the building blocks of proteins

can be put together in many arangements whose proteins play many roles

there are more than 300 but only 20 are coded for in genetics and are common

backbone is carbon with an amino and a COOH

each has a distinct attached R group with properities that determine the amino acid's role in the protein

the partial positive on the oxygen and negative on the nitrogen can interact

divided based on R group properities

polar (uncharged (no net charge but can have a partial charge), acidic, basic)

non polar

most have N and C in their R group except for two non polar amino acids

tend to be in the interior of proteins when in a aquous enivorment to make the protein more stable

when embedded in a membrane the nonpolar amino acids will be exposed on the surface to interact with the non polar fatty acids in the interior of the membrane

tryptophan which has and H group but has 9 C still making it insoluable

methionine has a S group but it does not participate in H bonding or ionic bonding in our cases so it is non polar

non polar

isoleucine, leucine, valine

have branched chain R groups

the catabolism of these amino acids requires a common pathway that when interrupted causes maple suryp urine disease (MSUD)

maple surpy urine disease

caused by a defect in the pathway that breaks down branched chain amino acids

urine has a distinctive odor due to build up of these amino acids

neurotoxicity is caused by build up in the blood

mental retardation

if treated with a special diet in time symptoms can be avoided

in normal catabolism phenylaline is converted to tyrosine

when defective this causes phenylketonuria (PKU)

causes neurotoxicity due to build up of phenylalanine in the blood

mental retardation

can be treated with a special diet and symptoms avoided if caught in time

aspertame is broken down into phenyaline fyi

smallest amino acid due to smallest R group

is a major part of collagen which has the structure (GLY-X-Y)n

mutations can cause ostrogenesis imperfecta

because glycine is small if it is mutated and replaced by anything else it will cause issues

glycine is important in collagen so mutations can cause multiple bone fractures and normally death in utero

R group is bonded with the amino acid main structure

structure is then rigid around the alpha C, one conformation only

it has special structural roles ex: collagen

if put where it isnt suposed to be it can cause problems due to the rigidity

methyl group donor in methlyation reactions due to the methyl on the end of its sulfur group

polar or non polar but it is group in non polar because for our porposes it does not participate like the other polar amino acids do

have uncharged, acidic, or basic R groups

R groups can participate in hyrogen or ionic bonds

allowing reaction with eachother, aqueous enivornments, exposed protein surfaces, enzyme/substrate

ASP and GLU

net negative charge at physiological pH

LYS and ARG

net positive charge at physiological pH

HIS is also included but at physiological pH its R group is mostly uncharged so the net +1 is not used in calculations but it can carry a charge in specific situations

SER, THR, TYR

hydroxyl group and be phosphorlyated in the presence of proteins

can turn on an off enzymes or participate in signal transduction

two CYS residues can interact to make a disulfide bond strenghtening the structure overall

oxidation reaction

can be N or O linked to the amide group of an ASN (N linked) or the hydroxyl of a SER or THR (O linked)

can attach to oligosacchrides and glycoproteins

important in cell surface recognition, antigens, extracellular matrix and mucins

dependent on glycocidic bond

protective glycoproteins in the digestive tract

precursor for synthesis of catecholamines including dopamine, epinepherine, and norepinephrine

function as neurotrasmitters in the brain or as hormone regulators of carbs and lipid metabolism

the first three are common to almost all proteins

1: primary

2: secondary

3: tertiary

4: quaternary: only applies to proteins with more than one polypeptide chain

the sequence of amino acids

this sequence is defined by a gene

have distinctive begining and end sequences that cannot be reversed and still perform the same function in biology it starts with the amine and ends with the COOH

alpha helix

beta sheet

commonly involve hydrogen bonding of polar peptide bonds

secondary structure

possible because peptide bonds are polar

the oxygen has a negative charge that can H+ bond with the partial positive of the amide hydrogen on a nearby pepride bond

this makes a helix where the R groups are facing outwards from the core of the chains

because R groups are rather close a stretch of amino acids with bulky or charged R groups of the same polarity can interfere with formation

proline is too rigid for the alpha helix and causes kinks

secondary structure

possible because of the polar peptide bond

H+ bonds are created by strings of peptides that fold back on eachother

not coiled tight

hydrogen bonds are perpendicular to the peptide bonds in the backbone

final three dimensional shape of a single polypeptide

R group of the amino acids interact to stabilize the structure

there are 4 main interactions

disulfide bonds

hydrophobic interactions

hydrogen bonds

ionic bonds

disulfide bonds are made by oxidation between two cysteine residues in a chain

this covalent bond adds lots of stability to the protein

only covalent bond in proteins outside the primary sequence

the partial positive on hydrogen bound to O or N can bind to negative charges or partial negatives on other atoms like O from a carboxyl or the carbonyl O in a peptide bond

H can also bind with surrounding water

only when there is more than one polypeptide chain

interactions between chains include hydrophobic, hydrogen bonds, and ionic bonds

ex: hemoglobin has 4 polypeptides; 2 alpha chains and two beta chains

Arginine Arg R

Histidine His H

Lysine Lys K

Serine Ser S

Threonine Thr T

Asparagine Asn N

Glutamine Glu Q

Tyrosine Tyr Y

Cysteine Cys C

alanine Ala A

Valine Val V

isoleucine Ile I

Leucine Leu L

Methionine Met M

Phenylalanine Phe F

Tryptophan Trp W

Glycine Gly G

Proline Pro P

tyrosine

(what is it the precursor to?)