MGD Flashcards
(286 cards)
0
Q
How are monomeric units joined to form macromolecules?
A
- Covalent bonds
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
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.
3
Q
What may happen if the interactions are broken?
A
- Loss of structure and therefore function.
4
Q
What is meant by amphipathic?
A
- Both a polar and non-polar end (hydrophilic and hydrophobic)
5
Q
What are the main roles of proteins?
A
- Structural support
- Immune protection
- Ligands in cell signalling
- Catalysts
- Transporters
- Machines
- Ion channels
- Receptors
6
Q
What is a zwitterion?
A
- NH3+
- COO-
- Both present.
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.
8
Q
What does polar mean?
A
- Non-symmetrical for electronegativity
9
Q
Determine which of the following are hydrophobic/hydrophilic:
- Non-polar
- Polar uncharged
- Polar charged
A
- Non-polar: hydrophobic
- Polar: Hydrophilic
10
Q
If the pH of a solution is LESS than the pK value what happens?
A
- Protonation
11
Q
If the pH of a solution is greater than the pK value what occurs?
A
- Deprotonation
12
Q
How does a peptide bond form?
A
- Elimination of a water molecule to form a peptide bond between two amino acids
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.
14
Q
What is the isoelectric point? (pI)
A
- The point at which there is no overall net charge.
15
Q
If the pH is smaller than the pI what happens?
A
- Protonation as there are many H+ present to join.
16
Q
If the pH is greater than the pI what occurs?
A
- Deprotonation as there are many OH- present to take H+ away.
17
Q
What are the different types of peptide lengths?
A
- Peptide
- Oligopeptide
- Polypeptide
- Protein
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.
19
Q
What are the two termini on primary amino acid structures called?
A
- Amino
- Carboxyl
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.
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
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.
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)
24
How does a Beta pleated sheet form?
- 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.
25
What is the difference between a parallel and antiparallel beta pleated sheet?
- Antiparallel the binding O and H are DIRECTLY opposite each other.
- Parallel the binding O and H are diagonal to each other.
26
What are the roles and characteristics of globular proteins?
- Roles: Catalysts, regulation
- Compact shape
- Several types of secondary structure
- e.g: haemoglobin
27
What are the roles and characteristics of fibrous proteins?
- Roles: Support, shape and protection
- Long strands/sheets
- Single type of repeating secondary structure
- e.g: collagen
28
Give 4 characteristics of collagen.
- Triple helix
- Gly-X-Y repeating sequence
- H bonds between chains
- Striated due to the staggered arrangements.
29
How are collagen fibrils formed?
- Covalently cross-linked collagen molecules.
30
What are motifs and domains and what type of structure are they?
- 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.
31
How are membrane proteins folded and why?
- '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.
32
What types of bonds/forces are present in the 4 types of protein structure?
- Primary: Covalent (peptide)
- Secondary: H bonds
- Tertiary & Quaternary: Covalent (disulphide), Ionic, H bonds, Van der Waals and hydrophobic interaction.
33
What is hydrophobic interaction?
- Interaction between hydrophobic side chains due to displacement of H2O
34
How do disulphide bonds form?
- Between Cysteine residues
| - Oxidise the cysteine to join via disulphide bond
35
Where are molecules with disulphide bonds found?
- Secretions as move into harsh conditions so need greater strength.
36
What is protein denaturation?
- Breaking of bonds to unfold proteins.
37
What factors can cause denaturation and why?
- Heat: Increase vibrational energy
- pH: Alters ionisation states of amino acids.
- Detergents/organic solvents disrupt hydrophobic interactions.
38
Is folding of proteins random?
| How is it sped up?
- No
| - Molecular chaperones needed.
39
What is amyloidoses?
- Accumulation of mis-folded proteins.
40
What are amyloid fibres?
- Misfolded, insoluble for of a naturally soluble protein.
| - This can cause disease.
41
What does a Haem group consist of?
- Protoporphyrin ring and Fe atom bound to 4 N atoms of the ring.
42
How can Haem groups carry oxygen?
