Test 3 BICH 410

What are the two requirements for life

Ability to self replicate

Ability to catalyze chemical reactions efficiently and selectively

What is a disadvantage of uncatalyzed reactions

Too slow to maintain life as we know it

What are the two types of biological catalyst

Enzymes

Ribozymes

What do most biological catalysts use

Enzymes

What are enzymes

Enormous catalytic power

High specificity for substrates

Accelerate chemical reactions

Where do enzymes function

Aqueous systems under very mild conditions of temperature and pH

Enzymes are the agents of

Metabolism

Every chem is, step of a metabolic pathway is catalyzed by

An enzyme

Free energy is

Large and exergonic

Enzymes bind at a specific molecule called _____ at a specific site on the enzyme surface called the ______

substrate

Active site

Catalytic power

Enzymes accelerate reactions by as much as 10^16 times greater than uncatalyzed

Enzymes accomplish there feats in aqueous solutions under mild temperatures and pH

Specificity

Extraordinary ability of an enzyme to catalyze one particular far action on a specific reactant called the substrate to produce a specific product

Enzymes can be very

Specific or broad

Active site

Specific site where an enzyme binds

Regulation of enzymes occurs

Control over amount of enzyme expressed

Reversible metabolic inhibitors and activators

How is specificity controlled

The structure of the enzyme

The unique fit of the substrate to the active site of the enzyme controls the selectivity for substrate and the product yield

Cofactors

May be one or more inorganic ions such as Fe2+, Mg2+, Zn2+

Can carry out their catalytic function relying solely on their structure

Many require no protein components

Coenzymes

Complex organic or organomteallic molecules

Actively involved in catalysis often serving as intermediate carriers of functional groups in converting substrate into product

How are coenzymes bound

Loosely bound by the enzyme and freely diffuse in and out of the active site

Bound tightly by the enzyme some are covalently attached

Protethic groups

Tightly bound or covalently bound coenzymes

Holoenzyme

Catalytic active enzyme with its coenzyme (or cofactor) bound

Apoenzyme

Protein with the Prost ethic group (or cofactor) removed

Cofactors are derived from

Vitamins

Vitamins

Organic nutrients required in small amounts from our diet

-ase

Traditional way to name an enzyme was to add the suffix

Oxidoreductases

Oxidation reduction reactions

Most abundant and common

E.C.1

Transferases

Transfer C,N, or P functional groups

Hexokinase

Transfer P groups to and from ATP

E.C.2.

Hydro leases

Cleavage of covalent bonds with water

Break down into two parts

H2O is a reactant

E.C.3

Urease

Lyases

Group additions to break double bonds or group eliminations that yield double bond

E.C.4

Aldolase

Fructosediphosphatealdioase

Isomerase

E.C.5

Rearrange molecules

Isomerazation reactoons

Ligases

Least common

E.C.6

Formation of bonds using the energy of AtP hydrolysis

Single bonds (endergonic)

the noncovalent interactions involved in substrate binding to the enzymes active site are the same interaction involved in

Tertiary and quartenary structure

What interactions are important in substrate specificity

Electrostatic

H bonding

Dipole dipole

Hydrophobic

Van der waal

Specificity of a substrate comes from

The complementary surfaces of the substrate molecule and the surface of the active site

Shape, polarity, charge

Substrates of different geometries or with different functional groups ____

Cannot productively bind to the enzymes active site

One of the first theories of specificity was the

Lock and key hypothesis

The enzyme is considered the

Lock

The substrate is considered the

Key

The lock and key model captures the

Nature of specificity

Enzymes in the lock and key hypothesis are

Not rigid like locks

Enzymes are

Flexible and dynamic molecules

Most enzymes undergo

Conformational changes upon substrate binding

The induced fit model of specificity

Hypothesizes that the shape of the enzymes active site changes upon substrate binding in a process of dynamic recognition between the substrate and the enzymes

What does the substrate alter

The confirmation of the enzyme so that the protein and the substrate will fit together precisely

Enzymes are ___ in both the both of chiral substrates and in chemistry of their reaction

