Topic 7: Modern Genetics Flashcards Preview

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Flashcards in Topic 7: Modern Genetics Deck (126):
1

Define genome

The total of all the genetic material in an organism

2

Where is the DNA found in prokaryotes?

In plasmids/chromosomes

3

Where is the DNA in eukaryotes?

In the nucleus, mitochondria and chloroplasts

4

What are exons?

Coding regions of DNA

5

What are introns?

Non-coding regions of DNA

6

Define gene sequencing

A method of analysing the individual base sequence along a DNA strand or an individual gene

7

What does PCR stand for?

Polymerase chain reaction

8

What is the purpose of PCR?

To amplify small samples of DNA by making more copies of it. Makes it easier to analyse

9

Summarise the stages of PCR

- Add DNA sample to mixture of enzymes, primers + nucleotides
- Heat mixture to 94 degrees
- Cool mixture to 55 degrees
- Raise temperature to 72 degrees

10

Why is taq polymerase used in PCR rather than normal DNA polymerase?

Thermicus aquaticus is an extremophile which is adapted to being at high temperatures. Its polymerase doesn't denature at the temps of PCR like normal DNA poly.

11

What is Taq an abbreviation for?

Thermic aquaticus (a bacteria)

12

What are primers?

Small sequences of DNA that must join to the beginning of the strand before copying can begin. Act as a starting point for DNA synthesis.

13

What is needed in the mixture that DNA is added to before PCR begins?

Taq polymerase
Primers
Buffer
Good supply of four bases

14

Why is the DNA initially heated to 94 degrees in PCR?

To break the hydrogen bonds between the DNA strands so that they become available for replication

15

Why is the temperature cooled to 55 degrees in PCR?

Allows primers to bind to complementary regions on the DNA

16

Why is the temperature raised for a second time to 72 degrees in PCR?

Optimum temperature for the Taq polymerase. Allows it to add onto the primers and extend the DNA strands

17

What are the uses of PCR?

DNA profiling
Gene sequencing

18

What is gene sequencing?

A method to determine the base sequence in a particular gene

19

Explain the basic principles in gene sequencing

- DNA cut up into fragments
- PCR done in mixture of normal and terminator bases
- Terminator bases have fluorescent dye to mark them
- Different length fragments made
- Separate with gel electrophoresis
- Compare to a DNA ladder to find nucleotide positions

20

What are the uses of DNA sequencing?

Predicting the amino acid sequence of a protein
Understanding genes and proteins used in non-communicable diseases

21

What is DNA profiling?

A method by which people can be identified and compared via the patterns in their DNA

22

What are satellites?

Short sequences of DNA that can be repeated up to 100s of times in the introns

23

What are micro-satellites?

Short sequences of DNA between 2-6 bases long that can be repeated between 5 and 100 times in the introns

24

What are mini-satellites?

Short sequences of DNA between 10-100 bases long and repeated 50-100s times in the introns

25

What principle is DNA profiling based on?

While everyone has satellites on the same loci on their homologous chromosomes, the number of times they are repeated differs between everyone

26

Summarise the stages of DNA profiling

Isolate DNA
Restriction enzymes
Gel electrophoresis
Southern blotting
Gene probes

27

What are restriction endonucleases?

Special enzymes that cut DNA at recognition sites on the intron sequence

28

Why are restriction endonucleases added to the DNA being profiled?

To cut around the repeating satellites and make different sized fragments which can then be separated out by gel electrophoresis

29

Summarise the stages of gel electrophoresis

DNA samples put into wells in agarose jelly with dye
Known DNA samples put in for comparison
Current applied
-vely charged DNA attracted to the +ve anode
Bands separate
Shone under UV light and identified

30

Why is DNA negatively charged?

Bc of the negatively charged phosphate group

31

Why is dye added to the DNA in gel electrophoresis?

So that the DNA can be seen on the plate

32

What is the relationship between size and speed of movement of DNA fragments in gel electrophoresis

Smaller fragments move faster and further

33

Explain the process of Southern blotting

Alkaline solution denatures DNA and separates it
Nylon filter put on it and draws up DNA - appears as blots
DNA covalently bound to filter using UV light

34

What are gene probes?

Complementary pieces of DNA which are labelled with a fluorescent molecule or radioactive isotope

35

What information can be found from the DNA profile produced in DNA profiling?

The number of microsatellites per fragment and the number of repeats

36

What are the uses of DNA profiling?

Paternity testing
Forensic science

37

What are housekeeping proteins?

Proteins found in all cells regardless of differentation

38

In what ways can you study cell differentiation?

Gel electrophoresis
Gene probes

39

How can you use gene probes to find a specific gene?

Specific probe is used for a specific gene
Heat DNA
Mix with fluorescently labelled mRNA
Hybridise at complementary points
Probe is labelled so it marks the genes

40

What are the two stages involved in the expression of a gene

Transcription
Translation

41

What are transcription factors?

Proteins that bind to DNA in the nucleus at promoter regions and control transcription. Can turn a gene on or off

42

What are promoter regions?

Areas on DNA which transcription factors bind to. Usually found right before the starting point of the gene

43

What are repressors?