- Fe2+ can make two additional binds to O2 one on each side of the plane.
43
The haemoglobin has two histidine residues what are their roles?
- Proximal: binds the Fe group to the protein.
| - Distal histidine stabilises.
44
When an oxygen molecule binds to the haem group what happens and how does this affect the O2 affinity?
- 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
45
Why is a sigmoidal shaped PO2 curve significant?
- Allows for oxygen to be loaded/unloaded in the lungs/tissues depending on pO2
46
What is the role of 2,3 bisphosphoglycerate?
- 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.
47
How does BPG decrease the affinity for oxygen?
- By stabilising the T state so the affinity doesn't increase with more O2.
- (Lower affinity = further to the right)
48
What is the Bohr effect?
- Binding of H+ and CO2 lowers the affinity.
| - More acidic so more O2 needs to be unloaded.
49
Why is CO poisonous to humans?
- 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
50
How do foetuses obtain O2?
- HbF has a higher binding affinity for oxygen than HbA does (normal haemoglobin)
- So the oxygen transfers from the mother to the foetus.
51
What are hue he secondary subunits that form:
- HbA
- HbF
- HbA2
- HbA: 2 alpha, 2 beta
- HbF: 2 alpha, 2 gamma
- HbA2: 2 alpha, 2 delta
52
What is the mutation responsible for sickle cell anaemia?
- Glutamine -> Valine
| - Charged hydrophilic -> uncharged hydrophobic.
53
How do sticky hydrophobic pockets form?
- Valine allows deoxygenated HbS to polymerase.
54
What is the effect of sickle cell anaemia?
- 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.
55
What is a thalassaemia?
- Imbalance of beta/alpha globin chains
56
What is a beta thalassaemia and what are the effects?
- Absent/lower B-globin chain production
- Alpha chains are unable to form stable tetramers
- Only form ppt.
- Symptoms after birth
57
What is alpha thalassaemia?
- 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.
58
What is the transition state?
- The high energy intermediate that lies between substrate and product
59
What is the activation energy?
- The minimum energy the substrate must have to allow reaction.
60
What are the roles of enzymes?
- 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)
61
What clinical roles do enzymes have?
- Inheritable genetic disorders
- Overactive enzyme can = disorder
- Measurement of enzyme activity for diagnosis (TSH/T4)
- Inhibition of enzymes by drugs.
62
What is an active site and it's role?
- 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.
63
What does a reaction rate-substrate concentration graph look like?
- Curve
| - Rate of increase is decreasing until it plateaus when all active sites are filled.
64
Finish the equation: Vo =
- Vo = Vmax (S) / Km + (S)
65
What does Vmax stand for?
- The maximum rate of reaction when all enzyme active sites are saturated with substrate.
66
What is Km?
- The substrate concentration that gives half maximum velocity
67
What does a low Km signify?
- Low Km = High affinity for the substrate
| - High Km = Low affinity for the substrate
68
If you double the amount of enzyme what happens to the standard rate?
- The standard rate DOESNT double.
69
On a Lineweaver-Burk plot what does the x and y intercepts signify?
- x intercept: -1/Km
| - y intercept: 1/Vmax
70
What is the y axis and x axis on a Lineweaver-Burk plot?
- y axis: 1/V (1/rate)
| - x axis: 1/(S)
71
Give an example of an irreversible inhibitor and why is it irreversible?
- Sarin nerve gas
| - Very tightly bound
72
What types of reversible binding is there?
- Competitive and non-competitive
| - Non-covalent bonds used, so freely dissociates.
73
What are the effects on Vmax and Km of competitive inhibitors?
- Increased Km (more substrate required, decrease in affinity)
- Vmax doesn't change ((S) can outcompete the inhibitor)
74
What is the effect on Vmax and Km for non-competitive inhibitors?
- Km doesn't change: (Affinity is the same)
| - Vmax decreases: (Fewer active sites available as prevents binding)
75
What is an isoemzyme?
- Different forms of the same enzyme that have different kinetic properties
76
What is product inhibition?
