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
negative feedback - how exactly does the end product stop the pathway
- End product binds on regulatory sites
- enzyme undergoes conformational change to stop pathway
how does protein phosphorylation change the function of the protein
- phosphorylation causes a conformational change
- turns it on/off depending on protein
protein phosphorylation - explain how it works
- Kinase – adds a phosphate
- Phosphatase – removes a phosphate
explain other types of covalent protein modifications
different post-translational modifications can alter proteins
explain motor protein myosin
- myosin is an ATPase
- can walk along actin filaments during muscle contraction by hydrolyzing ATP
explain protein complexes
- they are made of individual proteins that collaborate to perform a specific task
- the function is coordinated by the hydrolysis of ATP
explain how you can gather proteins to study them
- Take out of source tissue, if it is abundant
- Producing them artificially, If not abundant but you know the gene that expresses the protein
explain homogenization
- breaking cells and tissues
- can do it in 4 ways:
1. break cells with high-frequency sound (ultrasound)
2. use a mild detergent to make holes in the plasma membrane
3. force cells through a small hole using high pressure
4. sheer cells between a close-fitting rotating plunger and the thick walls of a glass vessel
how do you isolate protein complexes
- Immobilize protein and fish out proteins that you know interacts with it
- Can then break the interaction on proteins and break off a singular specific protein
