Enzymes Flashcards
Define enzyme
Enzymes are proteins that act as catalysts for biochemical reactions
True or false: enzymes are consumed in the reaction
False
True or false: enzymes are the most effective catalysts
True
Enzymes are usually what kind of protein?
Globular proteins
True or false: enzymes undergo all the reactions of proteins including denaturation
True
Name three things enzyme activity is effected by
Temperature, alterations in pH, and other protein denaturants like microwaves, heavy metals etc.
*Enzyme inhibitor
Drugs and compounds that modify drug action
Name the two types of enzymes
Simple and conjugated enzymes
*Simple enzyme
Composed only of protein (amino acid chains)
*Conjugated enzyme
Has a non-protein part in addition to a protein part
*Apoenzyme
Protein part of a conjugated enzyme
*Holoenzyme
The biochemically active conjugated enzyme
*Apoenzyme+cofactor =
Holoenzyme
*Cofactor
Non-protein part of a conjugated enzyme
*Substrate
Reactant in an enzyme catalyzed reaction
Cofactors are important
for the chemically reactive enzymes
What is a cofactor
Cofactors are small organic molecules or Inorganic ions
Organic molecule cofactors
also called co-enzymes or co- substrates
Co-enzymes/co-substrates are derived from
dietary vitamins
Inorganic ion cofactors
Typical metal ion cofactors - Zn2+, Mg2+, Mn2+, and Fe2+
• Nonmetallic ion cofactor - Cl-
• Inorganic ion cofactors derived from dietary minerals
Role of iron cofactor
oxidation/reduction
Role of copper cofactor
oxidation/reduction
Role of zinc cofactor
Helps bind NAD
Role of biotin coenzyme
carries COO-
Role of coenzyme A
carries CH2-CH3
Role of NAD coenzyme
carries electrons
Role of FAD coenzyme
carries electrons
Role of heme
Binds ions, O2, and electrons; contains iron cofactor
Role of Flavin
binds electrons
Role of Retinal
converts light energy
Nomenclature of enzymes
Most commonly named with reference to their function
– Type of reaction catalyzed
– Identity of the substrate
*substrate
the reactant in an enzyme-catalyzed reaction:
– The substrate is the substance upon which the enzyme “acts.”
– E. g., In the fermentation process, sugar is converted to alcohol, therefore in this reaction sugar is the substrate
-ase
identifies it as an enzyme
-in
can also identify an enzyme ex: pepsin, trypsin, chymotrypsin
Oxidase
catalyzes an oxidation reaction
Hydrolase
catalyzes a hydrolysis reaction
Predict the function of the following enzymes.
a. Maltase
b. Lactate dehydrogenase
c. Fructose oxidase
d. Maleate isomerase
a. Hydrolysis of maltose;
b. Removal of hydrogen from lactate ion;
c. Oxidation of fructose;
d. Rearrangement (isomerization) of maleate ion
Name the six major classes on enzymes
- Oxidoreductases
- Transferases
- Hydrolases
- Lyases
- Isomerase
- Ligases
Oxidoreductases
Oxidation-reductions
Transferases
an enzyme that catalyzes the transfer of a functional group from one molecule to another
Hydrolases
Hydrolysis reactions
Lyases
Reactions involving addition or removal of groups form double bonds
Isomerase
Isomerization reactions
Ligases
Reactions involving bond formation coupled with ATP
True or false: Oxidation and reduction reactions are always linked to one another
True
An oxidoreductase requires
a coenzyme that is either oxidized or reduced as the substrate in the reaction.
The two major subtypes of transferases
Transaminases and Kinases
Transaminases
catalyze transfer of an amino group to a substrate
Kinases
catalyze transfer of a phosphate group from adenosine triphosphate (ATP) to a substrate
Kinase inhibitors
Newer drug classes for treating cancer, inflammation
A hydrolase reaction involves
the addition of a water molecule to a bond to cause bond breakage
Carbohydrases
catalyze the hydrolysis of glycosidic bonds in oligo- and polysaccharides
Proteases
catalyze the hydrolysis of peptide bonds in proteins
Esterases
catalyze the hydrolysis of peptide bonds in proteins
Lipases
catalyze the hydrolysis of ester bonds in triacylglycerols
Dehydratase
effects the removal of the components of water from a double bond
Hydratase
effects the addition of the components of water to a double bonds
A ligase requires =
ATP hydrolysis because such reactions are energetically unfavorable and simultaneous input of energy obtained by a hydrolysis of ATP to ADP
*The active site
Relatively small part of an enzyme’s structure that is actually involved in catalysis
*Functions of the active site
Place where substrate binds to enzyme
– Formed due to folding and bending of the protein.
