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Chemistry for the Life Sciences > DNA > Flashcards

DNA Flashcards

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1
Q

In order to function, a cell must have…

A

…a means of storing information

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2
Q

A cells information is used for two things which are…

A

1 – encoding all the processes which allow the cell to metabolise and grow – ‘live’
2 – encoding within itself the means to replicate the information – ‘reproduce’

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3
Q

Information flows through the cell in…

A

…one direction

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4
Q

What is the cell’s information store known as?

A

DNA genome

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5
Q

What is the DNA genome used to do?

A

information is transcribed from the store in the form of mRNA

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6
Q

What happens with the mRNA transcripts after transcription ?

A

the transcripts are translated into functional molecules which control metabolism and utilise energy (from breaking chemical bonds) in order to grow and replicate

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7
Q

Where are hydrogen bonds located in the nucleotide subunits

A

Between nucleotide subunits holding the two strands together.

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8
Q

mRNA is…

A

…Transcribed from dna store. mRNA is then turned into proteins through translation.

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9
Q

Define translation

A

the synthesis of a polypeptide specified by an mRNA

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10
Q

How is information content of DNA stored?

A
  • the information content of DNA is stored as the sequence of bases A, C, G and T
  • i.e. the exact order that the bases occur is important as to what they encode
  • Bases are part of nucleotides – the subunits of a polymer
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11
Q

What are the building blocks of the DNA polymer?

A

the building blocks (monomers) of the DNA polymer are deoxyribo-base triphosphates

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12
Q

What constitutes a nucleotide?

A
  • A phosphate group
  • Sugar
  • Organic base
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13
Q

What do each of the nucleotides consist of?

A

each of the nucleotides consists of a purine or pyrimidine molecule attached to a deoxyribose (sugar) molecule and three phosphate groups

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14
Q

What parts of the nucleotide is polar (hydrophilic) and non polar (hydrophobic)?

A
  • Phosphate is polar and hydrophilic
  • Base is less polar and hydrophobic
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15
Q

How many rings do purines have?

A

2

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16
Q

How many rings do pyrimidines have?

A

1

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17
Q

Uracil is only in…

A

RNA

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18
Q

What bases are pyrimidines?

A
  • Cytosine (C)
  • Thymine (T)
  • Uracil (U) [RNA only]
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19
Q

Describe deoxyribose and ribose?

A
  • The sugar in DNA is Deoxyribose.
  • Ribose is a 5-carbon sugar. (Found in RNA)
  • Deoxyribose is lacking an oxygen on the 2’ carbon.
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20
Q

What bond joins the base and deoxyribose?

A

The bond that joins the base and the deoxyribose is an N-glycosidic bond.

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21
Q

How are N-glycosidic bonds formed?

A
  • the formation of the N-glycosidic bond is a dehydration reaction in which one molecule of water is eliminated by loss of the OH group of a sugar and a H group of a base.
  • a bond forms between the 1’ N of the pyrimidine (in this case) and the 1’ C of the deoxyribose
  • this forms a nucleoside – addition of a phosphate group is required to form a the nucleotide
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22
Q

How are nucleotides bound within a dna strand?

A

The monomers (nucleotides) are covalently joined within each strand via phospho-diester bonds between the 3’ C of one deoxyribose unit and the 5’ C of the next deoxyribose unit.

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23
Q

The dna strand has a…

A

…polarity

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24
Q

Why does the DNA strand have a ploarity?

A

The DNA strand has a polarity i.e. ends with different properties;
a phosphate group at one end and deoxyribose at the other end.

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25
Q

The phosphate end is called the…

A

…5’ end.

26
Q

The deoxyribose end is called the…

A

…3’ end

27
Q

In what sequence/order is the information contained in the sequence read?

A

The information contained in the sequence of bases is “read” starting at the 5’ end.

28
Q

The x shape is classic of…

A

…a helical structure

29
Q

What is the classic shape of a helical structure?

A

An x shape.

30
Q

Rosalind Franklin used one image
to…

A

… calculate the dimensions of DNA

31
Q

Rosalind Franklin and Maurice
Wilkins collected…

A

…x ray diffraction images.

32
Q

How many nucleotides are there
in one complete helical repeat?

A

34

33
Q

What do notches in the x ray diffraction images represent?

A
  • The notches illustrate the distance between the different bases.
  • Each notch is a nucleotide/base.
34
Q

Describe the triple helix model by Linus Pauling.

A

Triple helix model states that the phosphates form the helical core, with the bases pointing outwards, which is impossible under normal conditions.

35
Q

Who created the Triple Helix model?

A

Linus Pauling

36
Q

What is Paulings model also known as?

A

Triple helix model

37
Q

What is triple helix model also known as?

A

Paulings model

38
Q

How many hydrogen bonds between C and G base pairs?

A

C and G base pairs have 3 hydrogen bonds between them. Slightly stronger and more stable bonds.

39
Q

How many hydrogen bonds between A and T base pairs?

A

A and T base pairs have only 2 hydrogen bonds between them.

