What are three ways to increase the rate of a chemical reaction, including hydrolysis?
1.) Increasing the temperature (adding energy in the form of heat)
2.) Increasing the concentration of the reacting substances.
3.) Adding a catalyst
What is a catalyst?
A catalyst is a substance that participates in the reaction yet emerges from the reaction in its original form.
Living systems use catalysts called _____ to increase the rates of chemical reactions.
Enzymes
What are enzymes?
An enzyme is usually a protein that acts as a catalyst to speed up the rate of a chemical reaction without being consumed itself.
What is a major exception of enzymes?
Ribozymes are RNA molecules that act as catalysts
What makes enzyme different from non-biological catalyst?
Faster rate, moderate reaction conditions, and reaction or substrate specificity.
Enzymes speed up biochemical reactions at rate enhancements of ___ to ___.
10^8 to 10^12
What is a moderate condition?
Physiological condition with a temperature of 20-40 Celsius, pressure of 1 atm, pH 6-8 not including the digestive enzymes, and substrate concentration 1-20 mM.
Most enzymes are highly specific to their what?
Substrates
_____ has broad substrate specificity.
Chymotrypsin
Chymotrypsin hydrolyzes _____ and _____ bonds after Phe, Tyr, or Trp.
Peptide bonds; Other amide or ester bonds
Enzymes are usually named after what?
The reaction they catalyze
Pyruvate decarboxylase does what?
Removes a carboxylate group from the substrate pyruvate.
All biological reactions involve either the _____ if some substance to another, or its _____, or the _____ of that substance.
Addition; removal; rearrangement
What are six major classifications of enzymes?
1.) Oxidoreductases-Oxidation/reduction reactions
2.) Transferases- Transfer of functional groups
3.) Hydrolases- Hydrolysis reactions
4.) Lyases- Group elimination to form double bonds
5.) Isomerases- Isomerization reactions
6.) Ligases- Bond formation c
Enzymes have _____ sites.
Active
_____ bind to enzymes at the active site.
Substrates
_____ _____ are an exemplary class of enzymes that have a common set of amino acids (red) in their active site.
Serine proteases
What are the three things you can do to increase the rate of a reaction?
Temperature, concentration, and catalyst.
What makes ribosomes different from the typical enzymes?
Ribosomes are made from RNA, not typical protein.
What makes enzymes different from non-biological catalyst?
Faster, more specific, conditions milder.
T/F Only biological catalysts are not permanently altered or consumed as a result of the reaction.
FALSE
What statements are true regarding the difference between biological and nonbiological catalyst?
Only biological catalysts have complex, specific structures. Biological catalysts are more specific in regard to the substances on which they act. Biological catalysts can work under relatively mild conditions. Reaction rate enhancement is greater in biol
What determines the rate of a reaction?
The height of the activation energy barrier
The _____ the activation energy barrier, the _____ likely the reaction is to occur.
Higher; less
The sign of Delta G indicates what?
The spontaneity of a reaction.
If Delta G is <0 the reaction is _____. If Delta G is >0 the reaction is _____.
Spontaneous; not spontaneous
Enzymes work by _____ the activation energy for a reaction.
Lowering. It does this by interacting with the reacting molecules such that they are more likely to assume the transition state.
A catalyst _____ the reaction.
Speeds up, because as more reacting molecules achieve the transition state per unit time, more molecules of product can form per unit time.
An enzyme _____ the height of the activation energy barrier by _____ the energy of transition state.
Lowering; lowering
An enzyme does NOT alter what?
The net free energy change for a reaction.
The minimum amount of energy required to bring out a chemical reaction is called what?
Activation energy
How do you find the rate of enhancement?
Catalyzed rate/uncatalized rate
What are the three fundamental mechanisms which enzyme use to lower the activation energy?
Acid-base catalysis (An enzyme can use acid catalysis, base catalysis or both!), Covalent catalysis (also called nucleophilic catalysis) and Metal ion catalysis.
During acid catalysis, the catalyst acts as an acid by what?
