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First Quarter > BioChemistry Exam 1 > Flashcards

BioChemistry Exam 1 Flashcards

1
Q

Structural Forces

A
  • covalent bonds are strongest chemical bonds
  • they support linear structure
  • complex 3D structure is supported by weaker non-covalent interactions
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2
Q

Electrostatic Forces

A
  • depend on the distortion of electron distribution in a molecule
  • polar molecules have developed permanent dipole moment
  • partial separation of charge due to distortion of electron distribution
  • EN can distort electron pattern
  • the geometry of covalent bond influence electrostatic forces
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3
Q

Examples of electron distorted molecules

A
  • Ionic, charge-charge interactions have long range forces and are non-directional
  • Charge dipole interactions, depend on the orientation of dipole
  • Dipole-Dipole interaction depends on mutual interactions
  • Dipole-induced dipole, both induced dipole interactions only occur at short distances
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4
Q

Va Der Waal radii

A

closest molecular packing b/w molecules

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5
Q

Hydrogen Bonds

A

-they are the strongest weak bonds
90% of force due to partial charge interactions
10% is due to electron sharing b/w H’s and H-bond acceptors
-stabilize ordered structure of large molecules
bond length due to partial electron sharing
directionally with the acceptor electron pair makes a straight line

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6
Q

Power of the H-Bond

A
  • High surface tension, cohesiveness
  • High specific heat, requires a lot of energy to break
  • high viscosity, can form bond with other polar molecules
  • lower density as a skid, large distance b/w 2 molecules in H-bond
  • flickering cluster - water molecules are consistently rearranging
  • bridge - can link large molecules to provide interactions
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7
Q

Water as a solvent

A 
Hydrophillic
Hydrophillic mechanism 
Hydrophobic
Hydrophobic effect
Amphipathic
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8
Q

Hydrophillic

A

any charged molecule

  • alchohols, aldehyde,ketones,amides,ions all dissolve in water
  • even molecules with internal H-bond will swap with water to allow for more dynamic interactions
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9
Q

Hydrophillic mechanism

A

hydration shell

  • energetically favorable dipole-charge or dipole-dipole
  • the dielectric constant of water decreases the electrostatic force of ions that would pull them back together
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10
Q

Hydrophobic

A

non-polar molecule

-no H bonds or charge = no solubility

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11
Q

Hydrophobic effect

A
  • water forms a clathrate or cage aroun non-polar molecules
  • increases clathrates decreases entropy, so they obey the 2nd law of thermodynamics, hydrophobic molecules cluster together to exclude water. water still forms a single clathrate around hydrophobic cluster
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12
Q

Amphipathic

A

single molecule with one region polar, one region non-polar

  • fatty acid and detergents
  • in water, they form a layer on surface of water, with polar region interacting with water
  • with agitation. amphipathic molecules will form single layer miscalls or a lipid bilayer
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13
Q

pH and pOH

A
  • EN forces of oxygen can induce a covalent bond with an H from a neighbouring water molecule
  • hydronium ion is quite unstable, H+ ion bounces b/w a series of H2O molecules until it associates with another hydronium ion, making it water once again
  • the movement of H+ is what creates current in water
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14
Q

Measuring Ionization

A

chemical reaction has an equilibrium, Keq is the measured terms of conc. of product and conc. of reactants

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15
Q

Amino Acid - Protein Monomer

A
  • protein polymers are composed of 20 common monomers differing from each other by a residue or R group
  • amino acids are names for a central carbon atom bounded to an amino group, carboxyl group, hydrogen, and an R group
  • they are zwitterions at physiological pH b/c they have the dual poles
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16
Q

Characteristics of Amino Acids

A

-the alpha carbon is chiral, asymmetric such that the mirror image is not superimposable
-D vs L = Dextrorotary bends polarized light to the right
Levorotary bends polarized light to the left
- R vs S = organic chemistry organization in which order of molecules around the chiral centre increase in MW. L-amino acids are also in the S configuration, increasing molecular weight counter clockwise

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17
Q

D-Serine in the Brain

A
  • NMDA receptor is both voltage gates as well as ligand gated receptor that influences learning and memory
  • discovered in 1990 and in 2006 D-serine was shown to be an important co-agonist of NMDA receptor signalling
  • D-serine racemase synthesizes D-serine from L-serine
  • D-serine deficiency is seen in Schitzophrenia as well as genetic polymorphisms and racemes gene
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18
Q

