need to rembember for exam 2

conjugated protein glycoprotein

covalently bonded to carbs

conjugated protein lipoproteins

covalently bonded to lipids

conjugated protein metalloproteins 

metal ions for structure stabilization or catalytic force

conjugated protein phosphoproteins

covalently bonded to phosphate groups used to activate or deactivate

a protein or provide binding sites for protein attachment

conjugated protein hemoproteins

proteins containing heme group for oxygen transport or electron transfer

conjugated protein nucleoproteins

protein combined with a nucleic acid (DNA or RNA)

enzyme

a biological catalyst (protein or RNA). Enzyme name ends in “ase”

substrate

reactant of an enzyme catalyzed reaction

turnover number

number of substrate molecules that are converted to product over a given time period

cofactor

nonprotein substance that binds to the protein and is required for catalysis

trace metals

Cu⁺²,Fe⁺², Mn⁺², Mg⁺², Co⁺², Zn⁺²

proximity effect

bring reactants together

orientation effect

hold reactants at the required distance and orientation for the reaction

energy effect

lower activation energy by inducing a strain on the bonds of the substrate

catalytic effect

provide acidic, basic and other types of functional groups that are required for catalysis

class of enzymes: oxidoreductase

catalyze simultaneously oxidation-reduction reactions

oxidoreductase subclass dehydrogenase

requires 2 hydrogen atoms from substrate to form double bond and requires FAD or NAD⁺ as coenzyme

• FAD (removes H from 2 covalently bonded carbon atoms to form alkene)

• NAD⁺ (removes H from 2 covalently bonded OH and C to form carbonyl group)

class of enzymes: transferases

transfer of functional group (amino or phosphoyl) between substances

transferases subclass kinases

transfer phosphoyl group (-PO₃^2-)

transferases subclass transaminase

transfer amine group (-NH₃⁺)

class of enzymes: hydrolase

catalyze hydrolysis of substrates (water lysis), substrate breaks bonds by adding H to the product on one side of the broken bonds and an OH group to the other product)

hydrolase subclass lipases

hydrolyze ester bonds in lipds

hydrolase subclass proteases

hydrolyze peptide bonds (backbone amides)

hydrolase subclass nucleases

hydrolyze phosphate ester bonds in DNA/RNA

hydrolase subclass amylases

hydrolyze the 1,4 glycosidic bonds in amylase (starch)

class of enzymes: isomerase

catalyze the rearrangement of atoms in a substrate to produce an isomer

class of enzymes: lyases

catalyze elimination of functional group by forming or breaking double bond

class of enzymes: ligases

catalyze bond formation with ATP hydrolysis, split phosphate(s) from ATP to provide energy to form bond

competitive inhibition

inhibitor is molecule that resembles substrate and competes for same binding site as enzyme

noncompetitive inhibition

inhibitor binds at site separate from active site, changes conformation of protein stopping the substrate from bonding

uncompetitive inhibtion

substrate can bind to the active site but inhibitor blocks substate from forming product or product from leaving as inhibitor binds near active site 

irreversible inhibition

inhibitor goes into active site and covalently bonds with residue not allowing substrate to bond, put into degradation or lysosomes as body views enzyme and unneeded since substrate can’t bond to it

allosteric regulation

inhibitor binding at different site changing conformation of enzyme either increases enzyme activity (positive) or decreases it (negative)

feedback control

allosteric regulation of metabolic pathway either product inhibits 1st enzyme to save energy (negative control) or product enhances activity of 1st enzyme (positive control)

covalent modification (not irreversible inhibition)

type of allosteric where addition of phosphate group can conformational change in enzyme structure that either activates or deactivates

zymogens

enzyme synthesized as inactive form (proenzyme) no longer protein segment must be removed before enzyme is active

genetic control (done at DNA level)

affects amount of enzymes able to be controlled

water soluble vitamin

hydrophilic, contain OH and COOH group, not stored in body, forms coenzymes

thiamine (vitamin b₁)

water soluble

cofactor form: thiamine pyrophosphate

basic function: decarboxylation

riboflavin (vitamin b₂)

water soluble

cofactor form: flavin adenin dinucleotide (FAD: flavin mononucleotide (FMN)

basic function: oxidation-reduction

niacin (vitamin b₃)

water soluble

cofactor form: nicotinamide adenine dinucleotide (NAD⁺): nicotinamide adenine dinucleotide phosphate (NADP⁺)

basic function: oxidation-reduction

pantothenic acid (vitamin b₅)

water soluble

cofactor form: coenzyme A

basic function: acetyl group transfer

pyridoxine (vitamin b₆)

water soluble

cofactor form: pyridoxal phosphate

basic function: transamination

cobalamin (vitamin b₁₂)

water soluble

cofactor form: methylcobalamin

basic function: methyl group transfer

ascorbic acid (vitamin C)

water soluble

cofactor form: vitamin C

basic function: antioxidant; collagen synthesis, healing of wounds

biotin

water soluble

cofactor form: biocytin

basic function: carbon carrier

folic acid

water soluble

cofactor form: tetrahydrofolate

basic function: methyl group transfer

fat soluble vitamin

smt

vitamin A (retinol)

fat soluble

provitamin: B-carotene

functions: vision; cell growth and differentiation; antioxidant for lipids

vitamin D (calciferol)

fat soluble

provitamin: 7-dehydrocholesterol

functions: bone health-absorption of calcium and phosphate in the gut and maintenance of their serum levels

vitamin E (a-tocopherol)

fat soluble

provitamin: none

functions: strong antioxidant; prevents oxidative damage of vitamin A, LDLs, and cell membranes

vitamin K (phylloquinone)

fat soluble

provitamin: none

functions: synthesis of prothrombin for blood clotting

coenzyme

Organic cofactors typically found in Redox enzymes (examples: vitamins & derivatives of vitamins)

apoenzyme

protein minus its cofactor/coenzyme

Holoenzyme

catalytically active enzyme (apoenzyme with its cofactor/coenzyme

active site

pocket in enzyme where catalysis takes place