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Semester 1 > MGD > Flashcards

MGD Flashcards

1
Q

N Terminus Formula

A

NH3+

Amino Group

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2
Q

C Terminus Formula

A

COO-

Carboxyl group

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3
Q

Define: Aliphatic

A

Long carbon chained (not carbon ringed)

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4
Q

What characteristic does a difference in electronegativity cause in amino acids?

A

Polarity

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5
Q

What is pKa?

A

Acid Dissociation Constant

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6
Q

For a low pKa…

Accept or Donate H+?

A

Donate

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7
Q

Formation of peptide bonds…

Hydrolysis or condensation reaction?

A

Condensation Reaction

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8
Q

Where do peptide bonds form?

A

Between the amino group of one amino acid and the carboxyl group of another.

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9
Q

Are polypeptides Trans or Cis in natural circumstances?

A

Trans - If it were cis, the R groups would clash.

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10
Q

Define: Isoelectric point

A

The pH at which the overall charge of a protein is zero.

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11
Q

Protonated or deprotonated protein if:

pI > pH

A

Protonated - Solution donates H+ to protein

Smallest always donates H+

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12
Q

Haemoglobin Alpha helix:

How many amino acids per turn?

A

3.6 amino acids per turn

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13
Q

What’s the structure of antiparallel Beta sheets?

A

Beta strands running in opposite directions; joined by Hydrogen bonds.

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14
Q

Define: Motifs

A

Folding patterns containing more than 1 type of secondary structure.

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15
Q

Define: Domains

A

Part of a polypeptide chain which specifically fold to produce a distinct shape. Normally to produce a region with a specific role (eg. Active site of an enzyme).

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16
Q

What is a chaperone?

A

A protein which prevents a polypeptide from folding incorrectly.

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17
Q

How are amyloidoses formed?

A

When misfolded proteins clump together - form amyloid fibres which are very strong.

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18
Q

Draw the curve for haemoglobin - what are the key values?

A

Sigmoidal curve
10kPa = ~95%
4kPa = 50%
0kPa = 0%

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19
Q

Name the allosteric inhibitor which reduces haemoglobin’s affinity for oxygen.

A

2,3-bisphosphoglycerate (2,3-BPG)

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20
Q

Draw the line for an increased CO2 level. Name this effect.

A

Shift to the right.

Bohr effect.

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21
Q

Adult haemoglobin subunits?

Fetal haemoglobin subunits?

A 
Adult = 2 alpha, 2 beta
Fetal = 2 alpha, 2 gamma
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22
Q

Does fetal haemoglobin have a higher or lower affinity for oxygen than maternal haemoglobin? Why?

A

Higher affinity for oxygen so that oxygen will move from mother to fetus. If it was the same, the fetus would not receive oxygen from the mother’s bloodstream.

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23
Q

What is the Michaelis-Menten equation?

A

Vo = (Vmax*[s])/(Km + [s])

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24
Q

What is the Lineweaver-Burk plot equation?

A

1/Vo = (((Km)/Vmax) * 1/[s]) + 1/Vmax

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25
Q

Competitive inhibitor effect on Km and Vmax?

A

Vmax remains the same but Km increases.

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26
Q

Non-competitive inhibitor effect on Km and Vmax?

A

Km remains the same but Vmax decreases.

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27
Q

Define: Km

A

The concentration of substrate required to meet 1/2 Vmax.

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28
Q

Define: Vmax

A

The maximum rate of a reaction if [s] is infinite.

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29
Q

Define: Isoenzymes

A

Different forms of an enzyme.

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30
Q

Define: Product inhibition

A

This is when a product can act as a competitive inhibitor.

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31
Q

What states does haemoglobin have and when do they change?

A

T (Tense) state and R (Relaxed) state.

T state when no oxygen is bound. Then R state when oxygen begins to bind.

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32
Q

Define: Proteolytic cleavage

A

The cutting of a protein sequence at a specific point.

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33
Q

Define: Zymogen

A

An inactive precursor.

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34
Q

List 4 short term and 2 long term methods of regulation of protein activity.

