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3 Genetics > 16 Molecular Basis of Inheritance > Flashcards

16 Molecular Basis of Inheritance Flashcards

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1
Q

What is ’transformation’?

A

When the phenotype and genotype of a cell change due to the uptake of external DNA

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2
Q

How is ’transformation’ typically induced?

A

By bacteria which are engineered to insert DNA into other cells.

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3
Q

What are viruses which infect bacteria called?

A

‘Bacteriophages’

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4
Q

What are ‘Bacteriophages’?

A

Viruses which infect bacteria

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5
Q

What is an example of a ‘Bacteriophage’?

A

T2

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6
Q

What is ’T2’?

A

A bacteriophage

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7
Q

How can proteins be distinguished from DNA experimentally?

A

By adding radioactive phosphorus which is found in DNA but not proteins.

Alternatively radioactive sulphur can be used as it is found in proteins but not DNA.

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8
Q

What are bases of DNA?

A

Adenine, Thymine, Cytosine, and Guanine

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9
Q

How does DNA consist of structurally?

A

A long polymer made up of individual ’nucleotides’

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10
Q

What is the structure of each DNA nucleotide?

A

It has a central pentose sugar (‘deoxyribose’).

At the 1’ end of the sugar is a nitrogenous base i.e. A, C, T or G.

At the 5’ end of the deoxyribose is an inorganic phosphate group.

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11
Q

How does a DNA nucleotide differ from an RNA nucleotide?

A

A DNA has a central ‘deoxyribose sugar’ which has one less oxygen atom than the ‘ribose’ sugar of RNA.

Both sugars are pentoses.

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12
Q

What does 1’, 2’ and so on refer to?

A

This refers to the number of the Carbon in the deoxyribose.

They are labelled clockwise from the first Carbon at the top. (the first Carbon is actually at 90º, at the top is an Oxygen atom)

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13
Q

How are DNA nucleotides joined?

A

The phosphate group of one joins to the 3’ Carbon of the other’s deoxyribose sugar.

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14
Q

What are A, C, T and G collectively known as?

A

Nitrogenous bases.

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15
Q

What are ‘Chargaff’s rules’?

A

1) the base composition varies between species i.e ratio of A to G
2) within a species, the number of A and T bases are equal and the number of G and C bases are equal.

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16
Q

What is the basic structure of DNA?

A

It is a double helix.

It has a ’sugar-phophsate’ backbone ie. ribose-phosphate-ribose-phosphate. Between the two backbone are base pairs, with each consisting of complementary nitrogenous bases.

The nitrogenous bases are held together by hydrogen bonds

The helix is “right-handed,” curving up to the right

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17
Q

How are the complementary nitrogenous bases of base pairs held together?

A

By hydrogen bonds

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18
Q

What is the rule that there are equal number of A’s and Ts called as well as equal C’s and G’s called?

A

Chargaff’s rule.

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19
Q

How are the sugar-phosphate backbones in the double helix arranged?

A

They are ‘antiparallel’ in that one runs 5’ to 3’ and one runs 3’ to 5’

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20
Q

What does ‘antiparallel’ mean?

A

They are parallel but run in opposite directions.

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21
Q

What is it called when something i.e. the sugar phosphate backbones are parallel but run in opposite directions?

A

Antiparallel

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22
Q

How can nitrogen bases de grouped?

A

Into ‘purines’ (adenine and guanine) and ‘pyrimidines’ (thymine and cytosine)

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23
Q

What are ‘purines’?

A

Nitrogenous bases which consist of two organic rings

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24
Q

What are ‘pyrimidines’?

A

Nitrogenous bases with a single ring

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25
Q

Why is A pairing to T and C to G important structurally?

A

Pyrimidines have a single ring and thus are smaller than purines.

Therefore if a purine join to a purine it would be too wide and a pyrimidine-pyrimidine would be too narrow.

Therefore the fact that purines bind only to pyrimidines ensures that the DNA double helix has a uniform diameter.

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26
Q

What are the basic theoretical models for DNA replication?

A

The ‘conservative model’, ’semiconservative model’ and the ‘dispersive model’

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27
Q

What is the ‘conservative model’?

A

The two parental strands reassociate after acting as templates for new strands

This leads to restoring the parental double helix while leading to a double helix of entirely new genetic material.

