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Z OLD Molecules, Genes and Disease > Molecular Techniques and Diagnosis > Flashcards

Molecular Techniques and Diagnosis Flashcards

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1
Q

What produces endonucleases?

A

Bacteria

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2
Q

What do endonucleases do?

A

Recognition and degradation of foreign DNA

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3
Q

What are specific endonucleases also known as?

A

Restriction enzymes

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4
Q

What do specific endonucleases do?

A

Cleave phosphodiester bonds inside DNA

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5
Q

What is the specific place recognised and cut by a restriction enzyme called?

A

Restriction site

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6
Q

What is usually formed on cutting with a restriction enzyme?

A
  • (Mostly) palindromes of 4,5,6,8 bp

- (Mostly) staggered cuts, leaving ends

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7
Q

What is special about palindromes?

A

They read the same in the forward and backwards direction

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8
Q

What happens if a cut leaves sticky ends?

A

If they come back together, they will be held together by hydrogen bonds

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9
Q

What can be produced in contrast to sticky ends?

A

Blunt ends

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10
Q

How is DNA protected?

A

Methlation

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11
Q

What happens in methylation?

A

Methyl groups are added on my some enzymes

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12
Q

What can restriction enzymes be used to do?

A

Isolate DNA fragments

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13
Q

What is the purpose of DNA gel electrophoresis?

A

Separates DNA fragments produced

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14
Q

What happens in DNA gel electrophoresis?

A
  • DNA samples loaded in wells
  • Moves along agarose
  • DNA fragments move from -ve electrode to +ve electrode
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15
Q

What is the purpose of the agarose in DNA gel electrophoresis?

A

Acts as molecular sieve

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16
Q

Why do DNA fragments move from the -ve to the +ve electrode?

A

As DNA is -vely charged

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17
Q

What fragments move furthest in DNA gel electrophoresis?

A

The smallest

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18
Q

What are DNA fragments separated on the basis of in DNA gel electrophoresis?

A

NAME?

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19
Q

What is required for gel electrophoresis?

A
  • Gel
  • Buffer
  • Power supply
  • Stain/detection
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20
Q

What is the gel in gel electrophoresis?

A

A matrix that allows for separation of DNA fragments

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21
Q

What is the purpose of the buffer in gel electrophoresis?

A

Allows charge on DNA samples across gel

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22
Q

What is the buffer in gel electrophoresis?

A

A liquid containing salt

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23
Q

What does the power supply in gel electrophoresis do?

A

Generates charge difference across the gel

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24
Q

What is the purpose of the stain in gel electrophoresis?

A

To identify the presence of the separated DNA

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25
Q

What is often the stain in gel electrophoresis?

A

A molecule that sits between bases of DNA that fluoresces when light shines

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26
Q

What are the uses of restriction analysis?

A
  • To investigate the size of DNA fragments
  • To investigate mutations
  • To investigate DNA variation
  • To clone DNA
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27
Q

What is DNA ligase?

A

A ‘molecular glue’

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28
Q

What does DNA ligase do?

A

Makes new phosphodiester bonds

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29
Q

What is DNA ligase used for?

A

To join DNA of interest to DNA of vector

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30
Q

How can DNA ligase be used to join DNA of interest to DNA of vector?

A

DNA fragments cut with the same restriction endonuclease has the same overhanging fragments, and so can be mixed with DNA ligase

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31
Q

How can the same effect as cutting two pieces of DNA with the same restriction endonucleases be achieved?

A

By using different restriction enzymes giving the same complementary sequences

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32
Q

What are plasmids?

A
  • Small circular dsDNA

- ‘Mini-chromosomes’

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33
Q

Where are plasmids found?

A

In bacteria

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34
Q

What do plasmids do?

A

NAME?

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35
Q

What do plasmids have the ability to do?

A

Transfer to other bacteria

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36
Q

What do plasmids often carry?

A

Antibiotic resistance genes

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37
Q

What happens in the process of gene cloning?

A
  • DNA of interest is joined with a plasmid vector, forming a recombinant DNA molecule
  • Recombinant DNA molecule is introduced into bacterium, where replication will take place
  • Cells containing recombinant DNA are selected, identified and isolated
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38
Q

What is the process of introducing the recombinant DNA molecule into the bacterium called?

A

Transformation

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39
Q

Why clone human genes?

A
  • To make useful proteins
  • To find out what genes do
  • Genetic screening
  • Gene therapy
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40
Q

How is mammalian proinsulin mRNA obtained?

