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Semester 1 > MGD Sessions 7-11 > Flashcards

MGD Sessions 7-11 Flashcards

1
Q

What can be said about the specificity of bacterial endonucleases?

A

High

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2
Q

What do bacterial endonucleases commonly recognise and cleave?

A

Palindrome restriction sites

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3
Q

Which bond of the DNA sequence is cleaved by a bacterial endonuclease?

A

Phosphodiester

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4
Q

What are ‘sticky’ cuts?

A

Staggered cuts made by endonucleases which anneal w/complementary sequences to the overhang

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5
Q

What are ‘blunt’ cuts?

A

Double stranded ends created by endonucleases

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6
Q

How do bacteria protect their own DNA?

A

Methylation to block restriction enzymes

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7
Q

What is the general rule for the number of restriction sites present where n is the number of bases in the restriction site?

A

n^4

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8
Q

What is DNA ligase?

A

Enzyme that creates phosphodiester bonds b/w any sequences that have the same overhang or complementary blunt ends

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9
Q

Why will DNA move towards the anode in an electric field?

A

Phosphate group makes it negatively charged

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10
Q

What characteristic does DNA gel electrophoresis use to separate DNA fragments?

A

Size (also shape when plasmids-sorry!)

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11
Q

What are the 4 requirements for DNA gel electrophoresis?

A

Gel
Buffer
Power supply
Stain/detection

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12
Q

What type of plate is used in DNA gel electrophoresis to investigate long DNA w/larger size differences?

A

Agarose

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13
Q

What kind of plate is used to investigate DNA fragments with only one nucleotide differences?

A

Polyacrylamide gel

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14
Q

Why is restriction analysis used?

A

Clone DNA
Investigate mutations
Investigate size of DNA fragments
Investigate DNA variation

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15
Q

What can be used to identify the point mutation of one nucleotide as seen in sickle cell disease?

A

Restriction analysis

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16
Q

Why is a buffer needed in DNA gel electrophoresis?

A

Allows charge on the DNA samples across the gel

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17
Q

Describe how gene cloning is carried out.

A

Choose plasmid vector w/antibiotic resistant gene –> cut plasmid and gene of interest w/same restriction enzyme –> ligate –> recombinant DNA molecule –> transformation –> secreted by bacterial cells

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18
Q

What is the importance of the antibiotic resistance gene in the plasmid vector for gene cloning?

A

Can introduce antibiotic to see which bacteria have undergone transformation and taken up the recombinant plasmid

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19
Q

How is proinsulin synthesised by bacteria?

A

Mammalian proinsulin mRNA from pancreas –> reverse transcriptase –> proinsulin cDNA –> joint to plasmid –> recombinant plasmid –> infect E. Coli –> transformed bacterium synthesises proinsulin

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20
Q

Why do we clone human genes?

A 
Gene therapy
Make useful proteins
Find out what genes do
Genetic screening
Smaller initial sample needed for analysis
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21
Q

What happens in the first stage of PCR?

A

Heat to 95 degrees
Add 2 oligonucleotides unique to region to act as primers
Add heat stable Taq polymerase

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22
Q

Why are oligonucleotides used in PCR to act as primers?

A

Small pieces anneal easier

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23
Q

Which direction do the primers in PCR work?

A

5’ –> 3’

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24
Q

What happens to the temperature of the PCR during the second stage?

A

Cooled to RT

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25
Q

How does DNA renature in PCR?

A

Complementary bases realign upon cooling

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26
Q

Why is PCR used?

A

Amplification
Investigate variation/genetic relationships
Identify small deletions/insertions
Investigate single base mutations

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27
Q

In which direction will proteins move if placed in an electric field?

A

Towards anode or cathode

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28
Q

What properties can be used to separate proteins?

A

Size
Shape
Charge

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29
Q

What four things are required for protein electrophoresis?

A

Gel
Buffer
Power supply
Stain/detection

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30
Q

Why must separation of proteins by electrophoresis be further tested?

A

Relies on intrinsic properties of proteins so can be attributed to folding or other factors which need to be narrowed down

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31
Q

Which characteristic of proteins does SDS page investigate?

A

Size

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32
Q

How does SDS-PAGE only consider one factor affecting protein separation?

A

Protein denatured to remove tertiary and secondary structure

SDS binds to give standard overall -ve charge

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33
Q

How are proteins separated by isoelectric focusing?

A

Uses basis of charge

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34
Q

How is isoelectric focusing carried out?

A

Stable pH gradient established in vertical tube w/electric field applied –> protein added and moves until it reaches pI –> stain

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35
Q

What is 2D-page?

A

IEF put on top of SDS-polyacrylamide slab which allows separation of complex protein mixtures

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36
Q

What is proteomics?

A

Study of proteins

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37
Q

What are the 5 stages in proteomics?

A 
Digest protein w/trypsin
Perform mass spectrometry
Generate list of peptide sizes
Use database of predicted peptide sizes for known proteins 
Identify protein
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38
Q

What method can be used for protein analysis but has fewer options than for DNA electrophoresis?

A

Specific cleavage of proteins

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39
Q

What does enzymatic cleavage recognise?

A

Proteins after certain amino acids

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40
Q

How many segments would you expect to see in proteolysis of normal haemoglobin when using Endo-Arg-C?

A

4

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41
Q

What method of protein analysis can cyanogen bromide and hydroxylamine be used for?

A

Chemical cleavage

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42
Q

What an epitope?

A

Name given to a.a. an antibody can bind with

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43
Q

How does the production of polyclonal and monoclonal antibodies differ?

A

Polyclonal from many B lymphocytes

Monoclonal from 1

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44
Q

How many different antibodies are there in monoclonal and polyclonal antibodies?

A 
Monoclonal = 1 identical
Polyclonal = multiple different
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45
Q

Are monoclonal or polyclonal antibodies specific to one antigen?

A

Both are

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46
Q

How many epitopes does a polyclonal antibody bind to?