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28
Q

What is the ’semi-conservative model’?

A

The two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand.

This forms two helices. Each has one parental strand and one newly synthesised strand.

29
Q

What is the ‘dispersive model’?

A

Each strand of both daughter helices contains a mixture of old and newly synthesized DNA.

30
Q

What model of DNA replication actually happens?

A

The ’semi-conservative model’

31
Q

What is the basic concept of DNA replication?

A

The parental molecule has two complementary strands of DNA.

The two strands of the parental helix separate to form two ’template strands’

Complementary nucleotides are along the two ’template strands’ so that two new helices are formed.

32
Q

How does DNA replication begin?

A

Along the DNA molecule will be multiple (one if bacteria) ‘origins of replication’ which are regions of DNA where the DNA strands are separated to form two template strands.

As the DNA opens up it forms a ‘replication bubble’ i.e -o- which spreads so that it is -c=c- and so on

33
Q

How are the DNA strands separated during DNA replication?

A

At the ends of each ‘replication bubble’ is a Y shaped region called the ‘replication fork’ where the strands are actually separated.

Enzymes called ‘helicases’ perform the actual unwinding of the double helix.

After the strands separate ’single strand binding proteins’ attach to the exposed template strand to prevent the two strands from rebinding.

In the unseparated region ahead of the ‘replication fork’ ’topoisomerase’ breaks swivels and reattaches the double-strands to relieve the tension form unwinding.

34
Q

What are the main structures involved in unwinding during DNA replication?

A

Topoisomerase, helicase and ’single-strand binding proteins’

35
Q

What does ’topoisomerase’ refer to?

A

The enzyme which breaks, swivels and reattaches the double stands ahead of the ‘replication fork’ to relieve tension

36
Q

What does ’replication fork’ refer to?

A

The actual split in the two DNA molecules at the edges of the replication bubble

37
Q

What does ’helicase’ refer to?

A

The enzymes which separate the two strands of DNA during replication

38
Q

What does ’single-strnad binding proteins’ refer to?

A

The proteins which bind to the unwound strands to prevent them from rebinding.

39
Q

What happens when the DNA helix has been unwound during replication?

A

A short RNA ‘primer’ is added by ‘primase’.

This primer allows ‘DNA polymerase’ to bind to the template strand and begin duplication, moving from 3’ of the template strand to 5’.

DNA polymerase adds each nucleotide in the form of ’nucleoside triphosphate’ which is a ’nucleoside’ (sugar+nitrogenous base) with three phosphate groups.

Two phosphate groups are removed to provide energy for duplication. This leaves a DNA nucleotide i.e. one phosphate, sugar and nitrogenous base.

40
Q

What are some specific examples of DNA polymerases?

A

DNA polymerase I and DNA polymerase III which are found in E. Coli.

DNA polymerase is used for general replication whereas DNA polymerase III is used to replaces the RNA primers with DNA

In eukaryotes there are at least 11 different types.

41
Q

How specifically is the energy needed for DNA replication provided?

A

Each nucleotide is added in the form of ’nucleoside triphosphate’ which consists of a nucleoside (sugar + nitrogenous base) and 3 phosphate groups.

Two of the phosphate groups are removed to yield a molecule of pyrophosphate (P-P) which is hydrolysed to provide energy for replication

42
Q

What does ’nucleoside’ refer to?

A

A sugar + a nitrogenous base

43
Q

What does ’nucleotide’ refer to?

A

A sugar + nitrogenous base + phosphate group

44
Q

In what direction is DNA replicated?

A

DNA polymerases can add nucleotides only to the free 3’ end of a primer or growing DNA strand, never to the 5’ end Thus, a new DNA strand can elongate only in the 5’ → 3’ direction

(it moves 3’ to 5’ down the template molecule)

45
Q

What is a consequence of the unidirectional nature of DNA polymerase?

A

As the replication bubble expands one strand is in the correct direction. Therefore DNA polymerase can move down it as normal. This strand is called the ‘leading strand’.

Due to the antiparallel nature of DNA the other template strand will be going in the opposite direction. Therefore replication of the ‘lagging strand’ is more difficult.

46
Q

How is the ‘lagging strand’ replicated?

