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)
Steps in PCR:
• Denaturation of helical DNA (94-96 ̊C)
• Annealing (68 ̊C)
• Elongation (72 ̊)
from T. aquaticus can withstand the temperature constraints of PCR
Taq polymerase
was first recognized and described in the late 1700s
Biological catalysis
What did they study in 1700s when recognizing biological catalysis?
digestion of meat by secretions of the stomach
Continued studying in 1800s
conversion of starch to sugar by saliva and
various plant extracts
he concluded that fermentation of sugar into alcohol by yeast is catalyzed by
“ferments”
Louis Pasteur (1850)
In __, 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.
in 1897 Eduard Buchner
What did buchner discovered in yeast extracts could ferment sugar to alcohol?
fermentation was promoted by molecules that continued to function when removed from cells.
He later gave the name enzymes (from the Greek “en” = inside and “zymos” = yeast) to the molecules detected by Buchner.
Frederick W. Kühne
Made the isolation and crystallization of urease; it was a breakthrough in early enzyme studies
James Sumner in 1926
postulate of Sumner
he postulated that all enzymes are proteins
(2) They crystallized pepsin, trypsin, and other digestive enzymes and found them also to be proteins.
1930s John Northrop and Moses Kunitz
Who wrote treatise titled Enzymes?
J. B. S. Haldane
He made the remarkable suggestion
that weak bonding interactions between an enzyme and its substrate might be used to
catalyze a reaction.
J. B. S. Haldane
Living organisms seethe with _ _
metabolic activity
Virtually all of these transformations are mediated by _
enzymes
proteins (and occasionally RNA; ribozymes) specialized to catalyze metabolic
reactions.
enzymes
it catalyze the reactions that break down food molecules to allow the cell to harvest energy
enzymes
They also catalyze the biosynthetic reactions that
produce the great variety of molecules required for cellular life.
enzymes
Enzymes also catalyze the biosynthetic reactions that produce the great variety of _ _ _ _ _
molecules required for cellular life.
Enzymes are highly effective catalysts for an enormous diversity of chemical reactions because of their _ _ _ _ _ _ _ _ _ _
capacity to specifically bind a very wide range of molecules.
Enzymes _ _ _ _ _ _ _ the prelude to making and
breaking chemical bonds.
bring substrates together in an
optimal orientation,
Enzymes catalyze reactions by _ _ states, the highest-energy species in reaction pathways.
stabilizing transition
3 mechanism of enzyme catalysis
- enzyme + substrate
- enzyme-substrate complex
- enzyme + product
An additional chemical component either one or more inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+
cofactor
By selectively stabilizing a transition state,
an enzyme determines which one of several potential chemical reactions actually
takes place.
complex organic or metalloorganic molecule
coenzyme.
how are metal ions taken?
Almost any type of diet will provide adequate amounts of needed metallic cofactors because they are needed in very small (trace) amounts.
5 parts of holoenzyme
- cofactor (tung bilog)
- catalytic site (space)
- coenzyme (katung sa sulod)
- apoenzyme (kanang pinakadako)
- holoenzyme (overall)
hala ka maam, Why do apoenzymes need cofactors?
Cofactors provide additional chemically reactive functional groups besides those present in the amino acid side chains of apoenzymes.
how are coenzymes taken?
synthesized within the human body using building blocks obtained from other nutrients.
A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions is called a
holoenzyme
coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a
prosthetic group
The protein part of such an enzyme is called the
apoenzyme or apoprotein
Once the cofactor binds to the apoenzyme (b), the _ _ _ _ _ _ _ , the enzyme-substrate complex forms, and the reaction occurs.
active site takes on the correct configuration
NAD+ to NADP+
huhu how
alternate name name for all cofactor
coenzyme
conjugates enzyme always contains a
nonprotein part
what is the interaction of cofactors with apoenzymes?
they can, but do not have to be, covalently bonded to the apoenzyme
a sugar that can be stored indefinitely on
the shelf with no deterioration
glucose
Its reaction with oxygen is strongly exergonic (can release energy), but it doesn’t occur under normal
conditions
thermodynamic potentiality
, enzymes can catalyze such _ _ _, causing them to proceed at extraordinarily rapid rates.
thermodynamically favorable reactions
6 MAJOR CLASSES ON THE TYPES OF REACTIONS AND ENZYMES
oxidoreductase
Transferase
Hydrolase
Lyase
Isomerase
ligase
catalyzes an oxidation–reduction reaction.
