Enzymes are undoubtedly the most important molecular machines composed of ----- OR ------.
proteins or RNA
To proceed at a viable rate, most reactions require an --------- -------- -----.
initial energy input
DEFINE activation energy (Ea)
A chemical reaction occurs when colliding molecules possess a minimum amount of energy called the activation energy (Ea)
-More commonly called free energy of activation (DG‡) in biochemistry.
Catalysts increase reaction rate by lowering WHAT?
activation energy
DEFINE The free energy of activation (DG‡).
the amount of energy to convert 1 mol of substrate (reactant) from the ground state to the transition state
WHERE WOULD ONE FIND EXOTHERMIC (-DELTA G) ON THIS?
Many reactions that are spontaneous (-DG) will proceed at imperceptibly ---- rates, because they do not have the energy or correct orientation.
SLOW
The likelihood of a reaction ------- with increasing the temperature or using a catalyst
improves
T OR F?
Living systems cannot increase temperature without the risk of damaging structures, so they use catalysts (enzymes)
TRUE
Enzymes can increase reaction rate up to ----- TO ----.
107 TO 1019
T OR F?
Enzymes are very specific for substrates AND are not permanently altered.
TRUE
Each enzyme has a ----- ------ ----- to bind the substrate
specific active site
T OR F?
The active site also has amino acid side chains that take an active role in the catalytic process
TRUE
T OR F?
The active site is used to optimally orient the substrate to achieve the transition state at a lower energy via charge, hydrophobic interactions, H bonds
TRUE
DEFINE HOW TO Stabilize the transition state.
Stabilize the transition state---lowers energy barrier
Ultimately pulls the molecule into a state that most closely resembles the transition state.
T OR F ?
Enzymes do not change the thermodynamics of a
reaction.
TRUE
Remember, If thermodynamically unfavorable will not occur.
IF + ΔG —enzyme can not change this aspect.
NAME the t wo models that describe enzyme binding of substrate.
LOCK & KEY
INDUCED FIT
T OR F?
Many enzymes require certain non-protein components to function.
TRUE
WHAT ARE COFACTORS? NAME SOME AND THEIR FUNCTION.
Na+, K+, Mg+2 Ca+2 ,Zn+2 (provide high positive charge)- binding small molecules, serve as electrophiles, oxidation reduction reactions.
DEFINE HOLOENZYMES
INTACT FUNCTIONAL ENZYMES WITH COFACTORS
THE PROTEIN COMPONENT OF AN ENZYME IS CALLED WHAT?
APOENZYME.
NAME THE Six major enzyme categories
1. Oxidoreductases ---ox/red
2. Transferases---transfer structural group
3. Hydrolases—break down via hydrolysis
4. Lyases---groups are removed by elimination to form a double bond or added to a double bond
5. Isomerases---Intramolecular rearrangement
6. Ligases---Join groups/structures together
WHAT IS THE FUNCTION OF THE ISOMERASES ENZYME GROUP?
INTRAMOLECULAR REARRANGEMENT.
WWHAT IS THE FUNCTION OF THE LYASES ENZYME GROUP?
groups are removed by elimination to form a double bond or added to a double bond
DEFINE DIFFUSION CONTROLED LIMIT.
108 TO 109
CONVERT SUBSTRATE TO PRODUCT ALMOST EVERY TIME INTERACT OR CATALYTIC PERFECTION.
Thermodynamics can predict whether a reaction is spontaneous, but cannot predict -------.
RATE
The rate or velocity of a reaction is the WHAT?
The change of a concentration of reactant or product per unit of time
DEFINE Initial velocity (VO)
a velocity at the beginning of a reaction when the concentration of substrate greatly exceeds enzyme concentration (often use some sort of colored reaction to measure)
Information about reaction rates is the quantitative study of enzyme catalysis, or -------- -------.
enzyme kinetics
IN ENZYME KINETICS, THIS REACTION (A -->P) IS WHAT TYPE OF ORDER?
1ST ORDER.
T OR F?
WHEN A ENZYME KINETIC IS ZERO ORDER, THE RATE IS NOT AFFECTED BY ADDING MORE SUBSTRATE, YOU CAN KEEP ADDING BUT NO CHANGE.
