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Fundamentals of the living cell > DNA Structure > Flashcards

DNA Structure Flashcards

1
Q

What is DNA present as in the nucleus?

A

Chromatin

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2
Q

What are the 4 major forms of DNA?

A

B form, A form, Z form and C form

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3
Q

What is the structure of the B form of DNA?

A
  1. 10 base pairs per turn in B-form
  2. B-form has major and minor grooves
  3. DNA in most of our cells is present as B form
  4. Angle between the glycosidic bonds of major groove is 240 while for the minor groove it is 120
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4
Q

What is the structure of the A form of DNA?

A
  1. Less common than B-form
  2. 11 base pairs per turn for A-form
  3. A-form of DNA found under dehydrating conditions (when relative humidity less than 75%)
  4. A-form 20-25% shorter than B-form (A-form also wider than B-form)
  5. Major and minor grooves of A-form a lot closer in size compared with B-form
  6. Bases aren’t perpendicular to the helical axis like they are in the B-form
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5
Q

What is the structure of the Z form of DNA?

A
  1. left hand conformational
  2. 12 base pairs per turn
  3. Transient (only active for short amount of time and then disappears) in high salt conditions
  4. Phosphodiester backbone forms a zigzag pattern thus causing the DNA to be named the Z-form
  5. Contains negative supercoiling
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6
Q

What is the structure of the C form of DNA?

A
  1. Found at relatively low humidity (66%)

2. Found in the presence of certain ions, e.g. Li+ and mg2+

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7
Q

Why are major and minor grooves present on DNA?

A

Because the glycosidic bonds that form within a base pair aren’t directly opposite each other

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8
Q

What is the function of the major and minor grooves of DNA?

A

DNA binding Proteins can bind to bases within the major and minor grooves to alter the structure of the DNA or to regulate transcription

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9
Q

Do proteins bind more favourably to the major or minor groove? Why?

A

Proteins bind more favourably to bases within major groove as there is more space for them to bind compared to minor groove

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10
Q

How do proteins gain the energy to bind to DNA?

A

Proteins gain energy needed to bind to bases within major and minor grooves by displacing H20 molecules associated with the major and minor grooves

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11
Q

Basic structure of DNA

A
  1. DNA made up of repeating sugar phosphate units linked by 3’-5 phosphodiester bonds
  2. Sugar called deoxyribose
  3. Both the 3’ and the 5’ positions connected to a deoxyribose sugar
  4. DNA base bonded to carbon 1 of the deoxyribose sugar
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12
Q

Why does single stranded DNA have polarity?

A

DNA strands have polarity due to the presence of the negatively charged phosphate group. This means DNA is acidic in nature.

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13
Q

Is DNA or RNA more stable? Why is this the case?

A

DNA more stable than RNA due to the extra oxygen present in the deoxyribose sugar compared with the ribose sugar found in RNA

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14
Q

What types of bases are the 4 different DNA bases?

A 
Cytosine = Pyrimidine base 
Guanine = Purine base 
Thymine = Pyrimidine base 
Adenine = Purine base
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15
Q

What are the complementary base pairs in DNA?

A

Cytosine and Guanine

Adenine and Thymine

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16
Q

Why do the bases pair up in the combinations that they do?

A

C and G pair up because they are able to form 3 hydrogen bonds
A and T pair up because they form 2 hydrogen bonds when they pair up

17
Q

What form of DNA does tRNA fold into?

A

A form of DNA

18
Q

Examples of unusual forms of DNA

A

Holliday junction
Tetraplex DNA
C and Z forms of DNA

19
Q

When is the Holliday junction used and what is it for?

A

Formed during homologous recombination. Homologous recombination used to fix double strand break repair (When breakages occur on both strand son DNA).

20
Q

Levels of DNA structure

A

Primary: Sequence of bases
Secondary: Helical structure
Tertiary structure: DNA supercoiling
Quaternary structure: Interlocked chromosomes

21
Q

What process allow for DNA to be packaged into the nucleus?

A

DNA supercoiling

22
Q

What is a nucleosome?

A

Basic building block of chromatin that represents the first level of chromatin structure

23
Q

How is a nucleosome formed?

A

Formed when the DNA double helix is wound around 8 histone proteins (an octamer of histones)
The octamer of histones includes 2 molecules each of 4 different types of histone protein: Histone 2A, 2B, 3 and 4.

24
Q

How are chromosomes formed?

A

Once DNA is coiled into the nucleosome Histone 1 binds to the outside of the nucleosome and to the linker DNA.
This allows for multiple nucleosomes to stick together thus forming a 30 nm fibre called the solenoid fibre
Solenoid fibre is then subject to higher order coiling and looping to become chromatin
Chromatin then condenses and coils even more to form chromosomes

25
Q

How do the histone proteins interact with DNA?

A

positively charged N-terminal tail interacts electrostatically with the negatively charged phosphate present with the DNA strands

26
Q

What is the structure of an E.coli chromosome?

A

Circular and organised into 50 independently supercoiled domains

27
Q

What does DNA damage cause the DNA to become?

A

DNA becomes mutated

28
Q

Examples of DNA damage and how each type damages the DNA

A

Deamination - Hydrolytic reaction which causes entire amine group of a DNA base to be removed. This causes cytosine to be hydrolysed to form uracil

Oxidative stress - Occurs when there’s an imbalance between processes that produce oxygen free radicals and the production of the antioxidants that detoxify them or repair the resulting damage

Radiation – UV light can cause area of DNA with 2 adjacent thymine bases to form thymine dimers by causing formation of cyclobutyl ring between the bases

Ionising radiation, E.g. x-rays and gamma rays, can break DNA chromosomes to cause leukaemia.

29
Q

Why is DNA repair is important?

A
  1. Maintains genome stability as DNA is chemically unstable

2. 50-100 different enzymes/proteins involved which means that there is a large investment for the cell

30
Q

What are the different types of DNA repair?

A

Direct repair - E.g. DNA photoreactivation (occurs when photons cleave the c-c bond of cyclobutyl ring formed during thymine dimerisation to reproduce the thymine monomers)
Base excision repair - Endonucleases cleave the DNA backbone on 5’ side of abnormal base, remove the damaged base. Other DNA strand used as a template for replacement of damaged base. Then DNA ligase catalyses formation of phosphodiester bonds once new base inserted.

31
Q

Which endonucleases are involved in base excision repair?

A

UvrA and UvrB recognise damage
UvrC makes incision in the DNA strand
UrvD removes abnormal base

Fundamentals of the living cell (11 decks)

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