– Usually a “crevice like” location in the enzyme
– Some enzymes have more than one active site
*Lock-and-Key model
Enzyme has a pre-determined shape for the active
site
– Only substrate of specific shape can bind with active site
*Induced Fit Model
Substrate contact with enzyme will change the shape
of the active site
– Allows small change in space to accommodate substrate (e.g., how a hand fits into a glove)
Forces That Determine Substrate Binding
- H-bonding
- Hydrophobic interactions
- Electrostatic interactions – salt bridge
*Absolute Specificity
An enzyme will catalyze a particular reaction for only one substrate
– This is most restrictive of all specificities (not common)
*Stereochemical Specificity
An enzyme can distinguish between stereoisomers
– Chirality is inherent in an active site (amino acids are chiral compounds)
– L-Amino-acid oxidase - catalyzes reactions of L-amino acids but not of D-amino acids.
*Group Specificity
nvolves structurally similar compounds that have the same functional groups.
*Linkage Specificity
– Involves a particular type of bond irrespective of the structural features in the vicinity of the bond
– Considered most general of enzyme specificities
Phosphatases
Hydrolyze phosphate–ester bonds in all
types of phosphate esters
Enzyme Activity
A measure of the rate at which enzyme converts substrate to products in a biochemical reaction
*Four factors affect enzyme activity:
– Temperature
– pH
– Substrate concentration
– Enzyme concentration
*The effect of temperature on an enzyme
Higher temperature results in higher kinetic energy which causes an increase in number of reactant collisions, therefore there is higher activity.
Optimum temperature
Temperature at which the rate of enzyme catalyzed reaction is maximum
Optimum temperature for human enzymes
37oC (body temperature)
*Increased temperature (high fever) leads to
decreased enzyme activity
*Drastic changes in pH can result in
denaturation of proteins
*Optimum pH:
pH at which enzyme has maximum activity
Most enzymes have optimal activity in the pH range of
7.0 - 7.5
Pepsin: Optimum pH =
1.5 – 1.6
Trypsin: Optimum pH =
7.8 – 8.7
*Effect of substrate concentration on an enzyme
At a constant enzyme concentration, the enzyme activity increases with increased substrate concentration
Substrate saturation:
the concentration at which it reaches its maximum rate and all of the active sites are full
Turnover Number:
Number of substrate molecules converted to product per second per enzyme molecule under conditions of optimum temperature and pH
True or False: Enzymes are not consumed in the reactions they catalyze
True
*Effects of enzyme concentration
At a constant substrate concentration, enzyme activity increases with increase in enzyme concentration
*The greater the enzyme concentration..
the greater the reaction rate.
- Describe the effect that each of the following changes would have on the rate of a reaction that involves the substrate sucrose and the intestinal enzyme sucrase.
a. Decreasing the sucrase concentration
b. Increasing the sucrose concentration
c. Lowering the temperature to 10oC
d. Raising the pH from 6.0 to 8.0 when the optimum pH is 6.2
a. Decrease rate b. Increase rate c. Decrease rate d. Decrease rate
*Extremeophiles
Organisms that thrive in extreme environments.
Hydrothermophiles
Thrive at 80o-122oC and high pressure.
Acidophiles
Optimal growth pH
Alkaliphiles
Optimal growth pH >9.0
Halophiles
Live in highly saline conditions (>0.2 M NaCl).
Piezophiles
Grow under high hydrostatic pressure
Cryophiles
Grow at temps
*Extremozyme
A microbial enzyme that is active at conditions that would inactivate human enzymes as well as enzymes present in most other organisms.
*Extremozymes are of high interest for industrial chemists…
Enzymes are heavily used in industrial processes
– Industrial processes require extremes of temp, pressure, and pH.
*Extremozyme Applications
- Biotechnology industry – Production of enzymes for industrial applications.
- Petroleum industry – Oil well drilling operations – degumming of guar gum.
- Environmental scavenging and removal of heavy metals
- Environmental clean-up using genetically engineered extremophiles.
- Laundry detergents used in cold wash cycles
Enzyme Inhibitor
a substance that slows down or stops the normal catalytic function of an enzyme by binding to it
Two type of enzyme inhibitors
Competitive and Noncompetitive Inhibitors
*Competitive Inhibitors
Compete with the substrate for the same active site
• Will have similar charge & shape
Noncompetitive Inhibitors:
Do not compete with the substrate for the same active site
• Binds to the enzyme at a location other than active site
Reversible Competitive Inhibition
A competitive enzyme inhibitor decreases enzyme activity by binding to the same active site as the substrate.
• Binds reversibly to an enzyme active site and the inhibitor remains unchanged (no reaction occurs)
• The enzyme - inhibitor complex formation is via weak interactions (hydrogen bonds, etc.).