TRUE
WHAT ENZYME KINETIC ORDER IS THIS AND HOW WOULD YOU CALCULATE THE RATE?
FIRST ORDER.
RATE = K = Y=MX + B
NAME THIS FORMAULA AND KNOW WHAT WOULD HAPPEN IF YOU HAD A LARGE K1 VALUE.
The Michaelis constant (Km).
The lower the value of Km (big k1 for instance) the greater the affinity of the enzyme for ES complex formation (fig 6.4).
So the lower the concentration of substrate needed to achieve a given rate (fig 6.4)
LABEL K1, K-1 AND K2.
NAME AND DEFINE EACH UNIT:
[S] = substrate concentration
Vmax= maximum velocity
vo= initial velocity(ZERO ORDER STATE)
Km= Michaelis constant experimentally
determined
DEFINE Catalytic perfection
Enzyme working at maximum capacity or at its diffusion controlled limit—i.e. how fast the substrate can get to
the active site (i.e. diffusion in aqueous). THINK MACROMOLECULAR CROWDING. WORKS FASTER, PROCESS COUPLED TOGTHER DUE TO SMALL SPACE.
IF THE Km WAS LOWER, (STEEPER SLOPE) WHAT WOULD IT MEAN?
Km is substrate [conc] at Vmax/2
IT WOULD MEAN THAT THE SUBSTRAIT IS GOING INTO A TRANSITION STATE FASTER.
WHAT IS THE Kcat VALUE?
The number of substrate molecules converted to product per unit time is kcat (turnover number)
Kcat is Vmax over total enzyme concentration (Et).
Kcat = Vmax/(Et).
THIS MEASURES THE ENZYME EFFICENCY.
DEFINE SPECIFICITY CONSTANT
Reflects the relationship between catalytic rate of enzyme and substrate binding affinity
It can be used when comparing different substrates for the same enzyme since it is a measure of efficiency.
the specificity constant.
Kcat/Km
Low Km and high kcat = high affinity and efficient.
WHAT WOULD BE THE EQUATION FOR THIS LINEWEAVER-BURK LINE?
THE LINEWEAVER-BURK PLOTS ARE RECIPROCAL OF WHAT?
Michaelis-Menten equation gives a linear representation.
DIVIDE EVERYTHING INTO 1 (1/Km)
NAME THE POSITIONS OF A LINEWEAVER-BURK PLOT.
Slope of the line Km/Vmax
1/Vmax is the Y intercept
-1/Km is the X intercept
T OR F?
Enzyme inhibition can be reversible or irreversible.
TRUE
NAME 3 TYPES OF REVERSIBLE ENZYME INHIBITION.
COMPETITIVE
NONCOMPTITIVE
UNCOMPETITIVE
T OR F?
Reversible inhibition can be counteracted by increasing substrate levels or removing the inhibitor
TRUE
Irreversible inhibition occurs when the inhibitor permanently impairs the enzyme HOW?
Covalent interaction
--------------- ----------- bind reversibly to the enzyme at the active site thus competing with substrate binding.
Forms enzyme-inhibitor (EI) complex
Michaelis-Menten Plot of Uninhibited Enzyme Activity Versus Competitive Inhibition.
Succinate dehydrogenase of the Krebs citric acid cycle is inhibited by -------.
malonate
------ ----------- can bind reversibly to the E or ES complex at a site other than the active site of enzyme
Noncompetitive Inhibitors
WHAT TYPE OF CHART IS THIS AND LABEL BOXES.
Michaelis-Menten Plot of Uninhibited Enzyme Activity Versus Noncompetitive Inhibition. SHAPE CHANGES, NEVER REACHES Vmax.
NAME THE TYPE OF ENZYME INHIBITOR WHO....
Changes enzyme conformation-prevents product formation.
Increased substrate concentration partially reverses inhibition.
NONCOMPETITIVE INHIBITORS
T OR F?
NONCOMPETITIVE INHIBITORS HAVE DIFFERENT Vmax BUT MAY HAVE SAME OR DIFFERENT Km?
TRUE
------------ Inhibitors: a type of noncompetitive inhibition that involves binding only the ES.
