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DNA Analysis & Interpretation > Lecture 1 - DNA Structure > Flashcards

Lecture 1 - DNA Structure Flashcards

1
Q

How many base pairs are there in the human genome?

A

~3 billion base pairs

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2
Q

What is DNA?

A

DNA is a polymer composed of two polynucleotide chains that coil around each other

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3
Q

How many core components do nucleic acids have?

A

Three

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4
Q

What are the core components of nucleic acids?

A
  • Base pairs that scan across and they are the true encodings we get information from
  • Phosphate Groups / Phosphodiesters which are along the outside of the backbone
  • Deoxyribose/sugar
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5
Q

How many bases are nucleobases made up of?

A

Four

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6
Q

What are the two types of nucleobases?

A
  • Pyrimidines and Purines
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7
Q

What bases are pyrimidines?

A
  • Cytosine
  • Thymine
  • Uracil
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8
Q

Where is uracil primarily found?

A

In RNA

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9
Q

What bases are purines?

A
  • Adenine
  • Guanine
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10
Q

What is the difference between thymine and uracil?

A

Uracil doesn’t have the methyl group that is present in thymine

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11
Q

What is cytosine complementary to?

A

Guanine

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12
Q

What is Adenine complementary to?

A

Thymine

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13
Q

How many hydrogen bonds are there between Adenine and Thymine?

A

2 Hydrogen bonds

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14
Q

What is the NH2 bond in Adenine?

A

It is a hydrogen bond donor

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15
Q

What is the N in Adenine?

A

Hydrogen bond acceptor

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16
Q

How many hydrogen bonds do guanine and cytosine have?

A

3

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17
Q

What is the double-bonded oxygen in guanine?

A

Hydrogen bond acceptor

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18
Q

What is the NH in Guanine?

A

Hydrogen bond donor

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19
Q

What is the NH2 bond in Guanine?

A

Hydrogen bond donor

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20
Q

What is the NH2 bond in cytosine?

A

Hydrogen bond donor

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21
Q

What is the C=N bond in cytosine?

A

Hydrogen bond acceptor

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22
Q

What is the C=O bond in cytosine?

A

Hydrogen bond acceptor

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23
Q

What is the C=O in thymine?

A

Hydrogen bond acceptor

24
Q

What is the NH bond in thymine?

A

Hydrogen bond donor

25
How is ribose produced?
It is metabolically produced from glucose Glucose gets reducted
26
How is deoxyribose generated?
Enzymes called ribonucleotide reductase catalyses ribose 5-phosphate in a deoxygenation process.
27
Why is it helpful that ribose is a sugar?
It can go from a planar structure to a cyclic structure.
28
What is a phosphate group?
It is a form of PO4-
29
What position does the phosphodiester link?
- In the 5' to 3' - This linkage drivers the helix structure - The asymmetric linkage gives DNA strands direction
30
What are the nucleobases?
- Adenine - Cytosine - Guanine - Thymine - Uracil
31
What are nucleosides?
- Adenosine - Guanosine - Cytidine - Thymidine - Uridine
32
What are the nucleotides?
- Adenosine 5'-phosphate - Cytidine 5'-phosphate - Guanosine 5'-phosphate - Thymidine 5'-phosphate - Uridine 5'-phosphate
33
Primary sequence
Sequence of nucleotides
34
Duplex formed with strand complementary sequence =
Duplex formed with strand complementary sequence = complementary bases in opposite order
35
Longer duplex with higher G-C content =
Longer duplex with higher G-C content = More stable
36
# What is the complementary sequence? ATGTCTTGAACA
1. Split strand into three base units - ATG TCT TGA ACA 2. Write down the complementary bases - TAC AGA ACT TGT 3. Reverse the order to give strand in the 5' to 3' format - TGT TCA AGA CAT
37
Double Helix Structure | General facts
- Right handed - 1 turn = 33Å - 10.5 nucleotides per turn - width = 20 Å - Minor groove - Major groove - 3.3Å base stacking distance
38
Why is a double helix needed?
- Negatively charged phosphate groups along the backbone has electrostation repulsion from each other. - Base pairs form hydrogen bonds - Stacking of nucleobases through hydrphobic / van der waals interacts compacts duplex vertically.
39
What would happen if the base pairs were separated?
Water would get inside the structure and disrupt the hydrogen bonding which isn't entropically favoured.
40
Why are the base pairs were closely packed in DNA?
To allow for pi stacking to occur and to prevent for a hydrophobic collapse.
41
What would happen if the phosphates were closly packed in DNA?
If the phosphates wre stacked on top of each other they would want to repel.
42
Alternatice Double Helix Forms
- B-DNA: Right handed - A-DNA: Right handed - Z-DNA: Left handed
43
B-DNA
- Right handed - Most common - Found in cells under physiological conditions
44
A-DNA
- Right handed - Occurs under dehydrated conditions or in hybrid DNA-RNA
45
Z-DNA
- Left handed - DNA undergone methylation - Common in some diseases - It still has rotation but is not packed as tightly - Occurs sporadically due to some diseases
46
Triplex
3rd strand binds in major groove
47
G-Quadruplex
- Found in telomeres (ends of chromosomes) - Protects DNA ends and stop DNA repair systems from trating them as damaged. - Allows copying of ends which wouldn't be possible with 3' end.
48
Examples of secondary structures
Triplex, B-DNA, etc
49
What can secondary structures form?
These in turn can form even larger tertiary structures if the sequences are right
50
Examples of tertiary structures?
- Hairpin - Stem-loop - Holliday junction
51
DNA vs RNA
DNA: - 2-deoxyribose - Thymine - usually double stranded RNA: - Ribose - Further possible H bonding - Phosphodiesters more easily hydrolysed - Uracil - Usually single stranded
52
RNA structures
RNA exists in mant complex structures: - Bulge - Bubble / interior loop - Stem-loop - Hairpin
53
Nucleosomes
- DNA is coiled around proteins called histones to produce nucleosomes, which are further packed to produce chromosomes - 8 protein units required for each nucleosome.
54
Nanotechnology
Predictable sequence-specific hybridisation can be used to create 3D nanostructures for a wide variety of nanotechnological applications
55

DNA Analysis & Interpretation (19 decks)

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