BIO2

Positively charged amino acid

• basic

• hydrophilic

• amino group

Negatively charged amino acid

• acidic

• hydrophilic

• phosphate, carboxyl

Polar (uncharged) amino acid

• neutral

• hydrophilic

• hydroxyl aldehyde, keto, sulfydryl

• polar R groups can undergo h-bonding with backbone and other polar R groups

nonpolar amino acid

• neutral

• hydrophobic

• methyl groups

Secondary Structure

• local interactions in the backbone

• h-bonds form between nearby amino and carbonyl groups on the same polypeptide chain

• alpha - helix or beta-pleated sheet

Tertiary Structure

• Non-local folding of a polypeptide

• 3D structure

• dependent on interactions between R groups

• H bonds, hydrophobic interactions, van der Waals, disulfide bonds, ionic bonds

Hydrophobic R-groups

• towards the interior of proteins structure

• due to hydrophobic interactions in aqueous solutions

Charged R broups

can form ionic bonds with each other

Two cystines can form

covalent disulfide bonds

Glycine

very small and flexible

Proline

bent and rigid

Quaternary Structure

• 2+ polypeptides

• stabilized by R group interactions

anabolic reactions

creating new bonds requires the input of energy (energy storage)

catabolic reactions

breaking bonds outputs energy. energy released in catabolic reactions fuels anabolic reactions

Entropy (S)

• a measure of disorder

• unusable energy

Delta G=

Delta H - T Delta S

Delta H (Enthalpy) =

H products - H reactants

delta H < 0

exothermic and favorable

Delta G=

G products- G reactants

Delta G<0

• free energy is released

• spontaneous

• exergonic

Delta G>0

• input of free energy required

• non spontaneous

• endergonic

Delta G = 0

reaction is reverseable

Enzymes

• reduce random movements of substrate and allow for close proximity and correct orientation of substrate molecules

• lower activation energy

• do not change delta G

• increase probability that exergonic reactions will occur

Substrates

binding to the active site of an enzyme is driven between interaction between substrate and R groups lining the active site.

Substrate specificity

due to H-bonds, electrostatic interactions, and hydrophobic interactions with R groups in the active site.

oxidoreductases

transfer electrons between molecules

A- + B = A + B-

transferases

transfer functional groups between molecules

AX + B = A + BX

Ligases

join two large molecules together

Lyases

Catalyze non-hydrolytic bond breakage or creates new bonds without water or oxidation.

Ligases, Lyases, Transferases, and Oxidoreductases can all

catalyze dehydration reactions by different mechanisms

Hydrolases

use water to break covalent bonds thus break down molecules

Isomerases

move functional groups from one location on a molecule to another to create an isomer.

Catalysts

optimize reactant geometry, making chemical reactions more likely to occur.

induced fit

enzyme changes shape as it binds to the substrate

Transition state

• when conformation changes in enzyme put strain on substrate

• highly reactive

• induced by r groups spontaneously forming temporary covalent bonds with substrate

inorganic cofactors

copper, zinc, iron, magnesium, or calcium ions

coenzymes

non protein/amino acid unit

prosthetic grups

permanently bound non protein helper molecules

proteases

enzymes that cleave peptide bonds and can activate or deactivate enzymes

the addition of carbs or small regulatory proteins

can modulate enzyme structure/function or location

phosphorylation by kinases

can turn enzyme function on or off

inhibitors

chemicals that bind to enzymes to slow the rate of chemical reactions

irreversible inhibition

when an inhibitor covalently binds to the active site of an enzyme

competitive inhibitors

compete with substrate for the active site of an enzyme

uncompetitive inhibitors

bind to enzyme-substrate complex, preventing the release of product

noncompetitive inhibitors

change enzyme structure by binding outside the active site (to allhosteric site)

feedback inhibition

when key metabolic enzymes are allosterically controlled by the final product of a pathway

High delta H =

high potential energy