Chapter 3: Section C: Interactions of proteins and ligands Flashcards Preview

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Flashcards in Chapter 3: Section C: Interactions of proteins and ligands Deck (15):


- any molecule bound to the surface of a protein
- electrical attractions
- hydrophobic interactions


binding site

- region of a protein to which a ligand binds


4 characteristics of protein binding sites

- chemical specificity
- affinity
- saturation
- competition


chemical specificity of protein binding sites

- protein binding sites are ligand specific
- based on binding site shape (protein tertiary structure)
- different binding sites have different degrees of chemical specificity


affinity of protein binding sites

- the strength of binding between the ligand and binding-site
- depends on true strength of attraction between the protein and ligand
- different proteins may have the same chemical specificity, but different affinities


saturation of protein binding sites

- the fraction of total binding sites that are occupied at any given time
- for a population of binding sites
- 100% saturated = all available binding sites are occupied
- 50% saturated = half of available binding sites are occupied
- for a single binding site, 50% saturated means that it is occupied by a ligand 50% of the time


saturation depends on what

- concentration of the unbound ligand in solution (% saturation increases ligand concentration until 100% reached)
- affinity of binding site for ligand...the greater the affinity f the binding site, the lower the ligand concentration required to achieve a certain degree of saturation
- affinity measured according to the ligand concentration necessary to produce 50% saturation)


competition of protein binding sites

- ligands that bind to same binding site compete with each other for that site


Regulation of the binding site characteristics

- mechanisms for controlling cellular functions often involve regulating protein activity
- change protein shape and therefore change binding sites
- regulate protein synthesis and degredation


protein shape is altered by what

- allosteric modulation
- covalent modulation


2 binding sites of allosteric modulation

- function (active) site
- regulatory site


functional (active) allosteric site

- binds the ligand that generates the physiologic function of the protein


regulatory allosteric site

- binds a modulator molecule alters the shape of the functional site
- turn on functional site
- turn off functional site
- increase or decrease binding - affinity



- interactions between functional binding sites of multimeric proteins
- binding of a ligand to one functional binding site increases the affinity of the binding sites on the other polypeptide chains --> progressive increase in affinity for the ligand as more and more binding sites are occupied


Covalent modulation

- covalent bonding of charged chemical groups to one or more of the protein's side chains
- usually occurs through the addition of a phosphate group by phosphorylation
--> protein kinase
--> introduces a negative charge that changes protein conformation, altering the functional binding sites
- dephosphorylation removes the phosphate group