A

Multiple

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47
Q

How many epitopes does a monoclonal antibody bind to?

A

1

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48
Q

How are monoclonal antibodies made using mice?

A

Inject mouse w/antigen 3-4 times at 2 week intervals

Mouse produces antigens which can be found in its blood

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49
Q

How are monoclonal antibodies formed using mice?

A

Fuse mouse spleen cells and myeloma cells

Select and grow either in vivo/vitro

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50
Q

Why are myeloma cells used to make monoclonal antibodies?

A

They are immortalised

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51
Q

What is the end product of Western blotting?

A

Immunoblot

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52
Q

What happens in Western Blotting?

A

Nitrocellulose replica of gel electrophoretogram
Bind primary antibody
Wash
Labelled enzyme-linked secondary antibody bound
Immunoblot

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53
Q

What is ELISA?

A

Enzyme-linked immunoabsorbent assay

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54
Q

What happens between each stage of binding in ELISA?

A

Wash

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55
Q

Describe the stages in ELISA.

A

Antigen coated well
Specific antibody binds to antigen
Enzyme linked antibody binds to specific antibody
Substrate added

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56
Q

What is proportional to antibody level in ELISA?

A

Rate of colour production

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57
Q

What indicates how many antigens are present when carrying out ELISA?

A

How much antibody is needed

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58
Q

What does a radioimmunoassay use in conjunction with the ELISA method to measure protein concentration in a solution?

A

Radiolabelled primary antibody

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59
Q

What do enzyme assays measure to assess if an enzyme is present and if so, how much?

A

Appearance of product/disappearance of substrate

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60
Q

What are two methods of continuous enzyme assay?

A

Spectrophotometry

Chemoluminescence

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61
Q

What are two methods of discontinuous enzyme assay?

A

Radioactivity

Chromatography

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62
Q

Why would an enzyme assay be used to measure serum enzymes?

A

Suspected metabolic disorders

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63
Q

Give examples of some serum enzymes that can be assayed for.

A

Alkaline phosphatase - bone
Gamma-glutamyl transferase - liver
Cardiac troponin I - heart (gold standard)
Amylase/lipase - pancreas

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64
Q

What can enzyme activity be used to measure?

A

Clinically important metabolites

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65
Q

What do bacteria produce that recognise and degrade foreign DNA which enters the cell?

A

Endonucleases

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66
Q

Is Western blotting a DNA hybridisation technique?

A

Nope

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67
Q

What is found in the 4 tubes used for Sanger Chain DNA hybridisation?

A

ssDNA template
dNTPs
DNA polymerase
One ddNTP per tube

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68
Q

What happens in the Sanger chain method of DNA hybridisation?

A

4 tubes with one ddNTP per tube
Incubate at 37 degrees Celsius
Separate lanes for separate tubes on DNA electrophoresis

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69
Q

How can a chromatogram be used for Sanger chain?

A

Fluorescently labelled ddNTPs detected by laser as they fall off thing capillary gel

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70
Q

What is the Sanger chain method useful of?

A

Easy and quick sequencing of large genes

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71
Q

What does Northern blotting use to detect RNA species after gel electrophoresis?

A

DNA

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72
Q

Why are dideoxynucleotide triphosphates used in DNA hybridisation?

A

Have a H at 3’ end so are a substrate of RNA polymerase but prevent elongation

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73
Q

Do DNA probes used for DNA hybridisation have to completely align to target sequence?

A

Nope, partial overlap at one end is enough

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74
Q

Why do probes not have 100% similarity to target sequence?

A

They would bind too tightly

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75
Q

What can ssDNA be labelled with to be used as a probe for DNA hybridisation?

A

Radioactive or fluorescent marker

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76
Q

What does Southern blotting use to identify DNA sequences after gel electrophoresis?

A

DNA probes

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77
Q

How is Southern blotting carried out?

A

Transfer DNA fragments to nylon/nitrocellulose
Hybridise filter w/labelled gene probe
Detect hybridisation by exposing filter to X-Ray film

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78
Q

How are the DNA fragments from gel electrophoresis transferred in Southern blotting?

A

Alkaline solution
DNA –> ssDNA
Capillary action onto filter
Voltage applied causing DNA to move

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79
Q

Why use Southern blotting?

A 
Allows detection in v. small amounts of DNA
Investigate gene structure
Identify mutations in genetic tests
Gene expansions
Variation/genetic relationships
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80
Q

How would you use Southern blotting to test for SCD?

A

Use allele specific probes

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81
Q

How does the DNA examined in Southern blotting differ to that which is the end product of the preceding gel electrophoresis?

A

dsDNA after gel electrophoresis

ssDNA in Southern blotting

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82
Q

What do antibiotics that inhibit bacterial cell wall synthesis have in their molecular structure?

A

Contain beta-lactam ring

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83
Q

What is the function of glycopeptide transpeptidase?

A

Cleaves peptide bond b/w D-alanine residues for cross linking in cell walls

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84
Q

What can bacteria produce in order to be resistant to beta-lactams?

A

Beta-lactamase to break ring

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85
Q

How does mec-A gene expression allow for beta-lactam resistance?

A

Provides different, lower affinity penicillin binding protein so transpeptidase is unaffected

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86
Q

How can bacteria acquire resistance to beta-lactams via vertical transmission?

A

Mitosis

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87
Q

How can bacteria acquire resistance to beta-lactams via horizontal transmission?

A

Conjugation tube and resistant plasmid
Transformation
Transduction (bacteriophages)

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88
Q

How do beta-lactams have specificity?

A

Only peptidoglycan is not X-linked so only bacterial cell walls are affected

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89
Q

Give an example of a clinical use of narrow spectrum beta-lactams.

A

Antistaphylococcal penicillin

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90
Q

Give an example of a clinical use of broad spectrum beta-lactams.

A

Aminopenicillin

Natural penicillin

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91
Q

What is erythromycin an example of?

A

Antibiotic that inhibits bacterial protein synthesis

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92
Q

Why can erythromycin be used instead of penicillin in patients who are allergic to penicillin?

