Chapter 4: Enzymes Flashcards
It is a rod-shaped bacterium originally discovered in a hot spring in Yellowstone National Park
Thermus aquaticus
Thermus aquaticus can survive at what temperature?
Temperatures between 50°C and 80°C
How do these organisms survive at these extreme temperatures that would cook the life-forms with which we are more familiar?
- the structure of the enzyme that carry out all the work of the cells
- held together by many more attractive forces
- these proteins are stable and functional even at temperatures above the boiling point of water
Why was the T. aquaticus discovery important?
It is used in PCR, since Taq polymerase from T. aquaticus can withstand the temperature constraints of PCR.
What is PCR?
- Polymerase Chain Reaction
- it is a laboratory technique for rapidly producing (amplifying) millions to billions of copies of a specific segment of DNA
Steps in PCR:
- Denaturation of helical DNA (94-96˚C)
- Annealing (68˚C)
- Elongation (72˚)
When was the Biological catalysis first recognized and described?
late 1700s
Biological catalysis was first recognized and described in studies on the ___
digestion of meat by secretions of the stomach
What examination takes place in the 1800s?
The conversion of starch to sugar by saliva and various plant extracts
In the 1850s, he concluded that fermentation of sugar into alcohol by yeast is catalyzed by “ferments”
Louis Pasteur
These ferments were inseparable from the structure of living yeast cells
Vitalism
In 1897, he 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
He gave the name enzymes
Frederick W. Kuhne
Etymology of the word Enzyme (Greek)
“en” means inside
“zymos” means yeast
In 1926, he’s discovery was a breakthrough in early enzyme studies
James Sumner
What was the discovery of James Sumner that brought a breakthrough in early enzyme studies?
The isolation and crystallization of urease
What was Sumner found out and his assumption?
- urease crystals consisted entirely of protein
- all enzymes are proteins
In 1930s, they found out that crys pepsin, trypsin, and other digestive enzymes are also proteins
John Northrop and Moses Kunitz
What did J. B. S. Haldane wrote?
A treatise titled Enzymes
What was the remarkable suggestion of Haldane?
That weak bonding interactions between an enzyme and its substrate might be used to catalyze a reaction
Protein that is specialized to catalyze metabolic reactions
Enzyme (occasionally RNA; ribozymes)
Enzymes catalyze the reactions that break down food molecules to allow the cell to ___ ____
harvest energy
Enzymes, also catalyze the biosynthetic reactions that produce the great variety of ______ _____ for ____ ___
molecules required for cellular life
How important is the Enzymes to life?
About a quarter of the genes in the human genome encode enzymes
Proteins are highly effective catalysts because of their?
capacity to specifically bind a very wide range of molecules
How does enzymes catalyze reactions?
By stabilizing transition states
What is called to enzymes that requires an additional chemical component?
Cofactor
What are the inorganic ions that serves as cofactors for enzymes?
- Fe2+/Fe3+
- Mg2+
- Mn2+
- Cu2+
- K+
- Mo
- Ni2+
- Zn2+
A complex organic or metalloorganic molecule
Coenzyme
Components of Holoenzyme
- Cofactor
- Catalytic Site
- Coenzyme
- Apoenzyme
Why do apoenzymes need cofactors?
Cofactors provide additional chemically reactive functional groups besides those present in the amino acid side chains of apoenzymes
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
Holoenzyme
The protein part of such an enzyme
Apoenzyme or Apoprotein
NAD+
Nicotinamide adenine dinucleotide
(oxidized form)
NADH
reduced form NAD+
NADP+
Nicotinamide adenine dinucleotide phosphate
(oxidized form)
FAD
Flavin adenine dinucleotide
(oxidized form)
Finally, some enzyme proteins are modified covalently by ______, _____, and other processes
- phosphorylation
- glycosylation
Example of organic compound that show little tendency for reaction outside the cell
Glucose
Glucose is a ____ that can be stored _____ on the shelf with ___ ________
- sugar
- indefinitely
- no deterioration
What is produce in most cell that quickly oxidized glucose?
carbon dioxide and water and releasing lots of energy
Glucose represents _____ _____
thermodynamic potentiality
What suffix identifies a substance as an enzyme?
- ase
Examples of enzymes that ends with a suffix -ase
- Urease
- Sucrease
- Lipase
What enzymes have a suffix -in in their names?
Digestive enzymes:
- Trypsin
- Chymotrypsin
- Pepsin
What are the prefixes denotes the type of reaction catalyzed by an enzyme?
