Organic Bio Chem Exam #3

amines

derivatives of amonia (NH3) in which one +H atoms are replaced with alkyl or aromatic groups

primary amine

CH3-N-H2

• one H is replaced with carbon

secondary amine

(CH3)2-N-H

• two H are replaced with carbons

tertiary amine

(CH3)3-N

• three H are replaced with carbons

IUPAC name for amines

• the e in the corresponding alkane name is replaced with -amine

  • methane → methanamine

• amines w/ a chain of 3+ carbon atoms are numbered to show the position of the -NH2 group and any other substituents

  • N-ethyl-N-methyl-1-propanamine

amino

when a compound contains more than one functional group, IUPAC rules state an oxygen-containing group will take priority over an -NH2 group and the -NH2 group is names as the substituent amino

aniline

amine of benzene (aromatic ring with NH2)

which amine has the highest to lowest boiling point / solubility

primary → secondary → tertiary

neutralization of amines

• an amine acts as a base and reacts with an acid to form ammonium salt

  • the lone pair on nitrogen accepts H+ from acid to give ammonium salt (no water is formed)

heterocyclic amines

consists of ring of five/six atoms, where one or two are N atoms

• purines and pyridimines

alkaloids

• anti depressants, stimulants

• nicotine, caffeine, morphine, codine, heroin, OxyCotin

neurontransmitters

excitatory: stimulating receptors to send more impulses

inhibitory: decreasing the activity of receptors

• acetylcholine: regulates muscle activation, learning, STM

• methamphetamine/amphetamine: increasing excitatory catecholamine neurotransmitters (dopamine, norepinephrine )

• dopamine: natural stimulant; gives energy and enjoyment (addicted behavior / schizophrenia)

• serotonin: helps to relax (low=depression, anxiety, OCD, eating disorder)

• histamine: produced by immune system in response to invaders (ex benadryl)

• glutamate: (most abundant) excitatory involved with learning and memory

• GABA drug

  • decrease GABA activity = schizophrenia

  • increase GABA activity: ALS Lou Gehrigs

amide

derivatives of carboxylic acids where a nitrogen group (-NH2) of a primary/secondary amine replaces the hydroxyl (-OH) group of acid

• CH3-C(=O)-NH2

amidation

the production of amides

• when a carboxylic acid reacts with ammonium of a ½ amine and heat

• accompanied by the production of water (condensation)

IUPAC naming of amides

• dropping the -oic acid or -ic acid from carboxylic acid and adding the suffix amide

• replacing -amine with -amide

physical properties of amides

• don’t have the population of bases seen in amines

• the more hydrogen bonding an amide forms, the higher the boiling point

• water solubility increases with number of positive hydrogen bonds

• primary amides have the highest melting points

• tertiary amides cannot form hydrogen bonds - lowest melting point

urea

• the simplest natural amide

• end product of protein metabolism

• excreted in urine

amides and medicine

• Tylenol: phenol, amide

• Barbiturates: sedatives, sleep inducers

acid hydrolysis of amides

produce carboxylic acid and an ammonium salt

base hydrolysis of amides

produce a carboxylic salt and an amine/ammonium

amino acids

• the building blocks of protein; monomers of protein polymer

• contain a carboxylic and group and an amino group on alpha carbon

ionization of amino acids

• the carboxylic acid donates on H+ to the amino group to give carboxylate and an ammonium group

• this ionized form is called zwitterion

classification of amino aicids

• nonpolar: with hydrocarbon side chains (hydrophobic)

• polar (neutral): with polar side chains

  • acidic side chains - negative charged

  • basic side chains-positive charged

peptide bond

• an amide bond

• forms b/w the carboxylic group of one amino acid and the amino group of the next amino acid

• contains an N (free H23N+) terminal written on the left

• contains a C (free COO-) terminal written on the right

IUPAC names for dipeptides

• an -yl ending for the N terminal (free H3N+) amino acid

• the full amino acid name of the free carboxylic group (COO-) at the c terminal

what are the four protein structures

1) primary

2) secondary

3) tertiary

4) quaternary

primary protein structure

specific sequence of amino acids

• the backbone of a peptide chain or protein

secondary protein structure

amino acids form hydrogen bonds within a single polypeptide chain or between polypeptide chains

• alpha helix, beta pleated, triple helix

alpha helix

coiled shape held in place by hydrogen bonds between the amide groups and carboxyl groups of the amino acids along the chain

beta sheet pleated

forms between adjacent polypeptide chains or within the same polypeptide chain when the rigid structure of amino acids proline causes a bend in the polypeptide chain

tertiary structure

an overall 3-D shape formed by the interactions and repulsions of amino acid residues in different parts of the chain

