispersed throughout the daughter molecule and mix with newly-synthesized DNA.
40
In 1958, Meselson and Stahl's experiments supported the ____ model.
Semi-conservative
41
How does a molecule of DNA replicate?
| (very broadly)
The helix is opened and both strands are copied, so the daughter molecule has one parental strand and one new strand
42
What three things are needed for DNA replication to proceed?
1. Something to copy
2. Something to do the copying
3. Enough relevant building blocks
43
During DNA replication, the parental molecule becomes the...
Template
44
The copying of DNA is facilitated by enzymes called...
DNA polymerase
45
The "building blocks" for new DNA are...
Nuceloside triphosphates
## Footnote
(sometimes the textbook will call these "nucleotide triphosphates", treat both as being correct)
46
A molecule that contains only a pentose sugar and a nitrogenous base is termed a...
Nucleoside
47
List the three stages of DNA replication.
1. Initiation - process starts
2. Elongation - synthesis of new DNA
3. Termination - process ends
48
What are the functions of DNA polymerase?
| (two)
1. Matches template strands with complementary nucleotides
2. Links incoming nucleotides to the daughter strand
49
DNA polymerase always synthesizes DNA from the ____ end to the ____ end.
5' to 3'
50
# True or false:
DNA polymerase can start the process of DNA replication.
False
Starting the process requires a primer.
51
The primer is made by ____ and extended by ____.
RNA polymerase ; DNA polymerase
52
The action of DNA polymerase in the 5' to 3' direction is termed...
Writing or synthesizing
53
The action of DNA polymerase in the 3' to 5' direction is termed...
Reading
54
Many prokaryotes contain a single circular DNA molecule called a...
Chromosome
55
DNA replication begins at the ____ and ends at the ____.
Origin of replication ; terminus
56
What is the function of initiator proteins in DNA replication?
Binds to the origin and separates the two strands of DNA.
57
DNA is catalyzed by ____, macromolecular complexes that contain DNA polymerase.
Replisomes
58
# True or false:
In prokaryotes, replication proceeds in one direction around the chromosome.
False
Replication proceeds in both directions simultaneously.
59
The region of DNA controlled by the origin is called the...
Replicon
60
List the three major types of DNA polymerase found in prokaryotes.
1. DNA polymerase 1
2. DNA polymerase 2
3. DNA polymerase 3
## Footnote
wow......so creative
61
What is the function of DNA polymerase 1?
Replaces the RNA primers with DNA in the completed molecule.
62
What is the function of DNA polymerase 2?
It is involved in DNA repair processes.
63
What is the function of DNA polymerase 3?
It is the main replication enzyme and responsible for most of DNA synthesis.
64
DNA polymerase has an exonuclease action in the 3' to 5' direction called...
"Proofreading"
65
An exonuclease activity is one that can...
Break the phosphodiester bonds at the end of the molecule
66
Proofreading allows DNA polymerase to...
Recognize and remove mis-paired bases.
67
# True or false:
DNA replication is a continuous process.
False
The process is semi-discontinuous.
68
The strand that is synthesized continuously from the initial RNA primer is the...
Leading strand
## Footnote
(in the diagrams in the textbook, it's on the bottom of the replication fork)
69
The strand that is synthesized discontinuously is the...
Lagging strand
## Footnote
(in the diagrams in the textbook, it's on the top of the replication fork)
70
Because the lagging strand is synthesized discontinuously...
It has multiple priming and synthesis events which make short DNA fragments
71
The short sequences of DNA synthesized on the lagging strand are called...
Okazaki fragments
72
# True or false:
Both the leading and lagging strands are synthesized in the same direction.
False
The lagging strand is synthesized in the opposite direction of the replication fork's movement.
73
List the steps involved in replication of the lagging strand.
1. Primase makes a short RNA primer
2. DNA polymerase 3 makes an Okazaki fragment from the primer
3. DNA polymerase 1 replaces the primers with DNA
4. DNA ligase seals the resulting gap in the backbone
74
The enzyme that makes RNA primer for the lagging strand is...
Primase
75
The enzyme responsible for sealing the "nicks" (gaps) in the backbone is...
DNA ligase
76
Enzymes that use energy from ATP to unwind the DNA strands are...