- Accumulation of the product of a reaction inhibits the forward reaction.
77
What does allosteric mean?
Binds to anywhere but the active site.
78
What does an allosteric activator/inhibitor do?
- Activator: Increases the proportion of enzymes in the R state (higher affinity)
- Inhibitor: Increases the proportion of enzymes in the T state (lower affinity)
79
Which enzyme is the main regulator of glycolysis?
- Phosphofructokinase
80
What activates/inhibits the forward reaction of the phosphofructokinase dependant step of glycolysis?
- Activators: AMP, Fructose-2-6-bisphosphate
| - Inhibitors: ATP (large amounts present no more is required) H+, citrate.
81
How does phosphorylation occur?
- Protein kinases
- Transfers the terminal Pi from ATP
- To the OH group of Ser, Thr, Thy.
- Condensation reaction.
82
How does dephosphorylation occur?
- Protein phosphatases catalyse:
| - Hydrolytic removal of phosphoryl groups from proteins
83
Why is amplification of enzyme cascades useful?
- Enzymes activate other enzymes
| - The number of affected molecules increases rapidly.
84
What are zymogens?
- Inactive precursors of digestive enzymes
| - Not needed all the time, only activated by specific proteolytic cleavage.
85
What are the common prefixes/suffixes for zymogens?
- -ogen
| - Pro- (if ends in -ase)
86
Give 5 uses of proteolytic cleavage.
- Zymogens
- Some protein hormones (Insulin)
- Blood clotting
- Developmental processes (tissue remodelling)
- Programmed cell death,
87
Outline the blood clotting cascade.
- 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
88
How does thrombin lead to a fibrin clot forming?
- 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)
89
How is the fibrin clot maintained?
- Positive feedback loop
| - When limited proteolysis by thrombin/factor Xa occurs this is the positive feedback so more Factor XII is formed.
90
How can clotting be stopped?
- 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
91
Outline how clots are broken down.
- Fibrinolysis
- Plasminogen is activated by t-PA/streptokinase to form plasmin
- Plasmin catalyses the fibrin -> fibrin fragments reaction
92
When looking at a nucleus, what are the light and dark patches?
- Light: Euchromatin, beads on a string, genes expressed
| - Dark: Heterochromatin, solenoid 30nm fibre, genes not expressed
93
What is a nucleosome?
- Histone wrapped in DNA
94
When DNA is wrapped into a chromosome are the genes expressed?
- No
95
What are genes?
- Stretch of DNA with a chromosomal locus
| - Codes for a protein and it's regulation
96
In the human genome how many chromosomes are they and how are they split?
- 24
- 22 autosomal
- 2 sex
97
What is a nucleotide comprised of?
- Nitrogenous base
- Deoxyribose sugar
- Phosphate molecule
98
What is a nucleoside comprised of?
- Nitrogenous base
| - Deoxyribose sugar
99
Which of the nitrogenous bases are:
1) Pyrimidines
2) Purines
- 1) Thymine, (Uracil), Cytosine
| - 2) Arginine, Guanine.
100
Which of the nitrogenous bases have
1) 2 H bonds
2) 3 H bonds
- 1) A & T(U)
| - 2) C & G
101
How are nucleotides connected?
- Phosphodiester bonds
102
In a polynucleotide which direction is polarity and how are the ends distinctive?
- 5' - 3'
| - 5'P - 3'OH
103
How are duplex structures formed?
- They are secondary structures of polynucleotides
- Strands are complimentary & antiparallel
- H bonds form between the antiparallel complimentary sequences
104
Give two examples of antiparallel strands of DNA/RNA
- RNA stem loops-tRNA
| - Right handed double helix
105
What are the roles of the major and minor group of the double helix?
Major is more exposed and allows enzymes to bond.
106
What are the four stages of the cell cycle?
- Growth 1: Cell content replication
- Synthesis: DNA replication
- Growth 2: Double check and repair
- Mitosis: Cell division
107
What are the stages of replication in prokaryotes?
- Initiation
- Elongation
- Termination
108
What happens in the initiation stage?
