proteins

amino acid

building block of protein

amino acid structure

• a-carbon

• h atom

• carboxyl group (COO-)

• amino group (NH3)

• R group

amino acid forms

exist as 2 stereoisomers

d- and l- amino acids

l amino acids used in protein synthesis

amino acid function

depends on the r groups of the aa

• polar, uncharged

• non polar, uncharged

• charged amino acids

polar, uncharged amino acids

• R groups contain NH2 ( amide) , SH (sulfhyde ) , OH (hydroxyl)

• r groups would be on the inside, hiding away from water

nonpolar, uncharged amino acids

hydrocarbon chains may have N or S atoms

• r groups would be on the inside, hiding away from water

charged amino acids

contain a literal charge

• contain negatively charged acids (eg COO-)

• contain positively charged bases (eg NH3+)

proteins structure ( simple description)

made of amino acids + peptide bonds

• 2 proteins = dimer

• 3 = trimer

• 4 =tetramer

primary structure

linear sequence of amino acids joined by covalent peptide bonds

secondary structure

a- helix, beta sheet or random coik

with peptide bonds + hydrogen bonds

tertiary structure

3d folding of a single polypetide chain

with peptide bonds, disulphide, bonds, ionic bonds, hydrogen bonds, vanderwaals interactions, hydrophobic interactions

• stablises the overall shape

quaternary structure

the formation of more than just one polypeptide

all the bonds = tertiary structure

peptide bonds

formed by condensation reaction

2 H FROM NH3+

O from carboxyl

covalent bond

hydrogen bonds

donors ( eg amine or hydroxyl of aa)

have H atom linked to a more electronegative atom of an acceptor ( eg COO or SH)

weak bond w -5kcal energy

disulphide bonds

formed between an oxidation reaction of cysteine molecules

S-S

very strong, form of covalent bonding

ionic bonds

weak in (aq)

NH3+COO-

low/ high ph affects ionic bonds

vanderwaals forces

exist between non polar

typically weak

hydrophobic interactions

exist between hydrophobic molecules far from water

stronger bonds

ph effect on proteins

ph affects proteins by chnaging the protonation state of the charged residues

neutral state of protein

• uncharged

• isoelectric point or pI

acid

• low pH

• increase in H+

• NH3+ part gets more H+

base

• high pH

• decrease H+

• NH2, negative part

which bonds would be effected by ph

• ionic bonds

• hydrogen bonds

isoelectric point

ph at which proteins r at zero charge

• positive and negative charges are balances

• dependent on the r groups

what does the pi also affect

it affects the solubility

• proteins interact w each other rather than water

• might pecipitate

• where solubility is lowest

oblique

angled - external oblique