A

It is synthesised in blocks called ‘Okazaki fragments’

1) Primase forms a short RNA primer at a region slightly down stream of the current end of the lagging strand.
2) DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment at the end of the lagging strand.

Note that the polymerase moves towards the origin of replication and thus against the direction of overall replication.

3) When the first Okazaki fragment is formed the DNA polymerase forms another.
4) The RNA primer between the Okazaki fragment is converted to DNA by DNA pol I.
5) The adjacent Okazaki fragments and the DNA region between them which used to by the RNA primer are all joined using ‘DNA ligase’

47
Q

What does ‘DNA pol’ refer to?

A

DNA polymerase

48
Q

What are the fragments of the lagging strand which form during ‘lagging strand’ formation called?

A

Okazaki fragments

49
Q

What does ’Okazaki fragments’ refer to?

A

the fragments of the lagging strand which form during ‘lagging strand’ formation

50
Q

What are the main enzymes involved in the actual replication of DNA and what are their functions?

A

Primase - forms RNA primers on both the leading strand and at the start of the lagging strand’s Okazaki fragments

DNA pol I - replicates DNA in the leading strand and forms the Okazaki fragments.

DNA pol III - replaces the RNA primer

DNA ligase - joins the Okazaki fragments and what used to be the RNA primer.

51
Q

What side does DNA polymerase add nucleotides?

A

It can only add nucleotides to the 3’ end of a RNA primer.

52
Q

How are the enzymes of DNA replication arranged?

A

In a ‘DNA replication complex’

53
Q

What does ’DNA replication complex’ refer to?

A

The fact that the enzymes that perform DNA replication i.e. helicase, polymerase are all joined together into one static ‘DNA replication complex’ through which the DNA is fed.

Therefore the DNA polymerase does not relay move down the DNA, the DNA moves along it etc.

54
Q

How is the ‘DNA replication complex’ held in place?

A

In eukaryotes it may be anchored to the nuclear matrix, a network of fibres which pass throughout the nucleus.

55
Q

After DNA has been replicated, what important steps occur?

A

The DNA is proofread for mistakes with any detected being fixed.

56
Q

What can proofreading of DNA be divided into?

A

Repair by the DNA polymerase and ‘mismatch repair’

57
Q

What is proofreading of DNA by DNA polymerases?

A

As the DNA polymerase adds nucleotides it checks them against the template strand.

If they do not match it removes it, inserts the correct nucleotide, then continues on replicating.

58
Q

What does ’mismatch repair’ refer to?

A

The repair of DNA mismatches by enzymes other than DNA polymerase.

59
Q

How does ‘mismatch repair work’?

A

One repair system is called the ’nucleotide excision repair’

In this system an enzyme detects a mismatch along the strand.

This triggers a ’nuclease’ to cut out the defective region.

DNA polymerase fills in the missing nucleotides.

DNA ligase seals it off.

60
Q

Besides mismatch repair, what is the ’nucleotide excision repair’ system used for?

A

The correction of spontaneous errors induced in DNA through radiation etc.

61
Q

What is an example of a specific form of damage that can occur to DNA?

A

UV light can cause a ’thymine dimer’ to form where two adjacent thymine bases join to each other.

62
Q

What does ’thymine dimer’ refer to?

A

A form of damage to DNA caused by UV light in which two adjacent thymine bases join to each other.

63
Q

What does ’xeroderma pigments’ refer to?

A

A disorder caused by an inherited defect in a nucleotide excision repair enzyme

Individuals with this disorder are hypersensitive to sunlight as the mechanisms to repair thymine dimers caused by UV light are not present.

Mutations in their skin cells caused by ultraviolet light are left uncorrected, resulting in skin cancer.

64
Q

In what direction does DNA polymerase move down the template stand and why?

A

It can only form the new strand in a 5’ to 3’ direction.

Therefore due to the antiparallel nature of DNA the polymerase must move 3’ to 5’ down the template strand.

65
Q

What type of nitrogenous base is adenine?

A

Purine

66
Q

What type of nitrogenous base is guanine?

A

Purine

67
Q

What type of nitrogenous base is thymine?

A

Pyrimidine

68
Q

What type of base of cytosine?

A

Pyrimidine

3 Genetics (9 decks)

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