A

Spectrum is similar

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93
Q

What is the mechanism of action for antibiotics that inhibit bacterial protein synthesis?

A

Binds to large subunit so prevents translation by stopping tRNA moving along chain - no transfer from A to P

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94
Q

Does a usual dose of erythromycin kill bacteria?

A

Nope, prevents protein replication

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95
Q

How do bacteria adapt to become resistant to antibiotics that inhibit bacterial protein synthesis?

A

Methylated 50S subunit so drug cannot bind

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96
Q

How do bacteria acquire resistance to antibiotics that inhibit bacterial synthesis?

A

Random genetic mutation passed on by vertical transmission

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97
Q

How do antibiotics that inhibit protein synthesis have specificity?

A

Bind to 50S subunit which is specific to prokaryotic cells

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98
Q

What is the clinical use of antibiotics that inhibit protein synthesis?

A

Upper and lower RT infections
STDs
Off-label for gastric emptying

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99
Q

What mechanism of action do rifamycins use?

A

Inhibits bacterial transcription

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100
Q

How can antibiotics inhibit bacterial transcription?

A

Penetrate cell wall –> allosterically blocks beta-subunit of RNA polymerase –> elongation inhibited

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101
Q

Why are antibiotics that inhibit bacterial transcription broad spectrum?

A

Their RNA polymerase target is similar in lots of prokaryotes

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102
Q

How do bacteria become resistant to antibiotics that inhibit their transcription?

A

Mutations in beta-subunit so RNA polymerase cannot bind

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103
Q

How can bacteria have different levels of resistance to antibiotics that inhibit their transcription?

A

Different point mutations give different levels of resistance

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104
Q

How do bacteria acquire resistance to antibiotics that inhibit their transcription?

A

Spontaneous mutations
Naturally non-susceptible
Multi/cross resistance

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105
Q

What is multi/cross resistance?

A

If a bacterium has developed resistance to an antibiotic it is likely to be resistant to a similar antibiotic

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106
Q

How do antibiotics that inhibit bacterial transcription have specificity?

A

Mammalian cells have 5-subunit RNA polymerase complexes so it is not affected

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107
Q

What are clinical uses of antibiotics that inhibit bacterial transcription?

A

Readily absorbed in GI tract for TB, leprosy and other mycobacteria

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108
Q

What effect does rifamycin have on urine?

A

Colours it red

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109
Q

Give an example of an antifolate.

A

Methotrexate

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110
Q

Why mechanism of action does methotrexate use?

A

Competitively inhibits DHFR –> inhibits purine and pyrimidine biosynthesis –> no DNA, RNA or protein synthesis

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111
Q

What cellular effects do antifolates in chemotherapy cause?

A 
DNA, RNA and protein synthesis inhibited
Impaired cellular transport
Reduced polyglutamate formation in CSM
Increased drug efflux
Increased levels of gamma-glutamyl hydrolase
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112
Q

How can a cell be resistant to antifolates?

A

Inherent/primary/acquired drug resistance

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113
Q

How can a cell have an acquired resistance to antifolates?

A

Transformation via vertical transmission
Transduction
Conjugation

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114
Q

How does somatic evolution allow for acquisition of antifolate resistance?

A

Causes higher genomic instability

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115
Q

Do antifolates have specificity?

A

Nope

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116
Q

Why is methotrexate not specific?

A

Mammalian and bacterial cells have highly similar DHFRs

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117
Q

What can low doses of antifolates be used for clinically?

A

Autoimmune disease e.g. RA and uncontrollable psoriasis

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118
Q

As well as being a competitive inhibitor for DHFR, how else do antifolates inhibit cell division?

A

Cofactor to methyltransferases which inhibit cell division

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119
Q

What is the active form of dihydrofolate which is not seen in cells susceptible to anitfolates?

A

Tetrahydrofolate

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120
Q

What are ethical consideration with genome sequencing?

A

Who would be interested in the genome - insurance?
Can the knowledge help prevent illness later in life?
Does it open up areas for discrimination?
Does the scientist or the participant own the sequence?

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121
Q

What types of primer must you have for DNA hybridisation in PCR?

A

Forward and reverse

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122
Q

Do both forward and reverse primers act 5’ to 3’ in PCR?

A

Yes

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123
Q

What happens if there is a mismatch between the 5’ end and primer in PCR?

A

Not critical reduction in how complementary it is

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124
Q

What happens if there is a mismatch between the 3’ end and primer?

A

Elongation is prevented

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125
Q

What does Northern hybridisation analyse?

A

RNA

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126
Q

Why is a copy of mRNA made regardless of sequence in reverse transcriptase PCR?

A

All mRNA have a poly-A tail

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127
Q

How does the cDNA formed in reverse transcriptase differ from genomic DNA?

A

Has no introns

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128
Q

What is real time PCR?

A

Fluorescent PCR products show how much is made in real time

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129
Q

How does reverse transcriptase PCR analyse RNA?

A

Lots of template indicates high levels of mRNA expression

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130
Q

What does microarray analyse?

A

1000s of genes at once

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131
Q

What tail is seen on the cDNA strand formed in reverse transcriptase PCR?

A

Poly-T

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132
Q

If a gene is only expressed in healthy tissue how will it appear in microarray?

A

Green

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133
Q

How do genes unique to cancer tissue appear in microarray?

A

Red

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134
Q

What is used to fluorescently label the genes in microarray?

A

Reverse transcriptase labelling

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135
Q

How does the resultant microarray indicate the genes present in a tissue?

A

Red and green dots appear in proportion to how much each tissue type expresses

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136
Q

Describe the process of microarray analysis.

A 
Extract DNA
Label w/2 fluorochromes
Mix in equal quantities
Read red and green fluorescence
Work out red:green ratio and align to database
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137
Q

What does a green spot indicate in array comparative genome hybridisation?

A

Deletion

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138
Q

What does a red spot on array comparative genome hybridisation indicate?

