AP Bio - Unit 2

Proteins, enzymes, metabolism

Organic compound

Organic compound

Compound containing carbon

Macromolecule

A type of molecul, examples include proteins, carbohydrates, nucleic acids

Carbon skeleton

The ‘skeleton’ of the organic molecules made up by carbon chains; differences in carbon skeletons are what make molecules complex and diverse

Hydrocarbons

Organic molecules of only hydrogen and carbon. Nonpolar, hydrophobic. They attach to carbon skeleton and can determine the properties of an organic molecule

Fats

molecules with long hydrocarbon tails

Hydroxyl group

OH- or -HO—

compound name: alcohol

polar

Carbonyl group

Compound name: ketone if carbonyl is in carbon skeleton, aldehyde if carbonyl is at end of skeleton

carboxyl group

Compound name: carboxylic acid or organic acid

it is an acid

amine group

it is a base

sulfhydryl group

polar but hydrophobic (only function group which is hydrophobic)

compound name: thiol

phosphate group

compound name: organic phosphate

a polyatomic ion

methyl group

compound name: methylated compound

nonpolar and not a functional group (the other six groups are functional), hydrophobic

functional groups

chemical groups which affect molecular function directly through reactions (sulfhydryl, carbonyl, carboxyl, amine, phosphate, hydroxyl)

ATP

adenosine triphosphate, a complicated organic phosphate. it has three phosphate groups, and loses one in hydrolysis to become ADP.

polymer

molecule with many blocks linked by covalent bonds

monomer

smaller molecules that act as building blocks for monomers

enzymes

macromolecules which speed up reactions without being used up in the reaction

dehydration synthesis

monomers are joined to form a polymer by covalently bonding to each other and releasing a water molecule (one molecule gives up a Hydrogen while the other molecule gives up a Hydroxide)

hydrolysis

polymers separated into monomers using water, hydrogen attaches to one monomer while hydroxide attaches to the other

defensive proteins

function: fight against disease

storage proteins

function: storage of amino acids

transport proteins

function: transport of substances

hormonal proteins

function: coordination of an organism’s activities

receptor proteins

functions: response of cell to chemical stimuli

contractile and motor proteins

functions: movement

structural proteins

function: support

proteins

biologically functional molecule that is made up of polymers of amino acids called polypeptides folded and coiled

amino acid

an organic molecule with both an amino and a carboxyl group

side chain/R group

the chain of an amino acid which determines the properties of the amino acids - it is connected to the alpha carbon or central carbon

amino acids with polar side chains are hydrophilic, amino acids with nonpolar side chains are hydrophobic. acidic amino acids have negative charged side chains, basic amino acids have positive charged side chains

peptide bond

formed when amino group of one amino acid and carboxyl group of other amino acid are joined through dehydration reaction. peptide bonds are what link amino acids in polypeptides together

primary structure

the linear chain of amino acids/sequence of amino acids which form the polypeptides of the protein

determined by inherited genetic information

secondary structure

regions stabilized by hydrogen bonds between atoms. coils and folds of the polypeptide chains formed by hydrogen bonds between sections of backbone.

examples: alpha helix and beta pleated sheet

alpha helix

coil held by hydrogen bonding between every fourth amino acid

beta pleated sheet

secondary structure of 2+ segments of polypeptide chain lying side by side, connected by hydrogen bonds between 2 parallel segments of polypeptide backbone

tertiary structure

three dimensional shape of polypeptide stabilized by interactions between side chains of amino acids. this includes “hydrophobic interactions”, when amino acids with hydrophobic side chains end up in clusters at core of protein, out of contact with water

disulfide bridges are another example of tertiary structure.

