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Medicine Semester 1 > MGD > Flashcards

MGD Flashcards

0
Q

How are monomeric units joined to form macromolecules?

A
  • Covalent bonds
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1
Q

In which 3 ways do prokaryotes differ from eukaryotes?

A
  • No separate nucleus
  • Cell wall and a plasma membrane
  • Lack membrane bound organelles
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2
Q

List the bonds that join macromolecules together to form complexes

A
  • Non-covalent:
  • H bonds
  • Ionic attractions/repulsion
  • Van der Waals
  • Hydrophobic effect.
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3
Q

What may happen if the interactions are broken?

A
  • Loss of structure and therefore function.
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4
Q

What is meant by amphipathic?

A
  • Both a polar and non-polar end (hydrophilic and hydrophobic)
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5
Q

What are the main roles of proteins?

A
  • Structural support
  • Immune protection
  • Ligands in cell signalling
  • Catalysts
  • Transporters
  • Machines
  • Ion channels
  • Receptors
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6
Q

What is a zwitterion?

A
  • NH3+
  • COO-
  • Both present.
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7
Q

What are the stereoisomers of zwitterions?

Which one is found naturally in the body?

A
  • L and D

- L is found naturally in the body.

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8
Q

What does polar mean?

A
  • Non-symmetrical for electronegativity
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9
Q

Determine which of the following are hydrophobic/hydrophilic:

  • Non-polar
  • Polar uncharged
  • Polar charged
A
  • Non-polar: hydrophobic

- Polar: Hydrophilic

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10
Q

If the pH of a solution is LESS than the pK value what happens?

A
  • Protonation
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11
Q

If the pH of a solution is greater than the pK value what occurs?

A
  • Deprotonation
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12
Q

How does a peptide bond form?

A
  • Elimination of a water molecule to form a peptide bond between two amino acids
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13
Q

What two things does an amino acid sequence determine in a protein?

A
  • The way in which the polypeptide chains fold

- The physical characteristics of the protein.

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14
Q

What is the isoelectric point? (pI)

A
  • The point at which there is no overall net charge.
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15
Q

If the pH is smaller than the pI what happens?

A
  • Protonation as there are many H+ present to join.
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16
Q

If the pH is greater than the pI what occurs?

A
  • Deprotonation as there are many OH- present to take H+ away.
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17
Q

What are the different types of peptide lengths?

A
  • Peptide
  • Oligopeptide
  • Polypeptide
  • Protein
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18
Q

What is a conjugated protein?

A
  • Some proteins contain covalently linked chemical components in addition to their amino acid chains.
  • e.g: Haem groups in haemoglobin.
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19
Q

What are the two termini on primary amino acid structures called?

A
  • Amino

- Carboxyl

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20
Q

Outline what is meant by primary, secondary, tertiary and quaternary structures.

A
  • Primary: Linear amino acid sequence of polypeptide chains
  • Secondary: Local spatial arrangement of polypeptide backbone.
  • Tertiary: 3D arrangement of all atoms in single polypeptide.
  • Quaternary: 3D arrangement of all protein subunits.
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21
Q

What are the characteristics of an alpha helix?

A
  • 3.6 amino acids per 0.54nm turn
  • H bonds are parallel to amino acid orientation
  • R groups are on the outside and so aren’t used in secondary structure.
  • Stability is affected by amino acid sequence
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22
Q

What affects do Proline and Glycine have on an alpha helix?

A
  • Pro: helix breaker, rotation around the N-C bind is impossible
  • Gly: helix breaker, tiny R group supports other conformations.
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23
Q

In an alpha helix where does the H bonds form?

A
  • C=O and N-H four amino acids apart (hence 3.6 aa per turn)
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24
Q

How does a Beta pleated sheet form?

A
  • When H bonds join two amino acid strands together, either parallel or antiparallel.
  • R group alternates between opposite sides of chain and so point in opposite directions.
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25
Q

What is the difference between a parallel and antiparallel beta pleated sheet?

A
  • Antiparallel the binding O and H are DIRECTLY opposite each other.
  • Parallel the binding O and H are diagonal to each other.
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26
Q

What are the roles and characteristics of globular proteins?

A
  • Roles: Catalysts, regulation
  • Compact shape
  • Several types of secondary structure
  • e.g: haemoglobin
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27
Q

What are the roles and characteristics of fibrous proteins?

A
  • Roles: Support, shape and protection
  • Long strands/sheets
  • Single type of repeating secondary structure
  • e.g: collagen
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28
Q

Give 4 characteristics of collagen.

A
  • Triple helix
  • Gly-X-Y repeating sequence
  • H bonds between chains
  • Striated due to the staggered arrangements.
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29
Q

How are collagen fibrils formed?

A
  • Covalently cross-linked collagen molecules.
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30
Q

What are motifs and domains and what type of structure are they?

A
  • Globular tertiary structure
  • Motifs: Folding patterns containing one or more elements of secondary structure.
  • Domains: Part of a polypeptide chain that folds into a distinct shape and has a specific functional role.
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31
Q

How are membrane proteins folded and why?

A
  • ‘Inside out’ arrangement
  • Hydrophobic on outside to interact with lipids
  • Hydrophilic on inside to for pores for water and water soluble molecules can pass through.
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32
Q

What types of bonds/forces are present in the 4 types of protein structure?

A
  • Primary: Covalent (peptide)
  • Secondary: H bonds
  • Tertiary & Quaternary: Covalent (disulphide), Ionic, H bonds, Van der Waals and hydrophobic interaction.
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33
Q

What is hydrophobic interaction?

A
  • Interaction between hydrophobic side chains due to displacement of H2O
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34
Q

How do disulphide bonds form?

A
  • Between Cysteine residues

- Oxidise the cysteine to join via disulphide bond

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35
Q

Where are molecules with disulphide bonds found?

A
  • Secretions as move into harsh conditions so need greater strength.
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36
Q

What is protein denaturation?

A
  • Breaking of bonds to unfold proteins.
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37
Q

What factors can cause denaturation and why?

A
  • Heat: Increase vibrational energy
  • pH: Alters ionisation states of amino acids.
  • Detergents/organic solvents disrupt hydrophobic interactions.
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38
Q

Is folding of proteins random?

How is it sped up?

A
  • No

- Molecular chaperones needed.

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39
Q

What is amyloidoses?

A
  • Accumulation of mis-folded proteins.
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40
Q

What are amyloid fibres?