A

Duplication

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139
Q

What is carried out after the first run through of array comparative genome hybridisation?

A

Dye swaps

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140
Q

Why use array technology?

A

Investigate 1000s of genes simultaneously
Investigate conditional gene expression
Investigate chromosome duplications/deletions

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141
Q

How many regions of DNA does DNA fingerprinting consider?

A

1

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142
Q

What shows copy number in DNA fingerprinting?

A

Mini satellites

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143
Q

What shows copy number variation in DNA profiling?

A

Small tandem repeats

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144
Q

Which gene technology does DNA profiling use?

A

PCR

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145
Q

Describe how karyotyping is carried out.

A

Arrest cells in mitotic metaphase
Isolate nuclei onto slide and stain chromosomes
Obtain pictures of chromosomes
Pair homologous chromosomes

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146
Q

How does karyotyping identify translocations, trisomies and monosomies?

A

Stain appears in places it isn’t expected

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147
Q

How is FISH carried out?

A

Prove DNA –> label w/fluorescent dye –> denature and hybridise

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148
Q

What is FISH?

A

Fluorescence in Situ Hybridisation

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149
Q

What indicates a difference in FISH analysis?

A

Absence so one of probe pair not seen

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150
Q

Why is FISH used?

A

Investigate chromosome number
Investigate chromosomes behaviour
Investigate chromosome structure

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151
Q

What aspects of chromosome structure can FISH analyse?

A

Translocations
Deletions
Duplications

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152
Q

What aspects of chromosome behaviour can be investigated by FISH?

A

Anaphase lag - fails to connect spindle/not included in reformed nucleus

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153
Q

What ethical considerations are there with using DNA analysis?

A

Abortion

Autosomal dominant with late onset: do older generations know/want to know they’re positive

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154
Q

Why are most mutations of the genome of little/no consequence?

A

Protein coding regions only make up 1-2% of all the DNA

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155
Q

Mutations at what location in the DNA are most likely to cause disease?

A

In or close to protein coding genes

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156
Q

What is the most common genetic mutation?

A

SNPs (snips) - single base substitutions

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157
Q

What base substitution makes up ~2/3 of SNPs?

A

C –> T

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158
Q

What is a transition base substitution?

A

Purine purine

Pyrimidine pyrimidine

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159
Q

What is a transversion single base substitution?

A

Pyrimidine purine

160
Q

What base change forms the basis of the vast majority of heritable diseases?

A

CG –> TA

161
Q

What is a silent genetic mutation?

A

Where there is no a.a. change

162
Q

What happens if there is a single base substitution in the splice site?

A

Disrupts RNA splicing

163
Q

What is a missense genetic mutation?

A

1 a.a. is substituted for another

164
Q

What usually causes a missense mutation?

A

Single base change

165
Q

Where do single base changes usually occur in the codon so that the substitution is silent?

A

3rd base

166
Q

What is a nonsense genetic mutation?

A

a.a. to stop codon

167
Q

What effects can a frameshift mutation have?

A

Reading frame altered

Premature translation stop

168
Q

What genetic mutations can cause a frameshift mutation?

A

Insertions
Deletions
Splice site mutations
Stop codon mutation

169
Q

What is conservative missense?

A

a.a. substituted with adjacent a.a. in the genetic code table which limit is the damage caused by mutation

170
Q

How can small insertions or deletions affect the reading frame in genetic expression?

A

Multiples of 3 maintain

Non-multiples of 3 cause frameshift and premature termination codons

171
Q

What are mRNAs with PTCs degraded by so little truncated or no protein is made?

A

Nonsense mediated decay

172
Q

What happens if there is a mutation in an intron splice site?

A

Intron not present in mRNA

Skip exon immediately adjacent to mutation

173
Q

What can occur during DNA replication to cause base changes?

A

Rare tautomer forms w/altered base-pairing

DNA strand slippage

174
Q

How can chemicals cause base changes?

A

Direct DNA base alteration

Disruption of DNA base stacking

175
Q

How can we be exposed to radiation which may cause base changes?

A

Exposure to UV light

Radioactive substances

176
Q

What briefly changes position and allows a brief change in base-pair method?

A

Proton

177
Q

What happens if the newly synthesised strand loops out due to imperfect base pairing during replication?

A

Addition of one nucleotide on the new strand

178
Q

What happens if the template strand loops out during replication?

A

Omission of one nucleotide on new strand

179
Q

What effect does nitrous acid have on nucleotide bases?

A

Replaces amino groups w/keto groups

180
Q

How are the C, A and G bases altered with exposure to nitrous acid?

A

C –> U
A –> H
G –> X

181
Q

What do the resultant U, A and H bases seen in nitrous acid exposure base pair with?

A

U w/A
H w/C
X w/C

182
Q

What does ethyl methane sulphate cause removal of so that 25% of base pairing is right?

A

Purine rings so apurinic sites can be paired w/any base during replication

183
Q

What type of molecule is identified in cooked meats and cigarette condensates which disrupts packaging of DNA bases and is a base stacking mutagen?

A

Heterocyclic aromatic amine

184
Q

How can a heterocyclic aromatic amine cause a single base deletion?

A

Forces bases further apart on DNA strand so DNA polymerase misreads

185
Q

Which cheap and effective DNA stain works in a similar way to the heterocyclic aromatic amine seen in cooked meats and cigarette condensates?

A

Ethidium bromide

186
Q

What is the effect of ionising radiation on interaction w/cellular molecules?

A

Produces ions

187
Q

What affect do UVA and B have on the skin?

A

Destroy vitamin A

188
Q

What affect do UVA, B and C have on the skin?

A

Damage collagen fibres

189
Q

What induces vitamin D in the skin?

A

UVB

190
Q

What action do UV light photons have on DNA?

A

Cause adjacent thymine bases to base pair with one another rather than across helix - thymine dimer formation

191
Q

How is thymine dimer formation usually resolved?

A

Spontaneously by photo-reactivation

192
Q

How are most errors in DNA corrected?