- Recognition of origin of replication
- Requires DNA polymerase
- Requires a kick start by primase.
109
Outline the elongation stage.
- Moving replication forks
- Helicase unwinds double helix
- DNA polymerase extends at 3' end
- DNA ligase joins lagging strands.
110
How does termination occur?
- Replication forks join and leading and lagging strands join by DNA ligase
- Number of chromosomes stays the same.
111
When a chromosome is replicated how many DNA molecules are formed from how many?
- 2 from 1
112
On a chromosome which is the p and q arm?
- p arm: shorter 'petit'
| - q arm: longer
113
In mitosis what are the 5 stages and what are their roles?
- 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
114
What are the results of mitosis?
- Production of 2 identical daughter cells
- Necessary for: epidermis, bone marrow, mucosa
- Cell division for somatic cells.
115
Name the position of a nucleus as it ascends up the chromosome.
- Metacentric
- Submetacentric
- Acrocentric
- Telocentric
116
What are the products of meiosis?
- Germline cell division
- 4 non-identical cells (½ content of parent cells)
- Diploid -> haploid
- Egg and sperm production
117
Outline meiosis.
- 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
What is the point of meiosis?
- Maintaining constant chromosome number from generation to generation
- Generation of genetic diversity: - Random assortment of chromosomes & Crossing over of genetic material
119
What is spermatogenesis?
- Production of sperm
- 1 spermatocyte (2n) -> 4 sperm (n)
- Spermatogenesis = 248 days
120
What is Oogenesis?
- Production of eggs
- 1 oocyte (2n) = 1 egg (n) and 3 polar bodies (these disappear)
- Takes ~ 12-50 yrs
121
What are the consequences of faulty meiosis?
- ⅓ of all identified miscarriages
- Infertility
- Mental retardation
122
What does homozygous mean?
- 2 alleles of a gene are the same
123
What does heterozygous mean?
- 2 alleles of a gene are different
124
What does hemizygous mean?
- Only one allele of a gene on the X chromosome (i.e. Males only)
125
What does dominant and recessive mean?
- Dominant: dominant determines the phenotype
| - Recessive: non-dominant allele in a heterozygous is recessive
126
How would you depict a carrier of a disease?
- Half is shaded in.
127
What are the characteristics of a autosomal recessive pedigree?
- Males and females are equally affected
- Can skip generations
- Parents are heterozygous carriers
128
What are the characteristics of an autosomal dominant pedigree?
- Rare
- Every affected individual has 50% chance of having affected offspring.
- CANT skip generations
- Males & females are equally affected
129
What are the characteristics of an X linked recessive pedigree?
- 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
What is codominance?
When one type of allele isn't dominant or recessive other another.
131
What is complementation?
- Inherited in a recessive manner
| - More than one gene can be involved in producing a phenotype
132
What is recombination dependant of?
- Distance between genes
| - Nearer they are/linked the more likely they are to become rcombinated
133
What is recombinant frequency?
- Unexpected phenotype due to recombination
| - Number of unexpected per expected
134
What is transcription and where in the cell does it occur?
- 'Copying the code'
| - In the nucleus.
135
What is translation in simple terms and where in the cell does it occur, and how does it reach here?
- 'Changing the language'
- Cytoplasm
- Via nuclear pores
136
What do the following prefixes mean -RNA?
- mRNA
- rRNA
- tRNA
- miRNA
- Messenger
- Ribosomal
- Transfer
- Micro (gene regulation)
137
What is a promoter sequence?
- A sequence of DNA that initiates gene expression.
138
What are the 3 stages of transcription?
- Initiation
- Elongation
- Termination
139
In transcription what is needed for initiation?
- Promoter recognition
- Transcription initiation factors
- RNA polymerase
140
What happens in elongation of transcription?
- 5'-3' chain growth
141
What is termination dependant on in transcription?
- Amino acid sequence
142
What are the 3 stages to change pre-mRNA to mRNA?
- Capping
- Tailing/polyadenylation
- Splicing
143
What is capping?