A

Short term:

  1. Allosteric inhibitors
  2. Change in substrate concentration
  3. Use of zymogens (proteolytic cleavage)
  4. Covalent modification

Long term:

  1. Change proteinsynthesis rate
  2. Change protein degredation rate
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35
Q

Difference between euchromatin and heterochromatin?

A

Heterochromatin is densely packed solenoids whilst euchromatin is beads-on-a-string.

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36
Q

In which are genes expressed - Heterochromatin or Euchromatin?

A

Euchromatin - Heterochromatin is densely packed solenoids where genes cannot be expressed as they are too tightly packed.

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37
Q

Composition of nucleotides?

A

Base + Sugar + Phosphate

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38
Q

Composition of nucleosides?

A

Base + Sugar

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39
Q

Define: Genome

A

The entire DNA sequence.

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40
Q

Two different sugars which could be in a nucleotide?

A

Ribose sugar or Deoxyribose sugar

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41
Q

What is a Purine base? Examples?

A

Double ring base.

Eg. Adenine + Guanine

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42
Q

What is a pyrimidine base? Examples?

A

A single ring base.

Eg. Cytosine, Thymine, Uracil

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43
Q

How many hydrogen bonds form between:
Guanine - Cytosine
Adenine - Thymine
Adenine - Uracil

A

3
2
2

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44
Q

What two types of groove are found in DNA? Which is the flexible groove?

A

Minor and Major grooves. Minor groove is flexible.

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45
Q

Name the phases in DNA replication.

A

Growth 1 - Cell content replication
Synthesis - DNA is replicated
Growth 2 - Checking and repair of DNA
Division - (EG. Mitosis)

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46
Q

What is G0 phase?

A

This is outside of the cell cycle and is when DNA is not replicating.

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47
Q

Equation of DNA replication? Which enzyme catalyses the reaction?

A

(dNMP)n + dNTP –> (dNMP)n+1 + PPi

Enzyme = DNA polymerase

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48
Q

Which enzyme joins the lagging strand to form a continuous piece of DNA?

A

DNA ligase.

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49
Q

Name of enzyme which unwinds DNA helix?

A

DNA helicase.

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50
Q

Define: Mitosis

A

Cell division for somatic cells which produces two identical daughter cells

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51
Q

Define: Meiosis

A

Cell division for gametes which produces 4 non-identical daughter cells (haploids).

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52
Q

Stages of Mitosis and their key features?

A

Prophase - Disintegration of nuclear membrane.

Prometaphase - Formation of spindle fibres.

Metaphase - Chromosomes align along centre of cell.

Anaphase - Spindle fibres pull chromosomes apart to opposite sides of the cell.

Telophase - Cell membranes reform.

Cytokinesis - Cells split apart.

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53
Q

Stages of Meiosis and their features?

A

Prophase 1: Nuclear membranes disintegrate. Homologous chromosomes also pair up and crossing over occurs. Spindle fibres also form
Metaphase 1: Chromosomes align.
Anaphase 1: Spindle fibres pull homologous chromosomes to opposite poles.
Telophase 1: Nuclear membrane forms.

Prophase 2: Nuclear membrane disintegrates.
Metaphase 2: Chromosomes align. Spindle fibres form.
Anaphase 2: Spindle fibres pull chromatids apart to give chromosomes at opposite poles.
Telophase 2: Nuclear membrane forms. 4 non-identical daughters cells have been made.

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54
Q

Define: Genotype

A

The genetic constitution of an individual.

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55
Q

Define: Phenotype

A

The observable characteristics determined by the genotype and the environment.

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56
Q

Name 3 ways genetic variation may arise.

A
  1. Crossing over
  2. Random assortment
  3. Mutations
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57
Q

Define: Hemizygous

A

Only one copy of an allele from the X chromosome.

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58
Q

Define: Codominance

A

Where two alleles will contribute to the phenotype in a heterozygotes.

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59
Q

Define: Complementation

A

When two genes code for a phenotype - can cancel each other out if both defected genes.

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60
Q

Enzyme, substrate and template for transcription?

A 
Enzyme = RNA polymerase
Substrate = Nucleotides
Template = DNA
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61
Q

Enzyme, substrate and template for translation?