Amino Acid functions

A
  • monomers of protein synthesis
  • precursors to hormones
  • in starvation of low carb diet: food
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19
Q

Essential Amino Acids

A

Lysine, Tryptophan, Phenylalanine, Methionine, Threonine, Leucine, Isoleucine, Valine, Histidine, Arginine
-the amino acids that cannot be made in the body

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20
Q

The 20 amino acids

A
  • 9 hydrophobic amino acids: 5 non-polar aliphatic, 2 non-polar aromatic, 2 polar aliphatic
  • Hydrophillic amino acids: 2 polar aliphatic with hydroxyl groups, 1 polar sulfurhydryl group, 2 polar uncharged carboxamide residues, 2 negatively carged carboxylate residues, 2 positively charged residues via amonia group, 1 that is polar from imodazole group
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21
Q

Glycine

A

Gly, G
non-polar Aliphatic R group
sterically small so it is involved in bends

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22
Q

Alanin

A

Ala, A
non-polar, Aliphatic R group
deamination results in pyruvate which is used in the Krebs cycle

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23
Q

Valine

A

Val, V

non-polar Apliphatic R group

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24
Q

Leucine

A

Leu, L

Non-polar Aliphatic R group

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25
Q

Methione

A

Met, M

Non-polar Aliphatic R group

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26
Q

Isoleucine

A

Ile, I
Non-polar Aliphatic R group
has a 2nd chiral carbon on the R chain

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27
Q

Proline

A

Pro, P
non-polar, is an aliphatic R group that forms a cyclical structure with the amino group to form Imino
reduces structural flexibility and H-bond capacity of the amino group

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28
Q

Phenylanine

A

Phe, F
non-Polar, Aromatic R group
extremely hydrophobic b/c it has an extremely stable benzene R group

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29
Q

Tyrosine

A

Tyr, Y
non, Polar Aromatic R group
important in enzyme active sites of signal transduction b/c it has am available H from the hydrozyl to give up

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30
Q

Tryptophan

A

Trp, W
non-polar, Aromatic R group
serves as a precursor for seratonin and melatonin

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31
Q

Serine

A

Ser, S
Polar, Aliphatic R group
found in enzyme active site b/c the H bond help initiate catalysis
used in signal transduction pathways

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32
Q

Threonine

A 
Thr, T
Polar, Aliphatic R group
found in enzyme active sites b/c H bond helps to initiate catalysis
used in signal transduction
C by the OH is delta + slightly positive
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33
Q

Cysteine

A

Cys, C
polar, Aliphatic R group
used in structural support anabolism and synthesis reactions b/c it can lose the H on the sulfur and bond to another Cysteine molecule to form Cystine

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34
Q

Aspartate

A

Asp, D
Polar, uncharged carboxylate
deamination makes oxaacetate a glucose metabolite
it is Acidic

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35
Q

Glutamate

A

Glu, E
Polar, uncharged corboxylate
deamination make alpha-ketoglutarate a glucose metabolite
Acidic

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36
Q

Asparagine

A

Asg, N

Polar, uncharged carboxamide

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37
Q

Glutamine

A

Gln, Q
Polar, uncharged carboxamide
-amino acid monomer
-precursor to glutamine, nuerotransmitter GABA, alpha-ketoglutarate
-monosodium glutamate (MSG) flavor enhancer
-Neurotranmitter

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38
Q

Lysine

A

Lys, K
positively charged residue
participate in enzyme active sites
Basic

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39
Q

Arginine

A

Arg, R
positively charges residue
participates in enzyme active sites
has the guanadium group

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40
Q

Histidine

A

His, H
imidazole ring pKa near 6
this ring is either uncharged or positively charged and serves in enzyyme active sites

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41
Q

more about the 20 Amino Acids

A

-selenocysteine is created during protein synthesis
contains selenium instead of sulfer at cysteine
the amino acid is used in all anti-oxidant enzymes such as glutahione peroxidases and thioredoxin reductases
-other amino acids have post-translation modifications that yeild new functions; hydroxylation, carboxylation, phosphorylation, and cleavage
-choosing 20, only energetically favourable isoforms and residue will be selected