UNcompetitive
NAME THE LOCATIONS WHERE REVERSIBLE ENZYME INHIBITION CAN OCCUR.
Competitive:bind reversibly to the enzyme at the active site.
Noncompetitive: can bind reversibly to the E or ES complex at a site other than the active site of enzyme.
Uncompetitive: binding only the ES.
LINE A NORMAL ENZYME-CATALYZED RXN.
B,C, & D ARE COMPOUNDS ADDED. IDENTIFY THE INHIBITORY ACTION.
B. COMPETITIVE. Km HAS ONLY CHANGED.
C. PURE NONCOMPETITIVE. Vmax HAS ONLY CHANGED.
D. UNCOMPETITIVE. BOTH Km & Vmax HAVE CHANGED.
COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
COMPETITIVE. Km HAS ONLY CHANGED.
COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
PURE NONCOMPETITIVE. ONLY Vmax HAS CHANGED.
COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
MIXED NONCOMPETITIVE.NOTICE HOW X & Y INTERSECT BELOWTHE HORIZONAL AXIS. (CAN ALSO INTERSECT ABOVE THE HORIZONAL AXIS).
COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
MIXED NONCOMPETITIVE.NOTICE HOW X & Y INTERSECT ABOVE THE HORIZONAL AXIS. (CAN ALSO INTERSECT BELOW THE HORIZONAL AXIS).
COMPETITIVE, NONCOMPETITIVE, MIXED NONCOMPETITIVE OR UNCOMPETITIVE.
UNCOMPETITIVE. BOTH Km AND Vmax HAVE CHANGED.
T OR F?
In vitro work does not always reflect in vivo reality
TRUE
Scientists use 3 METHODS to understand the catalytic mechanism of enzymes. NAME THEM.
X-ray crystallography,
chemical inactivation,
modeling
Essential features of catalysis are reaction between ------ & -------.
Electron-deficient atoms (electrophiles) and electron-rich atoms (nucleophiles)
Electrons flow from a nucleophile to an electrophile
----------- ------------ is a step-by-step description of a reaction
Reaction mechanism
Examples of reactive intermediates include WHAT? NAME 3.
free radicals,
carbocations,
carbanions
WHAT THE HELL IS THIS AND WHAT DOES IT PRETAIN TO? WHERE WOULD YOU FIND THE PRODUCT?
Energy Profile for a Two-Step Reaction of reactive intermediates. Products are on the bottom line of delta G on the right.
T OR F?
Mechanisms of only a few enzymes are known in significant detail
TRUE
Several factors contribute to enzyme catalysis. The most important are...NAME 3
1) Proximity and Strain Effects
2) Electrostatic Effects
3) Acid-Base Catalysis
DEFINE Proximity and Strain Effects
ENZYME CATALYSIS. The substrate must come in close proximity to the active site. Strained enzyme substrate complex during binding induces change closer to transition state.
DEFINE Electrostatic Effects OF ENZYME CATALYSIS.
Charge distribution in the largely anhydrous active site may help position the substrate
DEFINE Acid-Base Catalysis OF ENZYMES
Proton transfer is an important factor in chemical reactions.
Hydrolysis of an ester, for example, takes place better if the pH is raised.
Hydroxide ion catalysis
THE HYDROXIDE ION CATALYSIS IS WHAT TYPE OF CATALYSIS MECHANISM?
ACID-BASE CATALYSIS.
WHAT'S THE NEXT 2 STEPS? WHAT DOES IT REPRESENT?
Hydroxide Ion Catalysis.
--->
T OR F?
Side chains of many amino acids (e.g., histidine, lysine, and aspartate) can be used as general acids or bases OF ENZYME CATALYSIS.
Depends on state of protonation, based on pKa of functional groups
TRUE
T OR F?
More physiological is the use of general bases and acids (i.e. non OH- bases) FOR ENZYME CATALYSIS.
TRUE
DEFINE THE REACTION NAME THE THE NEXT 2 STEPS.
General Base Catalysis
--->
WHAT TYPE OF CATALYSIS TYPE IS THIS AND NAME THE NEXT 2 STEPS.
GENERAL ACID CATALYSIS.
T OR F?
In order to participate in catalysis, the amino acid has to be charged or polar. For example, chymotrypsin.