A
  • Misfolded, insoluble for of a naturally soluble protein.

- This can cause disease.

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41
Q

What does a Haem group consist of?

A
  • Protoporphyrin ring and Fe atom bound to 4 N atoms of the ring.
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42
Q

How can Haem groups carry oxygen?

A
  • Fe2+ can make two additional binds to O2 one on each side of the plane.
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43
Q

The haemoglobin has two histidine residues what are their roles?

A
  • Proximal: binds the Fe group to the protein.

- Distal histidine stabilises.

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44
Q

When an oxygen molecule binds to the haem group what happens and how does this affect the O2 affinity?

A
  • Fe is initially below the plane of the ring
  • O2 binding causes movement of Fe into plane of the ring
  • This consequently causes His F8 to move changing the overall protein conformation. T state -> R state
  • Increases the affinity for O2
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45
Q

Why is a sigmoidal shaped PO2 curve significant?

A
  • Allows for oxygen to be loaded/unloaded in the lungs/tissues depending on pO2
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46
Q

What is the role of 2,3 bisphosphoglycerate?

A
  • Lowers the affinity for oxygen.
  • Without it then saturation of haemoglobin is too high in the tissues and not enough oxygen would be released.
  • 8% - 66% difference with BPG.
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47
Q

How does BPG decrease the affinity for oxygen?

A
  • By stabilising the T state so the affinity doesn’t increase with more O2.
  • (Lower affinity = further to the right)
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48
Q

What is the Bohr effect?

A
  • Binding of H+ and CO2 lowers the affinity.

- More acidic so more O2 needs to be unloaded.

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49
Q

Why is CO poisonous to humans?

A
  • Blocks the haem groups from loading O2, CO instead.
  • Binds 250 times more readily than O2
  • Also acts to increase the affinity for O2 for unaffected subunits
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50
Q

How do foetuses obtain O2?

A
  • HbF has a higher binding affinity for oxygen than HbA does (normal haemoglobin)
  • So the oxygen transfers from the mother to the foetus.
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51
Q

What are hue he secondary subunits that form:

  • HbA
  • HbF
  • HbA2
A
  • HbA: 2 alpha, 2 beta
  • HbF: 2 alpha, 2 gamma
  • HbA2: 2 alpha, 2 delta
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52
Q

What is the mutation responsible for sickle cell anaemia?

A
  • Glutamine -> Valine

- Charged hydrophilic -> uncharged hydrophobic.

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53
Q

How do sticky hydrophobic pockets form?

A
  • Valine allows deoxygenated HbS to polymerase.
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54
Q

What is the effect of sickle cell anaemia?

A
  • Sickle shaped cells are more prone to lyse, due to constant change from normal to sickle shaped, (anaemia)
  • They are more rigid, so block microvasculature.
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55
Q

What is a thalassaemia?

A
  • Imbalance of beta/alpha globin chains
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56
Q

What is a beta thalassaemia and what are the effects?

A
  • Absent/lower B-globin chain production
  • Alpha chains are unable to form stable tetramers
  • Only form ppt.
  • Symptoms after birth
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57
Q

What is alpha thalassaemia?

A
  • Absent/reduced production of alpha chains
  • Different levels of severity due to multiple copies of the alpha chains present
  • Beta chains can form stable tetramers, but with a very high affinity for oxygen that won’t release easily.
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58
Q

What is the transition state?

A
  • The high energy intermediate that lies between substrate and product
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59
Q

What is the activation energy?

A
  • The minimum energy the substrate must have to allow reaction.
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60
Q

What are the roles of enzymes?

A
  • Facilitate the formation of transition state
  • Highly specific
  • No permanent change
  • No effect on reaction equilibrium
  • Increases the rate of reaction
  • Protein
  • May require associated cofactors (bound to proteins, required for protein’s biological activity)
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61
Q

What clinical roles do enzymes have?

A
  • Inheritable genetic disorders
  • Overactive enzyme can = disorder
  • Measurement of enzyme activity for diagnosis (TSH/T4)
  • Inhibition of enzymes by drugs.
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62
Q

What is an active site and it’s role?

A
  • The area in which substrates bind and where chemical reactions occur.
  • A cleft that excludes water
  • Only small part of the enzyme the rest is structural.
  • The substrate binds to the active site by multiple weak non-covalent bonds that mustn’t be too tight otherwise can’t release.
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63
Q

What does a reaction rate-substrate concentration graph look like?

A
  • Curve

- Rate of increase is decreasing until it plateaus when all active sites are filled.

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64
Q

Finish the equation: Vo =

A
  • Vo = Vmax (S) / Km + (S)
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65
Q

What does Vmax stand for?

A
  • The maximum rate of reaction when all enzyme active sites are saturated with substrate.
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66
Q

What is Km?

A
  • The substrate concentration that gives half maximum velocity
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67
Q

What does a low Km signify?

A
  • Low Km = High affinity for the substrate

- High Km = Low affinity for the substrate

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68
Q

If you double the amount of enzyme what happens to the standard rate?

A
  • The standard rate DOESNT double.
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69
Q

On a Lineweaver-Burk plot what does the x and y intercepts signify?

A
  • x intercept: -1/Km

- y intercept: 1/Vmax

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70
Q

What is the y axis and x axis on a Lineweaver-Burk plot?

A
  • y axis: 1/V (1/rate)

- x axis: 1/(S)

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71
Q

Give an example of an irreversible inhibitor and why is it irreversible?

A
  • Sarin nerve gas

- Very tightly bound

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72
Q

What types of reversible binding is there?

A
  • Competitive and non-competitive

- Non-covalent bonds used, so freely dissociates.

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73
Q

What are the effects on Vmax and Km of competitive inhibitors?

A
  • Increased Km (more substrate required, decrease in affinity)
  • Vmax doesn’t change ((S) can outcompete the inhibitor)
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74
Q

What is the effect on Vmax and Km for non-competitive inhibitors?

A
  • Km doesn’t change: (Affinity is the same)

- Vmax decreases: (Fewer active sites available as prevents binding)

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75
Q

What is an isoemzyme?

A
  • Different forms of the same enzyme that have different kinetic properties
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76
Q

What is product inhibition?

A
  • Accumulation of the product of a reaction inhibits the forward reaction.
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77
Q

What does allosteric mean?

A

Binds to anywhere but the active site.

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78
Q

What does an allosteric activator/inhibitor do?