A

Proofreading as polymerase detects mis-paired 3’ base in new strand

193
Q

What are the two types of DNA repair?

A

Nucleotide mismatch

Excision

194
Q

Give a brief description of nucleotide mismatch repair.

A

Reduces error rate further still after replication
Enzymes detect mismatched bases and replace them
Patch of DNA sequence replaced

195
Q

What types of damaged bases can be accumulated by DNA in excision repair?

A

Oxidised bases
Alkylated
Uracil
De-animated

196
Q

What is short patch repair?

A

Single nucleotide change in excision repair

197
Q

What is long patch repair?

A

Multiple nucleotide change in excision repair

198
Q

Which human genes encode mismatch repair enzymes?

A

MLH1
MSH2
MSH6

199
Q

What are commonly mutated in cases of non-hereditary non-polyposis colorectal carcinoma?

A

Genes encoding mismatch repair enzymes

200
Q

What do all cancer cells exhibit?

A 
Chromosomal instability
Microsatellite instability (unexpected expansion and contraction)
201
Q

The probability of picking up 6 successive mutations necessary to cause tumour is very low so why do we see cancer?

A

Early mutations affect functions which raise the probability of successive mutations

202
Q

What are BRCA1 and 2 involved in?

A

Detecting DNA damage and signalling cell-cycle checkpoints

203
Q

What do sporadic breast tumours rarely have which is commonly seen in inherited breast tumours?

A

BRCA1 or BRCA2 mutations

204
Q

How common are affected males in families affected by breast cancer?

A

Fairly

205
Q

What are oncogenes?

A

Specific retro-viruses assoc. w/cancers

206
Q

What do retrovirus studies show about oncogenes?

A

Contain genes that are able to transform cells to cancerous phenotype

207
Q

What are human genes that exhibit sequence similarity to viral oncogenes called?

A

Porto-oncogenes

208
Q

What functions do proto-oncogenes performs?

A

Range of cell cycle

209
Q

What change can activate proto-oncogenes into dominantly acting cancer causing oncogenes?

A

Key a.a. substitutions

210
Q

What mutations do inherited cancer genes tend to harbour?

A

Recessive

211
Q

What type of inheritance does development of cancer display?

A

Dominant

212
Q

What does initiation of a tumour require at the allele level?

A

Mutation to both copies or deletion of functional copy

213
Q

Compare the progression of inherited and sporadic cases of cancer.

A

Inherited: all cells carry one mutation –> 2nd mutation –> tumour founder cells w/ 2 mutations
Sporadic: somatic mutation in one cell –> 2nd mutation –> tumour

214
Q

Which type of cancer is more rare, hereditary or sporadic?

A

Sporadic

215
Q

How can homozygous its arise?

A

Loss of wild-type chromosome
Deletion
Point mutation
Mitotic recombination

216
Q

What is needed to b e able to advise relatives following a positive sweat test indicating CF?

A

Molecular test

217
Q

Is it possible to be a compound heterozygote for two different genetic mutations?

A

Yes e.g. 2 CTFR mutations in CF

218
Q

What is the most common genetic mutation that causes CF?

A

Delta F508 3 base pair deletion causing deletion of phenylalanine

219
Q

What method of genetic analysis will give a mix of normal and mutated sequences following PCR if the individual is heterozygous for a mutation?

A

Single-strand conformation polymorphism

220
Q

What change can be detected by silver staining in single-strand conformation polymorphism?

A

Single base mutation

221
Q

What are the three methods of obtaining foetal DNA?

A

Amniocentesis
Mother’s blood
Chorion villus biopsy

222
Q

When is amniocentesis carried out?

A

15-20 weeks

223
Q

What type of cells are sampled by amniocentesis and can be cultured for 2 weeks?

A

Non-dividing

224
Q

Which method of obtaining foetal DNA carried the highest miscarriage risk?

A

Chorion villus biopsy

225
Q

How is chorion villus biopsy performed?

A

Trans-cervical

Trans-abdominal

226
Q

When is chorion villus biopsy performed?

A

10-13 weeks

227
Q

What must be separated from maternal tissue in chorion villus biopsy?

A

Foetal villi

228
Q

What does multiplex ligation-dependent probe amplification (MLPA) principle perform?

A

Exon count

229
Q

How does MLPA principle work?

A

It’s ability to ligate 2 single strand together only if target DNA is still present in sample

230
Q

Why can PCR not be used for some inherited disorders such as osteogenesis imperfecta or Duchenne muscular dystrophy?

A

Arise through whole exon duplications or deletions so PCR gets product from remaining whole exons

231
Q

What probes are used in MLPA principle?

A

Two adjacent for forward and reverse primers

One has a ‘stuffer’ region of any length and no relation to target sequence

232
Q

What is the purpose of the ‘stuffer’ region in either the forward or reverse primer used in MLPA principle?

A

Varies fragment length for analysis by electrophoresis

233
Q

How does the electrophoresis graph for MLPA principle show deletions in one gene?

A

Peaks half height of those in control

234
Q

How are the highest order structures of DNA stabilised?

A

By hanging loops of DNA onto protein scaffold

235
Q

What is epigenetic modification?

A

Switching of chromatin b/w active and inactive forms

236
Q

What groups indicate chromatin is active?

A

Acetyl

237
Q

What groups indicate chromatin is inactive?

A

Methyl groups

238
Q

How can cells be accumulated at metaphase?

A

Spindle inhibitor
Hypotonic solution
Fixative

239
Q

What types of growth can be used to culture cells in vitro for karyotyping?

A

In suspension

On substrate

240
Q

What is used to describe abnormalities in karyotyping?

A

International System for Cytogenic Nomenclature (ISCN) 2013

241
Q

What tissues can be used to give specimens for karyotyping?

A 
Bone marrow
Blood (T-lymph)
Amniotic fluid
CVS
Solid tissue
242
Q

Why is nothing expressed on the short arm of an acrocentric chromosome?