- 5'-5' linkage created
| - Protects against degradation.
144
What is tailing?
- RNA polymerase cleaves the RNA using specific endonuclease
- ATP-> Pi adds adenines
- Protects against degradation.
145
What is splicing?
- Removes introns and binds exons together.
146
What does ORF stand for?
- Open reading frame.
| - The area to be translated
147
What is an endonuclease and an exonuclease?
- Endo breaks within polynucleotide and isn't specific
| - Exo degrades from 5' or 3' end depending on specificity.
148
What characteristics are there of the triplet code?
- Degenerative
- Non-overlapping
- No gaps
- (Codons)
149
In which direction is the template read and what does this produce?
- 5' to 3'
| - N to C polypeptide chain
150
Which are the initiation and termination codons for translation?
- Initiation: AUG
| - Termination: UAA/UAG/UGA
151
How is the tRNA molecule described?
- Clover model
| - It carries different amino acids
152
How does the tRNA recognise the start codon?
- The anticodon loop's 5'CAU3' recognises 5'AUG3'
153
What is Isoleucine and it's role?
- A nitrogenous base
- Complementary to any
- Only on 3rd base in triplet
154
Outline how translation produces a polypeptide.
- 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
How is translation terminated?
- Stop codon.
156
How are proteins sorted?
- 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
How do proteins know where they are destined?
- Intrinsic signals to govern transfer and localisation in cells
- Receptor to guide to correct membrane
158
What are the four components required for protein sorting?
- Intrinsic signal
- Receptor which directs to correct membrane
- Translocational machinery
- Energy for transfer
159
How are proteins imported into the mitochondrial matrix?
- 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
What is PDH deficiency and its effects?
- Pyruvate dehydrogenase deficiency
- Reduced uptake into mitochondria
- Helix breaking Proline destabilises
- Loss of one basic residue on hydrophilic face of amphipathic helix.
161
How are proteins imported into the nucleus?
- 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
What conditions are caused by the mutation of NLS?
- Swyer syndrome: Mutation of NLS in sex determining section of protein, outwardly female.
- Leri-Weill dyschondrosteosis: Skeletal development reduced, short stature.
163
What is constitutive secretion?
- Continuos process
- Proteins are packed into vesicles and continuously released via exocytosis
- e.g serum albumin, collagen
164
What is regulated secretion?
- 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
What is the difference between O linked and N linked glycosylation?
- 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
Outline the protein secretion pathway.
- 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
Outline the proteolytic processing of insulin.
- 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
Outline the synthesis of collagen.
| HINT: CHADPOGRL.
- 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
LEARN THE TABLE
- No really, learn it...
170
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
```
- Golgi: Trimming and modification of N linked oligosaccharides
O linked glycosylation
- ER: N linked glycosylation
Signal cleavage
Disulphide bind formation
```
171
What are the roles of restriction enzymes and how do they work?
- 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
How does gel electrophoresis work?
- 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
What are the requirements for gel electrophoresis?
- 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
Why do we use restriction analysis?
- Size of DNA
- Mutations
- Variation
- Clone DNA
175
What is the role of DNA ligase?
- 'Molecular glue'
| - Forms phosphodiester bonds
176
What are plasmids?
- Small circular dsDNA
- Found in bacteria
- Carry genes
177
How does gene cloning and introduction occur?
- 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
What is the point in gene cloning?
- To make useful proteins
- To find out what the role of genes are
- Genetic screening
- Gene therapy
179
Outline how PCR occurs.
- 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
Why do we use PCR?
- Amplify a specific DNA fragment
- Investigate single base mutations
- Investigate small deletions and insertions
- Investigate variation and genetic relationships
181
In protein gel electrophoresis what are the different ways in which the proteins can be separated?
- Size
- Shape
- Charge (when placed in an electric field)
182
How are serum proteins separated in electrophoresis?
- Intensity of the blue colour shows intensity of protein concentration.
183
What is SDS-PAGE?
- Separation of proteins depending on their size.
184
What does IEF stand for and what is it?