A

From the pancreas

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41
Q

How is proinsulin cDNA produced?

A

From mammalian proinsulin, by action of reverse transcriptase

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42
Q

How is cDNA cloned?

A
  • cDNA joined to plasmid, forming recombinant plasmid

- Recombinant plasmid infects E.coli, producing transformed bacteria

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43
Q

How is the PCR carried out?

A
  • DNA molecule heated to 95º c , denaturing it
  • Primers added
  • DNA cooled to RT, so renatures with primers attached
  • Add DNA polymerase
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44
Q

Why does heating the DNA molecule denature it?

A

The hydrogen bonds holding it together break

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45
Q

What do the primers in PCR do?

A

Define the region to be amplified

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46
Q

How does DNA polymerase extend the DNA molecule?

A

5’ to 3’, starting at primers

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47
Q

Why is thermostable DNA polymerase (Taq) used in PCR?

A

Because it means we don’t have to add new enzyme every time

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48
Q

Why is a pair of primers used in PCR?

A

The forward and reverse

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49
Q

What do the primers in PCR do?

A

Uniquely define the region to be copied

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50
Q

What does the temperature achieve in PCR?

A

Cycles of denaturing, annealing, and polymerising

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51
Q

What is used to cycle temperatures in PCR?

A

Thermocycler

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52
Q

What does repeated PCR result in?

A

Exponential increase in DNA

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53
Q

Why use PCR?

A
  • To amplify a specific DNA fragment
  • To investigate single base mutations
  • To investigate small deletions or insertions
  • To investigate variation and genetic relationships
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54
Q

What happens to proteins if placed in electric field?

A

They will move towards the anode or cathode

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55
Q

Why will proteins move towards anode or cathode in electric field?

A

They are charged molecules

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56
Q

What are proteins separated on the basis of?

A

NAME?

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57
Q

What are the requirements for gel electrophoresis?

A

The same as for DNA

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58
Q

What is the process for carrying out protein gel electrophoresis?

A

NAME?

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59
Q

In protein gel electrophoresis, what charge goes on what end?

A

Doesn’t matter, because proteins have different charge if looking at native proteins

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60
Q

What does protein gel electrophoresis produce?

A

Bands

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61
Q

What do darkly stained bands in protein gel electrophoresis indicate?

A

More protein present

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62
Q

What does SDS-PAGE separate proteins on the basis of?

A

Size

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63
Q

What does SDS-PAGE rely on using?

A

Unfolded proteins

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64
Q

Why does SDS-PAGE rely on using unfolded proteins?

A

Because the shape of protein affects how it moves in a gel, and it has an intrinsic charge

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65
Q

What is used to denature proteins in SDS-PAGE?

A
  • ß-Me

- SDS

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66
Q

What does ß-Me do?

A

Breaks disulphide bonds

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67
Q

What is the purpose of the addition of ß-Me and SDS in SDS-PAGE?

A

It removes the tertiary and secondary structure, to give a linear polypeptide change

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68
Q

What does SDS do?

A

Binds in a fixed way to amino acid sequence

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69
Q

What has happened after the addition of the agents in SDS-PAGE?

A

It now has a uniform negative charge, so can be separated by gel electrophoresis

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70
Q

What does SDS-PAGE allow for?

A

Analysis of proteins

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71
Q

What can be do if we know the size of a particular band produced by SDS-PAGE?

A

Go looking for it in a mixture of proteins

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72
Q

What can be looked for using SDS-PAGE?

A
  • Protein expression
  • Levels of protein
  • Protein presence
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73
Q

What basis are proteins separated on in isoelectric focusing (IEF)?

A

Purely charge

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74
Q

Describe the method for IEF

A
  • A stable pH gradient is established in the gel after application of an electric field
  • Protein solution added, and electric field reapplied
  • After staining, proteins shown to be distributed along pH gradient according to their pI values
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75
Q

Why does IEF work?

A

Because proteins migrate until they reach a pH equal to their pI. There is no net charge at pI, so they stop migrating

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76
Q

What does 2D-PAGE make use of?

A

IEF, followed by SDS-PAGE

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77
Q

What does 2D-PAGE separate based on?

A

Size and charge

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78
Q

What does 2D-PAGE allow for?

A

The separation of complex mixture of proteins

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79
Q

Where is 2D-PAGE important?

A

For diagnosing disease states in different tissues

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80
Q

How can 2D-PAGE be used to diagnose?

