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ESA 1 - RJS > MGD > Flashcards

MGD Flashcards

1
Q

What is the general structure of an amino acid?

A

NH2 - CH - R - COOH

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2
Q

What groups are present in an ionised amino acid?

A

NH3+ & COO-

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3
Q

Which amino acid isomer is found in nature?

A

L-isomer

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4
Q

What are the classes of amino acids and give examples?

A

Non-polar amino acids - glycine, alanine, valine, leucine, proline, phenylalanine, isoleucine
Polar, uncharged - Cysteine, glutamine, tyrosine, asparagine, threonine, serine
Polar, charged - Lysine, arginine, histidine, aspartate, glutamate

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5
Q

What is pK and how does it effect amino acids?

A

pK is the acid dissociation constant - how strong an acid is
if pH < pK = protonated
if pH > pK = deprotonated

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6
Q

What are the characteristics of a peptide bond?

A

Rigid and planar and in trans conformation

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7
Q

What is an isoelectric point?

A

The pH at which the protein has no overall net charge

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8
Q

What is the secondary structure of a protein and what are the bonds involved?

A

Local spatial arrangement of polypeptide backbone
Covalent (peptide) bonds
Hydrogen bonds

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9
Q

What is the tertiary structure of a protein and what are the bonds involved?

A 
3D arrangement of all atoms in polypeptide
Covalent (disulphide)
Ionic
Hydrogen bonds
Van der Waals
Hydrophobic
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10
Q

What is the quaternary structure of a protein and what are the bonds involved?

A 
3D arrangement of protein subunits
Covalent (disulphide)
Ionic
Hydrogen bonds
Van der Waals
Hydrophobic
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11
Q

Describe features of alpha-helix

A

3.6 amino acids per turn
0.54nm pitch
Right handed helix
R groups pointing outwards
Hydrogen bonds between C=O group and NH group 4 amino acids away

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12
Q

What amino acids are strong helix formers and breakers?

A

Formers: Alanine and leucine (small)
Breakers: Proline (no rotation around N-C bond), Glycine (R=H which supports other conformations)

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13
Q

Describe features of beta-sheet

A

Fully extended conformation
0.35nm between adjacent amino acids
R groups alternates between opposite sides of chain
Can be either parallel or antiparallel

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14
Q

Describe the features of the two types of tertiary structure of a protein

A

Fibrous - single type of repeating secondary structure, long strands or sheets - support, shape and protection
Globular - several types of secondary structure, compact shape - catalysis, regulation

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15
Q

Describe structure of collagen

A

Left handed triple helical arrangement of 3 alpha collagen polypeptide chains
Gly-X-Y repeating sequence
High degree of proline and hydroxyproline - Proline is correct geometry for extended alpha-chain conformation
Hydrogen bonds stabilise interactions between chains - due to hydroxyproline

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16
Q

What causes protein denaturing and how does this occur?

A

Heat - increases vibrational energy
pH - alters ionisation states of amino acids
Detergents/organic solvents - disrupts hydrophobic interactions

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17
Q

Describe the structure of heam

A

Protoporphyrin ring and Fe atom bound to 4 nitrogen atoms of the ring
Fe can bond to oxygen above the plane and histidine residue from protein on other side

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18
Q

What are the features of myoglobin?

A

Compact single chain
75% alpha-helical
1 heam group

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19
Q

What does binding of O2 to haem group do?

A

Pulls Fe into plane of ring changing from T state to R state

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20
Q

Describe the oxygen binding curves for myoglobin and haemoglobin

A

Myoglobin - hyperbolic

Haemoglobin - sigmoidal (cooperative binding)

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21
Q

Describe the structure of haemoglobin

A

2 polypeptide chains - alpha and beta
4 subunits, alpha 2, beta 2
Each chain has an associated heam group
Binding of oxygen causes a conformation change from T state to R state (oxygen binding promotes stability of R state)

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22
Q

What is T state and R state?