- 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
What is 2D-PAGE?
- Allows the separation of complex mixtures of proteins
- Using pH
- Used for diagnosing disease states in different tissues
186
What is proteomics?
- Protein identification
- Digest the protein with trypsin
- Mass spectrometry
- Generate a list of peptide sizes and compare to known data.
187
What is the difference between proteomics and molecular diagnosis?
- Proteomics: Analysis of all proteins expressed from a genome
- Molecular diagnosis: Analysis of a single purified protein
188
Antibodies can bind to specific protein targets know as ____
| Antibodies can bind to a few amino acids on a protein know as ___
- Antigens
| - Epitopes
189
What are polyclonal antibodies' characteristics.
- Produced by MANY Beta lymphocytes
- Multiple different antibodies
- Specific to 1 antigen
- Multiple Epitopes
190
What are monoclonal antibodies characteristics?
- Produced from ONE beta lymphocyte
- ONE identical antibody
- Specific to ONE antigen
- ONE epitope
191
Outline the process of western blotting.
- 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
What is ELSIA?
- 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
What are enzyme assays and the two different types?
| Give examples
- Methods of measuring product
- Continuous: Spectrophotometry, Chemoluminescence
- Discontinuous: Radioactivity, Chromatography
194
Why do we measure enzyme levels?
- Metabolic disorders in tissues
| - Diagnosis of diseases (serum enzymes, e.g after an MI)
195
What does dNTP and ddNTP stand for?
- dNTP: deoxynucleoside triphosphate
| - ddNTP: dideoxynucleoside triphosphate
196
What is the Sanger chain termination method?
- 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
Outline the process of DNA hybridisation.
- 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
What is southern blotting?
- 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
What is the difference between Northern and Southern blotting?
- Northern is with RNA
| - Southern is with DNA
200
How can DNA fingerprinting be used?
- 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
Why do we use microarrays?
- Investigate 1000s of genes simultaneously
- Investigate chromosome deletions/duplications
- Investigate conditional gene expression
202
What is RTPCR?
- Reverse transcriptase polymerise chain reaction.
- From mature mRNA to DNA
- mRNA and cDNA (complimentary)
- Using primers and restriction endonucleases forms amplified DNA.
203
What is karyotyping?
- Lining up all 22 autosomal and 2 sex chromosomes visually.
| - Easy to see where problem is and if male/female.
204
What is FISH?
- 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
Why do we use FISH?
- Investigate: Genes in situ (in the cell)
| Chromosomal number/structure/behaviour.
206
What are single base substitutions also known as?
- SNPs: Single nucleotide polymorphisms
207
What is the difference between transitions and transversions?
- Transitions: Purine to purine / Pyrimidine to pyramidine.
| - Transversions: purine to pyramidine or vice versa.
208
How many codon triplets and stop codons are there per amino acid typically?
- 1/2/3/4/6 codons
| - 3 stop codons
209
What is a missense mutation?
- One amino acid is substituted by another.
210
What is a silent mutation?
- Single base substitution which doesn't substitute the amino acid.
211
What is a nonsense mutation?
- Amino acid codon changes to a stop codon.
212
What is a frameshift?
- Reading frame of mRNA is altered in some way.
| - Insertions/deletions/splice-site mutations
213
What is meant by conservative missense mutations?
- Some amino acid substitutions are better tolerated than others.
- Due to their polarity/size/charge
214
When can base deletions/insertions not have an affect on the reading frame?
- When they're a multiple of 3
215
What happens if a single base pair is inserted/deleted?
- Frameshift
| - Premature termination codons (PTC)
216
What may occur if mRNA contains a PTC?
- Be degraded by nonsense mediated decay
- No/Very little protein's produced.
- A protective mechanism
217
What may occur if there is a mutation at an intron splice site?
- The adjacent exon may be skipped
218
What are the 3 main causes of mutation? Give examples
- 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
What is a Tautomeric shift and what can it lead to?
- 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
What happens when slippage occurs during replication?
| On newly synthesised and template.
- 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
What affect on the bases can chemicals have?