A 
Enzyme = Ribosome
Substrate = Amino acyl tRNA
Template = mRNA
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62
Q

Outline: Capping, Tailing and Splicing

A

Capping = Adding a 5’ cap to protect against degradation and plays a role in translation.

Tailing = Adding a polyA tail which protects against degradation

Splicing = Sequence dependent process which removes introns.

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63
Q

Enzymes used in degradation of polynucleotides?

A

Endonuclease - breaks from within polynucleotide

Exonuclease - breaks from 5’ or 3’ end inwards.

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64
Q

How many types of RNA polymerase in eukaryotes and prokaryotes?

A 
Eukaryotes = 3 types
Prokaryotes = 1 type
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65
Q

Name 3 features of a genetic code.

A
  1. Read in triplets
  2. Non-overlapping
  3. Degenerate
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66
Q

Name the enzyme which joins amino acid to tRNA to form Amino acyl tRNA

A

tRNA synthetase

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67
Q

Bacteria or Man:

Coupled translation and transcription

A

Bacteria - no nucleus so occurs all together.

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68
Q

Bacteria or Man:

Simpler promoters

A

Bacteria

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69
Q

Bacteria or Man

Three RNA polymerase types

A

Man - Bacteria only has 1 type

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70
Q

Why do we care about difference between man and bacteria transcription + translation?

A

We can use differences to our advantage - drugs can target bacteria aspects which aren’t found in humans.

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71
Q

Which type of amino acid stereoisomers are found in proteins?

A

L isomers

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72
Q

Which can pass through a lipid bilayer more easily:

Hydrophobic or Hydrophillic substances

A

Hydrophobic - Non-polar molecules which are “water hating”

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73
Q

Protonated or Deprotonated form of conjugate base, more present when:

pH > pKa

A

Deprotonated

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74
Q

Draw the general structure of an amino acid.

A

Amino group, side group, carboxyl group, hydrogen - all surrounding a carbon

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75
Q

3 factors which can be used to classify amino acids.

A
  1. The interaction with water at pH 7.0
  2. The charge on side chain when at pH 7.0
  3. Aromatic or aliphatic
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76
Q

Charge of amino acids in acidic protein?

A

Negative charge

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77
Q

Charge of amino acids in basic protein?

A

Positively charged

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78
Q

As there is no rotation around a peptide bond, what shape does this give atoms in the bond?

A

Atoms in the bond are planar

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79
Q

Define: Homomeric

A

When polypeptide chains in a quaternary structure are the same.

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80
Q

Define: Heteromeric

A

When polypeptide chains in a quaternary structure are different.

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81
Q

List bond types found in primary structure

A

Covalent bonds (peptide bonds)

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82
Q

List the bonds found in secondary structure

A

Hydrogen bonds

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83
Q

List the bonds found in tertiary and quaternary structure.

A

Hydrogen bonds, Ionic interaction, disulphide bonds, Van der Waals forces, and hydrophobic interaction.

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84
Q

Key features of alpha helix structures?

A
  1. Right hand helix
  2. 0.54 nm pitch
  3. 3.6 amino acids per turn
  4. Pro and Gly act as helix breakers.
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85
Q

Features of Beta sheets?

A
  • Parallel or antiparallel

- Many hydrogen bonds form structure

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86
Q

Define: Myoglobin

A

A single subunit protein which can carry up to 1 molecule of oxygen. No cooperative binding.

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87
Q

Define: Haemoglobin

A

A protein with 4 haem groups meaning that it can carry up to 4 oxygen molecules. Can cooperatively bond.

88
Q

Name 3 diseases which can be caused due to mutations in globin genes.

A
  1. Sickle cell anaemia (Hydrophillic Glutamate become hydrophobic Valine = sticky patch).
  2. Alpha thalassaemia (less/no alpha subunits in haemoglobin - Too high affinity for O2).
  3. Beta thalassaemia (less/no beta subunits in haemoglobin - structure can’t bind to O2).
89
Q

Define: Okazaki fragments

A

The fragments formed by the lagging strand - the fragments are then joined together by DNA ligase.

