lecture 8 Flashcards
negative regulator
proteins can have negative feedback inhibition
-when you make too much of something, it will be inhibited
-inhibiting activity of the enzyme will inhibit the pathway
(ex. lysine, methionine, threonine)
ligand
any substance bound by a protein
protein-ligand interactions are dictated by
noncovalent interactions
binding site
region of protein that associated with a ligand
what dictates the specificity of the binding sites
specific interactions between the binding site amino acids and the ligand
Y shaped molecule composed of two heavy chains and two light chains
antibodies
antibodies bind very specifically to
a target molecule called and antigen
antibodies contain two
antigen binding sites where the amino acid sequence is highly variable
how many different possible antibodies are there?
billions
Antibodies function
important for fighting infections
laboratory tool: molecule identification, quantification and localization
Enzymes (E)
biological catalysts that speed up the rate of the reaction
Enzymes bind to — forming an —
substrates (S)
enzyme-substrate complex (ES)
after the reaction has proceeded, the enzyme will be in contact with the product as an —- and will eventually release a —
enzyme-product complex (EP)
product (P)
Active site
the region of an enzyme that binds and catalyzes the substrate
only a few amino acid residues in the active site participate in catalysis
–> why are enzymes so large then?
to provide a folding framework for the active site– precisely aligns the active site residues.
optimizes binding energy in the transition state
Activation energy
the energy needed to go from the ground state to transition state
transition state
the maximum energy species formed on the reaction coordinate
3 ways that enzymes lower the activation energy
- aligns substrates in a favourable orientation
- rearranges the electron distribution
- physically strains the substrate to induce a reaction
lysozome
enzyme that breaks polysaccharide chains that form cell walls in bacteria
lysozome function
-performs hydrolysis rxn
-helps rxn overcome the activation energy
Enzyme active sites
–> what type of amino acids would you expect to find there?
polar or charged amino acids are more likely to be found in the active site
(more energetically favourable)
enzyme names generally end in…
“ase”
protease
cuts protein
hydrolase
cuts hydrogens off
many protons rely on small nonprotein molecules to perform particular functions
give two examples
Retinal: binds to the protein rhodopsin. retinal changes shape when the photon is absorbed
Heme: binds to the protein hemoglobin and allows reversible binding of oxygen
enzymes are not always
active
(this would not be efficient!)
Regulating protein activity
-regulation of gene expression
-regulation of protein degredation
-confining protein to specific compartments
-regulating protein activity directly
Feedback inhibition
the end product of a chain of enzymatic reactions reduces the activity of an enzyme earlier in the pathway
feedback inhibition effects are
almost instantaneous and the effects can be rapidly reversed if product levels fall
preventing an enzyme from acting is a form of
negative regulation
positive regulation
enzyme activity is stimulated
feedback inhibition can have multiple
points of control
ex. biosynthesis of amino acids
allosteric proteins
proteins that can exist in multiple conformations depending on the binding of a molecule to a site other than a catalytic site
allosteric proteins: ADP and ATP example
ADP levels increase as ATP levels decrease which signals the need for additional oxidation of sugars
(this is an example of allosterically regulated enzyme that is positively regulated by ADP)
protein phosphorylation
attaching phosphate groups to proteins is a very common method of regulating its activity
-target proteins become active via kinase, creates covalent bonds
3 characteristics of protein phosphorylation
-may cause conformational changes
-reversible
-involves the enzyme-catalyzed transfer of the terminal phosphate of ATP to the hydroxyl group of serine, threonine or tyrosine
protein kinase
enzyme that catalyzes the addition of a phosphate
protein phosphatase
enzyme that catalyzes the removal of a phosphate
–> phosphorylating can either activate or inhibit protein activity
phosphorylation can also create
docking
docking (in protein phosphorylation): 2 functions
- important for intracellular signalling proteins
-binding of a signal causes phosphorylation of tyrosine residues which allows other proteins to bind
examples of covalent modifications that can be done in the cell
-addition of an acetyl group
-attaching (poly) ubiquitin
-addition of fatty acids
many proteins will have multiple covalent modifications
GTP binding proteins
-for some proteins, the phosphate is transferred from GTP (guanosine triphosphate) instead of ATP
-can be turned “on” and “off”
“on”= bound to GTP
“off”= bound to GDP
reversible process.
GTP-binding proteins can affect the activity of other proteins.
motor proteins
generate forces responsible for muscle contractions and most eukaryotic cell movement
what is the “problem” for motor proteins?
if the movements are easily reversible, the proteins will move back and forth and not get anywhere!!
what is the “solution” for motor proteins?
the steps involved in the movement are (basically) irreversible.
A way to do this is to couple one of the conformational changes to the hydrolysis of ATP.
Protein machines
proteins often work in tandem with other proteins to function as a large multiprotein complex
hydrolysis of nucleoside triphosphates drives what (protein machines)
drives an ordered series of conformational changes in individual subunits which affects the entire complex
ex. DNA replication
