proteins Flashcards
structure of amino acid
carboxyl, carbon then amine
- all amino acids except glycine are chiral therefore optically active
almost all amino acids are __ enantioners
L
fisher projection for aino acids
acid base characteristics of amino acids
- have acidic and basic functionality, amphoteric (act as acid or base depending on env)
- have 2 protons that can dissociate, 2 Ka/Kb values
- in sol can be zwitterionic (pos pos an neg charge)
-
what is the isoelectic point
- pH lies between pKa1 and pKa2
- aa is neutral and exists as a zwitterion
explain the titration of amino acids
- amino acid acts as a buffer so pH changes slowly upon addition of base
- @pKa1 +NH3CH2COOH = +NH3CH2COO-
- when more base added all COOH deprot, mol is now electrically neutral (zwitterion) and pH =pI
- pKa2 reached when past pI
- after pKa2 mol mostly NH2CH2COO-
___ moles of base are requires to deprotonate 1 mole of mot amino acids
2 mol
one for COOH and one for NH3+
where is the buffering capacity of amino acids greatest?
near Ka1 and Ka2
- at isoelectric point bufferin capacity is minimal
how to determine how much prot and deprot aa you have
pH = pKa + log (depot/prot)
ex: 3.3 = 2.3 + log (deprot/prot)
1 = log(deprot/prot)
10 = deprot/prot
*10x as many zwitterions as fully protonated form
non polar amino acids
alanine, valine, leucine, isoleucine, proline, phenylalanine, glycine and tryptophan
polar amino acids
methionine, serine, threonine, cysteine, tyrosine, asparagine, glutamine
acidic amino acids
- aspartic acid, glutamic acid, aspartate, glutamate
- carry net eng charge at physiological pH
basic amino acids
- carry net pos charge at physiological pH
- arginine, lysine and histidine
study amino acid structures
what are pepties
composed of amino acid subunits
- also called residues
- linked by peptide bonds
2 aa = dipeptide, 3= tripeptide, and many = polypeptide
peptide reactions
- aa joined by peptide (amide) bonds formed via condensation rxn
- can hydrolyse by adding water w/ acid or base
what does trypsin so to peptide linkages? what about chymotrypsin
- certain enzymes digest chain at specific linkage
- trypsin cleaves at COOH end of arg and lys
- chymotrypsin cleaves COOH end oh phenylalanine, tyrosine and tryptophan
peptide properties
- terminal amino acid w/ a free alpha amino group = amino terminal (N terminal)
- other is carboxy (C-terminal)
- have 2 res structues so rotation along C-N bond is resticted
what are proteins
- polypeptides that can range from only a few -> thousands of aa
- are enzymes, hormones, memrbane pores, receptors, elements of ell structure
- have primary, secondary, tertiary and quat structures
describe the primary structure of an amino acid
- seq of amino acids listen from N term -> C term
- other levels depend on this sequence
- can determine primary strucute in lab vai sequencing
what is secondary structure
- local structure of neighbouring amino acids governed mianly by H bond interactions within and between peptide chains
- A helix and B pleated sheet
- most complex prot contain both
describe the alpha helix
- rod-like structure in whih peptide chain coils clockwise about central axis
- helix is stab by intramol h bonding between carbonyl oxygen atoms and amine hydrogen atoms 4 residues away
-
describe the beta pleated sheet
- peptide chains lie alongside eachother in rows
- intra mol h bondinh between carbonyl oxygen atoms on one chian and amine on another
- r groups point above and below
describe tertiary structure
- 3D shapre of the protein determined by hydrophilic and hydrophobic interactions between R groupds and distribution of disulfide bonds
- aa with hydrophobic R groups tend to be found closer together, and face inwards
- hydrophilic aa arrange themselves with T groups interacting with aqueous env
what is the effect of 2 cysteine mol
- can form a disulfide bond, created loop in tertiary structure
what happens when proline is present in chain
- cannot fit into alpha helix, will cause a kink in the chain
what are the 2 major classifications of proteins based on tertiary structure
- fibrous (ex collagen) found in long sheets or strands
- globular (ex myoglobin) spherical in shape
what is quaternary structure
- some proteins contain more than one polypeptide unit
- quat structure refers to the way in which these subunits arrange themselves to yield a functional protien molecule
ex: hemoglobin is composed of 4 polypeptide chains
what are conjugated proteins
- derive part of function from ovaletly attached molecules called prosthetic groups
*at least one portion of thier structure is not made of protein (could be orgnic mol or metal ions)
- many vit are prosthetic groups
- playmajor role in determining the function of proteins
ex: the heme group in myo and hemoglobin
what are proteins that have lipid, carbohydrate and nuceltic acid prosthetic groups refered to as
lipoproteins, glycoproteins and nucleoproteins respectively
what are albumins and globulines
- primry globular in nature and function as carriers or enzymes
what are scleroproteins
- fibrous proteins that act as structural proteins
whar are chromoproteins
proteins bound to pigmented molecules
what are metalloproteins
proteins complexed around a metal ion
explain denaturing proteins
- also called melting
- protein loses 3 structure and revert to a random coil state
- caused by detergent or changes in pH, temp or solute cnoc
- weak intermolecular forced keeping the proteins table and functional are disrupted
- damage usually permanent
*some gentle denaturing agents do not permanently disrupt the protein and remocal may allow protein to renature and therefore regain function