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42
Q

Purifying Proteins

A

First you need to turn the protein into a salt and then by dialysis you can seperate them out from the others

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43
Q

Salting Out

A

Proteins are least soluble in water when the pH = pI, at this point amonium sulfate is used to precipitate a population of the protein

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44
Q

Dialysis

A

separating large proteins from smaller solutes by placing the prtein solute in a porous bag with defined pore size
placed in large volume buffer to encourage diffusion of the smaller solutes

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45
Q

6 types of Chromatography

A

uses a gell that binds to the proteins to separate them out by size, charge or affinity

  • Ion exhange chromatography
  • Afiinity Chromatography
  • High Performance Liquid Chromatography
  • Electrophoresis
  • 2D Electrophoresis
  • Mass Spectrometry
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46
Q

ion Exhange Chromatography

A

uses resin coated with either (+) or (-) substance
a -ve charge resin will then attract all the +vely charge proteins in the solution and repel the negatively charge ones which can then flow thru the column

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47
Q

Affinity Chromatography

A

using binding affinity of a given protein
if you desire a protein that binds to gluciose you would coat a resin with glucose and only those proteins with stay in the column
-to remove them: add more glucose to outcompete the resin, add denaturant to encourage protein to release from resin

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48
Q

High Performance Liquid Chromatography

A

uses high pressure fluid containing unpurified protein and more specific resin to produce an increase resolution and it happens faster

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49
Q

Electrophoresis

A

applies an electric field to separate proteins in a resin not made of beads, but of polyacrylamide, a polymer of various size
it allows you to determine the MW of each protein in the solution

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50
Q

2D Electrophoresis

A

separates proteins by MW and by pI in a 2 step process
used when the MW of proteins are the same
1. separate by isoelectric focusing, proteins migrate in a pH gradient in an electric field to point where pH = pI
2. the gel from the first part is placed on polyacrylamide gel and proteins are separated by size

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51
Q

Mass Spectrometry

A

produce more accurate MW of the protein by accelerating it on an electric field of a gas
MALDI-TOF ionizes proteins in a matrix and accelerate them thru a flight tube. The small cations will hit the detector first

52
Q

Peptide Bone Primary Structure

A

Dehydreation reaction; enzyme reaction in which monomers join to form polymers, and produe a molecule of H2)
general polymer forms 4 classes: proteins, cholesterol, fats, and nucleic acids
is rigid, regular and provides beackbone of protein, it has resonance structures in aqueous solution and has a planar configuration
single bonds have great flexibility so primary structure rotation is at the C alpha - amine and the C alpha - carbonyl group
due to steric clashes some angles wont work
most common config. is trans
proline has cyclized R group so it will allow the molecule to configure in both Cis and Trans

53
Q

The 4 types of secondary structures

A

alpha hellix
beta sheet
beta trun
omega turn

54
Q

alpha helix

A

-carbonyl H-bonds with amino 4 residues upstream making them highly packed
-residues 1 and 4 are close together
-residue spaced 2 apart are on opposite sides of helix
-helices have srcew sense
Things that prevent this: proline binding to its own amino group
steric clashes of large residues disrupt the packing of the helix

55
Q

Beta-Sheet

A

Anti-parallel- All NH and CO H-bond with adjacent (1-1)
Parallel - One NH and CO H-bond is adjacent,
The next one is an H-bond 2 residues upstream

56
Q

Beta-turn

A

tpyically located on the protein surface so they are important in protein interactions
they are formed by a H-bond b/w residues 1-3

57
Q

Tertiary Structure

A

long, thermodynamic arrangement of amino acid residues in an environment that supports function
generally supported by R-group interactions
factors affecting it are: 1. hydrophobicity 2.electrostatic 3. H-bond 4.Van der Waals
globular proteins are formed
cysteine disulphide bonds are used to form cross links for structural support

58
Q

Globular Proteins

A

proteins that have a hydrophobic interior surrounded by a hydrophilic water shell

59
Q

Proteostasis

A

protein chaperones interact with partially folded or misfiled polypeptides and provide an environment for proper folding

  1. protein disulfide isomerase- enzyme that catalyzes disulphide bonds
  2. peptide prolyl cis trans isomerase- enzyme that catalyzes interconversion of cis and trans isomers of proline to achieve native state
60
Q