Helicases
77
____ coat the separated DNA strands to prevent them from recombining.
Single-strand binding proteins
(SSBs)
78
List two problems caused by unwinding DNA.
1. Supercoiling
2. Torsional strain
79
Supercoiling occurs when...
DNA twists on itself
80
Why is supercoiling a problem?
It can damage the DNA and block the progress of the replisome
81
Torsional strain occurs when...
DNA strands become too twisted
82
What is the function of DNA gyrase?
Relieves torsional strain
83
DNA polymerases are kept on track by a protein complex called a...
Clamploader
84
In order to synthesize both strands at the same time, DNA replication is thought to involve...
Looping the lagging strand
85
DNA gyrase and helicase work together to...
Open the DNA helix
86
DNA polymerase 3 is held to the DNA strands by the...
Beta clamp
87
Unbound nucleotides are prevented from reforming H-bonds by the action of...
SSBs
88
The beta clamp protein is released from DNA polymerase 3 when...
It contacts an Okazaki fragment on the lagging strand
89
# True or false:
Eukaryotic and prokaryotic DNA replication proceeds in exactly the same fashion.
False
90
List two factors that complicate DNA replication in eukaryotes.
1. Size of the genome
2. Structure of the genome
91
# True or false:
Eukaryotes only have one origin of replication.
False
They often have multiple origins.
92
Approximately how many origins of replication are needed in the human genome?
30,000
93
What additional problem is caused by eukaryotes having linear chromosomes?
They require a special mechanism to replicate the ends of the chromosomes
94
What are the two main types of DNA polymerase in eukaryotes?
DNA polymerase delta (δ)
DNA polymerase epsilon (ε)
95
The special structures at the ends of eukaryotic chromosomes which consist of short, repeated DNA sequences are called...
Telomeres
96
What are the functions of telomeres?
| (two)
1. Protect the ends of DNA from nucleases
2. Maintain linear chromosome integrity
97
# True or false:
Both the leading and lagging strands of eukaryotic DNA require extra steps to replicate their ends.
False
Only the lagging strands requires extra steps.
98
Without extra steps, what would happen to the end of the lagging strand in eukaryotes?
The cell would be unable to replicate it, causing the chromosome to shorten each time the cell divides.
99
Eukaryotes can replicate the last section of the lagging strand using...
Telomerase
100
Telomerase contains an RNA template that matches...
The repeating telomere DNA
101
How does telomerase work?
It binds to the telomere and extends the lagging strand with repeating stretches of DNA.
102
Telomere length has been linked to...
Senescence
(cell aging)
103
In humans, telomerase is expressed in...
Embryos and children
104
# True or false:
In human adults, telomerase is only active in stem cells.
True
This is why cells have a limited number of divisions they can undergo.
105
Most ____ cells have active telomerase and lack telomere shortening.
Cancer
106
List two ways that the DNA of a cell can become damaged.
1. Errors during replication
2. Impact of mutagens (radiation and chemicals)
107
# True or false:
No mistakes made during DNA replication are acceptable to the cell.
False
Some mistakes are acceptable and remain - this causes genetic variation.
108
How does the cell correct errors made during DNA replication?
DNA polymerase "proofreads" the new strands
109
Mutagens damage DNA by...
Increasing the number of mistakes and mutations above normal levels
110
There is a link between the failure of DNA repair systems and...
Cancer
111
List the two general categories of DNA repair mechanisms.
1. Specific repair
2. Nonspecific repair
112
Specific repair mechanisms are a very effective means of targeting...
A single type of DNA damage
113
Nonspecific repair mechanisms can repair multiple types of DNA damage using...
A single mechanism
114
The specific repair mechanism used to correct damage from exposure to UV radiation is...
Photorepair
115
How does UV radiation damage DNA?
It causes two adjacent thymines to covalently link (a thymine dimer) which results in replication errors.
116
How does photorepair work?
An enzyme absorbs visible light and uses it to cleave the thymine dimers
117
A nonspecific repair mechanism that removes and replaces damaged DNA is called...
Excision repair
118
After a damaged region is removed, DNA polymerase uses ____ as the template to replace it.
Information on the undamaged strand