A

Can look at changes by comparing normal conditions to disease conditions

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81
Q

What is protein identification also known as?

A

Proteomics

82
Q

How can proteins be identified?

A

Can take proteins from gel, and identify using mass spectrometry, using a database

83
Q

Describe the method for proteomics

A
  • Digest protein with trypsin
  • Perform mass spectrometry
  • Generate list of peptide sizes
  • Uses database of predicted peptide sizes for known proteins to identify protein
84
Q

How can specific cleavage of proteins be carried out?

A
  • Enzymatic cleavage

- Chemical cleavage

85
Q

What happens in enzymatic cleavage?

A

Enzymes break peptide bonds in particular protein sequences

86
Q

Give 2 examples of enzymes used in enzymatic cleavage

A
  • Trypsin

- Staphylococcal protease

87
Q

Give 2 examples of chemicals used in chemical cleavage?

A
  • Cyanogen bromide

- Hydroxylamine

88
Q

What is proteomics?

A

Analysis of all proteins expressed from a genome

89
Q

What is molecular diagnosis?

A

Analysis of a single purified protein

90
Q

What do antibodies do?

A

Bind to a specific protein targets called antigens

91
Q

What do antibodies recognise?

A

Epitopes

92
Q

What is an epitope?

A

A few amino acids on a protein

93
Q

What produces polyclonal antibodies?

A

Many B lymphocytes

94
Q

What are polyclonal antibodies?

A

Multiple different antibodies

95
Q

What are polyclonal antibodies specific to?

A

1 antigen

96
Q

How many epitopes do polyclonal antibodies have?

A

Multiple

97
Q

What must be done to obtain polyclonal antibodies?

A

You inject with the antigen 3-4 times at two week intervals, and then bleed. You can then get isolated antibodies from extracted blood

98
Q

What produces monoclonal antibodies?

A

1 B lymphocyte

99
Q

What are monoclonal antibodies?

A

1 identical antibody

100
Q

How many epitopes do monoclonal antibodies have?

A

1

101
Q

How to you obtain monoclonal antibodies?

A
  • Inject with antigen
  • Obtain spleen cells
  • Mix spleen cells with myeloma cells. Culture the myeloma line, and then fuse in polyethylene glycol
  • Select and grow hybrid cells
  • Freeze and thaw the cells as required
  • Can inject into mice to induce tumours, extracting the antibody this way, or grow the hybrid cells in mass culture and then extract the antibodies they produce
102
Q

What is the purpose of fusing the spleen cells with myeloma cells?

A

Gives immortal cell life, as they just keep dividing

103
Q

What hybrid cells do you select for when producing monoclonal antibodies?

A

The ones making antibodies of desired specificity

104
Q

What does the western blotting process involve?

A

Detection of proteins on SDS-PAGE gel by antibodies

105
Q

Describe the process of western blotting

A

NAME?

106
Q

What solid matrix is the SDS-PAGE usually transferred onto?

A

Usually nitrocellulose

107
Q

What does the transference of the SDS-PAGE onto a more solid matrix produce?

A

A replica of gel electrophoretogram that is a more permanent record

108
Q

What is important of the antibody used against the protein of interest?

A

It must be specific to the protein of interest

109
Q

Is the protein of interest in western blotting folded or unfolded?

A

Doesn’t mattter

110
Q

What must be true of the enzyme-linked second antibody?

A

It must have some sort of marker

111
Q

What is the purpose of the enzyme-linked second antibody?

A

Detects the binding of the first antibody

112
Q

What is produced from western blotting?

A

An immunoblot

113
Q

How is an immunoblot interpreted?

A

By the band, which appears in a specific place

114
Q

What can an immunoblot be used to determine?

A
  • The expression of protein

- How much protein’s being produced

115
Q

What can ELISA measure?

A

The concentration of a particular protein in solution

116
Q

What can ELISA be used to work out?

A

How much antibody binds at a given antigen concentration

117
Q

How can ELISA be used to work out how much antigen binds at a given antigen concentration?

A

By building up a standard curve

118
Q

Describe the process of ELISA?

A

NAME?

119
Q

What is the significance in the rate of colour formation in ELISA?

A

It is proportional to the amount of specific antibody

120
Q

How does radioimmunoassay work?

A

In the same way as ELISA, but uses radio labelled primary antibodies

121
Q

What are enzyme assays used to do?

A

Work out normal activity

122
Q

What can enzyme assays be used to do?

A

Compare against abnormal cases

123
Q

What do enzyme assays measure?