A
  • Activator: Increases the proportion of enzymes in the R state (higher affinity)
  • Inhibitor: Increases the proportion of enzymes in the T state (lower affinity)
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79
Q

Which enzyme is the main regulator of glycolysis?

A
  • Phosphofructokinase
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80
Q

What activates/inhibits the forward reaction of the phosphofructokinase dependant step of glycolysis?

A
  • Activators: AMP, Fructose-2-6-bisphosphate

- Inhibitors: ATP (large amounts present no more is required) H+, citrate.

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81
Q

How does phosphorylation occur?

A
  • Protein kinases
  • Transfers the terminal Pi from ATP
  • To the OH group of Ser, Thr, Thy.
  • Condensation reaction.
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82
Q

How does dephosphorylation occur?

A
  • Protein phosphatases catalyse:

- Hydrolytic removal of phosphoryl groups from proteins

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83
Q

Why is amplification of enzyme cascades useful?

A
  • Enzymes activate other enzymes

- The number of affected molecules increases rapidly.

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84
Q

What are zymogens?

A
  • Inactive precursors of digestive enzymes

- Not needed all the time, only activated by specific proteolytic cleavage.

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85
Q

What are the common prefixes/suffixes for zymogens?

A
  • -ogen

- Pro- (if ends in -ase)

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86
Q

Give 5 uses of proteolytic cleavage.

A
  • Zymogens
  • Some protein hormones (Insulin)
  • Blood clotting
  • Developmental processes (tissue remodelling)
  • Programmed cell death,
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87
Q

Outline the blood clotting cascade.

A
  • Intrinsic pathway (damaged endothelium) promotes binding of Factor XII
  • Extrinsic pathway (trauma) promotes factor III (tissue factor)
  • Both pathways converge on Factor X activation
  • Thrombin activation
  • Fibrin clot formation
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88
Q

How does thrombin lead to a fibrin clot forming?

A
  • It cleaves fibrinopeptides from central globular domain of fibrinogen
  • These link together to form a fibrin mesh/clot
  • Stabilised by cross-linked amide bonds catalysed by transglutaminase (thrombin activates it from protransglutaminase)
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89
Q

How is the fibrin clot maintained?

A
  • Positive feedback loop

- When limited proteolysis by thrombin/factor Xa occurs this is the positive feedback so more Factor XII is formed.

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90
Q

How can clotting be stopped?

A
  • Localisation of prothrombin: dilution of clotting factors by blood flow and removal by liver.
  • Digestion by proteases: protein C degrades Va and VIII (activated by thrombin binding to endothelial receptor thrombomodulin)
  • Specific inhibitors
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91
Q

Outline how clots are broken down.

A
  • Fibrinolysis
  • Plasminogen is activated by t-PA/streptokinase to form plasmin
  • Plasmin catalyses the fibrin -> fibrin fragments reaction
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92
Q

When looking at a nucleus, what are the light and dark patches?

A
  • Light: Euchromatin, beads on a string, genes expressed

- Dark: Heterochromatin, solenoid 30nm fibre, genes not expressed

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93
Q

What is a nucleosome?

A
  • Histone wrapped in DNA
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94
Q

When DNA is wrapped into a chromosome are the genes expressed?

A
  • No
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95
Q

What are genes?

A
  • Stretch of DNA with a chromosomal locus

- Codes for a protein and it’s regulation

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96
Q

In the human genome how many chromosomes are they and how are they split?

A
  • 24
  • 22 autosomal
  • 2 sex
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97
Q

What is a nucleotide comprised of?

A
  • Nitrogenous base
  • Deoxyribose sugar
  • Phosphate molecule
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98
Q

What is a nucleoside comprised of?

A
  • Nitrogenous base

- Deoxyribose sugar

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99
Q

Which of the nitrogenous bases are:

1) Pyrimidines
2) Purines

A
  • 1) Thymine, (Uracil), Cytosine

- 2) Arginine, Guanine.

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100
Q

Which of the nitrogenous bases have

1) 2 H bonds
2) 3 H bonds

A
  • 1) A & T(U)

- 2) C & G

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101
Q

How are nucleotides connected?

A
  • Phosphodiester bonds
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102
Q

In a polynucleotide which direction is polarity and how are the ends distinctive?

A
  • 5’ - 3’

- 5’P - 3’OH

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103
Q

How are duplex structures formed?

A
  • They are secondary structures of polynucleotides
  • Strands are complimentary & antiparallel
  • H bonds form between the antiparallel complimentary sequences
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104
Q

Give two examples of antiparallel strands of DNA/RNA

A
  • RNA stem loops-tRNA

- Right handed double helix

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105
Q

What are the roles of the major and minor group of the double helix?

A

Major is more exposed and allows enzymes to bond.

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106
Q

What are the four stages of the cell cycle?

A
  • Growth 1: Cell content replication
  • Synthesis: DNA replication
  • Growth 2: Double check and repair
  • Mitosis: Cell division
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107
Q

What are the stages of replication in prokaryotes?

A
  • Initiation
  • Elongation
  • Termination
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108
Q

What happens in the initiation stage?

A
  • Recognition of origin of replication
  • Requires DNA polymerase
  • Requires a kick start by primase.
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109
Q

Outline the elongation stage.

A
  • Moving replication forks
  • Helicase unwinds double helix
  • DNA polymerase extends at 3’ end
  • DNA ligase joins lagging strands.
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110
Q

How does termination occur?

A
  • Replication forks join and leading and lagging strands join by DNA ligase
  • Number of chromosomes stays the same.
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111
Q

When a chromosome is replicated how many DNA molecules are formed from how many?

A
  • 2 from 1
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112
Q

On a chromosome which is the p and q arm?

A
  • p arm: shorter ‘petit’

- q arm: longer

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113
Q

In mitosis what are the 5 stages and what are their roles?

A
  • Prophase: Chromosomes condense, kinetochore binds to centromere
  • Prometaphase: Spindles bind the centromeres
  • Metaphase: Chromosomes line up on equator
  • Anaphase: Spindles contract, pulling apart chromatids to poles
  • Telophase: Cleavage of nuclear envelope, spindles break down
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114
Q

What are the results of mitosis?

A
  • Production of 2 identical daughter cells
  • Necessary for: epidermis, bone marrow, mucosa
  • Cell division for somatic cells.
115
Q

Name the position of a nucleus as it ascends up the chromosome.

A
  • Metacentric
  • Submetacentric
  • Acrocentric
  • Telocentric
116
Q

What are the products of meiosis?

