Exam 2 Flashcards
(86 cards)
1
Q
Catalyst
A
- a substance that increases the rate or velocity of a chemical reaction without itself being changed in the overall process
- enzymes are biological catalysts (proteins)
2
Q
Substrate
A
- the substance that is acted on by an enzyme
3
Q
Enzymes are divided into 6 major classes to define their function more precisely
A
- Oxidoreductase
- Transferases
- Hydrolases
- Lysases
- Isomerases
- Ligases
4
Q
Oxidoreductases
A
- catalyze oxidation reduction reactions
- adds/removes electrons and protons from its substrate
ex: alcohol dehydrogenase (oxidation with NAD+)
5
Q
Transferases
A
- catalyze transfer of functional groups from one molecule to another
ex: hexokinase (phosphorylation)
6
Q
Hydrolases
A
- catalyze hydrolytic cleavage
(cleave bonds by adding a water molecule)
ex: carboxypeptidase A (peptide bond cleavage)
7
Q
Lysases
A
- catalyze removal or addition of a group from a double bond, or other cleavages involving electron rearrangement
- remove functional groups via non-hydrolytic reactions.
- Often result in formation of a double bond.
ex: decarboxylation
8
Q
Isomerases
A
- catalyze intramolecular rearrangement
2 Types
1) Mutases- transfer functional groups from one position to another
2) Epimerases- invert functional groups about asymmetric carbons
ex: maleate isomerase (cis-trans isomerization)
9
Q
Ligases
A
- catalyze reactions in which two molecules are joined
- use the energy from ATP hydrolysis to form bonds between two substrate molecules.
ex: pyruate carboxylase (carboxylation)
10
Q
Cofactor, or coenzyme
A
- an organic(nonprotein) small molecule that binds to an enzyme and is essential to carry out the catalytic reaction
- non protein components of enzymes that convert inactive “apoenzymes” to active “holoenzymes”
- not permanently altered by the reaction
- most are derived metabolically from vitamins
11
Q
Major example of the coenzyme of the Vitamin Niacin and function
A
- nicotinamide adenine dinucleotide (NAD+)
- oxidation reduction
- capable of acting as an oxidizing agent (reduced)
- conversion of alcohol to aldehydes or ketones, coenzyme of alcohol dehydrogenase
12
Q
Metalloenzymes
A
- metal ions that are bound in a prosthetic group like heme
- acts in the same way as a coenzyme,
13
Q
Example of carboxypeptidase A as a metalloenzyme
A
- zinc ion in carboxypeptidase A binds the water molecule that attacks the carbonyl of tee scissile bonds and acts as an electrostatic catalyst
14
Q
How does a reaction proceed?
A
- spontaneously due to random kinetic energy of reactants 3 types of kinetic energy 1. vibrational 2. rotational 3. translational
15
Q
What is heats affect on kinetic energy and rate of reaction
A
- increases them
16
Q
Transition State
A
- the unstable (energized) intermediate formed in an enzymic reaction that has properties of both the substrate and the product
- point in a reaction where reactants and products have the highest energy
17
Q
Activation energy
A
- the threshold energy required to produce the chemical reaction
18
Q
Enzymes speed up reactions by _______ the amount of activation required to start a chemical reaction
A
- lowering
19
Q
What does it mean that Enzymes are reversible
A
- typically they bring a chemical reaction to equilibrium instead of completing it
20
Q
Cellulase enzyme
A
- hydrolyzes cellulose
- used as a digestive aid and in biofuel production
21
Q
Collagenase enzyme
A
- hydrolyzes collagen
- promotes burn and wound healing
22
Q
Invertase enzyme
A
- hydrolyses sucrose
- used in manufacture of soft-centered candy
23
Q
Lipase enzyme
A
- hydrolyzes lipids
- digestive aid, improves cheese flavor
24
Q
pectinase enzyme
A
- hydrolyzes pectin
- clarifies fruit juices
25
protease enzyme
- hydrolyzes protein
| - used in detergents
26
Apoenzyme
- the nonfunctional protein component of an enzyme lacking its cofactor
27
Holoenzyme
- the functionally complete apoenzyme plus its cofactor
28
Two main types of cofactors
1. organic:
- coenzymes(CoA, NAD+, biotin)
2. Inorganic:
- assorted mineral ions (Mg2+, Zn2+)
29
Prosthetic groups
- tightly bound non protein (organic) components of proteins (heme)
30
Coenzyme A
- nucleotide cofactor
- derived from pantothenic acid
- carries acyl groups for metabolic processes
- acetyl-CoA most common acyl intermediates
31
Beri-Beri
- crippling disease
- death due to heart failure bc degeneration of nerve fibers and heart muscle
- dietary deficiency of vitamin B1 (Thiamine), consumption of rice
- Thiamine required by enzymes involved in glucose catabolism and conversion to fats
32
William Fletcher
- rice bran and germ contained accessory factors that reversed or prevented Beri-Beri disease in chickens and prisoners
33
Cassimir Funk
- accessory factors contained N-rich substances which he named Vital amines (essential for survival)
34
Water soluble coenzymes
1. NAD+/NADP+
2. FMN/FAD
3. coenzyme A
4. Vitamin C
35
Lipid soluble enzymes
1. Vitamin E
2. Vitamin D
3. Vitamin A
36
Vitamin C
- water soluble
- Dehydro” form scavenges free radical electrons within the aqueous compartment of cell.