- Oxidase
- Hydrolase
- Carboxylase
- Dehydrogenase
What type of reaction denotes the prefix oxidase?
Oxidation
What type of reaction denotes the prefix hydrolase?
Hydrolysis
What type of reaction denotes the prefix carboxylase?
Carboxylation
What type of reaction denotes the prefix dehydrogenase?
Dehydrogenation
The identity of the ____ is often noted in addition to the type of reaction
Substrate
Urease
catalyzes the hydrolysis of urea
Lactase
catalyzes the hydrolysis of lactose
What are six major classes of enzymes?
- Oxidoreductase
- Transferase
- Hydrolase
- Lyase
- Isomerase
- Ligase
Oxidoreductase
catalyzes an oxidation-reduction reaction
An oxidoreductase requires a _____ that is oxidized or reduced as the _____ is reduced or oxidized
- coenzyme
- substrate
It is an oxidation that increases the number of C—O bonds and/or decreases the number of C—H bonds
Oxidation reaction
Oxidation reaction:
Increases
The number of C—O bonds
Oxidation reaction:
Decreases
The number of C—H bonds
It is an reduction that decreases the number of C—O bonds and/or increases the number of C—H bonds
Reduction reaction
Reduction reaction:
Increases
The number of C—H bonds
Reduction reaction:
Decreases
The number of C—O bonds
How can the enzymatic browning of apple slowed or prevented?
- Cold water
- Refrigeration
- Boiling (denaure)
- Lemin Juice (acidic)
Transferase
catalyzes the transfer of a functional group from one molecule to another
Two major subtypes of Transferase
- Transaminase
- Kinases
It is the transfer of an amino group from one molecule to another
Transaminase
- transfer of a phosphate group from adenosine triphosphate (ATP)
- play a major role in energy harvesting processes involving ATP
Kinases
a product containing an additional
phosphate group
Phosphorylated product
Hydrolase
catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break
Why does the gelatin will not gel if fresh fruits is added?
because these fruits contain a protease (a hydrolase) that catalyzes the hydrolysis of peptide (amide) linkages in gelatin preventing the hydrogel from forming
Why does the gelatin gels when canned fruits is added?
The protease present is deactivated when the pineapple was cooked prior to packaging
Lyase
catalyzes the addition of a group to a double bond or the removal of a group to form a double bond in a manner that does not involve hydrolysis or oxidation
Isomerase
catalyzes the isomerization (rearrangement of atoms) of a substrate in a reaction, converting it into a molecule isomeric with itself
Ligase
catalyzes the bonding together of two molecules into one with the participation of ATP
Subclasses of Oxidoreductases
- Oxidases
- Reductases
- Dehydrogenases
Type of reaction catalyzed by the subclass of Oxidoreductases:
Oxidases
oxidation of a substrate
Type of reaction catalyzed by the subclass of Oxidoreductases:
Reductases
reduction of a substrate
Type of reaction catalyzed by the subclass of Oxidoreductases:
Dehydrogenases
introduction of double bond (oxidation) by formal removal of two H atoms from a substrate, with one H being accepted by a coenzyme
Subclasses of Tranferases
- Transaminases
- Kinases
Type of reaction catalyzed by the subclass of Tranferases:
Transaminases
transfer of an amino acid between substrates
Type of reaction catalyzed by the subclass of Tranferases:
Kinases
transfer of a phosphate group between substrates
Subclasses of Hydrolases
- Lipases
- Proteases
- Nucleases
- Carbohydrases
- Phosphatases
Type of reaction catalyzed by the subclass of Hydrolases:
Lipases
hydrolysis of ester linkages in lipids
Type of reaction catalyzed by the subclass of Hydrolases:
Proteases
hydrolysis of amide linkages in proteins
Type of reaction catalyzed by the subclass of Hydrolases:
Nucleases
hydrolysis of sugar-phosphate ester bonds in nucleic acids
Type of reaction catalyzed by the subclass of Hydrolases:
Carbohydrases
hydrolysis of glycosidic nonds in carbohydrates
Type of reaction catalyzed by the subclass of Hydrolases:
Phosphatases
hydrolysis of phosphate-ester bonds
Subclasses of Lyases
- Dehydratases
- Decarboxylases
- Deaminases
- Hydratases
Type of reaction catalyzed by the subclass of Lyases:
Dehydratases
removal of H2O from a substrate
Type of reaction catalyzed by the subclass of Lyases:
Decarboxylases
removal of CO2 from a substrate
Type of reaction catalyzed by the subclass of Lyases:
Deaminases
removal of NH3 from a substrate
Type of reaction catalyzed by the subclass of Lyases:
Hydratases
addition of H2O to a substrate
Subclasses of Isomerases
- Racemases
- Mutases
Type of reaction catalyzed by the subclass of Isomerases:
Racemases
conversion of D isomer to L isomer, or vice versa
Type of reaction catalyzed by the subclass of Isomerases:
Mutases
transfer of a functional group from one position to another in the same molecule
Subclasses of Ligases
- Synthetase
- Carboxylases
Type of reaction catalyzed by the subclass of Ligases:
Synthetases