A

The amount of product at any given time

124
Q

Are enzyme assays continuous or discontinuous?

A

Can be either

125
Q

Give 2 examples of continuous assays

A
  • Spectrophotometry

- Chemiluminescence

126
Q

Give 2 examples of discontinuous assays?

A
  • Radioactivity

- Chromatography

127
Q

Where may in be clinically important to measure enzymes?

A

NAME?

128
Q

What can measurement of enzymes in tissues detect?

A

Metabolic disorders

129
Q

What can measurement of serum enzymes do?

A

Diagnose disease

130
Q

Give 2 examples of clinically important serum enzymes

A

NAME?

131
Q

When can some important serum enzymes indicate disease?

A

When they are found in the serum, as they are not normally

132
Q

Give an important condition that abnormal presence of serum enzyme indicates?

A

A heart attack

133
Q

What is the gold standard diagnosis method of MI?

A

Measurement of cardiac troponin by ELISA

134
Q

What can enzymes be used to measure?

A

Clinically important metabolites

135
Q

Give an example of how enzymes can be used to measure clinically important metabolites?

A

Measurement of glucose conc. with glucose oxidase

136
Q

Where is measurement of glucose conc. using glucose oxidase used?

A

In biosensor of glucose

137
Q

What is required for the Sanger chain termination method?

A

NAME?

138
Q

How do the labelled nucleotides terminate polypeptide production?

A

They are dideoxy on C3 and C2

139
Q

What happens in the Sanger chain termination method?

A

The normal and labelled nucleotides are mixed together, producing coloured bands

140
Q

What is the significance of the bands produced in the Sanger termination method?

A

Each band is one nucleotide difference

141
Q

How is the Sanger chain termination method interpreted?

A

The computer reads it, detects the colour of the band and uses this to sequence the DNA

142
Q

Why has the cost of sequencing fallen?

A

Due to advancement of next generation sequencing

143
Q

What is the consequence of the falling cost of sequencing?

A

Becomes viable to get a genome sequence done

144
Q

What are the ethical considerations regarding DNA sequencing?

A
  • Who has access to the genome sequence
  • Can knowledge help prevent illness later in life
  • Does it open up areas for discrimination
  • Who owns the DNA sequence
145
Q

Who may be interested in knowing a persons genome information?

A
  • Family
  • Potential spouse
  • Doctors
  • Government
  • Police
  • Schools
  • Insurance companies
146
Q

How is DNA hybridisation using a probe carried out?

A
  • Denature the DNA
  • Make a probe that is complementary to the DNA sequence, and add a fluorescent or radioactive label
  • Renature the DNA. Some of the DNA will bind to the probes
147
Q

What is formed when DNA binds to a probe?

A

A heteroduplex

148
Q

What is the result of the formation of a heteroduplex?

A

The DNA can be seen in a blot

149
Q

What does Southern hybridisation use?

A

An allele-specific probe

150
Q

How can probes be made very specific?

A

Using oligonucleotides

151
Q

How can an probe using oligonucleotides detect disease?

A

A normal oligonucleotide will bind when the sequence is normal, but won’t bind as tightly with a mutant allele, as there is a mismatch. Vice versa for disease specific oligonucleotides

152
Q

What does PCR using allele specific primers mean

A

Only DNA with an allele complementary to the probe is detected, and so only amplify normal DNA (or mutant DNA)

153
Q

What would happen if you attempted PCR using allele specific primers with a mismatch at the 5’ end?

A

It wouldn’t matter that much, and so PCR can continue

154
Q

What would happen if you attempted PCR using allele specific primers with a mismatch at the 3’ end?

A

Very dramatic, as if the 3’ end was mismatched, Taq polymerase can’t bind as the template can’t be read

155
Q

What does Northern hybridisation look at?

A

How much of a gene is expressed, by looking at how much RNA is made

156
Q

What is the difference between Northern and Southern hybridisation?

A

RNA is used in Northern

157
Q

Why must care be taken in Northern hybridisation?

A

RNA degrades

158
Q

What happens in Northern hybridisation?

A

You make a gel with RNA, and separate the RNA fragments

159
Q

What can be seen from Northern hybridisation?

A

NAME?

160
Q

What can reverse transcriptase do?

A

Take copy of a single stranded mRNA, and make it into DNA

161
Q

What do you have when a gene is expressed?

A

mRNA

162
Q

What could you say if used mRNA to do PCR?

A

Could say when mRNA is made

163
Q

What must be done to mRNA to perform PCR?