A
  • Germline cell division
  • 4 non-identical cells (½ content of parent cells)
  • Diploid -> haploid
  • Egg and sperm production
117
Q

Outline meiosis.

A
  • Prophase 1: homologous pairs line up
  • Metaphase 1: pairs line up on equator (Crossing over to form recombinant DNA, chiasmata)
  • Anaphase 1: Chromosomes are pulled to poles
  • Telophase 1: Cleaving to form daughter cells
  • Normal mitosis afterwards
118
Q

What is the point of meiosis?

A
  • Maintaining constant chromosome number from generation to generation
  • Generation of genetic diversity: - Random assortment of chromosomes & Crossing over of genetic material
119
Q

What is spermatogenesis?

A
  • Production of sperm
  • 1 spermatocyte (2n) -> 4 sperm (n)
  • Spermatogenesis = 248 days
120
Q

What is Oogenesis?

A
  • Production of eggs
  • 1 oocyte (2n) = 1 egg (n) and 3 polar bodies (these disappear)
  • Takes ~ 12-50 yrs
121
Q

What are the consequences of faulty meiosis?

A
  • ⅓ of all identified miscarriages
  • Infertility
  • Mental retardation
122
Q

What does homozygous mean?

A
  • 2 alleles of a gene are the same
123
Q

What does heterozygous mean?

A
  • 2 alleles of a gene are different
124
Q

What does hemizygous mean?

A
  • Only one allele of a gene on the X chromosome (i.e. Males only)
125
Q

What does dominant and recessive mean?

A
  • Dominant: dominant determines the phenotype

- Recessive: non-dominant allele in a heterozygous is recessive

126
Q

How would you depict a carrier of a disease?

A
  • Half is shaded in.
127
Q

What are the characteristics of a autosomal recessive pedigree?

A
  • Males and females are equally affected
  • Can skip generations
  • Parents are heterozygous carriers
128
Q

What are the characteristics of an autosomal dominant pedigree?

A
  • Rare
  • Every affected individual has 50% chance of having affected offspring.
  • CANT skip generations
  • Males & females are equally affected
129
Q

What are the characteristics of an X linked recessive pedigree?

A
  • Hemizygous males and homozygous females
  • Disease is more common in males
  • Affected males can’t give it to sons.
  • Heterozygous female carriers have 50% chance of having affected sons.
  • Daughters of affected males = heterozygous
130
Q

What is codominance?

A

When one type of allele isn’t dominant or recessive other another.

131
Q

What is complementation?

A
  • Inherited in a recessive manner

- More than one gene can be involved in producing a phenotype

132
Q

What is recombination dependant of?

A
  • Distance between genes

- Nearer they are/linked the more likely they are to become rcombinated

133
Q

What is recombinant frequency?

A
  • Unexpected phenotype due to recombination

- Number of unexpected per expected

134
Q

What is transcription and where in the cell does it occur?

A
  • ‘Copying the code’

- In the nucleus.

135
Q

What is translation in simple terms and where in the cell does it occur, and how does it reach here?

A
  • ‘Changing the language’
  • Cytoplasm
  • Via nuclear pores
136
Q

What do the following prefixes mean -RNA?

  • mRNA
  • rRNA
  • tRNA
  • miRNA
A
  • Messenger
  • Ribosomal
  • Transfer
  • Micro (gene regulation)
137
Q

What is a promoter sequence?

A
  • A sequence of DNA that initiates gene expression.
138
Q

What are the 3 stages of transcription?

A
  • Initiation
  • Elongation
  • Termination
139
Q

In transcription what is needed for initiation?

A
  • Promoter recognition
  • Transcription initiation factors
  • RNA polymerase
140
Q

What happens in elongation of transcription?

A
  • 5’-3’ chain growth
141
Q

What is termination dependant on in transcription?

A
  • Amino acid sequence
142
Q

What are the 3 stages to change pre-mRNA to mRNA?

A
  • Capping
  • Tailing/polyadenylation
  • Splicing
143
Q

What is capping?

A
  • 5’-5’ linkage created

- Protects against degradation.

144
Q

What is tailing?

A
  • RNA polymerase cleaves the RNA using specific endonuclease
  • ATP-> Pi adds adenines
  • Protects against degradation.
145
Q

What is splicing?

A
  • Removes introns and binds exons together.
146
Q

What does ORF stand for?

A
  • Open reading frame.

- The area to be translated

147
Q

What is an endonuclease and an exonuclease?

A
  • Endo breaks within polynucleotide and isn’t specific

- Exo degrades from 5’ or 3’ end depending on specificity.

148
Q

What characteristics are there of the triplet code?

A
  • Degenerative
  • Non-overlapping
  • No gaps
  • (Codons)
149
Q

In which direction is the template read and what does this produce?

A
  • 5’ to 3’

- N to C polypeptide chain

150
Q

Which are the initiation and termination codons for translation?

A
  • Initiation: AUG

- Termination: UAA/UAG/UGA

151
Q

How is the tRNA molecule described?

A
  • Clover model

- It carries different amino acids

152
Q

How does the tRNA recognise the start codon?

A
  • The anticodon loop’s 5’CAU3’ recognises 5’AUG3’
153
Q

What is Isoleucine and it’s role?

A
  • A nitrogenous base
  • Complementary to any
  • Only on 3rd base in triplet
154
Q

Outline how translation produces a polypeptide.

A
  • p site and an a site in the ribosome
  • p site contains 1st amino acid
  • Binding of aminoacyl tRNA using ATP -> ADP + Pi
  • Peptide bond forms to make polypeptide
155
Q

How is translation terminated?

A
  • Stop codon.
156
Q

How are proteins sorted?

A
  • Ribosomes attach to ER membrane if protein is destined for membrane/secretory pathway via co-transitional insertion
  • Ribosomes remain cytosolic if protein is destined for cytosol or post-transitional import into organelles.
157
Q

How do proteins know where they are destined?

A
  • Intrinsic signals to govern transfer and localisation in cells
  • Receptor to guide to correct membrane
158
Q

What are the four components required for protein sorting?

A
  • Intrinsic signal
  • Receptor which directs to correct membrane
  • Translocational machinery
  • Energy for transfer
159
Q

How are proteins imported into the mitochondrial matrix?

A
  • Protein with signal is kept unfolded by chaperones
  • Signal binds the receptor
  • Protein is fed out via pores in outer membrane
  • Targeting signal is cleaved off.
160
Q

What is PDH deficiency and its effects?