Quarternary Structure

A

this is when one or more protein polymer interact with each other by 1. electrostatic 2. H-bond 3. Covalent 4. Van der Waal
2 identical subunits = homodimer
2 non-identical subunits = heterodimer
larger subunit collaborations are defined by representative proportions or a ratio 2 alpha and 2 beta

61
Q

Characterization of Folding Proteins

A

databases organized based on folding motifs

we use motifs to understand functional relationships b/w proteins b/w motifs is more conserved than the primary sequence

62
Q

Structure dictates function

A

alpha-keratin are superfamily of structural proteins
they are right handed alpha helix coils with a left screw sense
this supercoiling reduces the number of AA per turn
2 alpha helices complimentary and typically repetitive (7 residues)
complimentary residues interact via Van der Waal Ionic and Disulfides
-these cross links prevent break and restore the curl and the more sulphide bonds the greater the overall strength

63
Q

Collagen

A

skin, bone, tendon, cartilage, teeth, and cornea
3 poly peptide structure
no intramolecular H-bonds
left screw sense
superhelical twist that has right screw sense
has a typical repeating pattern of Gly-Pro-Hyp
fibbers are stabilized by: steric repulsion of proline and hydroxyproline, H-bond b/w Gly and CO of residues, each peptide has 3 residues per turn, w/ sterics proline H-bonds, some H-bond in Hyp too

64
Q

Hydroxyproline

A

is a chemical modification of proline where an hydroxyl group is added
allows for more H-bonding with collagen
non-Hyp collagen is weaker - seen in skin lesion, bleeding gums and weak blood vessels

65
Q

Scurvy

A

Vitamin C is an E source for the enzyme that hydroxylates proline
This also then turns alpha-kg to succitate

66
Q

Osteogenisis Imperfecta

A

mutation of glycine in collagen disrupts tightly coiled superhelix. Disorder ranges mid to severe, dpending on location and repitition of mutation

67
Q

Ehler-Danlos

A

also a mutation of glycine, but causes loose joints

X-linked recessive, autosome recessive, and autosome dominant

68
Q

Intrinscally Disordered Proteins

A 
function by molecular recognition only taking on induced fit when in complex with another protein
conribute to fuzzy complexes where in even in complex with other protein retain a segment of disordered structure offering a region of regulation
69
Q

Metamorphic Proteins

A

adopt on or more conformations under the same set of conditions
lymphotactin is a secreted protein important in chemotaxis of T cell by binding the XRC11 receptor and binds heparin to support directionality of chemotaxis

70
Q

Carbohydrate additions

A

post-translation modification in ER or Golgi and vesicles change solubility and functionality of protein

71
Q

Phosphorylations

A

adding phosphate group in place of the hydroxyl on serene, threonine or tyrosine creates a larger molecular complex that has negative charge, typically active in an enzyme

72
Q

Cleavage

A

Proopiomelanocortin is a preprohormone with unique function but when it is cleaved has 9 different functions: pigmentation, adrenal, opiate, and insulin activity

73
Q

Amyloidoses

A

are a collection of disorders which a soluble protein that normally secreted from the cell is secreted in a misfiled state and converted into insoluble extracellular amyloid fiber
proteins predisposed to making amyloid fibers typically contain aromatic amino acids that are stabilized in a B-sheet
accumulation of amyloid fibbers destroy cells

74
Q

Famous amyloids

A

Alzheimers Disease - extracellular amyloid B-peptide misfolds after cleavage of internal and external regions of the transmembrane protein amyoid B precursor protein
Parkinsons disease - a-synuclein aggregates to form Lewy Bodies
Huntingtons disease - huntington has a long polyglutamate repeat causing aggregate
Primary systemic amyloidoses - misfolded antibody light chains due to genetic or environmental factors
Secondary systemic amyloidoses - serum amyloid A protein: symptoms on highest accumulation of deposits
Organ Specific amyloidoses - pancreatic B islet cells produce soluble amylin, which is insulin agonist, can become an insoluble amyloid form that deposits in the pancreatic islets killing B cells and causing type 2 diabetes

