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(3) Biological Molecules > DNA > Flashcards

DNA Flashcards

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Organic Chemistry 101 flashcards
1
Q

What is a eukaryotic cell?

A

This is a cell that has a nucleus

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2
Q

What is a prokaryotic cell?

A

This is a cell that does not have a nucleus

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3
Q

How are the parts of the cell compartmentalised?

A

They are contained within organelles

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4
Q

What is the central dogma?

A

1) DNA replication
2) DNA is transcribed into RNA
3) the RNA is translated into a protein

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5
Q

What is the transforming principle?

A

S cells contain a chemical that is fatal
R cells do not contain this chemical
The chemical in dead S cell bacteria could be transformed into living bacteria to make them deadly- Living R cells are changed to S cells

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6
Q

What is a bacteriophage?

A

This is a virus that infects bacteria by sticking to bacteria surface and injecting its own genetic material

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7
Q

Which experiment established DNA as genetic material?

A 
Hershey and Chase: 1952
35S proteins
1) protein coats of phages are radioactively labelled
2) phages infect bacteria with GM
3) no radioactivity enters the cell
32P DNA
1) DNA of phases is radioactively labelled
2) phages infect bacteria with GM
3) radioactivity enters the cell
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8
Q

What makes up a nucleotide?

A

DNA backbone- phosphates and their esters (phosphate)
Carbohydrates- ribose and deoxyribose (sugar)
Organic bases (nucleoside bases)- AGTC (unit)

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9
Q

What is a nucleotide?

A

Nucleotides form the basic structural unit of nucleic acids such as DNA

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10
Q

What are the bases and are they purines or pyramidines?

A

Adenine
Guanine
(Purines)

Uracil
Thymine
Cytosine
(Pyramidines)

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11
Q

What is the difference between ribose and deoxyribose?

A

Deoxyribose contains one less OH group than ribose

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12
Q

At which parts of DNA does it assemble?

A

DNA is assembled 5’ to 3’ direction

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13
Q

Describe the structure of the double helix of DNA

A

Phosphates are on the outside
Bases and hydrogen bonding is on the inside
It contains 2 strands which are antiparallel

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14
Q

Are nucleic acids acidic?

A

No nucleic acids are not acidic
At pH 7, only one in 1000 will have a proton to donate
The phosphate normally exists as an anion

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15
Q

Are DNA bases basic?

A

No they are not

Bases at pH 7 are neutral

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16
Q

Why does DNA have an overall negative charge?

A

Phosphates on the backbone will be negatively charged and so DNA has an overall negative charge

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17
Q

What are the difference between DNA and RNA?

A

1) DNA has thymine as a base whereas RNA has uracil
2) DNA has 2’ deoxyribose
On a macro molecular level, DNA is double stranded whereas RNA is single stranded
But RNA can still bind to DNA
RNA is short lived

18
Q

Why does DNA have thymine instead of uracil?

A

Cytosine can easily lose an NH3 and become uracil
This means that if this happens, the dUTpase can recognise this as a mistake and replace it whereas if uracil was a natural base of DNA, adenine would be paired with it which would lead to incorrect replication

19
Q

How is cytosine converted into uracil?

A

Water attacks and NH3 leaves

20
Q

What is the difference between thymine and uracil?

A

There is one methyl group difference

21
Q

How is cytosine converted to uracil

A

Water is added and NH3 leaves
Slow rate
(See mechanism

22
Q

What is the role of DUTpase?

A

DUTpase seeks out mutated uracil (from cytosine)

Even though uracil has a similar structure to thymine, it does not affect thymine as the methyl group on thymine is differentiating

23
Q

Is DNA or RNA more stable?

A

DNA is more stable than RNA (RNA is short lived)
RNA is more chemically reactive
DNA has a phosphate ester backbone
RNA has a reactive 2’ OH group

24
Q

What happens when DNA mutates?

A

It is passed onto future generations due to DNA replication

25
Q

Where can RNA be attacked?

A

RNA can be attacked by a base at the 2’ OH group
(RNA is removed)
( see mechanism)
This reaction is catalysed by RNAse which is shed by human skin

26
Q

Why do A-T and C-G pair together?

A

They have complementary H bonding stabilisation
A-T has 2 hydrogen bonds
C-G has 3 hydrogen bonds and so is more stable

27
Q

What is pi- pi stacking?

A

Interactions and attraction between aromatic rings when close in space, this makes a stack
This causes stabilisation in the double helix
Flat and aromatic which means drugs can fit in the spaces

28
Q

What is the role of DNA polymerase?

A

DNA polymerase extends the DNA chain in the 5’ to 3’ directions

Catalysed the bond formation between 3’
(See mechanism)

29
Q

How is DNA sequences?

A

1) heat DNA to break
2) primer reanneals
3) DNA polymerase adds free bases to primer (complementary)
4) dideoxy nucleotide terminates the chain- leads to fragments with different lengths (fluorescent chain terminators)
5) capillary electrophoresis- size dependent, small leave first
6) laser reads fluorescent ends

30
Q

What do you require for DNA sequencing?

A

Template strand- primer bonds to small parts of strand
DNA polymerase
Free DNA bases
Dideoxy nucleotides (fluoresently labelled)

31
Q

Describe the fidelity of DNA polymerase in humans and viruses

A

Fidelity is the accuracy of the polymerase
Human has a high fidelity and so few errors
Viral polymerase works faster but less meticulous as it competes with the host

32
Q

What will viral polymerase accept?

A

It will accept bases that lack 3’ OH dideoxynucleotides

Accept variations to bases- fluorescent bases

33
Q

How does capillary electrophoresis work?

A

It separated based on charge and size

Electrosmotic flow- migration of positive ions to the negative cathode

34
Q

What happens when thymine is exposed to UV radiation?

A

UV radiation damage

The excited state leads to dimers of thymine

35
Q

What is DNA photolase?

A

DNA repair enzyme. It binds to UV-damaged DNA containing pyrimidine dimers and breaks the cyclobutane ring joining the two pyrimidines of the dimer.

36
Q

How do cells repair DNA?

A

Prevents mistakes before the double helix (in replication)

1) two enzymes detect that the bases don’t match
2) a third enzyme detects the correct DNA strand
3) the defective strand is replaced

37
Q

What is base exclusion repair?

A

1) cytosine can lose an amino group forming uracil
2) enzymes cut out the defect and then damaged nucleotide
3) DNA fills in the gap

38
Q

When is DNA damage a good thing?

A

DNA damage is only lethal to cells engaged in the cell cycle
In mitosis, cell death is triggered if there is not enough DNA (apoptosis)

39
Q

How can apoptosis be triggered?

A

If you can stop the S phase in cell division (synthesis of DNA) , you can trigger apoptosis
Block the synthesis of thymine, if there is not enough DNA, (convert to uracil) cell death is triggered at check point

40
Q

How is uracil converted to thymine?

A

2) removal of 2’OH
2) removal of phosphate
3) addition of CH3

You need 2’OH and proton- recognised by ribonucleotide reductase
(See mechanism)

(3) Biological Molecules (7 decks)

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