90
Q

Define: Semi Conservative Replication

A

In the daughter cell DNA, there is one strand which is original and another which is new.

91
Q

Define: Gene

A

A specific section of DNA that can code for a protein.

92
Q

Define: Allele

A

Different versions of a gene

93
Q

Define: Dominant

A

When an allele is expressed as a phenotype both in homozygotes dominant and heterozygotes.

94
Q

Define: Recessive

A

When an allele is only displayed as a phenotype when the person is a homozygotes recessive.

95
Q

Define: Codominance

A

When both alleles determine the phenotype in a heterozygotes.

96
Q

Protonated or deprotonated if:

pI less than pH

A

Deprotonated - protein donates H+ to solution

Smallest always donates H+

97
Q

What do transcriptional factors recruit?

A

They recruit RNA polymerase for transcription.

98
Q

Following transcription, how is the 5’ and 3’ ends modified?

A

5’ cap is added to the 5’ end and a polyadenine tail is added to the 3’ end. This is for protection from degredation.

99
Q

What is splicing?

A

This is the removal of introns from pre-mRNA to form mature mRNA.

100
Q

Difference between endonucleases and exonucleases?

A

Endonucleases degrades polypeptide from the inside whereas exonucleases only operate the the 5’ or 3’ end.

101
Q

What type of RNA polymerase is mRNA?

A

RNA polymerase 2.

102
Q

Ribosome subunits in eukaryotes 80s type?

A

60s and 40s subunit.

103
Q

Ribosome subunits in prokaryotes 70s type?

A

50s and 30s subunits.

104
Q

Give three features of triplets in DNA code.

A
  1. Degenerate
  2. Non-overlapping
  3. No gaps
105
Q

Name of tRNA once an amino acid has bound?

A

AminoacyltRNA

106
Q

What are the two sites in translation called?

A

P site and A site.

107
Q

True or False:

All mutations have negative effects.

A

False. Some substitution mutations have no effect due to the degenerative nature of DNA triplets.

108
Q

Give 3 ways bacterial gene expression is different to mammalian.

A
  1. Simpler promoter regions
  2. Different transcription factors
  3. Bacteria only have one type of RNA polymerase
109
Q

What is constitutive secretion?

A

Constant secretion.

110
Q

What is regulated secretion?

A

Secretion which is controlled - proteins released in response to a signal.

111
Q

Name the enzyme which removes signals from proteins.

A

Signal peptidase

112
Q

What effect does SRP have on a ribosome translating mRNA?

A

It causes protein synthesis to pause.

113
Q

Name 2 modifications which can occur in the Endoplasmic Reticulum.

A
  1. Disulphide bond formation (Protein Disulphide Isomerase)

2. N-linked glycosylation

114
Q

Name 2 modifications which can occur in the Golgi Apparatus.

A
  1. O-linked glycosylation

2. Modification of N-linked oligosaccharides.

115
Q

What is the structure of collagen?

A

Formed by three strands of Alpha collagen strands wrapped in a right-handed triple helix.

116
Q

Describe the structure of an alpha collagen chain.

A
  1. Every third unit is Glycine

2. Every other position is often Proline or Hydroxyproline. Hydoxyproline is formed using the enzyme prolyl hydroxylase.

117
Q

How do crosslinks form between collagen subunits to form collagen?

A

Lysyl oxidase catalyses the reation of Lysine into an aldehyde derivative. The aldehyde derivative then spontaneously forms a cross link.

118
Q

What is the signal in nuclear targetting?

A

Nuclear Localisation Signal

119
Q

Which are the two specialist proteins used in nuclear targetting?

A
  1. Importin

2. Ran-GTP

120
Q

What is the signal in Mitochondrial protein targetting?

A

Amphipathic signal on N terminus.

121
Q

Name two specialist proteins in mitochondrial protein targetting.

A
  1. Translocase of Outer Membrane

2. Translocase of Inner Membrane.

122
Q

What is the signal used in lysosomal protein targetting?

A

Mannose-6-phosphate signal on the N terminus.

123
Q

How do lysosomal proteins get from the Golgi Apparatus to the forming lysosome?

A

Transported in vesicles. Once at lysosome, receptor and phosphate removed from protein.