A
  • Pyruvate dehydrogenase deficiency
  • Reduced uptake into mitochondria
  • Helix breaking Proline destabilises
  • Loss of one basic residue on hydrophilic face of amphipathic helix.
161
Q

How are proteins imported into the nucleus?

A
  • Carrier protein recognises cargo protein with a NLS (nuclear location sequence)
  • Carrier protein binds to Ran-GTP
  • Change in shape displaces cargo protein
  • Imported carrier protein with Ran-GTP is recycled into cytoplasm
162
Q

What conditions are caused by the mutation of NLS?

A
  • Swyer syndrome: Mutation of NLS in sex determining section of protein, outwardly female.
  • Leri-Weill dyschondrosteosis: Skeletal development reduced, short stature.
163
Q

What is constitutive secretion?

A
  • Continuos process
  • Proteins are packed into vesicles and continuously released via exocytosis
  • e.g serum albumin, collagen
164
Q

What is regulated secretion?

A
  • Proteins release in response to a signal e.g. hormone

- Proteins are packed into vesicles but only released when signal is detected e.g. Insulin.

165
Q

What is the difference between O linked and N linked glycosylation?

A
  • N linked: Occurs mainly in the ER, carbohydrate added via N-glycosyl link to amide nitrogen on Asn
  • O linked: Occurs mainly in the Golgi, carbohydrate added via glycosidic bond to OH group of Ser or Thr
166
Q

Outline the protein secretion pathway.

A
  • Protein synthesis is initiated on free ribosomes
  • N terminal signal sequence produced
  • Recognised by the signal recognition particle (SRP)
  • GTP bound SRP direct the ribosomes synthesising the secretory protein to SRP receptors on cytosolic face of ER
  • SRP dissociates
  • Newly formed polypeptide is fed into ER via a pore in the membrane.
  • Signal is removed by signal peptidase
  • Ribosome dissociates and is recycled.
167
Q

Outline the proteolytic processing of insulin.

A
  • Initially synthesised in an inactive form, preproinsulin
  • Signal sequence is removed and 3 disulphide bonds form to create proinsulin
  • This is cut into 3 peptides by proteases, A, B and C
  • C is released, mature insulin consists of the A and B strands.
168
Q

Outline the synthesis of collagen.

HINT: CHADPOGRL.

A
  • Cleavage of signal peptide
  • Hydroxylation of Proline/Lysine residues
  • Addition of N linked oligosaccharides
  • Disulphide bond formation
  • Procollagen: Formation of triple helix
  • O linked glycosylation (addition of glucose)
  • Golgi then exocytosis
  • Removal of terminal peptides (Procollagen peptidase)
  • Lateral aggregation to form fibrils.
169
Q

LEARN THE TABLE

A
  • No really, learn it…
170
Q

Sort these into the areas where they occur:

  • O linked glycosylation
  • Trimming and modification of N linked oligosaccharides
  • N linked glycosylation
  • Signal cleavage
  • Disulphide bond formation
A 
- Golgi: Trimming and modification of N linked oligosaccharides
             O linked glycosylation
- ER: N linked glycosylation
         Signal cleavage
         Disulphide bind formation
171
Q

What are the roles of restriction enzymes and how do they work?

A
  • Recognition and degradation of foreign DNA
  • ‘Molecular scissors’
  • Specific endonucleases recognise and cut specific DNA sequences
  • Normally palindromes of 4/5/6/8 base pairs
  • Cuts are staggered to form ‘sticky ends’
  • Protection of own DNA by methylation
172
Q

How does gel electrophoresis work?

A
  • Wells with DNA
  • Negative and positive electrode.
  • DNA is negatively charged so will travel to positive end when in an electric field.
  • Smaller fragments will travel furthest through the gel.
173
Q

What are the requirements for gel electrophoresis?

A
  • Gel: matrix that allow separation
  • Buffer: allows for charge on DNA across the gel
  • Power supply: generates charge difference across the gel
  • Stain/detection: Identify the samples
174
Q

Why do we use restriction analysis?

A
  • Size of DNA
  • Mutations
  • Variation
  • Clone DNA
175
Q

What is the role of DNA ligase?

A
  • ‘Molecular glue’

- Forms phosphodiester bonds

176
Q

What are plasmids?

A
  • Small circular dsDNA
  • Found in bacteria
  • Carry genes
177
Q

How does gene cloning and introduction occur?

A
  • Plasmid vector is cut using restriction endonucleases,
  • DNA fragment is joined using DNA ligase
  • This forms a recombinant DNA molecule
  • Introduced into bacteria
  • These replicate and spread the new plasmid by vertical or horizontal means.
178
Q

What is the point in gene cloning?

A
  • To make useful proteins
  • To find out what the role of genes are
  • Genetic screening
  • Gene therapy
179
Q

Outline how PCR occurs.

A
  • Amplification of target DNA
  • Thermostable DNA polymerase
  • Pair of primers define the region to be copied
  • Temperature cycles of denaturing, H bond formation and polymerisation
  • Repeat to increase the DNA number.
180
Q

Why do we use PCR?

A
  • Amplify a specific DNA fragment
  • Investigate single base mutations
  • Investigate small deletions and insertions
  • Investigate variation and genetic relationships
181
Q

In protein gel electrophoresis what are the different ways in which the proteins can be separated?

A
  • Size
  • Shape
  • Charge (when placed in an electric field)
182
Q

How are serum proteins separated in electrophoresis?

A
  • Intensity of the blue colour shows intensity of protein concentration.
183
Q

What is SDS-PAGE?

A
  • Separation of proteins depending on their size.
184
Q

What does IEF stand for and what is it?

A
  • Isoelectric focussing
  • Proteins separation on basis of charge
  • They will migrate until they reach an area of pH that is the same as their pI
  • As there is no net charge at the pI, it won’t move any further.
185
Q

What is 2D-PAGE?

A
  • Allows the separation of complex mixtures of proteins
  • Using pH
  • Used for diagnosing disease states in different tissues
186
Q

What is proteomics?

A
  • Protein identification
  • Digest the protein with trypsin
  • Mass spectrometry
  • Generate a list of peptide sizes and compare to known data.
187
Q

What is the difference between proteomics and molecular diagnosis?