Oxidoreductase
why is oxidoreductase requires a coenzyme that is oxidized or reduced as the substrate is reduced or oxidized?
Because oxidation and reduction are NOT independent processes but linked processes that must occur together,
An organic oxidation reaction is an oxidation that: (2)
increases the number of C—O bonds and/or
decreases the number of C—H bonds
An organic reduction reaction is a reduction that:
decreases the number of C—O bonds and/or
increases the number of C—H bonds
Example of enzyme oxidoreductase
Phenolase and enzymatic browning
How is enzymatic browning be preventetd?
- immersion in cold water
- refrigeration
- boiing temperature
- lemon juice
catalyzes the transfer of a functional group from one molecule to another
Transferase
Transferase two major subtypes:
- transaminase
- Kinases
transfer of an amino group from one molecule to
another.
transaminase
- transfer of a phosphate group from adenosine
triphosphate (ATP) to give adenosine diphosphate (ADP) and a phosphorylated product
Kinases
enzyme that transfers amino group from one to another functional group
Transaminase
makes glucose + atp to ADP + glucose 6-phosphate
hexokinase
catalyze a reaction between a
glutamine residue in a protein and a lysine residue in the same or another protein, resulting to the formation of large polymers of protein that are very tightly linked to one another.
Transglutaminases
can be used to make consistent, uniform
portions of meat or fish from smaller scraps.
meat glue
catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break.
hydrolase
Examples of hydrolase:
maltase
lipase
protease
What does maltase break?
maltose into 2 glucose
What does lipase break?
triglyceride to glycerol and fatty acids
What does protease break?
fruit hydrolyses peptide linkage in gelatin, preventing the hydrogel from forming
catalyzes the addition of a group to a double bond or the removal of a
group (H2O, CO2
, NH3) to form a double bond in a manner that does not involve hydrolysis or oxidation
Lyase
Lyase example:
fumarase adding H20 in from fumarate to L-Malate
Example of isomerase:
Phosphoglyceromutase — from 3-Phosphoglycerate to 2-Phosphoglycerate
catalyzes the isomerization (rearrangement of atoms) of a
substrate in a reaction, converting it into a molecule isomeric with itself
isomerase
Pyruvate carboxylase :
pyruvate = oxaloacetate + ADP + P + H+
catalyzes the bonding together of two molecules into one with the
participation of ATP
Ligase
DNA Ligase
glues OH in phosphate group of DNA strands
What does the AMP nucleotide worked?
which is
attached to a lysine residue in the
enzyme’s active site, is transferred to
the 5′-phosphate.
How does the AMP—phosphate bond carried?
attacked by the 3′-OH, forming the covalent bond and releasing AMP.
To allow the enzyme to carry out further
reactions in AMP nucleotides,
ATP must replenish the AMP in the enzyme’s active site.
Subclasses of oxidoreductases (3)
oxidases
reductases
dehydrogenases
Subclasses of transferases (2)
Transaminases
kinases
Subclasses of hydrolases (5)
lipases
proteases
nucleases
carbohydrases
phosphatases
Subclasses of lyases (4)
dehydratases
decarboxylases
deaminases
hydratases
Subclasses of isomerases (2)
racemases
mutases
Subclasses of ligases (2)
synthetases
carboxylases
Which of the following statements concerning an enzyme substrate is incorrect?
a. substance upon which the enzyme “acts”
b. reactant in an enzyme-catalyzed reax
c. product in enzyme-catalyzed reaction
c
most enzymes end with suffix -ase, but few names end in:
a. ose
b. ine
c. in
c
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 the reaction:
(1) the free-energy difference (∆G) between the products and reactants
(2) the energy required to initiate the conversion of reactants into products (Ea).