Transcription factors which block transcription

44

How do enhancer sequences work?

Enhancer sequences change the structure of the chromatin of DNA which makes it easier or harder for RNA polymerase to bind

45

What is RNA splicing?

Post-transcriptional modification of mRNA

46

What happens in RNA splicing?

Introns are removed (and sometimes exons) and exons are put together

47

What are spliceosomes and what do they do?

They're enzymes which join exons together to form functional mRNA

48

How can one gene make many different proteins?

Because the exons of the gene can be joined together by the spliceosome in different ways. Means a different order of the bases so different amino acid sequence so different protein

49

What is epigenetics?

The study of changes in organisms due to modifications of gene expression rather than alteration of the genetic code

50

Name some intracellular systems which interact to control genes

DNA methylation
Histone modification
Non-coding mRNA

51

Name all the ways in which gene expression is controlled

RNA splicing
Transcription factors
DNA methylation
Non-coding mRNA
Histone modification

52

What is DNA methylation?

The addition of a methyl group to a DNA molecule

53

Where are methyl groups added on DNA?

Only on cytosine

54

What enzyme is needed in DNA methylation?

DNA methyltransferase

55

How does DNA methylation affect genes?

It silences the genes so they become inactive because it changes the shape of the nucleotides so transcription factors and RNA polymerase can't bind

56

What is DNA demethylation do?

Removes a methyl group from DNA and activates the gene

57

How can DNA methylation lead to disease?

Can suppress important genes such as tumour suppressor genes which leads to cancerous tumours growing.

58

What is histone acetylation?

Addition of an acetyl group to histone

59

What does histone acetylation produce?

Euchromatin - regions of chromatin with high transcriptional acitivity bc structure is loose and the chromatin is activated.

60

What does histone methylation produce?

Heterochromatin where chromatin is tightly coiled so regions have low or no transcription

61

What is non-coding RNA?

RNA transcribed from the non-coding regions of the chromosomes

62

How can ncRNA control transcription?

Coats chromosomes and deactivates it because of supercoiling which prevents transcription

63

What are stem cells?

Undifferentiated cells with the potential to develop into many different types of specialised cells from instructions in their DNA

64

What does totipotent mean?

Cells that are capable of producing every kind of adult and placental cell in the embryo

65

Give an example of totipotent cells

Embryonic stem cells

66

What does pluripotent mean?

Capable of producing almost every type of cell

67

Give an example of pluripotent cells

Stem cells found in the umbilical cord

68

What are multipotent cells?

Cells which can form a limited number of actdult cells

69

Where can adult stem cells be found?

In the tissues and organs of adults

70

What are the problems with adult stem cells?

Multipotent
Found in small cells
Hard to extract

71

What are the advantages of embryonic stem cells over other stem cells?

Totipotent so they can form a wide range of cells
Stay totipotent after cell division

72

What does the type of tissue a stem cell forms depend on?

The location of the stem cell

73

Describe the develop of an embryo to a somatic stem cell including what type of stem cell is formed

Embryonic stem cell (totipotent)
Blastocyst stem cell (pluripotent)
Fully differentiated somatic stem cell (multipotent)

74

What controls the changes that occur to stem cells?

Gene expression (controlled by epigenetic factors)

75

Give an example of epigenetic control in humans?

Turning fetal haemoglobin to adult haemoglobin by turning of the fetal globin strands and turning on the adult ones

76

Name the uses of stem cells in medicine

Stem cell therapy: new body parts and repairing damage to current body parts
Therapeutic cloning

77

Why are adult stem cells used in stem cell therapy over embryonic stem cells?

Easier to control the differentiation and is less likely to lead to cancer

78

How are stem cells used to make new body parts?

Grown on either a synthetic or collagen based framework and forms body part

79

What is the advantage of using stem cells to make new body parts?

Because they're the body's own cells they won't be rejected

80

What is therapeutic cloning?

An experimental method of producing large quantities of stem cells which can be used to treat diseases caused by fault genes.

81

Describe the method of therapeutic cloning

Remove body cell nucleus
Put into an ovum which has had body cell removed
Apply electric shock
Ovum divides and develops into embryonic stem cells
SCs cultured into required cell
Genetic diseases removed and cells inserted back into the patients

82

Why is an electric shock applied to the ovum in therapeutic cloning?

To fuse the nucleus and the ovum
To trigger the development of the ovum

83

What are the advantages of using stem cells in therapeutic cloning

Patient's own cells so they won't be rejected
Don't need to wait for a donor
Diseases can't be treated that couldn't before

84

What are the disadvantages of using stem cells in therapeutic cloning?

Experimental
Can cause cancer
Embryos destroyed in the process - unethical

85

What does iPSC stand for?

Induced pluripotent stem cells

86

How are iPSCs made?

Fibroblast cells had four genes coding for transcription factors put into them by a harmless retrovirus vector. Genetically engineered from multipotent to pluripotent

87

What are fibroblast cells?

Cells that are relatively unspecialised

88

What are the advantages of iPSCs?

