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MBB I > DNA > Flashcards

DNA Flashcards

(90 cards)

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1
Q

What are the components of DNA?

A

Deoxyribonucleotides

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2
Q

What are the components of a deoxyribonucleotide?

A

Deoxyribose sugar, Phosphate, Nitrogenous base

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3
Q

Name the bases of DNA and RNA.

A

Guanine, Cytosine, Adenine, Thymine, Uracil

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4
Q

What is the difference between Purines and Pyrimidines?

A

Purine = 2 rings. Pyrimidine = 1 ring.

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5
Q

Which bases are Purine?

A

Guanine, Adenine

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6
Q

Which bases are Pyrimidine?

A

Cytosine, Thymine, Uracil (RNA)

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7
Q

What bond do the base and sugar form?

A

Glycosidic bond

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8
Q

What is a nucleoside?

A

When the base and sugar combine without the phosphate

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9
Q

What is the primary structure?

A

DNA sequence

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10
Q

What are the different ends of DNA?

A

3’ end and 5’ end

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11
Q

What is the backbone known as and what does this mean?

A

Polyanion. Has multiple negative charges due to the phosphate groups.

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12
Q

Why is DNA double stranded and why does this help?

A

Due to polarity. Maintains stability.

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13
Q

What does antiparallel mean?

A

5’ and 3’ run in different directions

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14
Q

Explain the hydrogen bonds between the bases?

A

Hydrogen interacts with a negative molecule and becomes more positive. It will be attracted to another negative molecule.

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15
Q

How many hydrogen bonds are between C & G and A & T?

A

C & G = 3 bonds.

A & T = 2 bonds

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16
Q

What are some examples of Non-standard base pairing?

A

Watson-Crick. Hosteen.

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17
Q

Describe Base Stacking.

A
  1. Bases stack and interact
  2. DNA bases has alternating single bonds
  3. Pi orbitals allow free electron movement and overlap to form Pi conjugation
  4. Becomes more stable
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18
Q

Why does DNA twist?

A
  • Having a straight stack creates repulsion
  • Rotates 30 degrees they interact better
  • Twisting makes the DNA helix asymmetrical
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19
Q

What are Major Grooves?

A

Big gaps in the helix. Higher information content. Proteins can interact and bind.

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20
Q

What is the Minor Groove?

A

Small gaps in the helix. Less access to the bases.

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21
Q

What is electrostatic repulsion in the DNA helix?

A

Phosphate groups are negatively charged and repel on another. Can form ionic bonds.

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22
Q

What is ssDNA?

A

Single Stranded DNA - always pushes to become double

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23
Q

What is dsDNA?

A

Double stranded DNA

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24
Q

What is the effect of temperature on DNA?

A

Increases = more DNA becomes single stranded.