A

T-state - Low affinity state

R-state - High affinity state

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23
Q

Describe the role of 2,3-BPG

A

2,3-Bisphosphoglycerate - decreases affinity for O2, promoting release of oxygen in tissues
More present in high altitudes

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24
Q

Describe the role of CO2 and H+ in oxygen binding to haemoglobin

A

Binding lowers affinity for oxygen —> The bohr effect.
Metabolically active tissues produce CO2 and H+, this moves the oxygen binding curve to the right meaning that more oxygen is given up at the site of the metabolically active tissues.
This ensures that delivery of O2 is coupled to demand.

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25
Q

Describe the difference between maternal and foetal heamoglobin

A

Maternal, HbA - alpha2-beta2
Foetal, HbF - alpha2-gamma2
HbF has a higher binding affinity for O2 than HbA which allows transfer of O2 to foetal blood supply from mother

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26
Q

What are the features of an active site

A

Occupies a small part of the enzyme
Formed by amino acids from different parts of primary sequence
Clefts or crevices
Complementary shape to substrate
Substrates are bound by weak multiple bonds

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27
Q

What is the Michaelis-Menten model for enzyme catalysis?

A

Proposes that a specific complex between the enzyme and the substrate is a necessary intermediate in catalysis. Predicts that plot will be rectangular hyperbola
Vo = Vmax [S] / Km [S]
Vmax = maximal rate when all enzyme active sites are saturated with substrate
Km = Substrate concentration gives 1/2 maximal velocity

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28
Q

What is the significance of Km

A

Low Km = high affinity

High Km = low affinity

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29
Q

What is the lineweaver-burk plot?

A 
Rearrangement of michaelis-menten equation
1/V0 = (Km / Vmax [S]) + 1/Vmax
Straight line
Y intercept = 1/Vmax
X intercept = -1/Km
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30
Q

Describe reversible enzyme inhibitors

A

Competitive - Binds at active site, affects Km not Vmax

Non-competitive - Binds at another site on the enzyme, affects Vmax not Km

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31
Q

What are the methods of short term enzyme activity regulation

A

Substrate and product concentration - isoenzymes (different forms of same enzyme, different kinetic properties)
Enzyme concentration
Allosteric regulation - bind to allosteric binding site to either inhibit or activate (phosphofrucktokinase)
Covalent modification - phosphorylation
Proteolytic cleavage - Zymogens

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32
Q

Briefly describe blood clotting cascade

A

Two pathways that converge:
Intrinsic - damaged endothelial lining of blood cells promotes binding of factor XII - Ca2+ cofactor
Extrinsic - trauma releases tissue factor III
Converge to form factor X —> prothrombin to thrombin activation —> formation of fibrin clot from fibrinogen

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33
Q

Describe the role of carboxyglutamate (Gla) residues

A

The post-translational modification of blood clotting cascade factors and prothrombin in the ER of liver adds COOH groups into glutamate residues to form carboxyglutamate - requires vitamin K
Allows interaction within sites of damage through Ca2+ and brings together clotting factors

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34
Q

Describe formation of fibrinogen clot

A

Dancing crabs
2 sets of tripeptides - 3 globular domains linked by rods
Fibrinopeptides are removed by thrombin allowing polymerisation (globular C-terminal of beta and gamma with N-terminal of beta and alpha chains)

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35
Q

Describe the stopping of the clotting process

A

Dilution of clotting factors by blood flow
Digestion by proteases
Specific inhibitors (naturally occuring)
Plasminogen —> Plasmin causes fibrin to be digested (proteolytic cleavage)

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36
Q

Describe DNA packaging

A

Histone octamer core with DNA strand wrapped round twice (nucleosome) linking histone cores
Loosely packed = beads on a string = euchromatin = genes expressed
Tightly packed = selenoid = heterochromatin = genes not expressed

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37
Q

What is the difference between RNA and DNA?

A

OH replaced for H on 2’ carbon for DNA

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38
Q

How many rings does a purine have and what are the bases?

A

Two

A and G

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39
Q

How many rings does a pyrimidine have and what are the bases?

A

One

C, T and U

40
Q

Which bases pair and how many bonds made between them?