formation of a new bond between two substrates, with participation of ATP
Type of reaction catalyzed by the subclass of Ligases:
Carboxylases
formation of a new bond between a substrate and CO2, with participation of ATP
A thermodynamic property that is a measure of useful energy, or the energy that is capable of doing work
Gibbs Free Energy (G)
Two thermodynamic properties of how enzymes operate
- the free-energy difference (∆G) between the products and reactants
- the energy required to initiate the conversion of reactants into products (Ea)
The free-energy change provides information about the ______ but NOT the ____ of a reaction
- spontaneity
- rate
The free-energy change of a reaction (∆G) tells us if the reaction can take place spontaneously:
- A reaction can take place spontaneously; (∆G<0), ∆G is negative
- A system is at equilibrium and no net change can take place if ∆G is zero (∆G=0)
- A reaction cannot take place spontaneously; (∆G>0), ∆G is positive. An input of free energy is required to drive such a reaction
- The ∆G of a reaction is independent of the molecular mechanism of the transformation
- The rate of a reaction depends on the free energy of activation (∆G‡), which is largely unrelated to the ∆G of the reaction
A reaction that can release energy
Exergonic
A reaction that requires energy
Endergonic
Endergonic Reactions
- Reactio is not spontaneous
- Energy is absorbed
- ∆G>0
Exergonic Reactions
- Reaction is spontaneous
- Energy is released
- ∆G<0
How does an enzyme speed up a chemical reaction?
- by lowering the activation energy of the reaction
- The energy difference between reactant (substrate) and product is not changed. It is only the activation energy that is reduced
Enzymes alter only the ____ ___and not the ____ _______
- reaction rate
- reaction equilibrium
X‡ denotes the transition state:
- transitory molecular structure that is no longer the substrate but is not yet the product
- the least-stable and most-seldom occupied species along the reaction pathway because it is the one with the highest free energy
It is the difference in free energy between the transition state and the substrate
Gibbs free energy of activition or activation energy (∆G‡)
What is the first step in enzymatic catalysis?
The formation of an enzyme-substrate complex
Enzymes bind to and then alter the structure of the substrate to _____ the ______ of the ______ ____
promote the formation of the transition state
What is the evidence for the existence of an enzyme–substrate complex?
- At constant concentration of enzyme, the reaction rate increases with increasing substrate concentration until a maximal velocity is reached
- The spectroscopic characteristics of many enzymes and substrates change on the formation of an ES complex
- X-ray crystallography
Common features of the active sites of enzymes
- The active site is a three dimensional cleft, or crevice, formed by groups that come from different parts of the amino acid sequence
- 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
Models of Enzyme Action
- Lock-and-key model
- Induced fit model
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
The enzyme active site, although not exactly complementary in shape to that of the substrate, is felxible enough that it can adapt to the shape of the substrate
Induced fit model
The _____ ____ between enzyme and substrate is important for catalysis
binding energy
What is the binding energy?
Free energy released in binding
The full complement of ____ ______ is formed only when the _____ is converted into the _____ ___
- weak interactions
- substrate
- 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
It 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
The degree of enzyme specificity is determined by the ____ ___
active site
Types of Specificity
- Absolute specificity
- Group Specificity
- Linkage Specificity
- Stereochemical Specificity
Absolute Specificity
- the enzyme will catalyze only one reaction
Example of Absolute specificity
- Aminoacyl tRNA synthetases
- Catalase
Group Specificity
the enzyme will act only on molecules that have a specific functional group, such as hydroxyl, amino, or phosphate groups
Example of Group specificity
- Carboxypeptidase
- Hexokinase
Linkage 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
Example of Linkage specificity
- Phosphatases hydrolyze phosphate-ester
- Poteases hydrolyze peptide bonds
Stereochemical Specificity
the enzyme will act on a particular stereoisomer
It is a measure of the rate at which an enzyme converts substrate to products in a biochemical reaction
Enzyme activity
Factors that affect enzyme activity
- Temperature
- pH
- Substate concentration
- Enzyme concentration
It is a measure of the kinetic energy (energy of motion) of molecules
Temperature
At higher temperatures
molecules are moving _____
and ______ more ______
- faster
- colliding more frequently
What is the optimum temperature for human enzymes?