TRUE
----------- side groups function to orient substrate or stabilize transition state whereas charged catalytic groups function in the reaction
Noncatalytic
The active sites of enzymes are lined with ----- ----- that create a microenvironment conducive to catalysis
AMINO ACIDS
DEFINE AND NAME Alkali metals OF ENZYME CATALYSIS.
Alkali metals are usually loosely bound and play structural roles.
Na+, K+, Mg2+, and Ca2+
DEFINE AND NAME Transition metals.
Transition metals usually play a functional role in catalysis as part of a functional group.
Zn2+, Fe2+, and Cu2+
T OR F?
Metals are good Lewis acids (accept charge) and effective electrophiles.
TRUE
WHAT THE HELL IS......
1.Contain functional groups that amino acid side chains do not
2.Can be tightly or loosely bound and their structures are often changed by the catalytic process
3. Most are derived from vitamins
COENZYMES
NAME THE 3 COENZYME GROUPS.
1. electron transfer (NAD+),
2. group transfer (coenzyme A),
3. high energy transfer potential (nucleotides)
DEFINE Coenzymes
a group of organic molecules that are attached to enzyme and are essential for function.
IN ENZYME CATALYSIS,Temperature- the higher the temperature, the faster the reaction rate. WHY?
increased number of collisions.
DEFINE pH optimum
pH- hydrogen ion concentration affects enzyme function; therefore there is a pH optimum
T OR F?
Catalytic activity is related to ionic state of the active site
TRUE
T OR F?
Changes in ionizable groups could change structure of the enzyme: increase or decrease activity—remember bonds that stabilize tertiary structure—H bonds, salt bridges
TRUE
WHAT THE HELL IS Chymotrypsin?
It's basically,serine protease of 27kD
Serine proteases have a triad of amino acids in their active site (e.g., Asp 102, His 57, and Ser 195)
Hydrolyzes peptide bonds adjacent to aromatic amino acids—such tyrosine (Y), tryptophan (W), and phenylalanine (F) (carboxyl side).
Used to digest food.
Enzyme regulation is necessary for...NAME 3
Maintenance of ordered state
Conservation of energy
Responsiveness to environmental changes
ENZYME CATALYSIS REACTIONS ARE CONTROLED HOW?
Control is accomplished by:
genetic control,
covalent modification,
allosteric regulation,
compartmentalization
Genetic Control happens at the ----level and can lead to repression or induction of enzyme synthesis
DNA
Several covalent modifications in enzyme structure cause changes ------ ------.
IN FUNCTION
Types of covalent modification include NAME 3
phosphorylation,
methylation,
acetylation
THROUGHT COLVALENT MODIFICATION,Some enzymes produced and stored as ----- OR --------.
proenzymes or
zymogens (inactive precursor)
WHAT ARE allosteric sites?
Sites other than active site—can induce a conformation change and thus alter enzyme activity.
The Rate of An Enzyme-Catalyzed Reaction As a Function of Substrate Concentration PRODUCE WHAT TYPE OF LINE ON A GRAPH?
Sigmoidal curve, unlike Michaelis-Menten kinetics
Most allosteric enzymes are ---------- ------------.
multisubunit enzymes
NAME THE allosteric enzymes 2 theoretical models.
concerted and sequential
DEFINE THE concerted model OF THE ALLOSTERIC ENZYMES.
In the concerted model, all subunits are changed at once from taut (T) to relaxed (R) or vice versa with first binding of effector (e.g. activator or inhibitor). An activator shifts the equilibrium in favor of the R form; an inhibitor shifts in favor of the T form
DEFINE THE sequential model OF THE ALLOSTERIC ENZYMES.
In the sequential model binding of the ligand to one subunit, it triggers a conformational change that is passed to subsequent subunits
T OR F?
ENZYMES ARE EFFECTED BY Diffusion barriers—pathways connected do not need to wait for substrate to diffuse through crowded cell
TRUE
Diagnostic Enzymes
NAME ONE PROCEDURE.
myocardial infarction (MI) leads to heart muscle cell death.
---------- AND ---------have been used to diagnose MI replaced by cTnI (troponin assay for muscle damage
