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Biochemistry > Exam 2 > Flashcards

Exam 2 Flashcards

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)
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2
Q

Substrate

A
  • the substance that is acted on by an enzyme
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3
Q

Enzymes are divided into 6 major classes to define their function more precisely

A
  1. Oxidoreductase
  2. Transferases
  3. Hydrolases
  4. Lysases
  5. Isomerases
  6. Ligases
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4
Q

Oxidoreductases

A
  • catalyze oxidation reduction reactions
  • adds/removes electrons and protons from its substrate
    ex: alcohol dehydrogenase (oxidation with NAD+)
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5
Q

Transferases

A
  • catalyze transfer of functional groups from one molecule to another
    ex: hexokinase (phosphorylation)
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6
Q

Hydrolases

A
  • catalyze hydrolytic cleavage
    (cleave bonds by adding a water molecule)
    ex: carboxypeptidase A (peptide bond cleavage)
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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
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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)
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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)
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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
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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
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12
Q

Metalloenzymes

A
  • metal ions that are bound in a prosthetic group like heme

- acts in the same way as a coenzyme,

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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
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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
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15
Q

What is heats affect on kinetic energy and rate of reaction

A
  • increases them
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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
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17
Q

Activation energy

A
  • the threshold energy required to produce the chemical reaction
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18
Q

Enzymes speed up reactions by _______ the amount of activation required to start a chemical reaction

A
  • lowering
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19
Q

What does it mean that Enzymes are reversible

A
  • typically they bring a chemical reaction to equilibrium instead of completing it
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20
Q

Cellulase enzyme

A
  • hydrolyzes cellulose

- used as a digestive aid and in biofuel production

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21
Q

Collagenase enzyme

A
  • hydrolyzes collagen

- promotes burn and wound healing

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22
Q

Invertase enzyme

A
  • hydrolyses sucrose

- used in manufacture of soft-centered candy

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23
Q

Lipase enzyme

A
  • hydrolyzes lipids

- digestive aid, improves cheese flavor

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24
Q

pectinase enzyme

A
  • hydrolyzes pectin

- clarifies fruit juices

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25
Q

protease enzyme

A
  • hydrolyzes protein

- used in detergents

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26
Q

Apoenzyme

A
  • the nonfunctional protein component of an enzyme lacking its cofactor
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27
Q

Holoenzyme

A
  • the functionally complete apoenzyme plus its cofactor
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28
Q

Two main types of cofactors

A
  1. organic:
    - coenzymes(CoA, NAD+, biotin)
  2. Inorganic:
    - assorted mineral ions (Mg2+, Zn2+)
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29
Q

Prosthetic groups

A
  • tightly bound non protein (organic) components of proteins (heme)
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30
Q

Coenzyme A

A
  • nucleotide cofactor
  • derived from pantothenic acid
  • carries acyl groups for metabolic processes
  • acetyl-CoA most common acyl intermediates
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31
Q

Beri-Beri

A
  • 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
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32
Q

William Fletcher

A
  • rice bran and germ contained accessory factors that reversed or prevented Beri-Beri disease in chickens and prisoners
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33
Q

Cassimir Funk

A
  • accessory factors contained N-rich substances which he named Vital amines (essential for survival)
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34
Q

Water soluble coenzymes

A
  1. NAD+/NADP+
  2. FMN/FAD
  3. coenzyme A
  4. Vitamin C
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35
Q

Lipid soluble enzymes

A
  1. Vitamin E
  2. Vitamin D
  3. Vitamin A
36
Q

Vitamin C

A
  • 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
Q

Vitamin E

A
  • regeneration of vitamin E by ascorbic acid

- ascorbate regenerated by reacting with GSH

38
Q

Vitamin D deficiency

A
  • 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
Q

Vitamin A deficiency

A
  • 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
Q

Lock and key hypothesis

A
  • 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
Q

Induced fit model

A
  • 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
Q

How do substrates bind to enzymes?