No ethical objections bc no embryo is damaged
Not rejected by body
Source of pluripotent stem cells which can give rise to many cells
Divide indefinitely

89

What are the disadvantages of iPSCs?

Experimental
Low success rate
Expensive
Still a chance of becoming cancerous

90

What is genetic engineering?

Changing the genetic material of an organism by inserting genes of a different organism into it

91

What is recombinant DNA?

DNA which has been artificially made by combining constituents from different organisms

92

Describe the stages of producing recombinant DNA

- isolate the gene
- insert it into the vector DNA
- ligase glues it together
- introduced to host cell

93

How can genes be isolated when producing recombinant DNA?

Reverse transcriptase
Restriction endonucleases

94

Explain how reverse transcriptase can be used to isolate genes

Reverses the transcription of mRNA to produce an artificial strand of cDNA

95

Explain how restriction endonucleases can be used to isolate genes

They cut DNA at specific sites, making small pieces of DNA which are easier to work with
Form sticky ends which can be used to bind to the vector DNA

96

What are sticky ends and why are they needed?

Overhangs of exposed bases which are needed to form hydrogen bonds to complementary sticky ends on the vector DNA

97

Why is the vector DNA cut with the same restriction endonucleases when producing recombinant DNA?

So that it has complementary sticky ends to the sample DNA

98

What does DNA ligase do?

Sticks the sample DNA and the vector DNA together by reforming the sugar phosphate backbone

99

In what ways can you identify recombinant bacterium?

Using fluorescent markers which fluoresce under UV light
Replica plating

100

Explain the process of replica plating

Recombinant DNA is inserted into the plasmid which also carries genes for antibiotic resistance
Bacteria grown on master plate in complete media
Inverted and imprinted onto smooth velvet surface
Imprinted onto a fresh colony
Grown in different media
Compare to the master plate

101

What is the function of a vector?

To artificially carry foreign genetic material into another cell where it can be transcripted and translated

102

What are the characteristics of a good vector?

Targets correct host cell
No adverse side effects
Ensures the DNA is transcribed

103

Name vectors that can be used to produce recombinant DNA

Gene guns
Viruses
Liposome coating
Microinjection
Agrobacterium

104

Explain how gene guns work

The DNA is coated onto a gold/tungsten pellet which is then shot at high speed into the cell

105

Explain how viruses act as vectors

Harmless virus is engineered to carry a desirable gene which is then inserted into animal cells.

106

Explain how liposome coating acts as a vector

Gene is coated in liposome so it can fuse and pass through the phospholipid bilayer and pass on DNA

107

What are liposomes?

Spheres formed from the lipid bilayer

108

How can microinjection act as a vector?

DNA can be injected into cells using a micropipette then manipulated using a micromanipulator

109

What happens in knockout organisms?

A gene is silenced and the function that is then lost is observed

110

Why do we use knockout organisms?

To identify the function of a gene (through trial and error) and to use them as models for disease bc we can test on them for cures

111

Explain how mice are used as knockout organisms

Adult mice have embryonic stem cells
Modified so they're heterozygous for the gene
Bred to form homologous offspring who have lost that function

112

How do you know which of the knockout mice are carrying the homozygous gene?

The silenced gene has a marker on it

113

Which diseases can we use knockout mice to study?

Cystic fibrosis
Cancer
Parkinson's
Obesity

114

Generally, why have soya beans been genetically modified?

To improve the quality and yield of the crops
Have herbicide resistance
Have more oleic acid and less linoeic acid

115

Describe the method by which soya beans are genetically modified

Ti plasmid extracted from bacterium
Target gene inserted into plasmid
Inserted back into bacterium
Plant infected. Tumour grows with cells with new gene
Sample of cells taken and cultured to make whole new plants

116

What bacteria is used in the genetic modification of soya beans

Agrobacterium tumefaciens

117

What does the bacterium do in the genetic modification of soya beans?

Causes tumours called crown galls

118

Why are fatty acids altered when genetically modifying soya beans?

To stop oxidation of soya beans

119

Why do you want more oleic acid in soya beans?

Because they aren't easily oxidised
Monounsaturated

120

Why do you want less linoleic acid in soya beans?

Easily oxidised
Polyunsaturated

121

What are the main concerns with genetically modifying foods such as soya beans?

-ingesting foreign DNA
-unethical bc somtimes animals are used
-GM makes seeds infertile so new ones have to be used
-build up of antibiotic resistance
-new genes spread uncontrollably

122

What are terminator bases?

Dideoxynucleotides - hydroxyl group missing from carbon three so they stop DNA synthesis

123

Similarities between iPS cells and embryonic stem cells?

Give rise to many different type of cells
Divide indefinitely

124

Differences between iPS cells and embryonic stem cells?

iPS - adult, embryonic - younger
iPS - pluripotent, embryonic - totipotent
iPS - no rejection, embryonic - rejection
iPS from adult cells but embryonic cells from inner mass of morula

125

How do vectors carrying recombinant DNA get taken up by cells?

Mix bacterium and vector
Applying heat treatment

126

How are DNA profiles compared?

Looking at the total number of bands
Band width
Position of bands