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CHEM141 > DNA Structure, Storage, Replication And Repair - Done > Flashcards

DNA Structure, Storage, Replication And Repair - Done Flashcards

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1
Q

How many base pairs per DNA helical turn?

A

10 - 10.5

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2
Q

How wide are the minor and major groves in DNA respectively?

A

Minor groove - 1.2nm wide

Major groove - 2.2nm wide

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3
Q

What’s the significance of the major groove?

A

The edges of bases are more accessible and lots of enzymes use this as a binding site - transcription factors

Also a target for medicinal chemists to exploit

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4
Q

What is the mechanisms of intercalating drugs on DNA?

A

Planar (aromatic or heteroaromatic) systems slip between the layers of nuclei acid pairs and disrupt shape of helix

Affects enzyme binding

Often show preference for minor or major groove

Intercalating can inhibit topoisomerases

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5
Q

What is proflavine and what does it treat?

A

Intercalating antibacterial drug - used in WW1 to treat deep face wounds

Completely ionised at physiological pH - ion-ion pair anchor drug in

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6
Q

What does doxorubicin treat?

A

Anticancer drug

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7
Q

Where does doxorubicin bind?

A

At the major groove in DNA, charged amino group acts as anchor

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8
Q

Why is doxorubicin considered a Topoisomerase ll poison?

A

Because intercalation prevents normal action of enzyme

Crucial to replication and mitosis

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9
Q

Briefly describe the process of gene expression

A

Cell transcribes the nucleotide sequence of a gene into an RNA molecule.

Cell then transcribes RNA molecule into amino acid sequence of a protein.

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10
Q

Define what a gene is

A

A gene is a segment of DNA that contains the instructions for making a particular RNA and/or protein.

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11
Q

What is an organisms karyotype?

A

The full set of chromosomes

Karyotype of humans is 46 chromosomes

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12
Q

What is interphase?

A

Cell is actively expressing its genes, DNA can replicate and complete gene expression to proteins.

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13
Q

What is M-Phase?

A

The mitotic phase where chromosomes become more densely packed - cell division

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14
Q

What’s significant about the structure at the telomere?

A

Higher concentration of G-C base pairs - chemical knot tying the ends

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15
Q

What’s the purpose of the centromere?

A

Attaches duplicated chromosomes to mitotic spindle

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16
Q

Why are genes found far from the centromere?

A

To reduce error

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17
Q

What’s the complex of nuclear DNA with histone and non-histone proteins called?

A

Chromatin

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18
Q

What is a nucleosome?

A

Nucleosomes contain DNA wrapped around a protein core of 8 histone molecules - 2 molecules each of histones H2A, H2B, H3 and H4

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19
Q

How many base pairs are in a histone octamer?

A

147 base pairs - 1.7 turns of DNA in a left-handed coil per histone octamer

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20
Q

What are the properties of histones?

A

Long N-terminal tail

High proportion of +ve amino acids - Arg and Lys

  • Positive charge helps histones bind tightly to -vely charged sugar-phosphate backbone
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21
Q

What’s the role of topoisomerase l?

A

Relieve torsional stress of supercoiled DNA - only cleaves 1 strand

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22
Q

What’s the role of topoisomerase ll?

A

Cuts both DNA strands which are pulled apart to allow second strand to pass through - strands are then resealed

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23
Q

By what mechanism does topoisomerase ll break the sugar-phosphate backbone?

A
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24
Q

How do intercalating drugs interfere with topoisomerases?

A

By preventing replication transcription [artly by inhibiting topoisomerases function