A
  • non covalent forces
  • van der Waals
  • electrostatic
  • hydrogen bonding
  • hydrophobic interations
43
Q

Enzyme-Substrate reaction 3 steps

A

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
Q

enzyme-substrate complex vs transition state on rxn coordinate diagram

A
  • 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
Q

What do delta Gnon and delta Gcat stand for? what do we want to be larger in reaction coordinate diagram? How is this achieved

A
  • delta G non is the transition state
  • delta G cat is the Enzyme-substrate complex
  • Gcat
46
Q

Activation energy on rxn coord diagram

A
  • the initial energy state when the reaction begins

- reactants

47
Q

Transition state on rxn coord diagram

A
  • highest energy point on the diagram between the reactant and product
48
Q

General acid/base catalysis (GABC)

A
  • important in reactions involving proton transfer

- specialized case of electrostatic catalysis involving the transfer of a positive charge (H+)

49
Q

What is required for a reaction to be considered catalytic?

A
  • enzyme active site must be restored to its initial state
50
Q

Lysozyme mechanism of a specific enzyme catalyzed reaction

A
  • lysozyme cleaves a polysaccharide

- lysozyme employs GABC, substrate distortion(strain of D ring) and covalent catalysis to achieve its rate enhancement

51
Q

Chymotrypsin mechanism of a specific enzyme catalyzed reaction

A
  • 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
Q

Mechanisms of enzyme regulation

A
  1. activation
  2. inhibition
  3. modification
53
Q

Substrate level control of enzyme regulation

A
  • 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
Q

Why do enzymes need regulation?

A
  1. maintenance of ordered state
  2. conservation of energy
  3. environmental responsiveness
55
Q

Feedback control in enzyme regulation

A
  • 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
Q

Allosteric enzymes

A
  • 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
Q

Homoallostery

A
  • cooperative substrate binding
  • subunits undergo conformational changes individually
  • Shift from T to R form is induced by S
58
Q

Heterallostery

A
  • 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
Q

T form of monomers (taut)

A
  • low substrate, high inhibitor affinity
60
Q

R form of monomers(relaxed)

A
  • high substrate and activator affinity
61
Q

Covalent modification

A
  • 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
Q

Proenzyme

A
  • an inactive enzyme precursor (polypeptide) that must be proteolytically cleaved or hydrolyzed in order to become active
63
Q

zymogen

A
  • 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
Q

Ribozymes

A
  • RNA molecules that can act as enzymes
65
Q

kinetics

A
  • studies the rate at which reactions occur

- also shows the reaction mechanism (how it occurs)

66
Q

rate laws

A
  • 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
Q

integrated rate laws

A
  • how to calc amount left or time to reach a given amount
68
Q

half life

A
  • how long it takes to react 50% of the reactants
69
Q

Arrhenius equation

A
  • how rate constant changes with T
70
Q

Mechanisms

A
  • link between rate and molecular scale process
71
Q

Factors that affect rates

A
  1. concentration of reactants
  2. temperature
  3. catalysts
72
Q

rate of reaction equation

A

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
Q

Instantaneous rate in a plot of concentration(y) vs time (x)

A
  • 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
Q

Rate law: order

A
  • 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
Q

first order reaction characteristics

A
  • 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
Q

first order reaction equation

A 
ln(A)t=-k(t)+ln(A)o
t=time
-k=slope
(A)o=y intercept
- in y=mx+b form
77
Q

Second order reaction characteristics

A
  • 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
Q

How to determine first or second order when not given a graph

A
  • plug numbers into first order and second order equations

- determine which will have the right characteristics

79
Q

Half life equation

A

(A)t=.5 (A)o

  • because t1/2 is one half of the original A
  • if increase concentration of A
80
Q

reaction coordinate diagrams

A
  • 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
Q

Heat in a reaction coordinate diagram

A
  • 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
Q

Arrhenius equation

A
  • relationship between k and Ea
83
Q

molecularity in reaction mechanisms

A
  • tells how many molecules are involved in the process
84
Q

Multistep mechanism

A
  • one of the steps are slower than the others

- reaction cannot occur faster than this step, rate determining step

85
Q

rate enhancement equation

A
  • determines how much an enzyme must stabilize the transition state to achieve observed rate enhancements
  • indicates how much faster rxn occurs when catalyzed
86
Q

to lower activation energy barrier to maintain delta Gcat>delta Gnon do what?

A
  • delta H more negative or delta S more positive

Biochemistry (15 decks)

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