A 
A-T = 2 bonds
G-C = 3 bonds
41
Q

How are nucleotides joined together?

A

Via phosophodiester bonds moving from 5’ to 3’

42
Q

Describe the cell cycle

A 
Growth 1 = cell content replication
Cell cycle check point
S phase = DNA replication
Growth 2 = Double check and repair
Cell cycle check point
Mitosis = cell division
43
Q

Describe DNA replication

A

Initiation - recognition of origin of replication, requires recruitment of DNA polymerase and other specific proteins, requires kick-start by primase
Elongation - DNA polymerase moves along both strands making a copy (consistent for leading strand, in segments for lagging strand - DNA ligase fills in gaps), DNA helicase unzips double strand
Termination - 2 replication ends meet to produce 4 strands

44
Q

Describe the chromosome structure

A

Two chromatids joined together via centromere

Centromere can be metacentric, submetacentric or acrocentric

45
Q

Describe the phases of mitosis

A

Prophase - nuclear membrane disappears, spindle fibres form
Prometaphase - spindles attach to centromeres
Metaphase - chromosomes line up in centre
Anaphase - chromatids pulled to polar ends
Telophase - cells divide

46
Q

How does meiosis differ from mitosis?

A

Two rounds of mitosis
Production of four non-identical cells
Germ line cells

47
Q

What causes generation of genetic diversity?

A

Random assortment of chromosomes

Crossing over of genetic material

48
Q

Describe the difference between spermatogenesis and oogenesis

A

Spermatogenesis forms 4 sperm from one spermatocyte - takes 48 days
Oogenesis forms one mature ovum and 3 polar bodies - takes 12-50 years

49
Q

What is co-dominance?

A

Two alleles are neither dominant over the other

e.g. blood groups (A & B are co-dominant)

50
Q

What is complementation?

A

More than one gene involved in producing phenotype

51
Q

What is linkage and recombination?

A

Genes on same chromosome are linked
Genes on different chromosomes are not-linked
Recombination frequency between linked genes is dependent of the distance between the genes

52
Q

What is a person’s phenotype?

A

Physical characteristics or traits of genetic make up, genotype modified by environmental and developmental conditions

53
Q

What is a person’s genotype?

A

Genetic code it carries

54
Q

Describe the process of transcription

A

Initiation:
1. Recognition of TATA box
2. Transcription factors bind
3. RNA polymerase binds to transcription factors
4. ATP is required
Elongation:
1. Replication of leading strand with nucleotides
Termination:
1. RNA polymerase reaches stop sequence
2. 5’ capping by methylated guanine - prevents degradation
3. polyadenylation of 3’ end
4. Splicing of introns to make mature mRNA

55
Q

Describe the process of translation

A

Initiation:
1. 40S of rRNA binds to 5’ cap
2. Methionine tRNA binds to 40S (amino acid for AUG, initiation codon)
3. ATP moves 40S and met-tRNA to initiation codon
4. 60S rRNA binds
Elongation:
1. rRNA moves along adding aminoacyl-tRNA with corresponding amino acid to codon which forms a peptide bond
2. Translocation (moves from A site to P site using GTP)
Termination:
1. Stop codon reached - no amino acid is added
2. Hydroxylation of last amino acid to form OH group

56
Q

Describe the process of DNA gel electrophoresis

A

DNA fragments separated by size.
Placed on gel with cathode and anode, each DNA fragment moves towards positive end. The distance moved corresponds with size.
Requires: gel, buffer, power supply, stain

57
Q

What is restriction analysis?

A

Uses restriction endonucleases (resitriction enzymes) that recognise specific DNA sequences then cut at that site to leave sticky ends.
It is possible to cut and paste DNA fragments together - DNA modification.
Useful for gene cloning - adding DNA into a plasmid and allowing bacteria to reproduce, extract the plasmid for analysis

58
Q

Describe PCR

A

Polymerase chain reaction amplifying a small amount of DNA into large numbers of replications
3 steps:
1. DNA is heated to 95C to separate strands
2. Sample is cooled to 55C and sequence-specific primers anneal to target DNA
3. Sample is heated to 72C to allow DNA synthesis by Taq polymerase (thermostable)

59
Q

Describe SDS-PAGE

A

Detergent SDS denatures protein molecules and masks the proteins charge which its large negative charge, allowing separate by molecular weight.