Stereospecific

Enzymes are composed of _____ and or

L- amino acids

Asymmetric active sites

what do catalyst not affect

Reaction equilibrium

Corresponding free energy change

what are the two pathways we are looking for form a substrate to product

path for the uncatalyzed reaction

path for the catalyzed reaction

the change in free energy is

independent upon which of these paths the reaction takes

if the catalyst change the equilibria of a reaction then

would violate the laws of thermodynamics

ground state

is the starting point

contribution to the free energy of the system by the average substrate or product our biochemical standard condition

reaction coordinate

the free energy of a system is often plotted against the progress of the reaction

the equilibria between S and P reflect

the difference in the free energies of their ground states

What characteristics does this graph show

P has lower ground state than S

ΔG’ is negative, and spontaneous

position of equilibria not affected by catalysis

what will thermodynamic parameters tell us

is a reaction is exergonic or not

thermodynamic potential of a factor

what does a favorable oror equivalently a large negative ΔG’

does NOT tell us anything about the rate of the reaction

the rate of reaction is

dependent on the pathway going form reactants to products

what opposes the conversion of S→P (an d vice versa)

energy barrier

the energy barrier consists of

energy required to bring reactants together

the energy required for the alignment of reacting groups

the energy required for the transient formation of unstable charges

the energy for bond rearrangements

other transformations required for the reaction to proceed in either direction

transition state

the top of the hill

what happens at the transition state

either direction on the reaction coordinate is down hill

the probability of reverting back to the substrate is equal to the probability of going on to product formation

activation energy

the difference in the energy levels between the ground state and the transition state

the activation energy is designated

ΔG++

the greater the activation energy

the slower the reaction

where does the intermediate occur

between the two activation energies

occupy the valleys between transition states

rate determining step

the overall rate of the conversion of reactants to products is determined by the slowest step (highest activation energy)

reaction rates can be increased by

raising temperatures which increases the population of molecules with sufficient energy to overcome the energy barrier

the activation energy can be elowered by

adding catalyst

catalysts enhance reaction rates by

lowering activation energy

binding energy

the energy derived from enzyme-substarte interactions

binding energy is a major source of

energy used to lower the activation energy

binding energy contributes to

specificity

binding energy is optimized in

the reaction transition state

enzyme active sites are NOt complementary to

the substrate but to the transition state

what would happen if an enzyme were completely complementary to the substrate

the substrate fit the enzyme as a key fits a lock then the ES would be incredibly stable and low in energy and have less free energy than the free substrate

weak non-covalent interactions are formed in

ES complex

if an enzyme were completely complementary to the substrate such that the substrate fit the enzyme as a key fits a lock then

the ES would be incredibly stable and low in energy and have less free energy than the free substrate

a perfect complementary ES results in

an increase in the activation energy since any changes in ES complex towards the transition state would interrupt optimized binding interaction

the binding energy is maximized when

the substrate reaches the transition state

free energy of a substrate binding lowers the

lowers the activation energy by binding the substrate tightest at the transition state

weak noncovalent forces between enzymes and substrate are a

major driving force in enzymatic catalysis

_____ of enzymes require cofactors

1/3

prosthetic group

covalently attached to active site of enzyme (require biotin coenzyme)

biotin

needed from diet can synthesize vitamin from body

coenzyme A

fatty acid metabolism

co-substrate

holoenzyme

enzyme w cofactor bound

100% enzymatic activity

apoenzyme

0% enzymatic activity

just enzyme w/o cofactor inactive form

how is an enzyme potrayed

as rigid but it is actually NOT rigid

why don’t we want the surface of a substrate to be perfect

it will then become an inhibitor

transition state analogs

very tight binding to the enzyme active site

affinity of the enzyme for the transition state may be as high as

10^-15 M

stable molecules that mimic the transition state are called

transition state analogs

transition state analogs bind much tighter than the

substrates or products

catalytic antibodies dont have

catalytic power of enzymes

abzymes

generated to accelerate reactions

antibody that binds to a substrate and catalyzes a specific chemical reaction, just like an enzyme.

what is another name for catalytic antibodies

abzymes

kinetics is a took used to

evaluate reaction mechanisms that provide descriptions of the individual steps that occur along a reaction pathway

kinetics is a study of

a chemical system whose composition changes with time

how can the changes in kinetics be described

by stoichiometric rate equations

a chemical reactions stoichiometry does NOT refflect

the sequence of molecular events that are involved