disulfide bridges

covalent bonds that reinforce shape of protein, formed where two cysteine monomers have their sulfurs bond together

quaternary structure

association of two or more polypeptides (some proteins only, not all)

denaturation

when aspect of proteins environments are altered, weak bonds and interactions get destroyed, protein loses shape

metabolism

totality of an organism’s chemical reactions, arises from orderly interactions between molecules

metabolic pathway

each step of the pathway is a reaction where a molecule is altered, each reaction catalyzed by enzymes

catabolic pathways

metabolic pathways which release energy by breaking down complex molecules into simpler ones (ex: cellular respiration)

anabolic pathways

consume energy to create complex molecules from simple ones

thermodynamicss

study of energy transformations in a collection of matter

system

whatever is being studied in a case of thermodynamics (ex: water bottle is an isolated system, it cannot exchange energy/matter with its surroundings, in contrast to open systems which can)

1st law of thermodynamics

energy can only be transferred and transformed, not created or destroyed

2nd law of thermodynamics

every energy transfer or transformation increases the entropy of the universe

entropy

measure of disorder of matter (ex: disorder caused by thermal energy reused as heat from body, not all energy is used for motion)

spontaneous process

process which can occur without input of energy, which automatically increases universe’s entropy, only when moving towards equilibrium

free energy

portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system

exergonic reaction

a reaction which proceeds with net release of free energy, so exergonic reactions are spontaneous

endergonic reaction

reaction which absorbs free energy from surroundings and stores it in molecules (nonspontaneous)

chemical work

work of cell: pushing of endergonic nonspontaneous reactions (ex: combining monomers into polymers)

transport work

work of cell: pumping of substances across membranes against the direction of spontaneous movement

mechanical work

work of cell: contraction of muscle cells, movement of chroosomes during cellular respiration

high energy bonds

reactants have high energy relative to the energy of the produces (ex: phosphate bonds of ATP)

phosphorylation

transfer of a phosphate group from ATP to some other molecule, such as the reactant

phosphorylated intermediate

recipient of phosphate group from ATP in phosphorylation; after reception, it becomes more reactive and less stable than the original molecule. it is necessary in coupling exergonic and endergonic reactions

Activation energy

energy required for molecules to be able to break bonds so they can enter transition state and be able to change bonds/react

induced fit

when the substrate enters the active site of the enzyme, the site’s shape changes slightly because of interactions between the side chains of amino acids of both substrate and enzyme. the active site fits more tightly around the substrate

catalysis mechanisms

different ways for enzyme to catalyze reaction

direct involvement catalysis

enzyme’s active site directly participates in chemical reaction. it may even form brief covalent bonds of substrate and sidechain of amino acid of the active site

template/orientation catalysis

in reaction with 2 or more substrates, enzyme’s active site may give template for substrates to come together in proper orientation for them to react with each other

stretch catalysis

the active site may stretch the substrate towards transition state form: the stretching can break chemical bonds in order for the substrate to form new ones in the reaction

microenvironment catalysis

enzyme’s active site may produce a microenvironment conducive to the type of reaction the substrate will participate in (ex: if substrate is acidic amino acid, active site may be pocket of low pH)

enzyme saturation

concentration of substrates is so high that all enzymes are already binded to a substrate and remaining substrates wait for reaction to be over so they can enter empty active sites

cofactor

nonprotein helpers for enzymes, bind either loosely or tightly to enzyme; an organic molecule cofactor is called a ‘coenzyme’ (ex: vitamins)

enzyme inhibitorsc

certain chmicals which inhibti actions of certain enzymes - inhibition is usually reversible, but is permanent if inhibitor is covalently bonded to the enzyme

competitive inhibitors

actively compete with substrate for the active site - they are inhibitors which bind to the active site

non-competitive inhibitors

doesnt directly competr with substrates, bind to a different part of the enzyme so that it changes shape and the active site is ineffective

allosteric regulation

protein’s function at one site is afected by binding of regulatory molecule to another site; allosteric enzymes which have activators

feedback inhibition

metabolic pathway switched off by inhibitory binding of its end product to enzyme which acts early in pathway, preventing cell from wasting chemical resources

activator

binds to allosteric sites of enzyme so active site is better fit for the substrate

inhibitor (allosteric)

binds to another site of the enzyme (apart from activator/active site) so that the active site is a worse fit for substrate

kinase

enzymes which take place in phosphorylation