Donating a proton
If a catalyst symbolized (H-A) donates a proton to the ketone's oxygen atom, it reduces the unfavorable carbanion character of the transition state, thereby lowering its energy and hence lowering the activation energy barrier for the reaction. This is an
Acid catalysis
Base catalysis _____ the energy of the transition state and thereby _____ the reaction.
lowers; accelerates
In a general base catalysis, H+ is _____ by a base to _____ the free energy of the transition state.
Abstracted; lower
Some _____ can play a role in acid-base catalysis.
Amino acids, including: Asp, Glu, His, Lys, Cys, and Tyr.
What happens in covalent catalysis?
In covalent catalysis, a covalent bond forms between the catalyst and the substrate during formation of the transition state.
Covalent catalysts _____ reactions by forming a _____ bond between enzyme and substrate.
Accelerate; covalent. Forms a covalent bond with the substrate in the middle of the reaction.
Enzymes that use covalent catalysis under go a two-part reaction process, so the reaction coordinate diagram contains _____ energy barriers with the reaction intermediate _____ them.
Two; between
Many of the groups that make good acid-base catalysts also make good covalent catalysts because they contain what?
Unshared electron pairs
A covalent catalysis needs what two things?
Nucleophile and electrophile
What is a nucleophile?
An electron-rich group in search of an electron-poor center.
What is an electrophile?
A compound with an electron deficiency.
Metal ions as catalysts occurs when?
Metal ions participate in enzymatic reactions by mediating oxidation-reduction reactions, or by promoting the reactivity of other groups in the enzyme's active site through electrostatic effects. Ex: Alcohol dehydrogenase
T/F Enzymes are not limited using only one of these mechanisms.
TRUE
The case study for Chymotrypsin utilized what?
Acid base catalysis and covalent catalysis.
Serine proteases have what three conserved amino acids in their active sites? These 3 amino acids form what?
Asp 102, His 57, and Ser 195. They form the catalytic triad.
In the catalytic triad, Asp 102 _____ His 57. His 57 acts as a general _____ and later as a general _____. Ser 195 acts as a _____.
Anchors
Base;acid
Nucleophile
The catalytic mechanism of chymotrypsin and other serine proteases: Step 1- after the peptide substrate enters the active site
1.) Removal of the Ser hydroxyl proton by His 57 (a base catalyst) allows the resulting nucleophilic oxygen (a covalent catalyst) to attack the carbonyl carbon of the substrate.
The catalytic mechanism of chymotrypsin and other serine proteases: Step 2-Tetrahedral intermediate
The tetrahedral intermediate decomposes when His 57, now acting as an acid catalyst, donates a proton to the nitrogen of the scissile peptide bond. This step cleaves the bond. Asp 102 promotes the reaction by stabilizing His 57 through hydrogen bonding.
The catalytic mechanism of chymotrypsin and other serine proteases: Step 3- Acyl-enzyme intermediate (Covalent intermediate)
The departure of the C-terminal portion of the cleaved peptide, with a newly exposed N-terminus, leaves the N-terminal portion of the substrate (an acyl group) linked to the enzyme. This acyl-enzyme intermediate is a relatively stable covalent complex. Wa
The catalytic mechanism of chymotrypsin and other serine proteases: Step 4- In the second tetrahedral intermediate
His 57, now an acid catalyst, donates a proton to the Ser oxygen, leading to collapse of the intermediate, resembling step 2.
The catalytic mechanism of chymotrypsin and other serine proteases: Step 5
The N-terminal portion of the original substrate, now with a new C-terminus, diffuses away, regenerating the enzyme.
Name the three categories of chemical catalysis.
Acid-base catalysis, Covalent catalysis, and Metal ion catalysis.
Which amino acids side chains can act as either an acid or a base?
Aspartate (Asp, D) -Charged
Glutamate (Glu, E) -Charged
Histidine (His, H) -Polar
Lysine (Lys, K) -Charged
Cysteine (Cys, C) -Polar
Tyrosine (Tyr, Y) -Polar
The three conserved amino acids that make up the catalytic triad in chymotrypsin are what?