124
Q

Name 2 enzymes which are resident to the Endoplasmic reticulum.

A
  1. Protein Disulphide Isomerase

2. Signal Peptidase

125
Q

What is the signal found in those enzymes which are resident to the Endoplasmic reticulum.

A

KDEL signal on the C terminus.

126
Q

Give an example of an allosterically regulated enzyme. Name an activator and an inhibitor.

A 
Enzyme = Phosphofructokinase
Activator = AMP
Inhibitor = ATP
127
Q

Name 4 bond types in tertiary structure of proteins

A
  1. Hydrogen bonds
  2. Ionic bonds
  3. Van der Waals
  4. Covalent bonds (disulphide bond)
128
Q

How does pH change protein shape?

A

pH causes ionised form of amino acids to change and therefore hydrogen bonds and ionic bonds is altered. Different bonding causes tertiary structure to change, hence a shape change.

129
Q

What is the amino acid and base change that causes Sickle Cell disease?

A

Conversion of Thymine to Adenine.

Amino acid change of Glutamate to Valine.

130
Q

Give the roles of the following:

  1. Golgi Apparatus
  2. Nucleus
  3. Nucleolus
  4. Endoplasmic Reticulum
  5. Lysosome
  6. Ribosome
  7. Cell Membrane
  8. Mitochondria
  9. Cytoplasm
A
  1. Export proteins + detoxification reactions
  2. DNA synthesis + repair
  3. RNA processing + ribosome assembly
  4. Export proteins + detoxification reaction + lipid synthesis
    + membrane synthesis + protein synthesis
  5. Cellular digestion
  6. Protein synthesis
  7. Transport of ions & small molecules + Cell morphology
  8. ATP synthesis
  9. Metabolism of carbohydrates, amino acids and
    nucleotides + Fatty acid synthesis
131
Q

What type of ribosomes do eukaryotes have? Composition?

A

80s type (60s + 40s)

132
Q

What type of ribosomes do prokaryotes have? Composition?

A

70s type (50s + 30s)

133
Q

Name the cytoskeleton components in eukaryotes

A
  1. Microfilaments
  2. Intermediate filaments
  3. Microtubules
134
Q

Name the cytoskeleton component in some prokaryotes

A
  1. Flagellum
135
Q

Hydrophobic - Polar or Non-polar?

A

Non-polar

136
Q

Hydrophillic - Polar or Non-polar?

A

Polar

137
Q

What is a zwitterion?

A

A neutral molecule with both positive and negative charge.

138
Q

What effect does CO2, H+ and 2,3-Bisphophoglycerate have on the haemoglobin sigmoidal curve?

A

Causes a shift to the right as affinity for oxygen decreases. Bohr effect.

139
Q

What effect does CO have on haemoglobin sigmoidal curve?

A

Shift to the left - CO blocks some haem groups by permanently binding and causes the affinity to other haem groups to increase.

140
Q

What is the mutation in sickle cell sufferers?

A

Single base mutation of Adenine to Thymine causing Glutamate to become a Valine.

141
Q

What is wrong in Alpha Thalassaemia sufferers?

A

Missing alpha subunits from haemoglobin - infinity to oxygen increases meaning that less oxygen is released to tissues.

142
Q

What is wrong in Beta Thalassaemia sufferers?

A

Missing beta subunits from haemoglobin - structure is unstable.

143
Q

Alpha or Beta Thalassaemia?

  • Detected at birth
A

Alpha thalassaemia as alpha subunits are normally found in foetuses. Beta subunit is not normally found until later as foetus haemoglobin contains gamma subunits instead.

144
Q

Define: Activity

A

The process of exerting energy to accomplish an effect.

145
Q

Define: International Unit of enzyme activity

A

The amount of enzyme that is required to catalyse the reaction of 1 micromole of substrate under specific conditions.

146
Q

Give an example of two zymogens and their active enzymes.

A

Pepsinogen –> Pepsin

Trypsinogen –> Trypsin

147
Q

How does plasminogen become plasmin for breakup of a clot.

A

Plasminogen (zymogen) is activated by t-PA and streptokinase to form plasmin. Plasmin converts Fibrin to Fibrin fragments.