• hydrophilic interactions, hydrophobic interactions, salt bridges, hydrogen bonding, disulfide bonds

hydrophilic interaction

occur b/w the external aqueous environment and polar amino acid sequence (polar parts on surface)

hydrophobic interactions

occur b/w nonpolar amino acid residues forming a nonpolar center at the interior of a gobular protein

salt bridges

ionic interactions b/w the charges of the acidic and basic residues of amino acid residues

disulfide bonds

covalent bonds that form when the -SH groups of two cystine residues

gobular proteins

• have compact, spherical shapes formed when sections of the polypeptide chain fold over the top of each other as a result of the interactions b/w amino acid residues

• carry out the work of cells: synthesis, transport, metabolism

myogoblin

gobular protein that stores oxygen in skeletal muscle

fibrous protein

consist of long, tin fiber-like shapes involved in the structure of cells and tissues

• alpha keratins: hair, wool, skin, nails

• beta keratins: feathers, scales

quaternary structure

• two polypeptides chains or subunits (hemoglobin)

• help together by same stabilizing interactions as tertiary

denaturation

• disruption in the interactions b/w residues that stabilize the secondary, tertiary, or quaternary

• does not affect amide bonds b/w amino acids

• protein is no longer biologically active

factors that denature proteins

• temp

• pH

• adding certain organic compounds

• adding heavy metal ions

• mechanical agitation

protein hydrolysis

• peptide/amide bonds break

• occurs in stomach when enzymes (ex trypsin) catalyze the hydrolysis of proteins to give amino acids

enzymes

biological catalysts that increase rate of reactions by changing the way a reaction takes place (lowering the activation energy)

• they are not changed in the process of the reactions

• nearly all enzymes are gobular proteins with a unique 3D shape

• have specific amino acid residues within the active site that interact with functional groups of the substrate to form hydrogen bonds, salt bridges, and hydrophobic interactions

absolute specificity

catalyzes one type of reaction for one substrate (ex urease)

group specificity

catalyzes one type of reaction for similar substrates (ex hexokinase)

linkage specificity

catalyzes one type of reaction for a specific type of bond (ex chemotrypsin)

enzyme-substrate (ES) complex

forms with combination of an enzyme and substrate; provides alternative pathway for reaction with lower activation activity

enzyme-product (EP) complex

forms after reaction; amino acid R groups catalyze the reaction

lock-an-key model

rigid structure binding to rigid enzyme

induced fit model

more dynamic; the active site is flexible enough to adapt to the shape of substrate

naming of enzymes

• ends with -ase

• identifies the reacting substance

• describes the function of the enzyme

• can be a common name (mostly digesting enzymes like pepsin)

amylase

digests carbohydrates

protease

digests proteins

lipase

digests fat/lipids

oxidoreductase

oxidation-reduction

• oxidases: catalyze the oxidation of a reaction

• dehydrogenases: catalyze the removal/addition of 2 H atoms

transferase

transfer of atoms

• transaminases: catalyze the transfer of amino acids

• kinases: catalyze the transfer of phosphate groups

hydrolases

hydrolysis

• protease: catalyze hydrolysis of peptide bonds in proteins

• lipase: catalyze the hydrolysis of ester bonds in proteins

• nuclease: catalyze the hydrolysis of phosphate ester bonds in nucleic acid

lyase

remove or add molecule to another

• decarboxylase: catalyze the removal of CO2 from a substate

• deaminases: catalyze the removal of NH3 from a substate

• dehydratase: catalyze the removal of H2O from a substate

• hydratase: catalyze the addition of H2O from a substate

isomerase

catalyze arrangement of atoms within a molecule

• isomerase: catalyze the conversion between cis/trans bonds

• epimerase: catalyze the conversion of D/L isomers

ligase

catalyze the joining of two molecules using ATP

• synthetase: catalyze the combination of 2 molecules

• carboxylase: catalyze the addition of CO2

factors affecting enzyme activity

temperature, pH, concentration of enzymes/substrate

optimal temp? what happens if temp falls above/below?

mostly around 37C (body temp)

• range: 10-50C

• shows little activity at low temp

• lose all activity at high temp due to denaturation

optimal pH? what happens if pH falls above/below?

mostly around 7-7.4

• range: 6-8

• lose activity in low/high pH as tertiary structure is denatured

enzyme concentration v enzyme activity

increased rate of reaction; binds more substrate with enzyme

substrate concentration v enzyme activity

increases rate of reaction until saturated with enzymes with substrate

enzyme regulation

rates of enzymes are controlled by regulatory enzymes

• increases reaction rate when more substrate is needed

• decreases when substrate is not needed

allosteric enzymes

binds with regulatory molecule at the allosteric site that is different from the active site; changed the shape of the enzyme, and therefore active site

positive regulators/effectors

active site becomes MORE active

negative regulators/effectors

slows down or turns off the enzyme

feedback control

generally occurs when end product is high; end product acts as a negative regulator and binds to allosteric site

covalent modification

enzyme activity is modified by covalent bonds to a group on the polypeptide chain that are formed or broken

zymogen / proenzymes

produced in their inactive form and can be activated at a later time when they are needed; full polypeptide chain before the tail is removed