Enzymes Flashcards
What is an enzyme?
A specific protein that speeds up the rate of a reaction by lowering the activation energy of a reaction.
- They are not changed or consumed in the reaction
- are sensitive to temperature and pH
- do not affect equilibrium
- do not change thermodynamic parameters (G, S, H)
What is the structure of an enzyme?
- scaffolded for support and position the active site
- then the active site has a binding site and a catalytic site
Catalytic site
Part of enzyme that is very specific and where the reaction is catalyzed
Binding site
Where the substrate interacts with enzyme through intermolecular interactions
Positions the substrate so it is properly in the catalytic site
Substrate
What is being changed by the enzyme
Ligand
Any Substance enzyme interacts with - encompasses both substrate and regulatory molecules
Orthosteric Regulatory Elements
Interact with enzyme at its active site
Allosteric Regulatory Elements
Bind/interact with enzyme at some other place, other than the active site
Induced fit model
Enzyme and substrate affect each other
-initial binding undergoes conformational shifts that allow closer binding and more efficient catalyst
Lock and key
Substrate fits into enzyme like a key to a lock - perfect fit with no changes in structure to get a better fit
This is inadequate to explain enzymes interactions with their substrates
Oxidoreductases
Catalyze oxidation/reduction reactions
Ex: alcohol dehydrogenase, superoxide dismutase
Transferases
Transfer fictional group between molecules
Ex: aspartame transaminase
Creatine kinase
DNA polymerase
Hydrolases
Catalyze hydrolysis
Ex: angiotensin converting enzyme
Pancreatic lipase
Lactase
Isomerases
Catalyze isomerization
Ex: Ribose-5-phosphate isomerase
Ligases
Join molecules together with covalent bonds
Ex: aminoacyl tRNA synthetase
Glutamine synthetase
Pyruvate carboxylase
Kinase
Adds a phosphate group to a molecule (phosphorylates
Phosphatase
Removes a phosphate
Name the different types of enzyme regulation
Negative feedback
Positive feedback
Feed forward regulation
Cooperativity
Negative feedback
Downstream products inhibit the pathways to the products
Stimulus —> sensor —> control —> effector
If you have negative inhibition of an enzyme, the products of the reaction end up inhibiting the enzyme upstream in the pathway
Positive feedback
Downstream products amplifies initial stages of a reaction
Feed forward regulation
Products at an earlier step in the pathway regulate the enzyme
Cooperativity
Where the binding of one substate makes it easier to bind the next
Characterized by a sigmodal curve
Hill coefficient
Expresses the degree of cooperativity of an enzyme or protein
>1 is positively cooperative
<1 is negatively cooperative
=1 non-cooperative
What is the vmax?
The maximum rate of reaction
When X is fully saturated and rate of reaction can’t increase
What is Km
Concentration of the substate that corresponds to 1/2 vmax
Can be used to measure the affinity and enzyme has for a substrate
Michaelis-menten plot
Reaction rate on y axis
Substrate concentration on x axis
1/2 vmax = rate where substrate conc = km
Lineweaver-Burk plot
Double-reciprocal transformation of Mich-Men, 1/v is on the y 1/Conc. of substate is on the x axis Y intercept = 1/vmax X intercept = -1/km
Competitive inhibitors
Bind at active site
Increase Km
Vmax stays the same
You can out compete them with more substrate
Non competitive inhibitor
Bind allosterically
Lower Vmax
Km stays same
Uncompetitive inhibitor
Prevent enzyme from letting go of substate
Vmax decreases
Km decreases
Mixed inhibition
Inhibitor binds at the allosteric site or binds the enzyme substrate complex
Vmax is always decreased
Km depends on if the mixed prefers binding the free enzyme or if it prefers the complex
Km increases if it prefers free
Km decreases if it prefer complex
Glycosytion
Form of regulating/modifying enzymes by adding carbohydrate moieties
Zymogens
Aka proenzymes
Enzymes that need to be cleaved to be active
Cofactors
Chemical compounds that help enzyme carry out its biological function
Ex: Mg2+, cu2+, coenzymes (if it’s a cofactor that acts in an enzyme), vitamins
Prosthetic groups
When a coenzyme is very tightly bonded to its enzyme
Ex: heme
Holoenzyme
Enzyme together with its coenzyme and/or metal
Apoenzyme
Enzyme without the coenzymes needed for to function
Primary Structure
amino acids held together by covalent bonds (the peptide bonds holding each one together). These are strong, hard to break, so primary structure resilient
Secondary Structure
formed by hydrogen bonds between the amine and carboxylic acid groups of the amino acid backbone
ex: alpha helices, beta sheets
Tertiary Structure
formed by hydrogen bonding and interactions between the side chains of the amino acids to form a 3D structure
environment plays role in how the side chains will behave
ex: hydrophobic side chains moving the protein so they are enclosed by hydrophilic proteins when in an aqueous environment
-oxidizing environments that cause formation of disulfide bonds
-reducing environments (often by a reagent, such as 2-mercaptoethanol) to break those bonds
disulfide bridges contribute heavily to tertiary structure b/c covalent
ex: hydrogen bonding, van der waals, disulfide bridges, salt bridges
Quaternary Structure
At least two subunits (full tertiary structure of a protein = 1 subunit) coming together via intramolecular bonds
Common Denaturing Agents
temperature
high and low pH extremes (this would interfere with charges, or break disulfide bridges if reducing environment)
once you remove the denaturing conditions, proteins are able to fold/reassemble again
What breaks primary structures?
proteases
these target specific amino acid residues