A
  • Proteomics: Analysis of all proteins expressed from a genome
  • Molecular diagnosis: Analysis of a single purified protein
188
Q

Antibodies can bind to specific protein targets know as ____

Antibodies can bind to a few amino acids on a protein know as ___

A
  • Antigens

- Epitopes

189
Q

What are polyclonal antibodies’ characteristics.

A
  • Produced by MANY Beta lymphocytes
  • Multiple different antibodies
  • Specific to 1 antigen
  • Multiple Epitopes
190
Q

What are monoclonal antibodies characteristics?

A
  • Produced from ONE beta lymphocyte
  • ONE identical antibody
  • Specific to ONE antigen
  • ONE epitope
191
Q

Outline the process of western blotting.

A
  • Nitrocellulose replica of gel electrophoresis
  • Binding of primary antibody
  • Binding of enzyme-linked secondary antibody
  • Immunoblot (proteins that are bound to the antibody are drawn up through the blot to form the stain)
  • Radioactive/fluorescent marker is used.
192
Q

What is ELSIA?

A
  • Used to measure the concentration of proteins in solution
  • Antigen joined by specific antibody, joined by enzyme-linked antibody.
  • Substrate is added which forms a coloured product
  • The rate of colour formation shows the concentration of the antibody.
193
Q

What are enzyme assays and the two different types?

Give examples

A
  • Methods of measuring product
  • Continuous: Spectrophotometry, Chemoluminescence
  • Discontinuous: Radioactivity, Chromatography
194
Q

Why do we measure enzyme levels?

A
  • Metabolic disorders in tissues

- Diagnosis of diseases (serum enzymes, e.g after an MI)

195
Q

What does dNTP and ddNTP stand for?

A
  • dNTP: deoxynucleoside triphosphate

- ddNTP: dideoxynucleoside triphosphate

196
Q

What is the Sanger chain termination method?

A
  • Add dNTPs and polymerase to cause termination at complimentary sites on complimentary strand.
  • This causes different lengths of DNA to be formed which can be measured in the gel.
  • Mark the fragments
197
Q

Outline the process of DNA hybridisation.

A
  • Heat to 95 degrees C, causing DNA to denature
  • Cool to room temperature, DNA renatures
  • Strength of the new strand depends on the number of H bonds formed between complimentary base pairs
198
Q

What is southern blotting?

A
  • Digest DNA with restriction enzymes
  • Separate DNA fragments by gel electrophoresis
  • Transfer DNA fragments to nylon (blotting)
  • Introduce labelled complimentary gene probe (hybridise filter)
  • Detect hybridisation by exposure to X-Ray film
199
Q

What is the difference between Northern and Southern blotting?

A
  • Northern is with RNA

- Southern is with DNA

200
Q

How can DNA fingerprinting be used?

A
  • Using gel electrophoresis half of the DNA should belong to the mother and other half to the father.
  • PCR is used for amplification
  • Used in paternity tests and forensics.
201
Q

Why do we use microarrays?

A
  • Investigate 1000s of genes simultaneously
  • Investigate chromosome deletions/duplications
  • Investigate conditional gene expression
202
Q

What is RTPCR?

A
  • Reverse transcriptase polymerise chain reaction.
  • From mature mRNA to DNA
  • mRNA and cDNA (complimentary)
  • Using primers and restriction endonucleases forms amplified DNA.
203
Q

What is karyotyping?

A
  • Lining up all 22 autosomal and 2 sex chromosomes visually.

- Easy to see where problem is and if male/female.

204
Q

What is FISH?

A
  • Fluoresce in situ hybridisation
  • Probe DNA
  • Label with fluorescent dye
  • Denature and hybridise, those that fluoresce must be the wanted DNA, only those complimentary to the probe will fluoresce.
205
Q

Why do we use FISH?

A
  • Investigate: Genes in situ (in the cell)

Chromosomal number/structure/behaviour.

206
Q

What are single base substitutions also known as?

A
  • SNPs: Single nucleotide polymorphisms
207
Q

What is the difference between transitions and transversions?

A
  • Transitions: Purine to purine / Pyrimidine to pyramidine.

- Transversions: purine to pyramidine or vice versa.

208
Q

How many codon triplets and stop codons are there per amino acid typically?

A
  • 1/2/3/4/6 codons

- 3 stop codons

209
Q

What is a missense mutation?

A
  • One amino acid is substituted by another.
210
Q

What is a silent mutation?

A
  • Single base substitution which doesn’t substitute the amino acid.
211
Q

What is a nonsense mutation?

A
  • Amino acid codon changes to a stop codon.
212
Q

What is a frameshift?

A
  • Reading frame of mRNA is altered in some way.

- Insertions/deletions/splice-site mutations

213
Q

What is meant by conservative missense mutations?

A
  • Some amino acid substitutions are better tolerated than others.
  • Due to their polarity/size/charge
214
Q

When can base deletions/insertions not have an affect on the reading frame?

A
  • When they’re a multiple of 3
215
Q

What happens if a single base pair is inserted/deleted?

A
  • Frameshift

- Premature termination codons (PTC)

216
Q

What may occur if mRNA contains a PTC?

A
  • Be degraded by nonsense mediated decay
  • No/Very little protein’s produced.
  • A protective mechanism
217
Q

What may occur if there is a mutation at an intron splice site?

A
  • The adjacent exon may be skipped
218
Q

What are the 3 main causes of mutation? Give examples

A
  • Sequence changes during replication: Tautomeric shifts/DNA strand slippage
  • Chemicals: Direct alteration of DNA bases/Disruption of DNA base stacking
  • Exposure to radiation: UV/Radioactive substances
219
Q

What is a Tautomeric shift and what can it lead to?

A
  • 4 bases in DNA, proton briefly changes position.
  • Leading to altered base pairing properties
  • They behave as an altered template base during replication.
  • Anomalous base-pairing: Tautomeric forms cause C to bind to A and T to G
220
Q

What happens when slippage occurs during replication?

On newly synthesised and template.

A
  • If newly synthesised strand loops out: addition of one nucleotide on new strand
  • If the template strand loops out: omission of one nucleotide on new strand.
221
Q

What affect on the bases can chemicals have?

A
  • Amino acids are replaced with Keto groups.
  • C -> U and binds with A
  • A -> H and binds with C
  • G -> X and binds with C
  • EMS causes removal of purine rings.
222
Q

Outline what base stacking mutagens are and what causes it.

A
  • IQ found in cooked meats and cigarette condensations
  • Disrupts packaging of DNA bases and causes SNPs at GC base pairing.
  • Intercalation of IQ forces the bases apart leading to misreading by DNA polymerase and a deletion of a single base.
223
Q

Give 4 examples of ionising radiation.