- 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
Outline what base stacking mutagens are and what causes it.
- 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
Give 4 examples of ionising radiation.
- Solar
- X-rays
- Nuclear
- Environmental sources (Radon)
224
What are the main effects of UV A,B and C?
- 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
What is thymine dimer formation and how is it caused?
- UV light
| - Causes adjacent Thymine bases to pair together.
226
What is nucleotide mismatch repair?
- After replication enzymes detect mismatched bases in the new strand and replace them.
227
What is excision repair?
- DNA accumulates damaged bases by: Oxidation/De-aminated/Uracil/Alkylated
- Repaired by base excision repair.
228
What are the 6 characteristics of cancerous growth.
- 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
All cancer cells exhibit what two things?
- Chromosomal instability
| - Micro-satellite instability.
230
What are BRCA1 and BRCA2 responsible for? And how do their effects make screening more cost effective?
- Inheritable breast cancer
| - Only effects certain populations (Families with known history are more likely to affect males)
231
When are oncogenes dangerous?
- When they have been activated and changed from proto-oncogenes to oncogenes
- Caused by key amino acid substitutions.
232
How is a cancerous tumour initiated?
- Only when both copies are mutated or the functional copies are deleted. (Proto-oncogenes and tumour suppressor)
- Knudson's two hit theory
233
Is cancer more likely to occur in sporadic or heritable conditions and why?
- 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
What is SSCP mutation scanning?
- 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
What are the 3 main ways of obtaining foetal DNA?
- Amniotic fluid cells (15-20 wks)
- Chorion villus biopsy (10-13wks)
- Foetal DNA in mother's blood (no risk of miscarriage)
236
How are karyotypes arranged?
- In decreasing size order
| - Except 22 and 21
237
How are chromosomes grouped?
- Similar size
| - Location of centromere
238
What is special about acrocentric chromosomes?
- Nucleus near the top
| - Satellites
239
How are chromosomes reported?
- 1st number of chromosomes
- 2nd sex chromosomes observed
- e.g normal female: 46XX
240
When would you be inclined to use karyotyping?
- Parental screening (especially >35yrs/family history)
- Birth defects (malformation/mental development impairment)
- Abnormal sexual development (Turner/Klinefelter)
- Infertility
- Recurrent foetal loss
- Leukaemia
241
How does diagnosis help?
- Accurate prognosis
- Better management from an earlier age
- Understanding reproductive risks
- Prenatal-chance to terminate
242
What is polyploidy and give an example report for one.
- When the number of chromosomes is a multiple of 23
- e.g. Tetraploidy: 4n: 92XXXX
- Life is impossible.
243
What is the cause of polyploidy?
- Polyspermy: fertilisation of an egg by more that none sperm.
244
What is aneuploidy?
- 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
What is anaphase lag?
- When chromosomes are left behind at cell division due to defects in spindle function/attachment to chromosomes.
- Lagging chromosomes can be lost entirely.
248
What are the only 3 viable autosomal trisomies?
- Trisomy 21: Down syndrome
- Trisomy 18: Edwards syndrome
- Trisomy 13: Patau syndrome.
249
What are the symptoms of Down syndrome?
- 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
What are the karyotype reports for Edwards and Patau syndrome?
- Edwards: 47XX+18 (5-15 days lifespan)
| - Patau: 47XY+13 (80% die within first year)
251
What happens when there is more than one X chromosome in a human cell?
- The only one is active
- Others are inactivated and form Barr bodies
- These are seen at the peripheral of cell nucleus.
252
What is Turner syndrome?
- 45X
- Phenotypic females
- Short, broad chested, low set ears, webbed neck, CV problems, infertile.
253
Why is having a single X chromosome a problem?
- Turner syndrome patients are monosomic for genes in PAR1 and PAR2
254
What is triple X syndrome?
- 47XXX
- 2 of 3 chromosomes are inactivated
- Symptoms: Tall, small head, delayed motor skills/speech, learning disabilities
- Auditory processing defects
- Scoliosis.
