Chapter 4: Enzymes Flashcards
is a rod-shaped bacterium originally discovered in a hot spring in Yellowstone National Park
Thermus aquaticus
is a laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA, which can then be studied in greater detail
Polymerase Chain Reaction (PCR)
Biological catalysis was first recognized and described in the late _____ , in studies on the ____ __ ___ __ ____ __ __ ____
- 1700s
- digestion of meat by secretions of the stomach
Research continued in the ____ with examinations of the ____ _ ___ _ ___ _ ___ __ ____ ____ ____
- 1800s
- conversion of starch to sugar by saliva and various plant extracts
In 1850s, he concluded that fermentation of sugar into alcohol by yeast is catalyzed by “ferments.”
Louis Pasteur
postulated that these ferments were inseparable from the structure of living yeast cells
- a doctrine that the functions of a living organism are due to a vital principle distinct from physicochemical forces.
Vitalism
discovered that yeast extracts could ferment sugar to alcohol, proving that fermentation was promoted by molecules that continued to function when removed from cells.
Eduard Buchner
When did Eduard Buchner discovered yeast extracts?
1897
later gave the name enzymes to the molecules detected by Buchner
Frederick W. Kühne
name of enzymes came from greek words…
“en”= inside
“zymos”= yeast
The isolation and crystallization of urease
James Sumner in 1926
_____ _____ found that urease crystals consisted entirely of protein, and he postulated that __ ____ __ ____
- James Sumner
- all enzymes are proteins
in 1930s they crystallized pepsin, trypsin, and other digestive enzymes and found them also to be proteins.
John Northrop and Moses Kunitz
wrote a treatise titled Enzymes
J.B.S. Haldane
Enzymes catalyze the reactions that ___ ____ food molecules to allow the cell to ______ _____
- break down
- Harvest energy
Enzymes also catalyze the biosynthetic reactions that produce the great variety of ____ ____ __ ____ ___.
- molecules required for cellular life.
Enzymes catalyze reactions by stabilizing transition states, the highest-energy species in reaction pathways.
- Stabilizing Transition
those that require a specific cofactor.
Conjugated enzyme
Two basic components of conjugated enzyme
- Cofactor - nonprotein component
- apoenzyme- protein component
either one or more inorganic ions
Cofactor
a complex organic or metalloorganic molecule
- a NONPROTEIN compound that is necessary for the functioning of an enzyme.
coenzyme
A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein
Prosthetic Group
A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions
- the active site formed by apoenzyme and cofactor together
Holoenzyme
The protein part of such an enzyme
apoenzyme or apoprotein.
______ is NOT an absolute
requirement for a coenzyme to be an active part of an enzyme
Permanent attachment
the suffix that identiefies a substance as an enzyme
suffix ‘-ase’
The suffix___ is still found in the names of some of the first enzymes studied
suffic ‘-in’
Classifications of enzyme is based on _____
based on reaction that they catalyze
Classifications of Enzymes
- Oxidoreductase
- Transferase
- Hydrolase
- Lyase
- Isomerase
- Ligase
catalyzes an oxidation–reduction reaction
Oxidoreductase
Subclasses under oxidoreductase
- Oxidases (oxidation of substrate)
- Reductases (reduction of substrate)
- dehydrogenases
introduction of double bond (oxidation) by formal removal of two H atoms from a substrate, with one H being accepted by a coenzyme
Dehydrogenases
catalyzes the transfer of a functional group from one molecule to another.
Transferase
2 major subtypes of transferase
a. Transaminase
b. Kinase
A subtype of transferase that transfer an amino group from one molecule to another.
Transaminase
A subtype of transferase that transfer phosphate group from adenosine triphosphate (ATP) to give adenosine diphosphate (ADP) and a phosphorylated product
Kinase
catalyzes a HYDROLYSIS REACTION in which the addition of a water molecule to a bond causes the bond to break.
Hydrolase
- catalyzes the ADDITION OF A GROUP to a double bond or the REMOVAL OF THE GROUP (H2O, CO2, NH3) to form a double bond in a manner that does not involve hydrolysis or oxidation
Lyase
catalyzes the ISOMERIZATION (rearrangement of atoms) of a substrate in a reaction, converting it into a molecule isomeric with itself.
Isomerase
catalyzes the BONDING TOGETHER of two molecules into one with the participation of ATP
Ligase
A thermodynamic property that is a measure of useful energy, or the energy that is capable of doing work.
Gibbs Free Energy (G)
A reaction can take place spontaneously only if ∆G is negative
- (∆G<0)
exergonic
if ∆G is zero (∆G=0).
A system is at equilibrium and no net change
A reaction cannot take place spontaneously if ∆G is positive (∆G>0)
- An input of free energy is required to drive such a reaction
endergonic
The ∆G of a reaction _____ only on the free energy of the products (the final state) _____ __ ___ ____ of the reactants (the initial state).
- Depends
- minus the free energy
The ∆G of a reaction is _____ of the molecular mechanism of the transformation
- independent
The rate of a reaction ___ on the ___ _____ of activation (∆G‡)
- Depends
- free energy
How does an enzyme speed up a chemical reaction?
It changes the path by which the reaction occurs, providing a lower energy route for the conversion of the substrate into the product(s).
- The enzymes speed up reactions by lowering the activation energy of the reaction
Common features of the active sites of enzyme
- The active site is a three-dimensional cleft produced by groups from various amino acid sequences.
- The active site takes up a small part of the total volume of an enzyme.
- Active sites are unique microenvironments.
- Substrates are bound to enzymes by multiple weak attractions.