75
Q

Antioxdants

A

because amyloids are protein misfolds in the ER it is cause by cell stress it accumulate unfolded proteins and triggers the unfolded protein response to increase the concentration of chaperones
Paeoniflorin and glycyrrhizin are chemicals in some herbal remedies that increase heat to shock proteins
cells with amyloids can be removed by fusion with lysosomes
cellular stress may also be avoided with increase antioxidants

76
Q

Cellular Prion Protein

A

is expressed in every cell of the body
in neurones it is important for neuroplaticity
in the immune system it is important for T cell signalling and cross linking antibodies
inherited mutations such as in fatal familial insomnia
disease onset and pathology are variable and cause spongiform encephalopathy

77
Q

co-factor

A

single metal molecule

78
Q

co-enzyme

A

more complex molecule

79
Q

ligand

A

molecule bound reversibly by a protein

80
Q

binding site

A

site on protein complementary to the ligand in shape, charge and solubility properties

81
Q

induced fit

A

structural adaptation between protein and ligand upon binding

82
Q

quantification of protein

A

at equlibrium protein + ligand = protein-ligand
dues to the structure of the binding site each protein has a unique affinity for the ligand
this is know as the rate of association Ka
the dissociation constant is Kd
the use of the equation is to find how many binding sites on the protein are occupied by a ligand
theta is the fraction of binding sites occupied by ligand in total

83
Q

Myoglobin

A

is an oxygen storage protein in muscle tissue
is a globular protein primarily composed of a-helices that bind prosthetic group, heme
this heme is buried deep in the protein structure so overall protein flexibility and movement in solution allows O2 to navigate and bind to heme
does not have any quarternary structures

84
Q

Heme

A

is a photoporphyrin ring containing 4 pyrroles

the nitrogen of each pyrrole is involved in a coordinate covalent bond with the ferrous iron

85
Q

coordinate covalent bond

A

where the shared electrons of the bond only come from one of the molecules acting in the bond

86
Q

Histidine in Myoglobin

A

Nitrogen from the imidazole ring of histidine in myglobin makes another coordinate covalent bond with ferrous iron creating a covalent in reaction of the prosthetic heme group to the protein and stabilizing iron
this histidine is known as the proximal histidine
there is also another histidine on the myglobin that binds to the distal end of Oxygen preventing the release of a superoxide

87
Q

prosthetic group

A

a type of co-factor that binds to an enzyme where the loosely bound co-factor is a co-enzyme and the tightly bound co-factor is a prosthetic group

88
Q

O2 in Myglobin

A

binds to the 6th iron binding site, the electron shift such that iron moves into the plan of the porphyrin ring, a 0.4A move
oxygen is highly EN so it pulls the electrons aways from Iron hard to make it Fe3+ and makes the oxygen a superoxide but is isn’t released due to the distal histidine imidazole ring H-bond to it

89
Q

Oxygen binding rates

A

myoglobin bind oxygen at rate of a hyperbolic curve when theta=Kd partial pressure is 2mmHg
problem is that at the lungs the mmHg is 100 and 40 in the tissue, so it makes myglobin a terrible transporting protein of O2

90
Q

Hemoglobin

A

is a tetramer composed of 2 a and 2 b chains of proteins each holding a single heme group
again these heme groups bound to the protein chains are attached to histidines.
has cooperative binding of oxygen to allow for transport
non-bound (O2 deoxy Hgb) favours the T state and bound (O2 oxy Hgb) brings it towards the R state
uses allosteric regulation to influence the binding and release of oxygen
can be poisoned by CO binding to Fe site
shown to have different qualities in the fetus where the fetal (a:y hemoglobin) hemoglobin has a higher affinity for O2 because of less + charges decreasing affinity for BPG

91
Q

cooperative binding

A

if the protein had a hyperbolic binding pattern all the time that the release of O2 would not happen at the tissues SO cooperative binding takes on a sigmoid curved
binding of 1 oxygen increases the affinity for the 2nd which influences the 3rd and 4th
this allows to higher R state partial pressure and still release at lower PP

92
Q

Quaternary structure change of Hemoglobin

A

-deoxyHgb takes on tight T state with each Heme group buried deep and tightly within the protein
since the O2 loading onto a heme causes a 0.4A movement and the proximal histidine is bound to the Fe the whole carboxyl terminal region of the subunit moves
-these carboxyl terminal regions are part of a:b interactions of hemoglobin, this causes a -conformation to the adjacent subunit making it more relaxed
-this addition of O2 allows for greater degree of rotation