- helps protect membrane damage by reacting with peroxyls and enhancing the activity of lipid soluble vitamin E
37
Vitamin E
- regeneration of vitamin E by ascorbic acid
| - ascorbate regenerated by reacting with GSH
38
Vitamin D deficiency
- CAUSES RICKETS
- not a true vitamin or cofactor bc can be synthesized in the body (no enzymic rxns)
- steroid hormone derived from cholesterol in presence of UV light
- Functions to promote Ca2+, PO43- & Mg2+ absorption in intestines.
- Inability to absorb Ca2+, PO43- & Mg2+ results in soft bones that bend during growth and development.
- Children are most susceptible.
39
Vitamin A deficiency
- get vitamin from animal products and B carotene from plants (carrots)
- Infants and are children most susceptible; high mortalities
- deficiency directly related to polish rice as a staple food in asia
* CAUSES BLINDNESS
40
Lock and key hypothesis
- Emil Fischer
- enzyme active site(lock) perfectly matches the shape of the substrate (key)
- only allows one substrate to bind to active site and be converted to product
41
Induced fit model
- Daniel Koshland
- substrates fit into active site like a flexible "hand in glove"
- both the enzyme and substrate are distorted on binding (conformational changes)
- substrate is forced into a conformation approximating the transition state
- enzyme keeps the substrate under strain
42
How do substrates bind to enzymes?
- non covalent forces
- van der Waals
- electrostatic
- hydrogen bonding
- hydrophobic interations
43
Enzyme-Substrate reaction 3 steps
1) binds to substrate (only reversible step)
2) conversion of enzyme-substrate complex to enzyme bound to product (intermediate)
- stabilized transition state
3) release of product (rapid)
44
enzyme-substrate complex vs transition state on rxn coordinate diagram
- ES complex is a stable intermediate that is thermodynamically favored (lower free energy G)
- transition state is an unstable state (highest free energy)
- EP is less favorable that E+P for maximum efficiency
45
What do delta Gnon and delta Gcat stand for? what do we want to be larger in reaction coordinate diagram? How is this achieved
- delta G non is the transition state
- delta G cat is the Enzyme-substrate complex
- Gcat
46
Activation energy on rxn coord diagram
- the initial energy state when the reaction begins
| - reactants
47
Transition state on rxn coord diagram
- highest energy point on the diagram between the reactant and product
48
General acid/base catalysis (GABC)
- important in reactions involving proton transfer
| - specialized case of electrostatic catalysis involving the transfer of a positive charge (H+)
49
What is required for a reaction to be considered catalytic?
- enzyme active site must be restored to its initial state
50
Lysozyme mechanism of a specific enzyme catalyzed reaction
- lysozyme cleaves a polysaccharide
| - lysozyme employs GABC, substrate distortion(strain of D ring) and covalent catalysis to achieve its rate enhancement
51
Chymotrypsin mechanism of a specific enzyme catalyzed reaction
- catalysis of peptide bonds hydrolysis by a serine proteases
- employs covalent catalysis, GABC and electrostatic stabilization
- involves stabilization of transition states and tetrahedral intermediate states
- oxyanion hole stabilizes the tetrahedral intermediate
52
Mechanisms of enzyme regulation
1. activation
2. inhibition
3. modification
53
Substrate level control of enzyme regulation
- direct interaction of substrates and products of each enzyme-catalyzed reaction with the enzyme itself
- the higher substrate concentration, higher rate of rxn
- a large change in S would be required to effect a significant change in enzyme, not used for regulation often
- high levels of product, which can bind to enzyme, inhibit the conversion of substrate to product (product inhibitor)
54
Why do enzymes need regulation?
