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30 Cards in this Set
- Front
- Back
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Ligand binding |
Specificity of ligand sand binding sites Coupled to conformational changes (induced fit) Conformational changes can affect others in one subunit (cooperativity) Interactions can be regulated |
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Functions of globular proteins |
Storage of ions and molecules (myoglobin, ferritin) Transport of ions/molecules (hemoglobin, serotonin transport) Defense against pathogens (antibodies, cytokines) Muscle contraction (actin, myosin) Biological catalysis (chymotrypsin, lysozyme) |
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Molecule that binds to a protein is a |
Ligand The region where it binds is binding site Binds via non covalent interactions that dictate protein structure |
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Quantitive description for binding |
Ka: association rate constant Kd: dissociation rate constant After some time process will reach equilibrium |
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Fraction of occupied bound sites |
Equilibrium dissociation constant The fraction of bound sites depends on free ligand concentration and Kd |
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Example of oxygen binding to myoglobin |
See pic |
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Specificity |
Lock and key model for certain ligands Based on: Size shape charge and hydrophobic/hydrophilic These characteristics are performed according to fisher |
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Induced fit |
Changes occur upon ligand binding Allows for tighter binding of ligand and high affinity for different ligands |
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Globing are oxygen binding proteins |
Oxygen molecule is captured with heme that is protein bound Myoglobin (storage in muscles) and hemoglobin (transfer of oxygen) |
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Binding of CO |
Similar size and shape to O2and can fit the same binding site. Bonds 20,000 times better than O2 due to lone pair being donated |
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Chromophore |
The heme group absorbs both in visible range and ultraviolet Deoxygenated blood appears purple and oxy hemoglobin blood is red |
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Could myoglobin transport O2? |
In lungs-13 kPa, binds oxygen In tissues-4 kPa, will not release it For effective transport affinity must vary: bind in lungs where pO2 is high and release in tissues where pO2 is low |
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Cooperativity |
Positive: increases affinity after first binding Negative: reduces affinity after first binding |
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Concerted v sequential cooperativity |
See pic |
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Allosteric regulation |
Cooperativity is an example of this Homotropic: normal ligand is the allosteric regulator Heterotropic: a different ligand affects binding of normal ligand |
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Subunit interactions in hemoglobin |
See pic Alpha 1 and 4 Beta 1 and 2 |
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R and T states of hemoglobin |
R: relaxed state, less interactions, more flexible, higher affinity for O2 T: tense, more interactions, more stable, low affinity for O2 O2 binding triggers T to R conformational change Involves breaking ion pairs btw alpha 1 and beta 2 |
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R and T states |
See pic |
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pH effect on binding: Bohr effect |
ph in lungs, 7.6 and tissues, 7.2 Lower in tissues due to active metabolizing generating H+ H+ binds to Hb and stabilizes T state which leads to release of O2 this increasing efficiency of transport |
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CO2 export |
Produced by metabolism in tissues 15-20% is exported in the form of carbonate on amino terminal residues of each polypeptide of Hb This process yields a proton that contributes to Bohr effect |
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2, 3 bisphoaphoglyverate regulates O2 binding |
Stabilizes T state, negative charge, bind to positive charge of Hb Allows release in tissue at high altitudes |
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Sickle cell mutation |
New valine side chain can bind to different Hb molecule to form a strand similar to amyloid IgE if proteins |
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Antigens |
Stimulate production of antibodies Recognized as foreign by immune system Coats proteins of bacteria and viruses Surface carbohydrates of cells or viruses |
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Antibodies |
Proteins that are produced by B cells and that specifically bind to antigens Binding will mark antigen for destruction Binds to small region of antigen (epitope) One antigen can have several epitopes |
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Immunoglobulin G |
Antibody with 2 heavy chains and 2 light chains (composed of variable and constant domains) Variable chains make up antigen binding sites (2 per antibody) which confers antigen specificity |
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Antigens bind via induced fit |
Antigen binding causes significant structural changes to that antibody |
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Review of muscle |
See pic |
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Myofibrils contain thick and thin filaments |
Thick: myosin Thin: actin |
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Atp and muscle |
See pic |
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Muscle contraction |
Ca binds to Troponin causing it to shift on tropomyosin exposing myosin binding sites Myosin heads bind to sites creating the power stroke |