• Competitive inhibition can be reduced by simply increasing the concentration of the substrate.
Reversible Noncompetitive Inhibition
- A noncompetitive enzyme inhibitor decreases enzyme activity by binding to a site on an enzyme other than the active site.
- Causes a change in the structure of the enzyme and prevents enzyme activity.
- Increasing the concentration of substrate does not completely overcome inhibition.
- Examples: Heavy metal ions Pb2+, Ag+, and Hg2+.
*Irreversible Inhibition
An irreversible enzyme inhibitor inactivates enzymes by forming a strong covalent bond with the enzyme’s active site.
– The structure is not similar to enzyme’s normal substrate
– The inhibitor bonds strongly and increasing substrate concentration does not reverse the inhibition process
– Enzyme is permanently inactivated.
– E.g., Chemical warfare agents (nerve gases) and organophosphate insecticides
Nerve gas Sarin:
Irreversible inhibitor of AChE causes muscular paralysis, convulsions, bronchial constriction, and death by asphyxiation
True or false: Cellular processes continually produces large amounts of an enzyme and plentiful amounts of products if the processes are not regulated
True
General mechanisms involved in regulation:
– Proteolytic enzymes and zymogens
– Covalent modification of enzymes
– Feedback control Regulation of enzyme activity by various substances produced within a cell
• The enzymes regulated are allosteric enzymes
*Properties of Allosteric Enzymes
• All allosteric enzymes have quaternary structure: – Composed of two or more protein chains
• Have at least two of binding sites:
– Substrate and regulator binding site
• Active and regulatory binding sites are distinct from each other:
– Located independent of each other
– Shapes of the sites (electronic geometry) are different
Binding of molecules at the regulatory site causes changes in the overall three dimensional structure of the enzyme:
– Change in three dimensional structure of the enzyme leads to change in enzyme activity
– Some regulators increase enzyme activity – activators
– Some regulators decrease enzyme activity - inhibitors
*Feedback Control:
A process in which activation or inhibition of the first reaction in a reaction sequence is controlled by a product of the reaction sequence
Regulators of a particular allosteric enzyme may be:
– Products of entirely different pathways of reaction within the cell
– Compounds produced outside the cell (hormones)
Feedback Control
Enzyme 1 inhibited by product D
A—–> B —-> C —-> D
Enz 1 Enz 2 Enz 3
*Proteolytic Enzymes and Zymogens
Mechanism of regulation by production of enzymes in inactive forms (zymogens).
• Zymogens, also known as pro-enzymes, are “turned on” at the appropriate time and place
– Example: proteolytic enzymes: Most digestive and blood-clotting enzymes are proteolytic enzymes
– Hydrolyze peptide bonds in proteins
*Covalent modification
A process in which enzyme activity is altered by covalently modifying the structure of the enzyme
– Involves adding or removing a group from an enzyme
*Most common covalent modification - addition and removal of phosphate group:
Phosphate group is often derived from an ATP molecule.
– Addition of the phosphate (phosphorylation) catalyzed by a Kinase enzyme
– Removal of the phosphate group (dephosphorylation) catalyzed by a phosphatase enzyme.
– Phosphate group is added to (or removed from) the R group of a serine, tyrosine, or threonine amino acid residue in the enzyme regulated.
*• Many common prescription drugs exert their mode of action by inhibiting enzymes
• Examples:
Penicillins, Kinase inhibitors, Solvaldi, Harvoni
*Sulfa drugs
Antibiotic:
A substance that kills bacteria or inhibits its growth
*Kinase inhibitors
–Tyrosine Kinase Inhibitors (TKIs)
• Many on market, under development
• Ex: Gleevec, BCR-ABL inhibitor for treating chronic myelogenous leukemia (CML)
*Solvaldi, Harvoni
Hepatitis C virus NS5B inhibitors
Penicillins all have structures..
containing a four-membered Beta- lactam ring fused with a five-membered thiazolidine ring
*Penicillin selectively inhibits ..
bacterial transpeptidase by covalent modification of serine residue
Transpeptidase catalyzes the formation
of peptide cross links between polysaccharides strands in bacterial cell walls
*Grapefruit Juice is an
Enzyme Inhibitor which inhibits Cytochrome P450
(CYP) enzymes present in the liver. This can have
an impact on drugs which are supposed to be metabolized causing higher drug concentrations and toxicity.
*enzyme-substrate complex
the intermediate reaction species that is formed when a substrate binds to the active site of an enzyme
*ACE Inhibitor
stands for
function
angiotensin-converting enzyme, octapeptide hormone
used to treat high blood pressure conditions as well as several heart conditions,
