Module C Flashcards
(C1-1) immune response-175
Has 2 complementary systems. Cellular immune system and humoral immune system.
Humoral targets bacteria and extracellular viruses
Cellular eliminates host cells, parasites, and foreign tissue.
(C1-1) antibody / immunoglobulin (Ig) vs. antigen, antiserum
Antibodies or Immunoglobin are proteins that bind to bacteria, viruses or large molecules to mark them for destruction. They are produced by B lymphocytes.
Antigen is any molecule or pathogen that can cause a response.
(C1-1) affinity vs. specificity
Affinity: how strong the bond between A and B are.
specificity: The number of bonds and shape of the two reactants determine specificity. Absolute specificity means enzyme will only bind to one thing.
(C1-1) epitope / antigenic determinant
The molecular structure which the T-cell receptors bind to is called the epitope. Substances less than 5000 Mr are generally not antigenic. However, they can bind to larger molecules to cause a response. These are called haptens.
(C1-1) immunoglobulin G (IgG) structure
Most common antibody molecule. Consists of two heavy chains and two light chains linked by disulfide bonds and non-covalent bonds. The heavy chains branch out, and at the point they branch out, they are attached to a light chain. Y shape.
(C1-1) heavy vs light chain-176
Heavy chain is the long chains that run compose the entire length of IgG, and light chains span only the fab domain
(C1-1) disulfide bond
Functional group of R-S-S-R, can also be called persulfide. Disulfide bonds hold the two heavy chains together and also link the heavy and the light chains in the fab domain together.
(C1-1) antigen-binding site
IgG antibodies have 2 identical antigen binding sites. The Fab domain of each branch has 1 binding site.
(C1-1) variable vs constant region
Constant region is found on the heavy chains and the light chains. These regions are called immunoglobulin fold and consist of beta sheets.
Each heavy and light chain has 1 variable region in which most of the variability is found.
(C1-1) Fc vs Fab domain
Fab is the Antigen Binding domain
Fc crystallizes readily. Fc consists of 2 different constant domains while Fab has 1 heavy chain constant, 1 light chain constant, 1 heavy and 1 light variable chain.
(C1-1) Fc receptor, macrophage
Marco-phages has a Fc receptor on its membrane which can bind to the Fc domain of the IgG antibody. Once bound, the marcophage will engulf the complex by phagocytosis.
(C1-1) polyclonal vs monoclonal antibody population
Monoclonal: all exactly identical, produced by identical B cells, binds to antigen in the same place
Polyclonal, produced by multiple B cells. Each one will bind to a different epitope of the same protein.
(C1-1) heterogeneous vs homogeneous population
homogeneous: recognize the same epitope
Heterogeneous:
(C1-1) B lymphocyte
Produces antibodies also called B cells.
(C1-1) clone
Identical cells.
(C1-2) TECHNIQUE: IMMUNOASSAYS
(C1-2) Sources: ModuleC-Binding: “Antibodies” section, p87-88, Fig. 3-31 through 3-33;
NnC 5.2 p178-179 ; 9.2 p334, Fig. 5-26; Fig. 9-17
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C1-2) immunoblot / Western blot
Allows for testing for the presence of minor components.
Uses electrophoresis
(C1-2) primary vs secondary antibody
Primary antibody: binds to the antigen serves as a test for the particular antigen
Secondary antibodies will bind to the primary if the primary is attached to the antigen
(C1-2) radiolabel
Using an isotopic version of a chemical, so we can trace where it goes.
(C1-2) immunofluorescence
Fixation of a cell (kind of like taxidermy)
Generally, they will introduce an antibody that will attach to the protein and then add a fluorescently died secondary antibody that will attach to the primary antibody.
(C1-2) ELISA
Enzyme-Linked Immunosorbent Assay
used to determine if the antigen is present and how much of it there is.
1. Antigen is plated
2. Antibody linked with enzyme is attached.
3.
(C1-2) colorimetric substrate
The substrate that is colored and used in immunofluorescence
(C1-2) immobilization / immunosorbent
techniques used to analyze proteins and enzymes in cells.
Immobilization is holding the enzyme and proteins in place while the reaction occurs.
Immunosorbent is the use of
(C1-2) direct vs indirect vs sandwich ELISA
Direct:
- Plastic is coated with antigen.