The free-energy change provides information about the _ but OT the _ _ _
spontaneity but NOT the rate of a reaction
A reaction can take place spontaneously only if ∆G is negative (∆G<0). Such reactions are said to be
exergonic
no net change can take place if ∆G is zero:
A system is at equilibrium (∆G=0)
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
is _ _ _ _ of the transformation.
independent of the molecular mechanism
The rate of a reaction depends on the ?
free energy of activation (∆G‡
)
How does an enzyme speed up a chemical reaction?
providing a lower energy route for
the conversion of the substrate into the
product(s).
Thus, enzymes speed up reactions by _ _ _ of the
reaction.
lowering the activation energy
Spontaneity (5)
> exergonic
equilibrium
endergonic
independent of the molecular mechanism
The rate of a reaction depends on the free energy of activation (∆G‡)
In the graph, what is changed and not changed?
The energy difference between reactant (substrate) and product is not
changed. It is only the activation energy that
is reduced.
transitory molecular structure that is no
longer the substrate but is not yet the
product
transition state X‡
The difference in free energy between the transition
state and the substrate is called _ _ of activation or simply the
Gibbs free
energy; activation energy
(∆G‡).
Enzymes bind to and then alter the structure of the substrate to ?
promote the formation of the
transition state.
Evidence 1: 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.
These changes are particularly striking if the enzyme
contains a
colored prosthetic group
Sequence of Crystallography:
crystal
diffraction pattern
electron density map
protein model
provided high-resolution images of substrates and
substrate analogs bound to the active sites of many enzymes
X -ray crystallography
The active sites of enzymes have some common features (5):
- 3D cleft or crevice
- small part of total volume
- unique microenvironments
- bounded by multiple weak attractions
- specificity
formed by groups that come from different parts of the amino acid
sequence
3D cleft; crevice
an enzyme that
degrades the cell walls of some bacteria
lysozyme
protein structure:
scaffold to support and position active site
bind and orient substrate
binding site
reduce chemical activation energy
catalytic site
Experiments show that the minimum size requires about 100 amino acid and that all amino acids in the protein
The active site takes up a small part of the
total volume of an enzyme.
the
cleft may also contain polar residues, some of which may acquire special properties
essential for substrate binding or catalysis. Why?
Active sites are unique microenvironments
Substrates are bound to enzymes by:
multiple weak attractions
3 weak attractions:
electrostatic interactions, hydrogen bonds, and van der Waals forces.
become significant in binding only
when numerous substrate atoms simultaneously come close to many enzyme atoms through the hydrophobic effect.
Van der Waals forces
Hence, the enzyme and substrate should have
complementary shapes
The directional character of hydrogen bonds between
enzyme and substrate often enforces a ?
high degree of
specificity
3 types of R groups:
- bind the substrate to enzyme active site
- maintain 3D structure of enzyme
- noninteracting groups helping determine the solubility of enzyme
The specificity of binding depends on the ?
precisely defined arrangement of atoms in an active site
explains the action of numerous
enzymes. It is, however, too restrictive for the action of many other enzymes.
The lock-and-key model (1890)
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
released by the formation of a large number of weak interactions between a complementary enzyme and its substrate
free energy; binding energy
the free energy that is released by the formation of a large number of weak
interactions between a complementary enzyme and its substrate
Binding energy
Only the _ can participate in most or all of the interactions with the enzyme and
thus maximize binding energy
correct substrate
- 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?
- stress
- facilitating
- modify the pH of microenvironment
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 extent to which an enzyme’s activity is restricted to (3)?
- a specific substrate, a specific group of substrates
- a specific type of chemical bond
- a specific type of chemical reaction.
Types of Specificity
- 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
Aminoacyl tRNA synthetases absolute specificity:
correct amino acid has the highest binding affinity for
the binding pocket of the catalytic site;
what affects more in absolute specificity?
differences in size and chemistry among amino acids suffice for effective discrimination.
catalyzes the conversion of hydrogen peroxide (H2O2
) to O2 and H2O.