37°C (normal body temperature)
If a person has a fever, the body temperature exceeds to ____ can be in a life-threatening situation because it can initiate _____ ______
- 40°C
- enzyme denaturation
- it can destroy bacterial enzyme with its high-temperature and high pressure
- it is used to sterilize medical instruments and laundry (in hospital)
Autoclaves
How can Autoclaves kill bacterial enzymes?
Super-heated steam is used to produce a temperature sufficient to denature bacterial enzymes
It is an equipment that sterilized instruments by dry heat (160°C) applied for at least 2 hours (h)
Dry air oven
How does autoclave works?
- works on the principle of the pressure cooker
- air is pumped out of the chamber, and steam under pressure is pumped into the chamber until a pressure of 2 atmospheres (atm) is achieved
The atmospheric pressure is greater than the vapor pressure
The water will not boil
The atmospheric pressure is equal to the vapor pressure
The water starts to boil
Atmospheric pressure alters the boiling point of water:
20,000 feet (6,000 meters)
Water boils at about 175°F (79°C)
Atmospheric pressure alters the boiling point of water:
10,000 feet (3,000 meters)
Water boils at about 194°F (90°C)
Atmospheric pressure alters the boiling point of water:
6,000 feet (1,800 meters)
Water boils at about 200°F (93°C)
Atmospheric pressure alters the boiling point of water:
Sea level
Water boils at about 212°F (100°C)
It is the pH at which an enzyme exhibits maximum activity
Optimum pH
Small changes in pH (less than one unit) can result in _____ ______ and subsequent loss of catalytic activity
enzyme denaturation
It helps maintain the optimum pH for an enzyme
Biochemical buffers
Physiological pH range
7.0-7.5
Pepsin, which is active in the stomach, functions best at ____
pH 2.0
Trypsin, which operates in the small intestine, functions best at ______
pH 8.0
Stomach and duodenal ulcers were thought to be due to ___
- excess stomach acid
- emotional stress
- spicy food
A clinical pathologist who had
examined many stomach biopsy specimens
J. Robin Warren
What did J. Robin Warren noticed in examining many stomach biopsy specimens?
Noticed a parallel between the severity of the inflammation and
the number of bacteria present
Who was the trainee doctor that Warren met in 1981?
Barry James Marshall
Marshall was unsuccessful in developing an animal model, so he decided to _____ ____ ____
experiments upon himself
absence of hydrochloric acid in the gastric secretions
Achlorhydria
What did Marshall and Warren discover after their experiment?
H. pylori (Helicobacter pylori), a bacterium that causes stomach ulcer and not stress and lifestyle
neutralizes gastric acid in the stomach
ammonia
The urease itself is protected from _____ by its complex ___ ____
- denaturation
- quaternary structure
- called “suicide bags” (Christian de Duve, 1956)
- they are membrane-bound vesicles containing about fifty different kinds of hydrolases that degrade large biological molecules into small molecules
Lysosomes
What would be the result if the hydrolytic enzymes of the lysosome were accidentally released into the cytoplasm of the cell?