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25
What does camptothecin treat?
Cancer - topoisomerase poison
26
What’s the method of action for camptothecin?
Stabilises the cleavable complex formed between DNA and topoisomerase l Cancer cell dies
27
What are fluoroquinolones?
Topoisomerase poisons They’re synthetic agents that target topoisomerase lV, bacterial homologues
28
What is the method of action of fluoroquinolones?
They inhibit replication and transcription of bacterial DNA by stabilising the bacterial topoisomerase - DNA complex Binding site only appears after the DNA has been ‘nicked’ and DNA strands are ready to be crossed over
29
How do fluoroquinolones lock to the enzyme?
Have a carboxylic acid which becomes charged at physiological pH as well as 2 R groups on opposite side
30
Why are chemical modifications to histone tail important?
Because modifications control which genes are switched on/off
31
What does a methyl group at K 9 mean on a H3 histone tail?
Heterochromatin formation, gene silencing
32
What does a methyl at K 4 and acyl at K 9 mean?
Gene expression
33
What does a phosphate at S 10 and acyl at K 14 mean?
Gene expression
34
Define epigenetic inheritance
The transmission of a heritable pattern of gene expression from one cell to its daughter cells that does not involve the DNA sequence
35
How can epigenetic transmission occur?
Parental cell divides, leaving half of the modified nucleosomes for each daughter cell. Proteins that recognise the same modifications they catalyse can then restore the parental modification pattern of nucleosomes - helping eukaryotic cells to ‘remember’ whether the gene was active
36
How many bases are wrong in the entire process of cell division?
1 - 3 letters wrong
37
What is structural important at replication origins?
Stretches of DNA rich with A - T
38
How many replication sites are in the human genome?
10,000 replication origins
39
What protein opens the DNA helix?
DNA helicase
40
What way can DNA only be synthesised in?
5’ —> 3’ direction
41
What direction is DNA always read in?
ALWAYS reads 3’ —> 5’ direction
42
What has DNA Polymerase evolved to do?
Evolved to use nucleotide triphosphates as substrates which are paired to the base in the template strand to grow the chain in 5’ —> 3’ direction
43
How is proofreading achieved?
Polymerisation and proofreading steps are tightly coordinated - happening in different domains If incorrect base is paired then it is removed and correct nucleotide is added and synthesis continues
44
What’s the proofreading domain known as?
A nuclease domain - E Results in error in 1 in every 10 million base pairs.
45
What is the strand that can grow in 5’—>3’ direction called?
The leading strand
46
What is the strand that can grow in 3’—>5’ direction called?
The lagging strand Grown discontinuously using back stitching - forms Okazaki fragments
47
What’s the function of DNA primase?
Creates an RNA primer - short sequence which provided a base-paired 3’ end as a starting point for DNA polymerase.
48
What’s the function of DNA polymerase?
Helps grow the chain from the primer Will form Okazaki fragments if on lagging strand template
49
What’s the function of nuclease enzymes?
Once the new Okazaki fragment reaches the primer of a previous fragment, nuclease cleaves off the primer
50
What’s the function of repair polymerase?
Replaces primer section with DNA
51
What’s the function of DNA ligase?
Joins sections of DNA together
52
What function group do all topoisomerase poisons possess?
A lactone ring - cyclic ester
53
What are chain terminating drugs?
Drugs that act as false substrates and are incorporated into the DNA chain during replication Chain can no longer be extended once added
54
What must chain terminating drugs have?
A triphosphate group A structure that makes it impossible for further building blocks to be added - No 3’ OH group to build from Also must be recognised by DNA template and interact with nucleic acids.
55
What drug is used to treat herpes? How does it achieve this?
Acyclovir - antiviral agent Is a substrate for viral thymidine kinase but not human - converting it to its monophosphate.
56
Why can the triphosphate not be used in chain terminating drugs?
Cannot be used because drug would be too polar to enter cells
57
After the mismatch repair mechanism what’s the overall efficiency of DNA replication?
1 error in every billion base pairs
58
How does sickle-cell anemia occur?
Occurs as a result of one uncorrected error in the gene for Beta-globin
59
What’s the significance of thymine dimers?
Ultraviolet radiation causes this Changes the structure of DNA - meaning those who cannot correct this have to avoid sunlight and are very susceptible to skin cancers
60
What two reactions are the most common to create serious DNA damage in cells?
Depurination - loses purine as polymerase skips over it - frameshift Deamination - cytosine amine is replaced by ketone - forming T not G as product
61
How does the mismatch repair system recognise a mistake?
Because a mutation can alter the secondary structure of DNA Hence repair proteins can recognise this
62
What’s the mechanism for the mismatch repair system?
1 - nuclease protein specific to the damage cleaves the phosphodiester linkages of the damaged nucleotide 2 - repair DNA polymerase replaces the gap created with correct nucleotide 3 - ligase enzyme joins the sections together
63
What do alkylating and metallating agents do?
They often form covalent bonds to nucleophilic centres in DNA with their highly electrophilic groups. This can disrupt/prevent replication and transcription - useful against cancer
64
What are possible toxic side effects of alkylating and metallating agents?
Protein alkylation
65
How are inter-strand crosslinks formed?
React with nucleic acid base on each chain of DNA duplex This crosslinks the strands - disrupting replication and transcription
66
How are intracellular-strand crosslinks formed?
Link two nucleophilic groups on the same chain That DNA portion then becomes masked from enzymes - stopping replication
67
What does a drug need to form inter/intra-strand crosslinks in DNA duplexes?
TWO alkylating groups
68
How can you find basic nitrogen’s on nucleic acids?
Nitrogen’s that have lone pairs orthogonal to the ring - not involved in aromaticity
69
How does miscoding lead to altering protein structure and function? Where can this be useful?
Guanine exists in keto form - though when alkylated it exists in enol form This makes it more likely to bind to thymine - useful in anticancer and antiparasitic drugs
70
What anticancer drug contains a aziridinium ion?
Nitrogen mustards, Chlormethine - crosslinks DNA so stop replication (Aziridinium ion HIGHLY electrophilic)
71
What do nitrosoureas treat and how do they function?
Anticancer drug Nitrosoureas decompose spontaneously in the body to form 2 active compounds
72
Give an example of a nitrosourea?
Carmustine Lomustine Streptozotocin
73
What do the active compounds of nitrosoureas do?
One carbamoylates lysine residues - inactivating DNA repair enzymes Other causes alkylation on O6 of guanine and N3 of cytosine
74
What is Busulfan and what does is do?
Anticancer drug Causes inter-strand crosslinking between guanine units.
75
What’s the general structure of Busulfan? What’s its role?
Busulfan has 2 sulfonate groups at either end of a 4 carbon chain Sulfonate groups are good leaving groups and so can crosslink 2 DNA strands, stopping replication (Inter-strand crosslinking)
76
What anticancer drug is neutral and unreactive?
Cisplatin
77
How is cisplatin activated and what’s its function?
Activated within cells by aquation Intra-strand crosslinking — N-7 and O-6 positions of adjacent guanine molecules
78
What is Calicheamicin Y1 and what does it do?
Anticancer agent that cuts DNA strands and prevents DNA ligase from repairing the damage
79
How does Calicheamicin Y1 act as a chain cutter?
It creates radicals on DNA structure that react with oxygen to form peroxy species and DNA chain fragments
80
Where does Calicheamicin Y1 bind?
Binds at the minor groove in DNA helix
81
What compounds work the same way as Calicheamicin Y1?
Bleomycins and podophyllotoxins

CHEM141 (12 decks)

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