93
Q

Allosteric Regulation

A

a molecule that binds to the protein outside the ligand binding site to influence the protein:ligand binding interactions
the best example of an allosteric regulator is Biphosphotglycerate which helps lower the affinity for O2 and stabilize the T state

94
Q

Biphosphoglycerate (BPG) (DPG)

A

is a negatively charged molecule that interacts a positively charged pocket between the 4 a:b subunits to stabilize the T state and lower affinity for O2

95
Q

Why lower affinity for O2

A

creates a more efficient offloading of O2 with rest and exercise
hemoglobin now has an O2 buffer- its is at a 97% saturation at the lungs and then can begin to release the O2 at 40mmHg in the tissue
in higher press as BPG increases->it binds to hemoglobin->favours the T state->unloads the O2 at tissue

96
Q

Fetal Hemoglobin

A

fetus needs to load O2 at tissue of 40mmHg but regular hemoglobin offloads at this pressure
you cannot just eliminate BPG to favour affinity because it would not be able to offload
a:y hemoglobin found in the fetus has 2 less + charges decreasing the affinity for - BPG, therefore it favours the R state to pick up more O2 but still has some affinity for BPG to offload O2 at fetal tissue
basically a great affinity at 40mmHg and then the same at lower pressure, steeper slope on graph

97
Q

CO and hemoglobin

A

CO has a 200 fold increase in affinity for hemoglobin than O2
CO binding favours the R state
CO binding causes the porphyrin pigment to become bright red in lips and doesn’t allow the release of O2 at tissues because it wants to stay R state

98
Q

Bohr Effect

A
  • O2 affinity of Hemoglobin is directly related to the concentration of H+ and CO2
  • as there is a decrease in pH (increase of H+ concentration) or increase of CO2 blood concentration then Hgb will favour the T state and want to release O2
  • if there is an increase in pH (decrease of H+ concentration) or a decrease of CO2 blood concentration then Hgb well favour the R state and want to pick up O2
  • CO2 binds to the free amine group on hemoglobin to make carbamate, this carbamate on amino group in the a:b interaction face favour the T state
  • as H+ rises the histidine becomes protonated and forms a salt bridge with asparagine(-) stabilizing the T state
99
Q

Relationship of CO2 and H+

A

since CO2 reacts with H2O to make carbonic acid then it will release more H+ into the blood decreasing the pH.

100
Q

Carbaminohemoglobin

A

transports 23% of CO2

101
Q

Haldane Effect

A

bind of the O2 to Hgb displaces CO2 from blood
Hgb:O2 is acidic and as the H+ is released from Hgb it combines with bicarbonate (HCO3-) to make carbonic acid which carbonic anhydrase then converts to H2O and CO2
prevents carbminohemoglobin formation
the haldane effect is responsible for 50% of CO2 exchange

102
Q

Haldane Effect

A

deoxygenation of the blood increases its ability to to carry CO2 and H+ ions.

103
Q

Hemoglobin A1c

A

is hemoglobin that is glycosylated
it is normal to have some glycosylated hemoglobin, but with increasing blood sugar, increase glycosylation occurs
HgbA1c is used as a measurement to represent evaluated blood sugar over long term compared to the glucose tolerance test

104
Q

Classic Sickle Cell Anemia

A

of the B chain there is a substitution of Valine for glutamate at residue #6
valine is a hydrophobic non-charged AA where glutamate is hydrophilic acid.
this exchange for valine forms deoxyhemoglobin and it then forms a fibrous chain with other B subunits, distorts the shape of RBC making it fragile, impedes circulation
oxyhemoglobin favour the R state and also displacing Valine such that it has no interaction with B subunits
the B subunits develop flat ends to lay together on each other

105
Q

Thalassemias

A

imbalance of a or b subunits
a-thalassemia- 100% b subunit therefore it cannot have cooperativity and thus does not real ease O2
b-thalassemia - 100% a aggregates and precipitates, lysing RBC
genetically there are 2 alleles for b subunits and 4 for a subunits

106
Q

ASHP

A

is an a hemoglobin that stabilizes proteins by helping to refold misfolded a-globulin
occupies a-globulin to prevent aggregation and precipitation
a:b stability is higher than a:ASHP, so a:b complexes are formed