A

No euchromatin present

243
Q

How are chromosomes assigned to groups A-G?

A

According to size and shape

244
Q

What chromosomes are in the D and G karyotype groups?

A

Acrocentric w/satellites on their p-arms

245
Q

How does the size of chromosome 22 relate to 21?

A

Bigger

246
Q

What does solid staining show in karyotyping?

A

Shape and size of chromosomes

247
Q

What is used in G banding of chromosomes to identify gene rich and gene poor areas for karyotyping?

A

Trypsin

248
Q

What does a karyotype report of 47,XX,+21 indicate?

A

Female w/trisomy 21

249
Q

What does a karyotype report of 46,XY,inv(7)(p11.2q11.23) indicate?

A

Make w/chromosome 7 inversion

250
Q

What would the karyotype report of a girl with a chromosome count of 46, derivative 20 from translocation 2 and 20 which is maternally inherited look like?

A

46,XX,der(20)t(2;20)(q.27.3;11.2)mat

251
Q

Why carry out cytogenetic analysis?

A

Prenatal diagnosis
Assess future reproductive risks
Better clinical management
Accurate diagnosis/prognosis of clinical problems

252
Q

What constitutional abnormalities indicate referral for cytogenetic analysis?

A 
Prenatal diagnosis
Birth defects
Abnormal sexual development
Recurrent foetal loss
Infertility
253
Q

What acquired abnormalities indicate referral for cytogenetic analysis?

A

Leukaemias

Solid tumours

254
Q

What is the main method of prenatal diagnosis in the first trimester of pregnancy?

A

Biochemistry and ultrasound looking at nuchal translucency

255
Q

Give four broad types of birth defect.

A

Dysmorphism
Congenital malformations
Metal retardation
Developmental delay

256
Q

How is trisomy 21 better known?

A

Down’s syndrome

257
Q

What genetic defect causes Williams syndrome?

A

Deletion 7q11.23

258
Q

What is the effect of the 22q11.2 microdeletion seen in Di George syndrome?

A

Significant heart defects

259
Q

What is aneuploidy?

A

Loss or gain of whole chromosomes due to errors of cell division in meiosis

260
Q

Which three trisomies are compatible with life?

A 
Down syndrome (+21)
Patau syndrome (+13)
Edwards syndrome (+18)
261
Q

What is the only viable fully monosomy syndrome?

A

Turner

262
Q

What does Turner syndrome cause?

A

Inactivated X

263
Q

What error occurs in the meiotic cell divisions during gamete formation?

A

Non-disjunction

264
Q

What results if there is non-disjunction in mitotic cell division?

A

Mosaicism

265
Q

What is mosaicism?

A

More than one cell population seen in an individual

266
Q

What is polyploidy?

A

Gain of a whole haploid set of chromosomes

267
Q

What is the most common cause of polyploidy?

A

Polyspermy

268
Q

How common is triploidy?

A

Relatively, occurs in 2-3% of all pregnancies

269
Q

Which polyploidy is often found as a cultural artefact on prenatal diagnosis?

A

Tetraploidy

270
Q

Is diploid/triploid mosaicism seen in live births?

A

Yep

271
Q

What is anaphase lag?

A

When chromosomes are left behind at cell division and are therefore not present in diagnosed cells

272
Q

What happens in cell division to cause anaphase lag?

A

Defects in spindle

Defects in attachment to chromosomes

273
Q

What can result from fertilisation by a normal gamete of a gamete which has undergone non-disjunction in meiosis I?

A

Trisomy
Monosomy
OK cell

274
Q

What causes trisomy 18?

A

Maternal meiosis II error

275
Q

What visible features indicate trisomy 18?

A 
Rocker bottom foot
Overlapping fingers
Low-set ears
Prominent occiput
Small lower jaw
276
Q

What is the modal lifespan of a neonate with trisomy 18?

A

5-15 days

277
Q

What visible effects may be seen in trisomy 21?

A

Hypotonia
Characteristic facial features
Intellectual disability
Heart defects

278
Q

What diseases are associated with trisomy 21?

A

Alzheimer’s

Leukaemia

279
Q

What effects can be seen in trisomy 13?

A

Multiple congenital abnormalities
Polydactyly
Single lobed brain

280
Q

What happens to the majority of neonates with trisomy 13?

A

Die in neonatal period

281
Q

What characterises Turner Syndrome?

A 
Mild learning difficulties
Heart defects
Neck webbing
Infertility
Hypotonia 
Short stature
282
Q

What do phenotypic differences depend on in Turner syndrome?

A

Parental origin of X chromosome

283
Q

What determines whether mosaicism occurs throughout the body or in specific tissues?

A

Time of mitotic disjunction

284
Q

When would mitotic disjunction not cause mosaicism?

A

If it occurs after first zygotic division

285
Q

Which cell line is usually lost when there is mitotic non-disjunction after the first zygotic division?

A

Monosomy

286
Q

How is the trisomy conceptus created by mitotic non-disjunction after the first zygotic division rescued to give mosaicism?

A

Anaphase lag

287
Q

When will the monosomy cell line not be lost in mitotic non-disjunction after the first zygotic disjunction?

A

If it involves X

288
Q

What is uniparental disomy?

A

Presence of homologous chromosomes from one parent

289
Q

What is heterodisomy?

A

Meiosis I error causing 2 homologous chromosomes from one parent

290
Q

What is isodisomy?

A

Error in meiosis II causing 2 identical chromosomes from one parent

291
Q

What is segmental uniparental disomy?

A

When only part of a chromosome is involved

292
Q

Name two conditions which are uniparental disomy involving chromosome 15.

A

Prader-Willi

Angelman syndrome

293
Q

Why do imprinted chromosomes show differential expression of specific genes in uniparental disomy?

A

Depends on parental origin

294
Q

What can cause uniparental disomy?

A 
Gamete complementation
Mitotic error
Trisomy rescue
Monosomy rescue
(2 separate must happen)
295
Q

What are the 8 cytogenic structural abnormalities?

