L 7. Protein Structure & Function II Flashcards
explain protein families
- within each family, amino acid sequences and the 3D shape closely resemble each other
- proteins within families may have different roles bc they have different enzymatic activity
define ligand
any substance that is bound to a protein
how to enzymes regulate metabolic pathways
one enzyme can catalyze a molecule and another enzyme will catalyze the same molecule and so on
how do enzymes catalyze reactions
- it lowers the activation energy
- so it requires less energy for a reactant to turn into a product
how do ligands bond to proteins
- they have to physically interact
- the ligand binds through noncovalent bonds
- the enzyme will fold and create a pocket for substrate to bind
ligand-protein binding - what happens at the pocket of the enzyme
- amino acids within particular areas in the protein will cause noncovalent bonds to interact with the ligand
- this will cause a conformational change in the protein resulting in the protein completing its task
structure of a protein - binding sites
bind and orient substrate/ligand
structure of a protein - catalytic site
reduces chemical activation energy
what are the ways a protein and ligand can bind
- Orientation/proximity
- Rearrangement of e-
- Strain
protein-ligand binding - orientation/proximity
- enzyme binds to two substrate molecules
- orientates them precisely to encourage a reaction
protein-ligand binding - rearrangement of e-
- binding of substrate to enzyme rearranges electrons in the substrate
- creates partial negative charge and positive charges that favor a reaction
protein-ligand binding - strain
- enzyme strains the bound substrate molecule
- forcing it towards a transition state to favor a reaction
explain enzyme substrate interaction
- substrate + enzyme are separate
- enzyme-substrate binds
- enzyme-product (substrate becomes product)
- enzyme + product separate
explain feedback inhibition (negative regulation)
- Prescence of end product stops the pathway
- Prevents further reactions down that pathway
negative feedback - What would happen if there were no feedback regulation?
the cell would keep making enzymes it does not need and wastes energy