- Then antibody with enzyme attached is added.
- substrate for the enzyme is added and observe color change
Indirect:
The enzyme is on a secondary antibody instead of the primary. This is useful since we would not have to make a new Ab-Enzyme complex for each different protein.
Sandwich, use of a capture enzyme plated onto the plastic first. The the antigen is added and indirect ELISA proceeds
(C1-3) BINDING AFFINITY
(C1-3) Sources: ModuleC-Binding: “Affinity” section, p531-537, p546-548, Eq. 12-3, 12-7,
12-13 through 12-15; NnC 5.1 p159-161, Table 5-1
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(C1-3) molecular recognition / interaction, noncovalent complex, unbound vs. bound
Non-covalent complex: Tertiary proteins form strong non-covalent bonds to form a quatenary structure
(C1-3) ligand vs. receptor
Receptor: is the protein, and the ligand is the substrate that binds to the receptor.
(C1-3) dissociation vs. binding reaction
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(C1-3) uni- vs bimolecular
Unimolecular is S->P. For unimolecular reactions, the rate is V=k[S] where k is the constant of the reaction.
Bimolecular:
(C1-3) dynamic equilibrium
Forward and reverse rates are equal. There is no net change in products or reactants.
(C1-3) binary vs. ternary complex
binary complex: two things make up a complex
eg. substrate and enzyme
ternary: three things in the complex.
eg. substrate, enzyme and co-enzyme.
(C1-3) dissociation constant (Kd) vs. association constant (Ka) / binding constant (Kb)
Ka= [PL]/[P][L] Kd= 1/Ka
Ka is the affinity of the ligand for the protein and Kd is the dissociation of the ligand-protien complex.
(C1-3) molar units equilibrium constant vs activity equilibrium constant
equilibrium constant may have units expressed in moles.
equilibrium activity constant does not have any terms.
(C1-5) HYPERBOLIC BINDING CURVE
(C1-5) Sources: ModuleC-Binding: “Affinity” section, p535-537, p546-548, Eq.12-9, 12-11,
Fig. 12-4; Fig. 12-11, 12-12; NnC 5.1 p160-161, Fig. 5-4, Eq. 5-8, Example 5-1
“Step-by-Step-Predicting Fraction Occupancy”
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(C1-5) saturable binding
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(C1-5) saturated vs. “half saturated”
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(C1-5) fractional saturation (f) / occupancy / occupancy probability
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(C1-5) binding curve / isotherm
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(C1-5) dimensionless (activity) vs. concentration axis
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(C1-5) hyperbolic curve
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(C1-5) log axis binding curve
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(C1-5) “essentially complete occupancy” / “predominantly complete occupancy”
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(C1-5) [L] / K ratio
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(C1-6) STANDARD FREE ENERGY OF A REACTION
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(C1-6) Sources: ModuleC-Binding: “Affinity” section, p533-535, Eq.12-4, 12-5, 12-8, Fig.
12-3, Table 12-1; NnC 13.1 p507-510 , Eq. 13-3, Table 13-1 through 13-3;
Biochemical convention: NnC 13.1 Conventions on p. 507; 13.2 p517
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(C1-6) “driving force” of a chemical reaction
Systems will tend towards lower free energy states.
Thus, if the delta Gibbs is negative, the reaction will occur spontaneously.
It is called the standard free energy, or delta Gibbs naught when the concentrations are 1 mole and T=298K.
(C1-6) free energy change, G in general usage (“deltaG”)
The amount of free energy change is the maximum amount of work that the reaction can do, or how much free energy was released due to the reaction.
Delta G= Delta G naught + RTlnQ
(C1-6) standard free energy change (in general)
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(C1-6) free energy content of a sample
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(C1-6) (standard) free energy of binding vs. (standard) free energy of dissociation
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(C1-6) standard free energy change without biochemical convention, G° (“delta-G-naught”)
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(C1-6) biochemical convention for standard state
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(C1-6) standard transformed equilibrium constant, K’ (“K-prime”) & free energy
change, G’° (“delta-G-prime-naught”)
delta-G-prime-naught= -RTlnKeq
The
(C1-6) prime-naught notation
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(C1-6) well-buffered aqueous solution
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(C1-6) sum of species vs. exact atomic species
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