60
Q

Describe the process of western blotting

A

SDS-PAGE followed by transferring the proteins to a membrane and specific proteins can be visualised using antibody binding

61
Q

Describe ELISA

A

Enzyme-linked immunoabsorbant assays

  1. Antibody of protein of interest is immobilised on solid support
  2. Solution with protein of interest is added, antibody binds to protein, rest is washed away
  3. Second antibody specific to protein applied with enzyme linked to it
  4. Binding of second antibody measured by assaying for activity of enzyme linked to it
62
Q

What is an enzyme assay?

A

Measuring enzyme activity by measuring substrate or product during reaction

63
Q

Describe DNA sequencing

A

Determination of the nucleotide sequence using the dideoxy chain termination method

64
Q

Describe southern blotting/hybridisation

A

Following DNA gel electrophoresis, fragments are transferred onto a solid membrane. A single-stranded DNA molecule labelled with radioactive or fluorescent tags used as a probe to find any complementary DNA sequences present on membrane

65
Q

What is karyotyping?

A

Full set of stained metaphase chromosomes of an individual organised according to chromosome number

66
Q

Describe FISH

A

Fluorescence in situ hybridisation

Fluorescent probes for a specific genes or DNA stretches are used

67
Q

What is a mutation?

A

A change in the genetic code either spontaneously or induced by mutagens creating a mutant allele or phenotype

68
Q

What is a point mutation? What are the two subgroups? What are the three types?

A

Base subsititution either a transition (purine to purine, pyrimidine to pyrimidine) or transversion (purine to pyrimidine)
They can be:
1. Silent mutation - no change to the amino acid
2. Missense mutation - replaces one amino acid for another
3. Nonsense mutation - changes amino acid for stop codon
Point mutations outside non-coding regions can cause change to protein binding sites, promoter sequences, splice sites etc

69
Q

Describe insertion or deletion with regards to mutations

A

A sequence that is either added or deleted, can be a single nucleotide up to millions of nucleotides long (tandem duplications).
They can cause a frame shift mutation if the number is not a multiple of 3 or no change in the reading frame but change in amino acid code if multiple of 3

70
Q

Describe DNA repair

A

Mismatch repair - post-replication process in which mismatched based is changed for the correct one
Excision repair:
1. Base-excision repair - single nucleotide due to oxidation, alkylation, hydrolysis or demaination
2. Nucleotide excision repair - repairs damage affecting 2-30 nucleotides caused by external agents e.g. chemical mutagens, UV, ROS

71
Q

What is normal karyotype nomenclature for a male and female?

A

Male - 46,XY

Female - 46,XX

72
Q

Name the types of numerical chromosomal abnormailities

A

Polypoidy - multiple numbers of all chromosomes

Aneuploidy - multiple copies of one chromosome

73
Q

Name the types of structural chromosomal abnormailities

A

Balanced - the exchange rearrangement of genetic material does not cause any missing or extra genetic information - inversion
Unbalanced - the structural chromosomal changes cause missing or extra genetic information - deletion, duplication

74
Q

What is an isochormosome?

A

Creation of two non-identical chromosomes, one is both p arms and other is both q arms

75
Q

What is translocation chromosome mutation?

A

Rearrangement of genetic material to a non-homologous chromosome - no loss of genetic material

76
Q

What is reciprocal translocation?

A

Exchange of genetic material between two non-homologous chromosomes - no loss of genetic material

77
Q

What is Robertsonian translocation?