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25
What is the melting temperature?
When 50% of DNA is single stranded. Below can still anneal
26
How does DNA anneal?
Trial and error
27
What does the melting temperature depend on?
Content of GC base pairs, size of DNA, ionic strength, pH
28
When does DNA replication happen?
During cell division - synthesis
29
During replication what are the 2 strands known as?
Template strand and complementary strand
30
Explain Semi Conservative replication
One parent strand and one new daughter strand
31
Where does DNA replication start?
Origins of replication
32
What is meant by bidirectional replication bubble?
Replicates in both directions. Known as a replication fork.
33
What enzymes separates the DNA strands?
Helicase - breaks hydrogen bonds.
34
What do SSB proteins do?
Straighten and prevent DNA from re-annealing
35
What is DNA polymerase?
Enzyme the catalyses DNA synthesis - there are 3 different ones
36
What does DNA polymerase need?
A template (bases). dNTPs (building blocks). Mg2+ (promotes reaction. Primer
37
What does DNA primase produce?
RNA primer
38
What direction does replication occur?
Runs from 5' to 3'
39
What happens during replication?
- Both strands synthesized at the same time by DNA polymerase III - Leading = continuous - Lagging - done in fragments
40
What are Okazaki fragments?
1000 to 2000 base pairs
41
What is the role of DNA polymerase I?
Finishes lagging strand. Removes RNA and replaces it with DNA
42
What is the role of DNA ligase?
Joins it together at the end
43
Why does DNA want complementary pairs?
More stable than mismatched pairs
44
How does DNA polymerase copy DNA accurately?
- It's active site prevents bond formation between mismatched pairs - Can make contact in minor groove and measure the correct distance - Can proofread its own work - Editing and synthesizing happens in separate parts of DNA polymerase
45
How does DNA polymerase synthesize the lagging strand?
Needs a free 3'OH to initiate. Requires an RNA primer. RNA primers in the middle are easily removed.
46
What is the End Replication Problem?
RNA primers at 5' cannot be replaced as there is no 3'OH existing. End up with DNA that is a little shorter than the parent. Called the terminal gap. Always shortening.
47
How does the DNA deal with the End Replication Problem?
Don't put important genes at the end of chromosomes. Adds tandem repeats of DNA - don't have function in gene expression. Repeated multiple times.
48
What are tandem repeats?
Telomeres. T and G rich
49
How do telomeres and protein complexes interact?
Associate with proteins to form a loop which protects the end of the genome
50
What is the importance of telomeres?
They are counted after each replication. Too little telomeres mean the cell will not replicate anymore.
51
What is the role of telomerase?
Adds telomeres to the end of DNA. Multicomplex of proteins and RNA - the RNA is complementary to DNA and acts as a template to lengthen the telomeres
52
Where is telomerase active?
Germ cells and cancer cells.
53
What is Heterochromatin?
Condensed. Few genes. Telomeres. Centromeres. Suppresses gene expression. Stability. Inactive.
54
What is Euchromatin?
Less condensed. Expressed genes.
55
What is chromatin?
DNA and its packaging
56
What happens if you treat chromatin with low concentrations salt?
- Adding competing bonds - Will destabilize the structure - Disturbs the intermolecular interactions
57
What happens if you treat chromatin with high concentrations of salt?
Will break strong interactions
58
What are you left with if you treat the nucleus with salt?
'beads on a string'
59
What is the string in 'beads on a string' structure?
DNA
60
What are the beads in 'beads on a string' structure?
Proteins → histones → nucleosomes
61
What charge would an interacting protein have?
Weak positive charged
62
How many histones are in a nucleosome?
4
63
What are the core histones?
H2A, H2B, H3, H4.
64
What is the octameric complex?
2 copies of the core histones which come together to form an octameric complex
65
How many base pairs of DNA are wrapped around a histone?
146bp
66
What are nucleosomes linked by?
Naked DNA
67
Why does DNA need to be packaged?
Body will recognise naked DNA like viral DNA
68
How many fold reduction is beads on a string?
6 fold
69
What is the 40 fold reduction known as?
30 nm chromatin fibre. Zigzag structure.
70
What histone clamps the 40 fold reduction?
H1 - changes the exit path of DNA from the nucleosome.
71
What fold is the entire mitotic chromosome?
10,000 fold shorter than extended DNA
72
What is RNA?
Ribonucleic acid
73
What are the roles of RNA?
Storage/transfer of genetic information. Structural. Catalytic. Rrgulatory.
74
Why should RNA be less table?
Don't want transcripts to stay forever as there will be no regulatory system. Gene will be constantly expressed
75
Why is RNA less stable than DNA?
1. 2'OH (not H) | 2. Single stranded
76
Why does having a 2'OH make RNA unstable?
OH can be activated → electrons transferred to phosphate → covalent bond between O and P → P releases its other bond → degrades the chain
77
Describe the secondary structure of RNA
Can become double stranded → hydrogen bonds between nucleotides → forms compicated structure → get a bulge, internal loop or a hairpin
78
Why does single stranded RNA twist?
- Promoted by base stacking and is strong | - On an angle = more stable
79
Describe folding of tRNA.
- Have an anticodon loop, interacts with mRNA | - Loop to bring the amino acid to the peptide bond
80
How many classes of histones are there?
5
81
What does the activity of telomerase do?
Avoid loss of chromosome ends
82
What do the daughter strands have in semiconservative DNA replication?
- Contains one of the parent strands | - Has the same (A+T) content as template strand
83
What is the role of helicase?
Moves along the DNA to separate strands. At the replication fork helicase is required to separate the strands.
84
What does the proof-reading activity of DNA polymerase increase?
Fidelity of replication at least on hundred fold
85
What is the overall dimension of a CG pair very similar to?
An AT pair
86
How many hydrogen bonds are formed in ice?
4
87
How are base pairs arranged in B-DNA?
- Base stacking contrubutes to the stability | - Base pairs are placed across the centre of the double helix
88
How are base pairs arranged in A-DNA?
Base stacking contributes to stability
89
How are 5' and 3' carbons linked in nucleic acids?
Phosphate group
90
What methyl group is located in the major groove?
Thymine

MBB I (4 decks)

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