Asp, His, and Ser.
An enzyme accelerates a biochemical reaction by?
Providing a more favorable pathway for the reaction.
The height of the activation barrier determines what?
The rate of the reaction.
The catalytic activity of enzymes also depends on what four alternative ways (non-chemical)?
1. Transition state stabilization
2. Proximity and orientation effects
3. Induced fit
4. Electrostatic catalysis
Stabilizing the transition state will _____ the activation energy.
Lower
Proximity and orientation effects
When enzymes bind substrates, the substrates are brought into proximity and in the correct orientation to make a chemical reaction favorable.
Induced fit is a conformational change of the enzyme brought on by the what?
binding of the substrate
What is one of the benefits of the mechanism induced fit?
One of the benefits is allowing the full immersion of the substrate into the center of the enzyme while still allowing come and going of the substrate by diffusion.
Induced fit: When hexokinase binds to glucose (the _____), a conformational change occurs in the enzyme to "_____" the substrate better.
Substrate; "fit
By sequestering substrates in the active site, an enzyme can eliminate the energy barrier imposed by the ordered solvent molecules, thereby accelerating the reaction. This phenomenon is sometimes described as what?
Electrostatic catalysis
Electrostatic catalysis lowers the activation energy by what?
Isolating the reactants from the aqueous environment. Without the water molecules the reactants are spared from overcoming the hydration shell in order to make contact.
Electrostatic catalysis helps reactants overcome what?
Hydration shell
What statement about stabilizing the transitional state of the substrate is true?
The stabilizing effect lowers activation energy. It does NOT have anything to do with Gibb's free energy or binding the substrate.
The transitional state of the substrate is the _____ stable form.
Least
What statement about proximity and orientation effect is true?
The mechanism essentially does the same thing as increasing substrate concentration.
T/F The conformation change of enzyme that utilizes induced fit mechanism is powered by the free energy change of the reaction.
TRUE
T/F The electrostatic catalysis is caused by the removal of hydration shell from the reactants.
TRUE
Chymotrypsin, trypsin, and elastase have very similar _____ bur differ significantly in their _____.
Structures; Specificity
The varying specificities of these enzymes are largely explained by the chemical character of the so-called _____, a cavity on the enzyme surface at the active site that accommodates the residue on the N-terminal side of the scissile peptide bond.
Specificity pocket
Enteropeptidase in our intestine initiate the activation of _____.
Zymogens
Inactive zymogens are activated by what?
Proteolysis
Zymogens are what?
Premature forms of an enzyme
What is autoactivation?
When an enzyme can turn itself
T/F Enteropeptidase can be found in the intestine and the pancreas.
FALSE, if found in the pancreas it would start there.
Trypsin cuts after basic amino acids because of the Asp reside at the bottom of its specificity pocket. What if you found trypsin mutant that cuts after acidic amino acid instead. What do you expect the mutation to be?
Asp to Lys. Lys is positive and Asp is negative.
What is the final step of coagulation?
The conversion of fibrinogen to fibrin. A series of proteolytic reactions involving a number of proteins and additional factors from platelets and damaged tissue.
Blood Coagulation requires a Cascade of _____.
Proteases
The enzyme responsible for cleaving fibrinogen to fibrin is known as what?
Thrombin
Like Trypsin, thrombin cleaves peptide bonds following Arg residues, but it is highly specific for the what?
Two cleavage sites in the fibrinogen sequence
The thrombin inhibitor is?
Anti-thrombin
Protease inhibitors limit what?
Protease activity
How are chymotrypsin, trypsin, and elastase similar and different from each other?
They all cut protein peptides but each cut after a different type of amino acid.
T/F The specificity pocket is a region on the serine proteases that selects for certain type of amino acid side chains. Once a correct side chain docks in the pocket a cut is made.
TRUE
T/F The reason our body has a thrombin inhibitor flowing in the blood stream is to prevent internal bleeding.
FALSE
What would happen if a person suffered a mutation which caused him/her to have no thrombin inhibitor in their blood stream?
They would have a blood clot very easily.