A
  • Solar
  • X-rays
  • Nuclear
  • Environmental sources (Radon)
224
Q

What are the main effects of UV A,B and C?

A
  • UVA/B/C: all damage collagen fibres, so has ageing effects.
  • UVB: Sunburn and skin cancer (overexposure)
  • UVA/B: Destroys Vitamin A in the skin
225
Q

What is thymine dimer formation and how is it caused?

A
  • UV light

- Causes adjacent Thymine bases to pair together.

226
Q

What is nucleotide mismatch repair?

A
  • After replication enzymes detect mismatched bases in the new strand and replace them.
227
Q

What is excision repair?

A
  • DNA accumulates damaged bases by: Oxidation/De-aminated/Uracil/Alkylated
  • Repaired by base excision repair.
228
Q

What are the 6 characteristics of cancerous growth.

A
  • Divide independently of external growth signals
  • Ignore external anti-growth signals
  • Avoid apoptosis (programmed cell death)
  • Divide indefinitely
  • Stimulate sustained angiogenesis (blood vessels forming from existing ones)
  • Invade tissues and establish secondary tumours
229
Q

All cancer cells exhibit what two things?

A
  • Chromosomal instability

- Micro-satellite instability.

230
Q

What are BRCA1 and BRCA2 responsible for? And how do their effects make screening more cost effective?

A
  • Inheritable breast cancer

- Only effects certain populations (Families with known history are more likely to affect males)

231
Q

When are oncogenes dangerous?

A
  • When they have been activated and changed from proto-oncogenes to oncogenes
  • Caused by key amino acid substitutions.
232
Q

How is a cancerous tumour initiated?

A
  • Only when both copies are mutated or the functional copies are deleted. (Proto-oncogenes and tumour suppressor)
  • Knudson’s two hit theory
233
Q

Is cancer more likely to occur in sporadic or heritable conditions and why?

A
  • Heritable: pre-existing mutation, only one more needed in any cell so more likely
  • Sporadic: only one cell mutated, second mutation must affect the same cell, so is less likely,
234
Q

What is SSCP mutation scanning?

A
  • Identify mutated region
  • Heat the amplified DNA to denature
  • Snap cool it, individual strands will adopt a sequence specific partly double stranded forms.
  • DNA’s electrophoresed and detected by silver, use known data to identify.
  • SSCP: Single strand conformation polymorphism.
235
Q

What are the 3 main ways of obtaining foetal DNA?

A
  • Amniotic fluid cells (15-20 wks)
  • Chorion villus biopsy (10-13wks)
  • Foetal DNA in mother’s blood (no risk of miscarriage)
236
Q

How are karyotypes arranged?

A
  • In decreasing size order

- Except 22 and 21

237
Q

How are chromosomes grouped?

A
  • Similar size

- Location of centromere

238
Q

What is special about acrocentric chromosomes?

A
  • Nucleus near the top

- Satellites

239
Q

How are chromosomes reported?

A
  • 1st number of chromosomes
  • 2nd sex chromosomes observed
  • e.g normal female: 46XX
240
Q

When would you be inclined to use karyotyping?

A
  • Parental screening (especially >35yrs/family history)
  • Birth defects (malformation/mental development impairment)
  • Abnormal sexual development (Turner/Klinefelter)
  • Infertility
  • Recurrent foetal loss
  • Leukaemia
241
Q

How does diagnosis help?

A
  • Accurate prognosis
  • Better management from an earlier age
  • Understanding reproductive risks
  • Prenatal-chance to terminate
242
Q

What is polyploidy and give an example report for one.

A
  • When the number of chromosomes is a multiple of 23
  • e.g. Tetraploidy: 4n: 92XXXX
  • Life is impossible.
243
Q

What is the cause of polyploidy?

A
  • Polyspermy: fertilisation of an egg by more that none sperm.
244
Q

What is aneuploidy?

A
  • Abnormal number of chromosomes not a multiple of haploid number.
  • Monosomy: Loss of 1 homologous pair of chromosomes 45X (Turner syndrome)
  • Trisomy: Gain of 1 homologous pair of chromosomes. 47XXY (Kleinfelter syndrome) or 47XX +21 (Down syndrome)
247
Q

What is anaphase lag?

A
  • When chromosomes are left behind at cell division due to defects in spindle function/attachment to chromosomes.
  • Lagging chromosomes can be lost entirely.
248
Q

What are the only 3 viable autosomal trisomies?

A
  • Trisomy 21: Down syndrome
  • Trisomy 18: Edwards syndrome
  • Trisomy 13: Patau syndrome.
249
Q

What are the symptoms of Down syndrome?

A
  • Mild-moderate intellectual disability
  • Congenital heart disease
  • Hypothyroidism
  • Constipation (lack of nerves in colon)
  • Infertility in males, reduced in females
  • Eye disorders
  • Hearing disorders.
  • Haematological malignancies
250
Q

What are the karyotype reports for Edwards and Patau syndrome?

A
  • Edwards: 47XX+18 (5-15 days lifespan)

- Patau: 47XY+13 (80% die within first year)

251
Q

What happens when there is more than one X chromosome in a human cell?

A
  • The only one is active
  • Others are inactivated and form Barr bodies
  • These are seen at the peripheral of cell nucleus.
252
Q

What is Turner syndrome?

A
  • 45X
  • Phenotypic females
  • Short, broad chested, low set ears, webbed neck, CV problems, infertile.
253
Q

Why is having a single X chromosome a problem?

A
  • Turner syndrome patients are monosomic for genes in PAR1 and PAR2
254
Q

What is triple X syndrome?

A
  • 47XXX
  • 2 of 3 chromosomes are inactivated
  • Symptoms: Tall, small head, delayed motor skills/speech, learning disabilities
  • Auditory processing defects
  • Scoliosis.
255
Q

What is Klinefelter syndrome?

A
  • 47XXY
  • Symptoms show after onset of puberty
  • Reduced testosterone production
  • Gynocomastia (Increased beast tissue)
  • Learning language and reading impairment
  • Treatment: hormones and surgery.
256
Q

What is XXY syndrome?

A
  • 47XXY
  • Phenotype: essentially normal
  • Slightly lower IQ levels.
257
Q

What is translocation?