A

Rearrangement of genetic material between 2 chromosomes - q arms of acrocentric chromosomes combine to from one super-chromosome with loss of both p arms

78
Q

Describe collagen synthesis

A

C - Cleavage of signal peptide
H - Hydroxylation of proline and lysine residues
A - Addition of N-linked oligosacchardies & galactose to hydroxylysine
D - Disulphide bonds form between aligned chains
P - Procollagen formed (triple helix)
O - O-linked glycosylation
G - Transport vesicle in golgi and exocytosis
R - Removal of terminal peptides (procollagen peptidase)
L - Lateral aggregation to form fibrils

80
Q

What are the components of a signal sequence?

A

It is located at the N-terminus of a protein
Contains:
1. Stretch of ~10-15 hydrophobic residues
2. 1 or more positively charged residues near amino terminus before hydrophobic sequence
3. Few polar amino acids within C-terminal region of signal sequence

81
Q

Describe the protein secretion pathway

A
  1. Protein synthesis initiated on free ribosomes & N-terminal signal sequence produced
  2. Signal sequence recognised by signal recognition particle (SRP)
  3. GTP-bound SRP directs ribosome to SRP receptor on ER
  4. SRP dissociates with hydrolysis of GTP - translocon opens
  5. Signal sequence cleaved by signal peptidase
  6. Protein synthesis continues
  7. Ribosome dissociates - translocon closes
  8. Protein folds
82
Q

Describe synthesis of insulin

A

Preproinsulin synthesised into the ER where signal sequence is cleaved (by sign 8al peptidase) and disulphide bonds are formed
Transported into Golgi where C peptide is cleaved by endopeptidases to give insulin (active)

85
Q

What modification occur in the ER?

A

Correct folding
Disulphide bonds formed
N-linked glycosylation

87
Q

How does genetic variation occur?

A

Random assortment of chromosomes during metaphase and crossing over

88
Q

What is N-linked glycosylation?

A

Sugars added to amine group on asparagine via N-linked glycosyl link
The sugars are assembled on a membrane lipid carrier and then transferred

89
Q

What modification occur in the Golgi?

A

O-linked glycosylation

90
Q

What is O-linked glycosylation?

A

Sugars added to hydroxyl of serene and threonine residues

Glycosyl transferase builds up sugar chain and attaches it via a glycosidic link

91
Q

What are the two types of intracellular secretion?

A

Constitutive secretion - continuous process, proteins packaged into vesicles and released continuously by exocytosis e.g. Serum albumin and collagen
Regulated secretion - proteins released in response to a signal (hormone), proteins packaged into vesicles but not released until stimulus received e.g. Insulin

92
Q

How is a protein targeted to the ER?

A

N-terminus signal that is removed - made of 6-12 hydrophobic amino acids & 1 or more basic amino acids

93
Q

How is a protein targeted to the mitochondria?

A

N-terminus signal that is removed - made of amphipathic helix 920-50) residues

94
Q

How is a protein targeted to a peroxisome?

A

C-terminus signal that remains - serine-lysine-leucine at C terminus

95
Q

How is a protein targeted to the nucleus?

A

Internal signal that is not removed - cluster of basic amino acids

96
Q

Describe the process by which a newly synthesised protein enters the mitochondria

A
  1. Chaperone keeps protein unfolded
  2. Signal binds to receptor
  3. Protein fed through pore in membrane
  4. Proteins moves through pore in inner membrane
  5. Targeting signal cleaved
97
Q

Describe the process by which a newly synthesised protein enters the peroxisome

A
  1. PTS binds to cargo
  2. Binds to peroxisomal import receptor
  3. Peroxisomal import receptor merges into the translocon
  4. PTS cargo complex dissociates in the cell and peroxisomal import receptor dissociates extracelllularlly
98
Q

Describe the process by which a newly synthesised protein enters the nucleus

A
  1. Importin binds to protein with nuclear localisation signal (NLS)
  2. Transported across membrane
  3. Ran-GTP binds inducing a conformational change
  4. Protein is displaced intracellularly
99
Q

Describe allosteric regulation

A

Sigmoidal relationship between rate and substrate concentration
Substrate binds making subsequent binding either easier or harder - R & T state
It binds to an allosteric binding site
Activator increase R state
Inhibitors increase T state

ESA 1 - RJS (6 decks)

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