148
Q

Which direction do we read DNA and RNA?

A

5’ to 3’.

149
Q

What are the types of bonds found between nucleotides in DNA?

A

Phosphodiester bonds

150
Q

Name 4 environmental factors which can cause a change in the genotype and/or the phenotype.

A
  • Mutagenic agent
  • Radiation
  • Diet
  • Lifestyle
151
Q

Name the 3 RNA polymerase types in humans.

A

RNA polymerase 1 = rRNA = Ribosomal RNA
RNA polymerase 2 = mRNA = Messenger RNA
RNA polymerase 3 = tRNA = Transfer RNA

152
Q

What type of bond forms between neighboring nucleotides?

A

Phosphodiester bonds

153
Q

What type of bond forms between neighboring amino acids?

A

Peptide bonds

154
Q

How many disulphide bonds are there in Insulin?

A

3 (2 between A and B + 1 amongst A)

155
Q

What are endoprotease and exoprotease?

A

Enzymes used in proteolytic processing.

156
Q

Why does procollagen have to be exocytosed before having the pro-segment cleaved off?

A

Procollagen becomes tropocollagen without the segment - tropocollagen can form fibrils and therefore form collagen fibres which are very large and can cause damage to cells if inside.

157
Q

What is the sequence found in proteins destined for the Peroxisomes?

A

Peroxisome Target Sequence

158
Q

What is the protein which binds to proteins destined for peroxisomes?

A

Peroxisomal Import Receptors

159
Q

How does Sanger Termination Method sequence DNA?

A

Fluorescent labelled terminator nucleotides are added into four different PCR setups (one for each nucleotide type - A,C,G,T). Then run the products in 4 different wells in gel electrophoresis. Can then read back the sequence, shortest (furthest travelled) to longest - this code gathered is complementary to the template strand.

160
Q

Why do terminator nucleotides not allow further binding beyond them?

A

No -OH group on the 3rd carbon meaning that phosphodiester bonds cannot form with any further nucleotides.

161
Q

How does restriction analysis work?

A

Restriction endonucleases (molecular scissors) can be used to cut DNA at specific recognition sites.

162
Q

What can you measure with restriction analysis?

A
  • DNA variation
  • DNA mutations
  • Size of DNA fragments
  • Gene cloning (not measured but uses this)
163
Q

How do we do gene cloning?

A
  • Get sample to replicate from restriction analysis
  • Cut plasmid with same restriction endonuclease
  • Add DNA segment and add to cut plasmids.
    Recombinant DNA should form.
  • Identify recombinant DNA and insert into bacteria
  • Allow bacteria to divide.
164
Q

Why does DNA move in gel electrophoresis

A

DNA is negatively charged so in a current, it is attracted to positively charged anode.

165
Q

What is the reference DNA sample we compare to called?

A

DNA ladder

166
Q

Temperatures + stages in a thermocycler?

A

95 degrees = Denaturation
55 degrees = Renaturation (annealing)
72 degrees = DNA synthesis

167
Q

Name 3 uses for PCR

A
  1. Replicate useful section
  2. Investigate single base pair
  3. Investigate small deletion/insertion
168
Q

What is isoelectric focusing?

A

This is protein electrophoresis which is dependent on the pI value of the protein. Gel has pH gradient and with a current, proteins will move until in a region where their pI = pH - this is when the charge is zero.

169
Q

What is SDS page?

A

Protein electrophoresis which is based on the molecular weight of a protein - to do this, uses SDS detergent splits protein into single chain (removes shape).

170
Q

What is 2D page?

A

This is isoelectric focusing followed by SDS page - this is done as some proteins may have the same pI value.

171
Q

How does western blotting work?

A

SDS page product is lifted onto a nylon sheet and then has primary antibodies added which are specific to certain proteins we are looking for in the sample. We then wash and add secondary antibodies which are specific to the primary antibodies. Secondary antibodies can carry fluorescent probes or enzymes to detect binding of primary antibodies.

172
Q

What is ELISA?