A 
Translocations
Inversions 
Deletions
Duplications
Insertions
Rings
Marker chromosomes
Isochromsomes
296
Q

What are reciprocal translocations caused by?

A

Two break rearrangements

297
Q

How do balanced reciprocal translocations compare to unbalanced?

A

Balanced have all genetic material present just rearranged –> asymptomatic
Unbalanced will have abnormal phenotype dependent on the regions of trisomy and monosomy

298
Q

What happens to create a normal/carrier phenotype in meiotic disjunction once the translocation has formed a quadrivalent?

A

Alternate chromosomes segregate together

299
Q

What happens after the quadrivalent has been formed in meiotic disjunction to create an abnormal phenotype that will be full term?

A

Non-homologous centromeres segregate together

300
Q

What happens in meiotic disjunction after the quadrivalent has been formed to create a massive degree of imbalance?

A

Homologous centromeres segregate together

301
Q

What type of chromosomes fuse together in Robertsonian translocations?

A

Acrocentric

302
Q

How does the chromosome count differ in balanced and unbalanced Robertsonian translocations?

A

45 in balanced

46 in unbalanced

303
Q

What is there a risk of in Robertsonian translocation?

A

Aneuploidy

304
Q

Why can homologous carriers of a Robertsonian translocation not have a normal pregnancy?

A

Only have Robertsonian gametes as empty gametes are not viable

305
Q

How do deletions arise?

A

Uneven pairing and recombination during meiosis

306
Q

What is the difference between a terminal and interstitial deletion?

A

Terminal - end of arm

Interstitial - middle of arms

307
Q

How do deletions affect karyotype?

A

Cause unbalanced

308
Q

What is needed to see micro deletions that can’t be seen by G-banding?

A

FISH

309
Q

What is prenatal aneuploidy screening?

A

Interphase analysis used for prenatal diagnosis of common aneuploidies

310
Q

What can be used with the FISH techniques to allow 2 analysts to blindly score 30 cells to look for abnormality?

A

Vysis aneuvysion probes

311
Q

What method of interphase analysis looks for different types of abnormalities such as translocations, gene rearrangements or amplifications?

A

Leukaemia-FISH

312
Q

What does microarray examine?

A

Whole genome at high resolution looking for copy number changes

313
Q

What does excess red indicate in comparative genomic hybridisation slide scanning?

A

More reference DNA and deletion of test DNA

314
Q

What does excess green indicate in comparative genomic hybridisation slide scanning?

A

More test DNA and duplication of test DNA

315
Q

Why are copy arrangements visible but balance not in microarray methodology?

A

Uses ratios of test and reference DNA

316
Q

What are the advantages of comparative genomic hybridisation slide scanning?

A 
Examines genome at high resolution
Targeted against known genetic conditions
Can be automated
Detailed info on genes
Better phenotype/genotype correlation
317
Q

What are the disadvantages of comparative genomic hybridisation slide scanning?

A

More expensive than karyotyping
Doesn’t detect balanced arrangements
Mosaicism may be missed

318
Q

What is non-invasive prenatal testing?

A

Analysis of cell free foetal DNA in maternal plasma at 9 weeks gestation

319
Q

Why is non-invasive prenatal testing tench only challenging?

A

DNA deteriorates rapidly

320
Q

What is non-invasive prenatal testing already approved for?

A

Congenital adrenal hyperplasia
X linked disorders (not haemophilia)
Achondroplasia
Thenatophoric dysplasia

321
Q

How is next generation sequencing carried out?

A

Sequence fragments of gDNA in parallel and realign to reveal entire reference genome

322
Q

What is the problem with next generation sequencing?

A

Massive amounts of data are hard to store

323
Q

What are the benefits of next generation sequencing?

A

Reduced cost and time - technology is quick but analysis is not

324
Q

What is whole exome sequencing?

A

Targeted sequencing of all exons

325
Q

What are the benefits of whole exome sequencing?

A

Reduced data in comparison to whole genome analysis
Easier to interpret
Has given rise to many reports of clinically significant de novo mutations

326
Q

How many pairs of cranial nerves are there?

A

12

327
Q

How many segmental/spinal nerves are there?

A

31 pairs

328
Q

What make up nerves?

A

90% glia

10% neurones

329
Q

What is the function of glia?

A

Create environment in which neurones can survive

330
Q

When are micro glia seen?

A

Inflammatory insult to CNS

331
Q

What is the function of microglia?

A

Act as phagocytic immune cells in the simple immune system of the CNS

332
Q

Which cells are macroglia?

A 
Astrocytes
Oligodendrocytes
Schwann cells
Ependyma
Satellite cells
333
Q

What is the function of astrocytes?

A 
Give brain and spinal cord shape
Acts as phagocytes
Form blood-brain barrier
Glucose --> lactate for neuronal nourishment
Support cellular matrix of NS
334
Q

What is the function of oligodendrocytes?

A

Myelinated up to 250 CNS axons at a time

335
Q

What is the function of Schwann cells?

A

Myelinated single PNS axons

336
Q

What is the function of ependyma?

A

Line ventricles and central canal of spinal cord for circulation of CSF

337
Q

What is the function of satellite cells in the PNS?

A

Physically support neurones

338
Q

What is the structure of the cell body of a neurone?

A 
4-120 micrometers
Various shapes
Contains centrally positioned nucleus and nucleolus
Missouri substance
Some have appendages called dendrites
339
Q

What is Nissl substance?

A

ER and Golgi apparatus

340
Q

How can a dendrite be identified if it is present on a cell body?

A

Widest part of cell

341
Q

How does myelination of axons vary?

A

Thin are not
Thick are heavily
Level varies b/w neuronal types

342
Q

How can conduction in an axon be expressed?

A

CV

6FD where F = level of atonal myelination and D = diameter

343
Q

Where is the axon hillock found in a neurone if present?

A

B/w axon and cell body

344
Q

What forms the grey matter of the nervous system?