Hydrogen peroxide is the only substrate it will accept.
catalase
examples of enzymes in group specificity:
carboxypeptidase
hexokinase
the enzyme will act only on molecules that have a 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.
linkage specificity
examples of linkage specificity:
Phosphatases hydrolyze phosphate-ester bonds; proteases hydrolyze peptide bonds
—the enzyme will act on a particular stereoisomer. Chirality is
inherent in an enzyme active site because amino acids are chiral compounds.
stereochemical specificity
Factors that affect enzyme activity:
(1) Temperature
(2) pH
(3) substrate concentration, and
(4) enzyme concentration
is a measure of the rate at which an enzyme converts substrate to
products in a biochemical reaction
enzyme activity
How does temperature affect?
As the temperature of an enzymatically catalyzed reaction increases, so does the
rate (velocity) of the reaction
Examples of temperature as a factor:
- fever
- autoclaves
- sterilization
is the pH at which an enzyme exhibits maximum activity.
optimum pH
clinical pathologist who had examined many stomach biopsy specimens
noticed a parallel between the severity of the inflammation and the number of bacteria present.
J. Robin Warren
optimum pH range:
pH range of 7.0–7.5
optimum pH of pepsin
2.0
optimum pH of trypsin
8.0
stomach and duodenal ulcers were thought to be due to:
excess stomach acid,
emotional stress and spicy food, among others.
looking for a research topic
and learned that Warren had a list of patients whose gastric biopsies showed “curved” bacteria.
Barry James Marshall
absence of
hydrochloric acid in the gastric secretions.
achlorhydria
Why does Marshall and Warren awarded nobel prize in medicine in 2005?
discovery of “the bacterium
Helicobacter pylori and its role in gastritis
and peptic ulcer disease.”
How do the enzymes present in the H. pylori bacterium can function in the acidic environment of the stomach?
The urease itself
is protected from denaturation
by its complex quaternary
structure.
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.
the number of substrate molecules transformed per minute by
one molecule of enzyme under optimum conditions of temperature, pH, and saturation.
turnover number
the active sites of all the enzyme molecules are occupied by a substrate
molecule.
at maximum rate of substrate concentration
enzyme concentration
The concentration of substrate in a reaction is much higher than that of the enzyme.
mechanism of enzyme action
Formation of an enzyme-substrate complex as an intermediate species provides an alternative pathway, with lower activation energy, through which a reaction can occur.
active site has a fixed geometric shape. only a substrate with a matching shape can fit into it
lock-and-key model
active site has a flexible shape that can change to accept a variety of related substrates. enzymes vary in their degree of specificity for substrates
induced-fit model
FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: TEMPERATURE
reaction rate increases; activity drops sharply as proteins are denatured
FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: PH
max enzymatic activity is possible only within a narrow pH range; outside range, the proteins are denatured and activity drops sharply
FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: SUBSTRATE CONCENTRATION
reaction rate increases with substrate concentration until full saturation occurs; then rate levels off
FACTORS THAT AFFECT THE RATE OF ENZYME ACTIVITY: ENZYME CONCENTRATION
reaction rate increases with increasing enzyme concentration; assuming enzyme concentration is much lower than that of substrate
microorganism
that thrives in extreme environments
extremophile
(optimal growth at pH levels of 3.0 or below
acidophiles
optimal growth at pH levels of 9.0 or
above
alkaliphiles
high salinity, a salinity that exceeds 0.2 M NaCl needed for growth
halophiles
a temperature between 80°C and 121°C needed to thrive
hyperthermophiles
a high hydrostatic pressure needed for growth
piezophiles
extremely dry conditions needed for growth
xerophiles
temperature of 15°C or lower needed for growth
cryophiles
enzymes present in extremophiles; microbial enzyme
active at conditions that would inactivate human enzymes
as well as enzymes present in other types of higher
organisms.
extremozymes
