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Assessment 1.2

Amino Acids and Peptides

Reactant-Product [A]+[B]----[C]+[D]-2nd order
[S]-----[P]- 1st order
Substrate reactant
Equilibrium Constant Keq=[C]x[D]/[A]x[B]
Keq= [P]/[S]
Equilibrium constant amount of substrate
Molarity Avogadro's Number- 6.02 x 10^23 mol
Thermodynamics moving forward equilibrium constant > 1
moving backwards (reverse) equilibrium constant < 1
^G`= -RTIn(Keq) R= Universal Gas Constant T= Temperature in Kelvin In(x)=2.303 log(x)
Keq > 1= - G tendency to move forward
Keq < 1= G tendency to move in reverse (backwards)
- G Don't know how long it'll take to occur, all we know is that it'll go forward
Enzymes change the rate that the reaction is occuring by lowering the Gact
globular proteins (soluble)
Globular highly folded proteins, water soluble
Fibrous elongated proteins, insoluble
Catalyst reduce the activation energy of reactions
All reactions have a activation energy called catalyst
Cofactor a small (relative to protein) molecule required for enzyme activity. May be organic or inorganice, tightly bound or loose
Coenzyme an organic factor that is loosely bound to the enzyme, like a substrate
examples: NADP(H),NAD(H), ATP
apoprotein the folded polypeptide chain of conjugated protein
holoprotein the complete, biologically active protein conjugate, consisting of the folded polypeptide chain(s) and any relevant cofactors, a apoprotein combined with its prosthetic group
Effect of pH and temperature on Enzyme as temperature increases the kinetic energy of the molecules increase, including that of substrate molecules
Too high of temp will denature the proteins
Lipase group of enzymes named after the activator
Active Sites the region of the enzymes that binds the substrate
substrates are bound by noncovalent bonds
If you change the active site on the amino acid it creates a big problem
Lock and Key Concept
Antibody can bind two of the same antigen
Enzyme has 5 active sites and only 2 substrates bond to the enzyme it is considered to be unsaturated
The enzymes are completely (filled) bonded to all active sites this is considered to be saturated
Enzymes can have more than one active site
Structural Mechanisms account for an enzyme's ability to reduct Gact Entropy Reduction, General Acid-Base Catalysis, and Covalen Catalysis
Entropy Reduction one or more substrates bind in active site with the correct orientation for reaction; randomness
The enzyme has to have a binding site
General Acid-Base Catalysis Substrate protons important for reactivity are accepted or donated by the amino acid in the active site
Accounts for the pH-dependence of enzyme activity.
Covalent Catalysis A transient covalent bond is formed between the enzyme and substrate-usally for cleavage. Makes uses of kinases.
Six Classes of Enzyme Reactions
1. Oxidoreductase Catalyze oxidation/reduction reactions, transfer of electrons from one compound to another, thus changing the oxidation state of both substrates
Dehydrogenases- transfer of H-
Oxygenases- Oxidizes with O2
Peroxidases- (i.e. catalase)
Phosphoralated- turning reaction on and off
Alcohol dehydrogenases occurs in the liver and breaks down alcohol
Formealdehyde- Formic Acid Example
2. Transferase Catalyze reactions in which a functional group is transferred from one compound to another. ex-kinases
kinases- adds a phosphate to protein, transfers to group with hydroxyl group(serine,tyrosine, & threonine)
AST-aspartate transaminase ALT- alanine transaminase Get these two reading from the blood analysis to find out the condition of the liver.
AST & ALT levels are both high if taking in too much APAP, excessive alcohol consumption which causes liver damage.
If both levels are high then something is going on with the liver. If AST level is high and ALT is normal then something else is going on within the body besides the liver.
3. Hydrolases cleave bonds by adding water across the bond
4. Lysases cleaves bonds but do so without addition of water
5. Isomerases no change of molecule, creating isomers by moving functional groups
6. Ligases/Synthetases catalyze formation of new chemical bond by coupling their formation of the cleave of a high energy compound.
Ligases differ from lyases in that they utilize the energy obtained from cleavage of a high energy bond to drive the reaction usually ATP.