- The specificity of binding depends on the precisely defined arrangement of atoms in an active site
Weak attractions that bounds the substrates to an enzyme
- electrostatic interactions
- hydrogen bonds
- van der Waals forces
the substrate may bind to ONLY CERTAIN CONFORMATIONS of the enzyme
Conformation selection
the intermediate reaction species that is formed when a substrate binds to the active site of an enzyme.
enzyme–substrate (ES) complex
Only a substrate whose shape and chemical nature are complementary to those of the active site can interact with the enzyme
Lock-and-key model for enzyme activity
The active site (although not exactly complementary in shape to that of substrate) is flexible enough that it can ADAPT TO THE SHAPE of the susbtrate
Induced-fit model for enzyme activity
The free energy released on binding
Binding energy
the full complement of such interactions is formed only when the substrate is ____ into the ____ ____.
- converted
- Transition state
a state in which the substrate is in an energetically unstable intermediate form, having features of both the substrate and the product
Transition state
What kinds of transition state changes might occur in the substrate that would make a reaction proceed more rapidly?
- The enzyme might put “stress”
on a bond and thereby promote bond breakage - An enzyme may facilitate a reaction by bringing two reactants close to one another and in the proper orientation for reaction to occur
- The active site of an enzyme may modify the pH of the microenvironment surrounding the substrate
Life cycle of HIV
- Binding
- Fusion
- Reverse Transcription
- Integration
- Replication
- Assembly
- Budding
Role of protease inhibitors
Protease inhibitors blocks new HIV from becoming mature HIV
- The degree of enzyme specificity is determined by the active site.
- is the extent to which an enzyme’s activity is restricted to a specific substrate, a specific group of substrates, a specific type of chemical bond, or a specific type of chemical reaction.
Enzyme specificity
types of specificity (enzyme)
- Absolute specificity
- Group specificity
- Linkage specificity
- Stereochemical specificity
- the enzyme will catalyze ONLY ONE REACTION.
- This most restrictive of all specificities is not common.
Absolute specificity
—the enzyme will act only on molecules THAT HAVE SPECIFIC FUNCTIONAL GROUP, such as hydroxyl, amino, or phosphate groups.
Group specificity
—the enzyme will act on a PARTICULAR TYPE OF CHEMICAL BOND, irrespective of the rest of the molecular structure
- is the most general of the common specificities.
Linkage specificity
—the enzyme will act on a particular stereoisomer
Stereochemical specificity
Factors that affect enzyme activity
- Temperature
- pH
- Substrate concentration
- Enzyme concentration
is a measure of the rate at which an enzyme converts substrate to products in a biochemical reaction.
Enzyme activity
is a measure of the kinetic energy (energy of motion) of molecules.
Temperature
How does temperature affects enzyme activity
- As the temperature of an
enzymatically catalyzed reaction increases, so does the rate (velocity) of the reaction. - The increased energy begins to cause disruptions in the tertiary structure of the enzyme
(denaturation)
is the pH at which an enzyme exhibits maximum activity
Optimum pH (between 7.0-7.5)
_____ ____help maintain the
optimum pH for an enzyme
Biochemical Buffers
Reaction rate incease with substrate concentration until full saturation occurs; then the rate levels off
Concentration of substrate
Increasing enzyme concentration will speed up the reaction. Once all of the substrate is bound, the reaction will no longer speed up.
Concentration of enzyme
is a microorganism that thrives in extreme environments, environments in which humans and most other forms of life could not survive
Extremophile
examples of extremophile environments
- hydrothermal areas (like of yellowstone national park)
- Hydrothermal vents on the ocean
Acidophiles (optimal growth at pH)
pH 3.0 or below
Alkaliphiles (optimal growth at pH)
pH 9.0 or above
Halophile
- high salinity that exceeds 0.2M NaCl
Hyperthermophile required temperature to thrive
between 80°C and 121°C
The enzymes present in extremophiles
extremoenzymes
_____ __ _____ _____within a cell is a necessity for many reasons; mainly due to energy conservation (If the cell runs out of chemical energy, it will die).
Regulation of enzyme activity
The (3) mechanisms exist by which enzymes within a cell can be “turned on”
(1) feedback control associated with allosteric enzymes,
(2) proteolytic enzymes and proenzymes/zymogens, and
(3) covalent modification
enzymes that have an additional binding site for effector molecules other than the active site
Allosteric enzymes
occurs when a product of the reaction binds to an allosteric site on the enzyme and affects its catalytic activity
feedback control associated with allosteric enzymes,
inactive form of enzyme; converted by proteolysis (hydrolysis of the protein) to the active form when it has reached the site of its activity.
Proenzyme or zymogen
allow the cell to control when and where an enzyme becomes active
Zymogen
is a process in which enzyme activity is altered by covalently modifying the structure of the enzyme through attachment of a chemical group to or removal of a chemical group from a particular amino acid within the enzyme’s structure
Covalents Modification
chemicals that can bind to enzymes and either eliminate or drastically reduce their catalytic ability
Enzyme Inihibitors
Three models of inhibition
(1) irreversible inhibition
(2) reversible competitive inhibition
(3) reversible noncompetitive inhibition
- Usually bind very tightly, sometimes even covalently, to the enzyme
Irreversible enzyme inhibitors
- inactivates an enzyme through noncovalent, more easily reversed, interactions.
- can dissociate from the enzyme
Reversible enzyme inhibitors
2 forms of reversible enzyme inhibitors
a. Reversible competitive inihibitors
b. noncompetetive enzyme inhibitors
often referred to as structural analogs
- the inhibitor and the substrate compete for binding to the enzyme active site
Reversible competitive inhibitors
a molecule that decreases enzyme activity by binding to a site on an enzyme other than the active site
- The substrate still occupies the active site but cannot catylyze the reaction due to the presence of the inhibitors
noncompetitive inhibitors