1. maintenance of ordered state
2. conservation of energy
3. environmental responsiveness
55
Feedback control in enzyme regulation
- feedback inhibition
- inhibition or activation of a key step(control points) in the pathway occurs through a allosteric enzyme mechanism
- efficient means to maintain homeostasis of reaction
- an increase in the conc of product leads to a dec in the rate of its production
- control generation of final product by slowing the first step of reaction so machine can regulate concentration of E
56
Allosteric enzymes
- occurs when the binding of a ligand results in a conformational change in an enzyme
- means other site (other shape) other than active site
- exhibit cooperativity in substrate binding (homoallostery) and regulation of activity by other effector molecules (heteroallostery)
57
Homoallostery
- cooperative substrate binding
- subunits undergo conformational changes individually
- Shift from T to R form is induced by S
58
Heterallostery
- inhibitors or activators
- if an enzyme molecule can exist in two conformational states (T and R), then its kinetics can be controlled by any other substance that binds to the protein
- Allosteric inhibitors shift towards T
- allosteric activators shift towards R
59
T form of monomers (taut)
- low substrate, high inhibitor affinity
60
R form of monomers(relaxed)
- high substrate and activator affinity
61
Covalent modification
- the reversible attachment (or modification) of a functional group to/on a protein or enzyme via a covalent bond
ex:
- phosphorylation/dephosphorylation
- oxidation/reduction
- proenzymes vs zymogens(irreversible)
62
Proenzyme
- an inactive enzyme precursor (polypeptide) that must be proteolytically cleaved or hydrolyzed in order to become active
63
zymogen
- irreversible
- an inactive enzyme precursor (polypeptide) that must be proteolytically cleaved or hydrolyzed in order to become active
- must be cleaved proteolytically in the intestine to yield active enzymes
64
Ribozymes
- RNA molecules that can act as enzymes
65
kinetics
- studies the rate at which reactions occur
| - also shows the reaction mechanism (how it occurs)
66
rate laws
- how the rate depends on amounts of reactants
- measure the rate at different starting concentrations
- k= rate constant
ex: if a reactant doubles, initial rate will double
67
integrated rate laws
- how to calc amount left or time to reach a given amount
68
half life
- how long it takes to react 50% of the reactants
69
Arrhenius equation
- how rate constant changes with T
70
Mechanisms
- link between rate and molecular scale process
71
Factors that affect rates
1. concentration of reactants
2. temperature
3. catalysts
72
rate of reaction equation
change in concentration/change in time
- average rate decreases as the reaction proceeds because as the reaction goes forward, there are fewer collisions between reactant molecules
73
Instantaneous rate in a plot of concentration(y) vs time (x)
- the slope of a line tangent to any curve at any point at the time
- if the ratio is not 1:1
use aA + bB -> cC+ dD
rate= (
74
Rate law: order
- tell the order of the reaction with respect to each reactant
- overall reaction order can be found by adding exponents on rxns in rate law
75
first order reaction characteristics
- depends on the first power of the concentration of the reactant
- the larger the k more rapid the rate
- use graph ln A vs t
- straight line with a decreasing slope of -k
76
first order reaction equation
```
ln(A)t=-k(t)+ln(A)o
t=time
-k=slope
(A)o=y intercept
- in y=mx+b form
```
77
Second order reaction characteristics
- 2 reactions come together to form the producy
- plot of 1/A vs time
- has a straight line
- with a slope of positive k
78
How to determine first or second order when not given a graph
- plug numbers into first order and second order equations
| - determine which will have the right characteristics
79
Half life equation
(A)t=.5 (A)o
- because t1/2 is one half of the original A
- if increase concentration of A
80
reaction coordinate diagrams
- show the energy of reactants and products (delta E)
- highest point is transition state
- species present at the transition state is called the activated complex
- energy gap between reactants and activated complex is activation energy barrier
81
Heat in a reaction coordinate diagram
- speeds the reaction, so the amount of molecules that can overcome the activation energy increases
- the curve will flatten and broaden
- reaction rate increases
82
Arrhenius equation
- relationship between k and Ea
83
molecularity in reaction mechanisms
- tells how many molecules are involved in the process
84
Multistep mechanism
- one of the steps are slower than the others
| - reaction cannot occur faster than this step, rate determining step
85
rate enhancement equation
- determines how much an enzyme must stabilize the transition state to achieve observed rate enhancements
- indicates how much faster rxn occurs when catalyzed
86
to lower activation energy barrier to maintain delta Gcat>delta Gnon do what?
- delta H more negative or delta S more positive