107
Q

Antibodies

A

are proteins produced by B cells made in bones
Millions of B cells are produced each with a unique binding site (5-10% of total B cell output generated daily)
serves as a flag for other cells of the immune system that can eliminate the antigen by phagocytosis, Cytolytic T cells can bind antibodies and deliver toxins to the cell associated with antigen
the antibody:antigen interaction takes on an induced fit which the overall structure changes upon binding (increasing avidity)
it is the non-covalent forces and the 3D shapes that dictate the protein:ligand interaction

108
Q

Ligand for antibodies

A

are called the antigen and it is the protein containing molecule that generate antibodies

109
Q

Epitope

A

is a specific region of the antigen that directly binds with the ligand binding site of the antibody

  • they can be sequential reisudes, so antibodies can bind a denatured antigen
  • can be unsequential in which the residues are in close proximity due to 3D structure
110
Q

Structures of the Antigen

A

constant region- base of y shape that serves as the ligand for receptors on macrophages
hinge region- disulfide bond that allow flexible rotation and contribute to antibody aggregation
heavy chain- inner arm of the y that contain a portion of antigen binding site
light chain- outer arm of the y that contains portion of antigen binding site

111
Q

The 5 isotopes (Constant Region)

A

the part that serves as the ligand for receptors of immune cells
isotype switching only occurs upon B cell activation (presence of antigen)
IgM-blood, naive B cells
IgG- blood
IgA- gut
IgE - respiratory and mucosal
IgD - less known, naive B cells

112
Q

The Variable Region (Heavy and Light Chains)

A

have a high variability in the antigen binding site is targeted specifically to the residues that will interact with antigen
light chain and heavy are b-sheets and the variable region is the b-turns and omega loops
also known as the hyper variable region of antibodies

113
Q

Generating Hypervariable loops

A

germline DNA contains multiple copies of regions coding for light and heavy chains known as Variable, Joining, Diversity, and Constant
does somatic recombination to initiate shuffling of the DNA regions
somatic hypermutation during exposure to antigen

114
Q

Somatic Recombination

A

involves enzymes known as recombinase activating gene (RAG) that initiate shuffling and joining of different regions of DNA during B cell development
is the only enzyme allowed to cut and segment from the germ line DNA

115
Q

Somatic Hypermutation

A

occurs during exposure to antigen, their process increases the affinity on antibody, and thus effective clearing of antigen
involves randon nicks in hypervarialbe region followed by homologous recombination
this process introduces mutations upon repair, some mutants are successful and have higher affinity while other die

116
Q

Case Study

A

5 year old kid with streptococci
low level of neutophils, lymphocyte normal, monocytes elevated, successful recovery from antibody IV antibiotics
has recurrent sinus infections
results: testing for antibodies showed no antibodies for streptococci, low IgG, IgA but high levels of IgM

117
Q

Antibodies in Biotechnology

A

capitalizing on the specificity, affinity and avidity of antibody:antigen complex to purify and identify proteins
-more specificity affinity chromatography
-western blot
-ELIZE
a single unique antibody binding a single qpitope on an antigen is generated by a single B cell

118
Q

more specificity affinity chromatography

A
  • if the ligand for a protein is not known an antibody can be generated and chemically bound to resin
119
Q

western blot

A
  • is a procedure with proteins separated by size on a gel are probed with an antibody
120
Q

ELIZE

A
  • enzyme linked immunosorbant assay
    antigen bound to antibody held to glass by electrostatic forces, enzyme linked antibody sent in with different epitope for same antigen, add substrate for enzyme that changed colour of product
121
Q

Clonal Expansion

A

a B cell that creates an antigen undergoes a clonal expansion or activation induced cell division, all the daughter cells make the same antibody

122
Q

Polyclonal

A

the antibody is derived (cloned) from more than 1 B cell

123
Q

Immunogen

A

any substance that can elicit an immune response, differs from antigen because some antigens have to be attached to immunogens to elicits an immune response

124
Q

Adjuvant

A

a substance that enhances the immunogenicity of substances mixed with it without forming stable connection with the antigen

125
Q

How good is clone after purification

A

concentration and purity
cross-reaction
comparison of affinity and avidity
does it work for my application

First Quarter (26 decks)

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