A

Enzyme-linked Immunoabsorbent Assay.
Add a sample to a well and cause it to bind. Add primary antibody which is specific to the protein we are looking for in a sample. Wash and then add secondary antibody which can carry enzymes or fluorescent probes - if these bind to the primary antibodies and are detected, it suggests that the specific protein is present.

173
Q

Name 5 ways that bacteria can become resistant to antibiotics.

A
  1. Increased rate of division (more mutations arise)
  2. Decreased drug uptake by cells
  3. Increased removal of drug from cells
  4. Increased transcription of target (overwhelm drug)
  5. Altered target (mutation causes lower affinity to drug)
174
Q

What is DNA hybridisation?

A

The binding of two complementary strands of DNA or RNA to form a structure though complementary base pairing.

175
Q

How can we use PCR to identify a single base mutation?

A

Use an allele specific primer which will only bind if no mutations have occurred. If there has been a mutation, the primer cannot bind and you will get no PCR product.

176
Q

How can we use restriction analysis to test for a specific allele?

A

We can use a specific restriction endonuclease which will only cut at a specific allele. If the allele is present it will cut, if not it won’t.

177
Q

Describe southern blotting.

A

Gel electrophoresis followed by DNA hybridisation. Can use specific probes which will bind to a fragment of interest if it is present. Lift result from electrophoresis using nylon membrane.

178
Q

How does nothern blotting differ to southern blotting?

A

Uses RNA rather than DNA.

179
Q

Describe reverse transcriptase PCR

A

Using an mRNA template, reverse transcriptase can make a cDNA strand which can then be put into a PCR setup to replicate it. We can use a gene specific primer in the setup meaning that only if the gene is present, the PCR will occur.

180
Q

Describe microarray

A

We have a microarray dish where specific complementary DNA sections are bound to it. We then add a sample, if the sample binds we know that it is the DNA of interest we are looking for.

181
Q

Describe DNA fingerprinting/DNA profiling

A

In our introns we have repeating sequences. The number of sequences vary for each individual and the number of repeats is similar for more closely related individuals.

In the method, we use restriction endonucleases which cut around the repeating sequences in an individual. We then enter these into PCR followed by gel electrophoresis. We can do this for multiple repeats and then compare the results with other people to identify how closely they are related.

182
Q

What is karyotyping

A

Images of chromosomes are taken and then lined up for comparison. Compares banding pattern, size, number etc.

183
Q

What is FISH?

A

Fluorescence In Situ Hybridisation.
Here we use fluorescent probes which are specific to DNA sequences of interest. We add this to their DNA and then observe any results in an image of their chromosomes. If the DNA sequence is present, the probe will bind. We can use probes which bind to mutations instead.

184
Q

What is a transition point mutation?

A

Purine –> Purine or Pyrimidine –> Pyrimidine point mutation.

185
Q

What is a transversion point mutation?

A

Purine –> Pyrimidine or Pyrimidine –> Purine point mutation.

186
Q

Name the 3 types of point mutation.

A
  1. Silent mutation
  2. Missense mutation
  3. Nonsense mutation
187
Q

What is frameshift and how is it caused?

A

This is when the open reading frame is shifted due to the insertion or deletion of a non-multiple of three nitrogenous bases.

188
Q

Give the 2 types of spontaneous mutation. Explain what causes them.

A
  1. Tautomeric shift - Within the 4 bases, sometimes a proton moves position causing rare forms of bases to arise. These different forms cause different base pairing properties so different DNA sequences are coded for.
  2. Slippage during replication - Occassionally, when there are repeated sequences (eg. AAAAAAAAA), the template or new strand loop out. As replication continues, this can cause a longer or shorter strand (dependent on which one looped out).
189
Q

What causes induced mutations?

A

Induced mutations are caused by chemicals or radiation.

190
Q

Name the 3 mechanisms the body has to prevent mutations.

A
  1. Proof reading by the DNA polymerase. Corrects 99% of mismatches.
  2. Nucleotide mismatch repair - Finds mismatch and replaces segment around it.
  3. Excision repair - Excision around incorrect base pair which is then replaced.
191
Q

Name the 6 features which cells gain to become tumorous.