A
  • No loss of genetic material just rearrangement between two homologous chromosomes
  • Consequences: Break point BETWEEN genes- no phenotype
    Risk of passing on derivative chromosome.
    Offspring may have diseased phenotype.
258
Q

What is reciprocal translocation?

A
  • No loss of genetic material

- Direct exchange of genetic material

259
Q

What is Robertsonian translocation?

A
  • Rearrangement of genetic material between two chromosomes: the q arms of 2 acrocentric chromosomes combine to form one ‘super chromosome’ with the loss of both p arms
  • Inappropriate recombination between these RNA genes can lead to a head to head chromosome translocation (fusion) and some genetic material can be lost.
260
Q

Write the karyotype report for the following:

  • Down syndrome male with a 14/21 Robertsonian translocation
  • 2 free chromosomes on 21 and translocated copy
  • Only one free chromosome 14 and translated copy.
A
  • 46 XY, -14, +t(14q;21q)
261
Q

What would be the report for a Down syndrome male involving a 21,21 Robertsonian translocation?

A
  • 46 XY, -21,-21, +t(21;21)
262
Q

What is an interstitial and a terminal deletion?

A
  • Interstitial - internally

- Terminal - ends

263
Q

What is the Philadelphia chromosome useful for diagnosing?

A
  • Chronic myelogenous leukaemia

- It’s a highly sensitive indicator.

264
Q

What are paints used for when trying to diagnose a disease?

A
  • Paints are chromosome specific FISH probes
  • Can be specific for one or more chromosomes or just part of one
  • Good for gross alterations, easy to see where the alteration is.
265
Q

For high resolution banding what techniques are used?

A
  • Multicolour FISH
  • Multicolour chromosome bonding
  • Fluorescent bond/chromosome specific probes are hybridised to chromosomes which can then be analysed by computers.
266
Q

How can flucloxacillin inhibit the production of a cell wall?

A
  • Flucloxacillin is structurally similar to the terminal amino acid on the peptide side chain.
  • It can bind to the transpeptidase enzyme and prevent it from working.
  • The Peptidoglycan layer of the cell wall cannot be maintained and so it is weakened and lysis occurs leading to cell death.
267
Q

What is the composition of a bacterial cell wall?

A
  • Peptidoglycan: strong cross linked layer of amino sugars.

- The cross links are formed between a glycine residue and an amino sugars (N Acetylmuramic acids)

268
Q

How do bacteria generally become resistant to beta lactam antibiotics?

A
  • Produce beta lactamases
  • This cleaves the antibiotic at the penicillin structure’s centre.
  • Rendering it useless.
269
Q

How does Flucloxacillin normally overcome bacterial resistance?

A
  • It has a bulky side chain that protects the penicillin ring.
270
Q

How have some bacteria become resistant to Flucloxacillin?

A
  • Change the structure of the protein that Flucloxacillin binds to.
  • Thus no longer binding to the transpeptidase so it remains active.
271
Q

How can bacteria obtain resistance?

A
  • Mutation in the gene coding for penicillin binding proteins
  • High error rate in bacterial DNA replication means mutations are common.
  • Vertically or horizontally via conjugation tubes.
  • Resitant bacteria soon become dominant as Flucloxacillin wipes out all non resistant strains.
272
Q

Why does Flucloxacillin not affect eukaryotic cells?

A
  • Eukaryotes don’t have cell walls so no Peptidoglycan cross linkages to break.
273
Q

What are the clinical applications of Flucloxacillin?

A
  • Therapy to treat skin and musculoskeletal disorders causes by staphylococci bacteria.
274
Q

How can an antibiotic that inhibits transcription inhibit cell growth?

A
  • No transcription
  • No translation
  • No protein synthesis
  • No cell growth.
275
Q

How does normal bacterial transcription occur?

A
  • One RNA polymerase transcribes all DNA
  • RNA polymerase binds DNA unwinding the double helix
  • mRNA is formed
276
Q

How does Rifampicin stop transcription?

A
  • Sterically blocks synthesis of 2nd or 3rd phosphodiester bonds
  • Polymerase dissociates from DNA
  • mRNA degrades.
277
Q

Why is Rifampicin only specific to prokaryotic cells?

A
  • Transcription in prokaryotes occurs in the cytoplasm and is done by only one RNA polymerase.
  • Different amino acid sequences between eukaryotes and prokaryotes RNA polymerases
  • Only specific to prokaryotic DNA dependant RNA polymerases.
278
Q

How can translation be inhibited in bacteria?

A
  • Bind to a 30s subunit of ribosome
  • Blocking the amino-Acyl tRNA to the A site of the ribosome complex.
  • Thus no more amino acids can join the polypeptide chain.
279
Q

What are the the three main ways that bacteria obtains resistance to translation preventing antibiotics?

A
  • Increase efflux of drug (ability to remove the drug from the bacterial cell so the conc is lower)
  • Limiting penetration of antibiotics (so less can enter the cell)
  • Decrease the ability to bind to the ribosome hence reducing affinity.
280
Q

Why is tetracycline only specific to prokaryotic cells?

A
  • Only affects 30s subunit of ribosomes

- Eukaryotes don’t contain 30s

281
Q

What is a folate and how is it incorporated into the body?

A
  • Needed to synthesise dNTPs
  • dNTPs are needed for DNA and RNA synthesis
  • Vitamin B9 from the diet.
282
Q

What is an anti-folate and it’s uses?

A
  • Impair the function of folates
  • Chemotherapy
  • Antibiotic agent.
283
Q

How is methotrexate an anti-folate? Outline it’s mechanism.

A
  • Methotrexate inhibits DHF
  • Dihydrofolate can’t become trihydrofolate
  • Trihydrofolates synthesise thymidylates
  • Which in turn synthesise RNA/DNA
284
Q

How is methotrexate specific?

A
  • It isn’t folates exists in both eukaryotes and prokaryotes
  • Possible to prevent the synthesis of folates.
  • Can’t distinguish between cancerous and non-cancerous cells.
285
Q

How can resistance to methotrexate occur?

A
  • Decrease retention
  • Increase levels of DHFR
  • Mutated DHFR binds less readily to methotrexate
288
Q

What occurs when non-disjunction occurs in mitosis?

A
  • Leads to two populations of cells with different karyotypes - Mosaic.
294
Q

What is the cause of aneuploidy?

A
  • Non-disjunction at meiotic cell division

- Creation of a gamete with a missing/additional (therefore both) chromosome.

Medicine Semester 1 (6 decks)

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