A

Neuronal cell bodies

345
Q

What are collections of cell bodies known as in the CNS and PNS?

A 
CNS = grey matter
PNS = ganglia
346
Q

How does a Schwann cell myelinated an axon?

A

Wraps itself round

347
Q

What diseases can demyelination axons?

A

Multiple sclerosis
Guillaine-Barre
Diabetes

348
Q

Why are beta-lactams considered suicide inhibitors?

A

Undergo partial reaction to form irreversible inhibitor in glycopeptide transpeptidase active site

349
Q

At what cross-sectional diameter do axons conduct faster if they are unmyelinated?

A
350
Q

What forms white matter in the CNS?

A

Myelinated neuronal axons

351
Q

What is the epineurium?

A

Ensheaths entire nerve

Interfacial binds attach adjacent fascicles

352
Q

What is the perineurium?

A

Ensheaths a nerve fascicle

353
Q

What is the endoneurium?

A

Ensheaths a single cell axon

354
Q

What happens to the axon when an axon is severed?

A

Compression causes nerve to split
Proximal segment seals to prevent leakage of cell contents
Nerve stump formed
Distal segment cut off from nutritional support and dies
Wallerian degeneration

355
Q

What happens in Wallerian degeneration?

A

Degradation of myelin sheath
Invasion by macrophages
Neurolemma remains and can reinnervate tissue if Schwann cells can reach

356
Q

What happens to the cell body when an axon is severed?

A

Puffs up with increased contents
Nucleus displaced to periphery
Chromatolysis

357
Q

What is an afferent neurone?

A

Neurone that carries signal from periphery to CNS

358
Q

What is an efferent neurone?

A

Neurone that carries signals from brain/spinal cord to periphery

359
Q

What forms the CNS?

A

Brain and spinal cord

360
Q

What is the CNS characterised by?

A

Protection of the cranium and vertebral column, suspended in CSF

361
Q

What is the CNS responsible for?

A

Sophisticated functions

362
Q

Where do segmental nerves which are attached to the spine go?

A

To PNS

363
Q

What are collections of neuronal cell bodies and axons called in the CNS?

A 
Bodies = nuclei
Axons = fibre tracts
364
Q

What are the constituents of the PNS?

A 
Axons of cranial nerves
Axons of spinal nerves
Ganglia
Nerve plexuses
Enteric nervous supply
365
Q

What does the PNS connect?

A

CNS target organs

366
Q

What are collections of neuronal cell bodies and axons called in the PNS?

A

Cell bodies = ganglia

Axons = nerves

367
Q

Explain the appearance of the spinal cord in cross section.

A

Grey matter centrally w/butterfly shape

White matter peripherally fully surrounding grey matter

368
Q

Are the CNS and PNS independent?

A

No, neurone can be in both at the same time

369
Q

How is the efferent somatic nervous system laid out?

A

1 spinal/cranial nerpurone carries output and terminates directly on effector organ

370
Q

How does the somatic nervous system progress during childhood?

A

Efferents underdeveloped at birth but are fully developed by puberty

371
Q

What type of control is the somatic nervous system under?

A

Voluntary

372
Q

What is the function of the autonomic nervous system?

A

Sub serves fundamental life functions incl. homeostasis

373
Q

What is the ANS activated?

A

In utero w/organogenesis

374
Q

How is the ANS controlled?

A

Not voluntarily

Change continuous output in two opposing systems

375
Q

What are the effector organs of the ANS?

A

Viscera
Smooth muscle
Secretory glands

376
Q

Where are the cell bodies of sympathetic nerve fibres located in the spine?

A

Thoraco-lumbar

T1-12 and L1-2

377
Q

What do axon lengths in the ANS depend on?

A

Which division they belong to

378
Q

Why is there lots of flexibility in the ANS?

A

Always 2 neurones, one w/cell body in CNS and one w/cell body in PNS

379
Q

What are White Rami communicates?

A

Neurones w/cell body in CNS

380
Q

What are Grey Rami communicates?

A

Neurones w/cell body in PNS

381
Q

What are most organs innervated by?

A

ANS

382
Q

Describe the ANS innervation of most organs?

A

Dual SNS and PNS which are mostly reciprocal so the balance determines the output

383
Q

Whoa receives sympathetic drive only?

A

Sweat glands

384
Q

What happens to the brain when there is over-activity of the PNS?

A

Dilates systemic blood vessels leading to shortage of substrates to brain

385
Q

What happens to the body if there is over-activity of the SNS?

A

Constriction of systemic blood vessels leading to shortage of substrate to the tissues

386
Q

What are all pre-ganglionic neurones?

A

Cholinergic

387
Q

Where are the pre-ganglionic neurones in the SNS located?

A

Spinal cord

388
Q

What do sympathetic post-ganglionic neurones express?

A

Nictoinic receptors

389
Q

What do the effector organs of the SNS express?

A

Variety of alpha and beta receptors

390
Q

What are the three modes of termination of signals in the SNS?

A

Synapse in chain at level of origin (paravertebral)
Synapse at different level up or down chain
Use specialised preganglionic nerves to not synapse in paravertebral chain

391
Q

Why are preganglionic neurones in the SNS short?

A

Majority of efferents synapse immediately after exiting the spinal cord

392
Q

Which receptors can exercise presynaptic inhibition in the SNS?

A

Alpha-1 + 2

Beta-1 + 2

393
Q

What do the long postganglionic neurones of the SNS secrete?

A

Noradrenaline/adrenaline

394
Q

Describe the neurones of the PNS.

A

Preganglionic: long and cholinergic
Postganglionic: short, in effector organ walls, cholinergic and express nitcotinic receptors

395
Q

What do effector organs in the PNS express?

A

Muscarinic receptors

396
Q

Which effector organ in the PNS behaves as a ganglion cell w/nitcotinic receptors?

A

Adrenal medulla

397
Q

Which effector organs are exceptions in the SNS?

A

Sweat and ejaculatory mechanisms which are cholinergic

Semester 1 (7 decks)

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