255
What is Klinefelter syndrome?
- 47XXY
- Symptoms show after onset of puberty
- Reduced testosterone production
- Gynocomastia (Increased beast tissue)
- Learning language and reading impairment
- Treatment: hormones and surgery.
256
What is XXY syndrome?
- 47XXY
- Phenotype: essentially normal
- Slightly lower IQ levels.
257
What is translocation?
- 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
What is reciprocal translocation?
- No loss of genetic material
| - Direct exchange of genetic material
259
What is Robertsonian translocation?
- 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
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.
- 46 XY, -14, +t(14q;21q)
261
What would be the report for a Down syndrome male involving a 21,21 Robertsonian translocation?
- 46 XY, -21,-21, +t(21;21)
262
What is an interstitial and a terminal deletion?
- Interstitial - internally
| - Terminal - ends
263
What is the Philadelphia chromosome useful for diagnosing?
- Chronic myelogenous leukaemia
| - It's a highly sensitive indicator.
264
What are paints used for when trying to diagnose a disease?
- 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
For high resolution banding what techniques are used?
- Multicolour FISH
- Multicolour chromosome bonding
- Fluorescent bond/chromosome specific probes are hybridised to chromosomes which can then be analysed by computers.
266
How can flucloxacillin inhibit the production of a cell wall?
- 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
What is the composition of a bacterial cell wall?
- 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
How do bacteria generally become resistant to beta lactam antibiotics?
- Produce beta lactamases
- This cleaves the antibiotic at the penicillin structure's centre.
- Rendering it useless.
269
How does Flucloxacillin normally overcome bacterial resistance?
- It has a bulky side chain that protects the penicillin ring.
270
How have some bacteria become resistant to Flucloxacillin?
- Change the structure of the protein that Flucloxacillin binds to.
- Thus no longer binding to the transpeptidase so it remains active.
271
How can bacteria obtain resistance?
- 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
Why does Flucloxacillin not affect eukaryotic cells?
- Eukaryotes don't have cell walls so no Peptidoglycan cross linkages to break.
273
What are the clinical applications of Flucloxacillin?
- Therapy to treat skin and musculoskeletal disorders causes by staphylococci bacteria.
274
How can an antibiotic that inhibits transcription inhibit cell growth?
- No transcription
- No translation
- No protein synthesis
- No cell growth.
275
How does normal bacterial transcription occur?
- One RNA polymerase transcribes all DNA
- RNA polymerase binds DNA unwinding the double helix
- mRNA is formed
276
How does Rifampicin stop transcription?
- Sterically blocks synthesis of 2nd or 3rd phosphodiester bonds
- Polymerase dissociates from DNA
- mRNA degrades.
277
Why is Rifampicin only specific to prokaryotic cells?
- 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
How can translation be inhibited in bacteria?
- 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
What are the the three main ways that bacteria obtains resistance to translation preventing antibiotics?
- 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
Why is tetracycline only specific to prokaryotic cells?
- Only affects 30s subunit of ribosomes
| - Eukaryotes don't contain 30s
281
What is a folate and how is it incorporated into the body?
- Needed to synthesise dNTPs
- dNTPs are needed for DNA and RNA synthesis
- Vitamin B9 from the diet.
282
What is an anti-folate and it's uses?
- Impair the function of folates
- Chemotherapy
- Antibiotic agent.
283
How is methotrexate an anti-folate? Outline it's mechanism.
- Methotrexate inhibits DHF
- Dihydrofolate can't become trihydrofolate
- Trihydrofolates synthesise thymidylates
- Which in turn synthesise RNA/DNA
284
How is methotrexate specific?
- 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
How can resistance to methotrexate occur?
- Decrease retention
- Increase levels of DHFR
- Mutated DHFR binds less readily to methotrexate
288
What occurs when non-disjunction occurs in mitosis?
- Leads to two populations of cells with different karyotypes - Mosaic.
294
What is the cause of aneuploidy?
- Non-disjunction at meiotic cell division
| - Creation of a gamete with a missing/additional (therefore both) chromosome.