40
Q

How does DNA naturally exist?

A

DNA exists naturally with two strands that are aligned so that the bases are on the inside and the sugar-phosphate backbone is on the outside

41
Q

How do bases form pairs?

A

The bases form pairs using hydrogen bonds to stabilise them.

42
Q

How do the two dna strands run?

A

The two strands run anti-parallel.

43
Q

The base core is known as a…

A

Hydrophobic base core

44
Q

The phosphate is known as a…

A

…Hydrophilic phosphate

45
Q

G and C and A and T pairings have the…

A

…same length,

46
Q

Chargraff’s rules state that …

A
  • DNA from any cell of all organisms should have a 1:1 ratio (base Pair Rule) of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine.
47
Q

What are hydrogen bonds formed between?

A

a donor atom with Hydrogen covalently
attached and a acceptor atom which attracts the hydrogen.

48
Q

Describe dipoles between base pairs.

A
  • O and N can have lone e- pairs that partake in H-bonding
  • the dipole to be from the lone pair (δ- charge) interacts with the dipole on H (δ+ charge), which forms due to the electronegative nature of O and N
49
Q

Describe structure of dna double helix

A
  • DNA has a helical structure.
  • But what is the biological reason for this?
  • The bases are hydrophobic – so they are repelled by water.
  • Within cells the DNA molecule is surrounded by water
  • The bases therefore try to avoid water.
  • if it had a ladder structure – there would be gaps where water would
    associate between bases
  • Twists allow for the removal of these spaces and brings the hydrophobic
    surfaces of bases close together
  • Bases are perpendicular to the sugar-phosphate backbone.
  • Resulting in bases stacking on each other.
50
Q

Advantages of stacking.

A

Stacking contributes to stability:-
* Hydrophobic effect
* Base pairs attract one another through van der Waals forces.

51
Q

How strong are Van der Waals forces?

A

Although van der Waals forces are small the overall net effect of all the atoms involved in van der Waals contacts is substantial.

52
Q

Van der waals forces induce…

A

…major and minor grooves in the dna structure.

53
Q

What is a consequence of the hydrogen bonding?

A
  • the sugar molecules attached to the glycosidic bonds are not directly opposite to each other
  • this results in the exposure of
    more of the surface of the bases
    at the major groove – these bases
    are then available for interacting
    with other molecules.
54
Q

B-DNA is….

A

…Right-handed and the form of most DNA under physiological conditions

55
Q

A-DNA is…

A

Right handed and Double-stranded RNA and some RNA-DNA hybrids

56
Q

Z-DNA is …

A

…Left-handed and occurs in certain GC-rich areas.
- Affects which proteins can bind. e.g. some viral proteins interact with Z-form DNA

57
Q

How is DNA replicated?

A
  • In order for any cell to reproduce it first has to copy its genetic material.
  • DNA polymerase catalyses addition of
    nucleotides to a DNA strand by a condensation reaction creating the ester bond
  • Strands grow at the 3’ end and require a template strand
  • Complementary nucleotides form base pairs with bases in the template strand and are then attached to the growing chain.– (A with T and C with G)
58
Q

Describe Replication forks.

A
  • replication forks can be seen
    in electron micrographs of
    chromosomes replicating
  • in eukaryotes there are
    multiple replication forks
    occurring at many places on
    the chromosome
  • in prokaryotes there tends to
    be one origin of replication
    only
59
Q

Describe the different molecules involved in DNA polymerization at the replication fork.

A

DNA is polymerised by a complex of proteins at the replication fork:
1 - DNA polymerase (catalyses the addition of bases to the 3’ end)
2 - Topoisomerase (unwinds the helix to prevent torsion)
3 - Helicase (melts the double stranded molecule)
4 - DNA primase (makes short RNA primers [gives a free 3’ end])
5 - Single stranded binding proteins (prevents premature annealing)
6 - DNA ligase (joins Okazaki fragments on the lagging strand)

60
Q

How do bases interact with other molecules?

A

In order to interact with proteins such as those involved in DNA replication, the bases in the major groove form intermolecular interactions with amino acids on the surface of proteins - these can be through Van der Waals forces or H bonding.

61
Q

How are new DNA strands built?

A

1) DNA strands run anti-parallel to one another
2) The enzyme Helicase unwinds the DNA double helix by melting the molecule.
3) DNA polymerase attaches to a ‘leading’ strand
4) DNA polymerase synthesises a new DNA strand in the 5’ to 3’ direction
5) Another DNA polymerase molecule attaches to the ‘lagging’ strand
6) DNA is synthesised in the 5’ to 3’ direction
7) Helicase continues to unwind the DNA double helix
8) Continuous synthesis proceeds on the ‘leading’ strand
9) DNA polymerase detaches from the ‘lagging’ strand, and rejoins further down
10) Synthesis of DNA continues on the ‘lagging strand’
11) DNA polymerase is unable to join up the fragments on the lagging strand
12) This is done by the enzyme Ligase which joins Okazaki fragments on the lagging strand.

Chemistry for the Life Sciences (12 decks)

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