A
  1. Independent division to growth signals
  2. Independent to external anti-growth signlas
  3. Avoid apoptosis
  4. Divide without biological ageing
  5. Angiogenesis can occur
  6. Can invade tissues
192
Q

Describe Array Comparative Genomic Hybridisation

A

This is where you get an array slide with DNA probes bound for all of the genome. You then get patient DNA probed with one colour and control DNA probed with another. Add both in equal quantities to the array slide and observe the colour change. If patient colour shows, patient has insertion. If control colour shows, patient has a deletion.

193
Q

Describe Euchromatin

A

DNA which is loosely wrapped around histone proteins to form beads on a string - it can be read for transcription.

194
Q

Describe Heterochromatin

A

Tightly wrapped DNA around histone proteins which is then folded into solenoid structures. These cannot be read for active transcription.

195
Q

How is sex determined by chromosomes?

A

With the presence of atleast one Y chromosome, the individual is phenotypically male.

196
Q

Define: Polyploidy

A

A cell or organism which can has gained whole haploid sets of chromosomes.

197
Q

Define: Aneuploidy

A

The gain or loss of a whole chromosome in a cell.

198
Q

Define: Monosomy

A

When one chromosome is missing in the cell. The individual has 45 chromosomes. One chromosome is now single.

199
Q

Define: Trisomy

A

When one chromosome has been gained. The individual now has 47 chromosomes. One chromosome is now triplets.

200
Q

Define: Balanced - in terms of chromosomes

A

This is when a structural change does not result in the loss of genetic material.

201
Q

Define: Unbalanced - in terms of chromosomes

A

This is when a structural change results in the loss of genetic material.

202
Q

Give 3 examples of mutations which can occur within a single chromosome.

A
  1. Deletion
  2. Duplication/Insertion
  3. Inversion (no loss of genetic material, just rearrangement).
203
Q

Give 3 examples of mutations which can occur with 2 chromosomes.

A
  1. Inversion (no loss of genetic material, just rearrangement to a non-homologous chromsome)
  2. Reciprocal translocation (no loss of genetic material, just swap between non-homologous chromosomes)
  3. Robertsonian translocation (loss of genetic material as q arms of 2 acrocentric chromosomes join whilst the p arms disappear).
204
Q

Write the nomenclature for a female who has lost some genetic material from the p arm of chromosome 7.

A

46, XX, 7p-

205
Q

Write the nomenclature for a male with downs syndrome.

A

47, XY, +21

206
Q

Give 3 congenital and 1 acquired reason for referral to karyotyping.

A

Congential:

  1. Birth defect
  2. Abnormal ultrasound scan of foetus
  3. Infertility

Acquired:
1. Leukaemia

207
Q

Name a protective method to stop Premature Stop Codons in insertion/deletion mutations from having an effect.

A

Nonsense Mediated Decay

208
Q

How does nitrous acid cause mutation?

A

Changes amino group to keto group.
C–>Uracil
A–> Hypoxanthine (binds to C)
G–> Xanthine (binds to C)

209
Q

How does EMS cause mutations?

A

Creates apurinic site - any base can bind to this so 3/4 times binding is wrong.

210
Q

How does IQ cause mutations?

A

Causes incorrect DNA base packaging; mostly causing single base deletions. Causes bases to be further apart at places, causing DNA polymerase to misread.

211
Q

Give the name of the two main metabolic pathways in Red Blood Cells

A
  1. Embden Meyerhof Pathway (glucose–> lactate + ATP)

2. Hexose Monophosphate Pathway (g-6-p –> NADPH)

212
Q

Amino Acyl-tRNA is charged or uncharged version of tRNA?

A

Charged

213
Q

What type of alpha chains make up the triple helix of Tropocollagen/procollagen?

A

2 X A1 chains

1 X A2 chains

214
Q

What type of alpha chains make up the triple helix of Tropocollagen/procollagen?

A

2 X A1 chains

1 X A2 chains

215
Q

What is I-Cell disease? How is it caused?

A

Fatal disease which causes Lysosome proteins to not be sent to lysosomes due to mis-targetting. This mis-targetting is due to an N-acetyl glucosamine phosphotransferase deficiency.

Semester 1 (4 decks)

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