A

PCR can’t work with RNA, so need to make it into RNA

164
Q

What does every mRNA have?

A

A long polyA tail

165
Q

What is required to make mRNA into DNA?

A

A T primer, that binds to the polyA tail, so there is a template to copy

166
Q

What type of DNA is formed from mRNA?

A

cDNA

167
Q

What happens once cDNA is made?

A

The RNA is degraded using nucleases

168
Q

What is used to degrade the RNA?

A

An enzyme that specifically degrades RNA

169
Q

What can you do once you have cDNA produced from RNA?

A

Continue PCR

170
Q

What do you need for PCR using cDNA?

A

Forward and reverse primers

171
Q

Why do you need forward and reverse primers for PCR with cDNA?

A

Forward primer uses template to make another strand, producing a double strand. Once you have double strand, CPR continues as normal

172
Q

What is microarray technology looking at?

A

Conditional expression, so what RNA is produced, and therefore what’s actually being expressed in healthy and tumour tissue

173
Q

What must always be done in microarray technology?

A

Comparison of two conditions

174
Q

Describe the process of microarray technology

A
  • Have samples of both cells, and isolate the RNA
  • Use reverse transcription labelling to make cDNA with coloured fluorescent probe
  • Combine targets by mixing in equal quantities
  • Hybridise to microarray- probes find complementary sequences on individual dots, and bind to it
175
Q

What will happen if a gene is switched on in a tumour tissue, but not under normal conditions?

A

We will only see the colour of the tumour cDNA marker

176
Q

When may we use array comparative genome hybridisation?

A

If we have a suspected chromosomal problem, but don’t know where in the genome is wrong

177
Q

Describe the process of array comparative genome hybridisation

A
  • Extract DNA from both cell types
  • Label DNA with two different flourochromes
  • Mix in equal quantities and hybridise with microarray slide
178
Q

What must we know about the microarray slide?

A

Must know which genes are represented by which dot on the slide

179
Q

What happens if there is nothing wrong at a certain position on the chromosome?

A

Equal colours

180
Q

What happens if there is a deletion at a chromosomal location?

A

Bits of DNA that don’t have one of the colours

181
Q

How can a disease be determined?

A

By working out red:green ratio

182
Q

Why use array technology?

A
  • To investigate 1000’s genes at the same time
  • Investigate chromosome deletions/duplications
  • Investigate conditional gene expressoin
183
Q

Where is array technology better than Northern and Southern blotting?

A

When you need to look at many genes, or don’t know what genes you want to look at

184
Q

What does array technology allow for?

A

Genome wide analysis

185
Q

When will array technology be used to investigate chromosome deletions/duplications?

A

When micro deletions/substitutions

186
Q

Why will array technology only used to investigate chromosome changes when they are small?

A

If they are bigger, can physically see them

187
Q

What does DNA fingerprinting use?

A

Minisatellites

188
Q

What are minisatellites?

A

DNA sequences that are repeated over and over again

189
Q

Why are minisatellites used in DNA fingerprinting?

A

They show copy number variation, and everyone has different number of copies, so they are highly variable regions

190
Q

What does DNA profiling use?

A

Small Tandem Repeats (STRs)

191
Q

What are STRs?

A

Like minisatellites but only a few bases

192
Q

How do we carry out DNA profiling?

A

Do PCR on one of the variable regions

193
Q

Where can DNA profiling be used?

A

NAME?

194
Q

What happens in Karyotyping?

A

Stain chromosomes, so can see banding patterns

195
Q

Give an example of a problem that could be seen using Karyotyping?

A

A translocation

196
Q

What is a translocation?

A

When bits of chromosomes have fused with other chromosomes

197
Q

What happens in FISH?

A
  • Label probe DNA with fluorescent dye

- Denature and hybridise with chromosomal DNA

198
Q

What is required for FISH?

A

Need to know what you’re looking for

199
Q

How does FISH work?

A

If you have a gene you suspect has something wrong with it, make probe DNA for that gene, and label inside a cultured cell. The probe will bind at the position the gene is in the chromosome, and give a fluorescent tag.

200
Q

What does chromosome painting do?

A

Labels all chromosomes a different colour

201
Q

What makes chromosome painting possible?

A

We know exactly whats on each chromosome, so can make probes for sequences of DNA on a chromosome, and label all probes from one chromosome in the same colour

202
Q

What are the uses of FISH?

A

NAME?

Z OLD Molecules, Genes and Disease (14 decks)

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