biochem topic 5

peptide bonds are broken by

hydrolysis

organisms must be able to ____ the rate of peptide bond hydrolysis

accelerate

• to recycle old proteins into newer forms (ex. regulatory proteins)

ways to increase rate of hydrolysis

1. increase temp (impractical since organisms can’t do that)

2. increase reactants (impracticle since we contain many molecules)

3. use a catalyst (ENZYMESSS)

isozymes

enzymes that are different protein structures and may carry different properties but catalyze same reaction

_______ determines rate of a reaction

height of activation energy

higher the activation energy

slower the reaction, less likely it will occur

when products have less free energy than reactants

reaction proceeds spontaneously

reactants can reform to original state, products and reform to original reactants

true

if reactants have more free energy than products

than reverse reaction occurs

cofactor

non-protein compound or metal ion that binds to enzyme and helps with catalytic activity

co-enzymes

vitamin derived cofactors

3 chemical catalytic mechanisms used by enzymes

1. acid-base

2. covalent

3. metal ion

catalytic triad

asp,his,ser

• present in same position of active site of many protease, conserved residues

• effective in breaking covalent bonds (peptide)

convergent evolution

unrelated proteins evolved to share similar traits

specificity pocket

cavity on enzyme active site that grabs desired residue to be cut

chymotryptsin cleaves peptide bonds after

large hydrophobic residues

scissile bond

chemical bond that’s targeted to be cleaved by enzyme

Zymogens

protease inhibitors that activate to prevent enzymes from eating tissues

proteolysis

enzymic breakdown of proteins into smaller proteins or amino acids

properties enzymes

1. Specific to the substrate (able to recognize out of many molecules)

2. accuracy (almost never make a mistake)

3. rapidity (can accelerate reactions billions or trillion times faster)

4. optimal conditions are mild (mild temp, neutral pH)

half life of peptide bond

20 years

• problem in digestive proteins

transition state

• Intermediate form between reactants and products

• highest point of free energy

• state where bonds are breaking and reforming

in order to react with enzyme, the two groups must come together and _____ with the correct ______

collide, orientation

mechanisms to lower activation energy

1. Enzyme binds 2 substrate molecules and orients them precisely to encourage a reaction between them

2. binding of substance rearranges electrons in substrate , creating partial negative and positive charges that favour a reaction

3. enzyme strains bound substrate , forcing it toward a transition state to favour a reaction

transition state analogues

• compounds that resemble the transition state, with similar geometry and charge distribution

• do not undergo chemical reactions

• drugs and antibiotics function as this (can shut down enzymes!)

enzyme’s active site is always matched to the

transition state

• tightly wraps itself around the substrate, forcing it into the transition state so it reaches desired reaction faster

chymotrypsin

• member of serine protease family

• features critical serine in its active site

• secreted by pancreas and breaks down dietary proteins

• hydrolysizes peptide bonds

• features catylitic triad (ser-his-asp)

nucleophilicity

the ability of a chemical species (a nucleophile) to donate a pair of electrons to an electron-deficient atom (an electrophile) to form a new covalent bond

specificity pocket of chymotrypsin

likes large aromatic amino acids

specificity pocket of trypsin

positively charged sidechain

specificity pocket of elastase

small amino acids

major serine protease

chymotrypsin, trypsin, elastase

first intermediate form of chymotrypsin

acyl-enzyme intermediate (covalent)

second intermediate form of chymotrypsin

tetrahedral

types of inhibitors

• reversible

• irreversable

reversable inhibitor

• Non-covalent bonding to enzyme

• can be removed

• competitive inhibition is most popular

• affects kM, not kmax

irreversible inhibitor

covalent bonding with an enzyme

permanent

• sometimes called suicide substrates (get stuck and can’t perform reaction)

the rate of the reaction is controlled by

the activation energy

• For the reaction to occur, enough energy (the “activation energy”) must be acquired to raise the reactant to the transition state

enzymes don’t change

difference in free energy between the reactants and products (∆G)

Free energy of activation (ΔGǂ )

the difference in free energy between the reactants and the transition state. It determines the rate of the reaction

transition state

1. An intermediate form between reactants and products

2. The point of highest free energy along the reaction pathway

3. A form that is different from both reactants and products

4. A state in which bonds are in the process of forming and breaking

Often the active site is found in

a cleft between two domains or subunits

• allows the substrate to be surrounded and the reaction environment to be controlled by the enzyme

• In the active site, multiple weak bonds are formed as substrate(s) bind, and the chemical and physical geometry of the site push the incoming molecule towards the transition state

nucleophilicity

measure of how quickly a chemical species donates an electron pair to form a covalent bond with an electrophile, typically carbon

oxyanion

a polyatomic ion that contains one or more oxygen atoms bonded to a central chemical element (usually a nonmetal) and carries a net negative electrical charge

Vmax is determined by

• independent factors

• unrelated to kM