- destruction of cellular molecules
- death of the cell
Lysosomal enzymes function optimally at _____
acid pH 4.8
Enzyme-catalyzed reaction must occur in two stages:
- formation of an enzyme-substrate complex
- Conversion of substrate into product and release of the product and enzyme
It is the region of the enzyme that specifically binds the substrate andcatalyzes the reaction
Active site
It is dependent on the amount of enzyme that is available
Reaction rate
It is the number of substrate molecules transformed per minute by one molecule of enzyme under optimum conditions of temperature, pH, and saturation
Turnover number
The concentration of substrate
in a reaction is much _____ than that of the enzyme
higher
It is a microorganism that thrives in extreme environments
Extremophile
Extremophile environments
- Hydrothermal areas of Yelllowstone National Park
- Hydrothermal vents on the ocean floor (temperatures and pressure are extemely high)
Microorganims that shows optimal growth at pH levels of 3.0 or below
Acidophiles
An extremophiles that shows optimal growth at pH levels of 9.0 or above
Alkaliphiles
An extremophiles that thrives in high salinity, a salinity that exceeds 0.2 M NaCl needed for growth
Halophiles
Organims that can thrive at a temperature between 80°C and 121°C
Hyperthermophiles
Organims that can thrive at a high hydrostatic pressure
Piezophiles
Organims that can thrive at an extremely dry conditions
Xerophiles
Organims that can thrive at a
temperature of 15°C or lower
Cryophiles
- enzyme present in extremophiles
- a microbial enzyme active at conditions that would inactivate human enzymes as well as enzymes present in other types of higher organisms
Extremozymes
Extremozymes have characteristics that have been found to be useful
can function in hot water and cold water wash (adapted)
The development of commercially useful enzymes using extremophile sources involves the following general approach:
- Samples containing the extremophile are gathered from the extreme environment where it is found
- DNA material is extracted from the extremophile and processed
- Macroscopic amounts of the DNA are produced using the polymerase chain reaction
- The macroscopic amount of DNA is analyzed to identify the genes present that are involved in extremozyme production
- Genetic engineering techniques are used to insert the extremozyme gene into bacteria, which then produce the extremozyme
- The process is then commercialized
Main reason why there is a necessity for the regulation of enzyme activity witin a cell
due to energy conservation (If the cell runs out of chemical energy, it will die)
Many mechanisms exist by which enzymes within a cell can be “turned on”
- feedback control associated with allosteric enzymes,
- proteolytic enzymes and proenzymes/zymogens, and
- covalent modification
Characteristics of allosteric enzymes:
- allosteric enzymes have quaternary structure
- have two kinds of binding sites
- two binding sites are distinct from each other in both location and shape
- Binding of a molecule at the regulatory site causes changes in the overall three-dimensional structure of the enzyme
Two kinds of binding site
- Substrate (active)
- Regulators (regulatory)
Structure of allosteric enzymes
Quaternary structure
Two different sites of attachment in the allosteric enzymes
- active site
- effector binding site
- inactive form of enzyme
- converted by proteolysis to the active form when it has reached the site of its activity
Proenzyme or zymogen
hydrolysis of the protein
Proteolysis
Example of proteolytic enzymes
most digestice and blood-clotting enzymes
It 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
Covalent modification
Most common type of protein modification
- Phosphorylation (by protein kinases)
- Dephosphorylation (by phosphatases)
Example of the active phosphorylated version of the enzyme
triacylglycerol lipase
Example of the active dephosphorylated version of the enzyme
glycogen synthase
chemicals that can bind to enzymes and either eliminate or drastically reduce their catalytic ability
Enzyme inhibitors
Example of Enzyme inhibitors
Arsenic and Penicilin
It binds to the thiol groups of cysteine amino acids in the proteins, interfering with the formation of disulfide bonds needed to stabilize the tertiary structure of enzymes
Arsenic
It inhibits several enzymes that are involved in the synthesis of bacterial cell walls
Penicillin
Three (3) modes of inhibition:
- irreversible inhibition
- reversible competitive inhibition
- reversible noncompetitive inhibition
- do not have structure similar to that of the enzymes normal substrate
- bind very tightly
- binding of the inhibitor to one of the R groups of an amino acid in the active site
- enzyme-substrate complex cannot form
- may interfere with the catalytic groups of the active site
Irreversible Enzyme Inhibitors
Irreverisble inhibitors include
- venom
- nerve gases
Two types of Reversible enzyme inhibitors
- Reversible competitive inhibitors
- Reversible noncompetitive inhibitors
- often referred to as structural analogs
- competitive, inhibitor and the substrate compete for binding to the enzyme active site
- the degree of inhibition depends on their relative concentrations
Reversible competitive inhibitors
The formation of an enzyme–competitive inhibitor complex is a _______ process because it is _____ by ____ _____
- reversible
- maintained by weak interactions
How can the competitive inhibition be reduced?
by simply increasing the concentration of the substrate
- a molecule that decreases enzyme activity by binding to a site on an enzyme other than the
active site - the inhibitor causes a change in the structure of the enzyme sufficient to prevent the catalytic groups at the active site from properly
Reversible noncompetitive inhibitors
Examples of noncompetitive inhibitors
Heavy metal ions:
- Pb2+
- Ag+
- Hg2+
Binding sites for these ions
Sulfhydryl (-SH; also called as thiol)
What enzymes are serine proteses?
Pancreatic Serine Proteases
Chymotrypsin
Trypsin
Elastase
Why are these enzymes called serine proteases?
because they have the amino acid serine in the catalytic region of the active site that is essential for hydrolysis of the peptide bond