Isoenzymes enzymes that catalyze the same reaction but differ in structure or sequence
Mechanisms of Enzyme Regulation
1. Product Inhibition direct, reversible inhibition at an enzyme's active site by the product of the enzyme-catalyzed reaction. whats going to happen
single Step glucose-------- Glucose -6-phosphate
2. Allosteric Regulation bind the enzyme at a location distinct from the active site and cause a conformational change in the protein
product inhibition- inhibits the same enzyme that produced the product
feedback inhibition- often involves a molecule producted "Downstream" in the pathway acting as an inhibitor
multi-step process A-B-C-D-E (product)
3.Covalent Modification or Phosphorylation regulation protein kinase transfer phosphate from ATP to Serine, Tyrosine Threonine
Phosphorylation can increase of deacres the enzymes catalytic activity
4.Protein Protein Interaction binding of an enzyme by another protein to form a complex can result in activation or inhibition of an enzyme
Calmodulin (EF hand, Ca2+ binding protein
5. Zymogen Cleavage zymogen- inactive form on a enzyme that can be activated
digestive enzymes are often synthesized as zymogens, then activated by on demand by the other proteases
proteases- protein cleaving enzymes
Enzyme regulation involves proteins that are inactive inhibitors
6.Enzymes Synthesis and Degradation Vmax is proportional to the amount of enzyme present
Increase Vmax add enzymes
How to measure the reactant rate? Measure how fast the product is producing
Increaseing the substrate the reaction rate will increase until saturation then it'll plateau (Vmax)
Enzymology Enzymes are markers for diseases. Damage cells release isozymes that are normally intracellular.
Creatine Phospho(kinase) CK is used to diagnose myocardial infarction. stored in the muscle
CK-BB- outside the brain
CK-MM-skeletal muscle and heart muscle
CK-MB- mostly in the heart; increased levels indicates something is wrong with the heart (attack)
CK and LDH are common enzymes used to diagnose myocardial infarctions. LDH 1 & 2 are the important ones
Examples of Therapeutic Enzymes
Tissue Plasminogen Activator dissolves blood clots
Asparaginase used in acute lymphoblasts leukemia
Lactase lactose intolerant
Substrate Concentration Km
doesn't effect velocity
low Km- higher affinity of enzyme to the substrate
Vmax depends on the character of the enzyme and the substrate, and on the amount of the enzyme, when it plateaus out
more enzyme=higher Vmax less enzyme= lower Vmax
adding more substrates not going to effect
Km appears as the substrate concentration at which the rate of catalysis in half Vmax
= 1/2 Vmax
1/2 is free and 1/2 is bound with substrates
Kcat is the turnover number (Vmax/total (E)) the enzyme's top speed
Kcat/Km is a measure of an enzyme's catalytic efficiency bigger=better
Enzyme Inhibition
1. Reverse Competitive Inhibition competitive inhibitor competes with the substrate for the active site of the free enzyme
lowers the effective product Vmax= stays the same, Km increases
Example: Lipitor lowers serum cholesterol by reversibly and competitively inhibiting HMG-CoA reductase
2. Uncompetitive Inhibition Binds to enzyme when substrate is also bound
Vmax=lowers Km=decreases
Example: Mycophenolate (Cellcept) suppresses the immune system following an organ transplant
3. Mixed and Pure Noncompetitive Inhibition binds free enzymes and enzyme substrate complex, but doesn't bind at the active sites
Vmax= lower Km=usually lower
Km= can increase (like a competitive inhibitor) or decrease (like an uncompetitive inhibitor)
Example: Caspofungin- used to treat yeast infections & Foscarnet- antiviral inhibits viral DNA polymerase and used to treat herpes virus
4. Irreversible Inhibition poisons the enzyme by covalently modifying the active site of the free enzyme
permanent damage
Vmax=lower Km=unchanged
Example: Sarin Nerve Gas- irreversible acetylcholinesterase inhibitor; nerve damage causing muscle contraction, pulmonary arrest and death
Lineweaver-Burk Plot K0.5 used instead of Km
Allosteric inhibitor shifts the curve to the right (makes it more sigmoidal) and increases K0.5
Allosteric Activator- shifts the curve to the left (makes it more hyperbolic) and decrease K0.5
Competitive Inhibitor line increasing with inhibitor (on graph) Km=increasing 1/v (Y intercept) stays the same
Uncompetitive Inhibitor Y intercept-different Km=decrease Vmax & Km=decrease
Noncompetitive or Mixed Inhibition Converge on X intercept. look at graphs!
Created by: lisagoette