amino acids, proteins and DNA

H H2N-C-COOH R • chiral C • 20 naturally occurring

because they have the f groups of amine (base) and carboxylic acid, they have both basic and acidic properties

low pH so high acidity so amine will be protonated. because high [H+] so more likely to act as proton acceptor NH2 —> NH3+ already high [H+] so acid less likely to deprotonate. links to le chatelier; the deprotonation is energetically unfavourable !!! also side groups

c acid is deprotonated COOH –> COO- low [H+] and high [OH-] so H+ is donated to base, OH-, forming water !!! also side groups

zwitter ion structure - name for when formal charge separation but overall electrically neutral molecule. so if side groups also give charges, not zwitterion acid is deprotonated and amine group is protonated !!! also side groups

• has a formal charge separation • H+ from c.acid protonates amine • overall neutral molecule

the no charge form of amino acid never occurs because COOH acts as acid and NH3 acts as base so they are weak buffers because if H+ OR OH- is added: +NH3[]COO- + HCl –> Cl- NH3+[]COOH - the chloride ion forms ionic bond with the nh3+ and the h+ protonated the carboxylate ion (conjugate base) +NH3[]COO- + NaOH —> NH2[]COO-Na+ +H2O - the Na+ forms ionic bond withcarboxylate ion and nh3 releases a proton (conjugate acid) the [] in the middle is the bit of the amino acid unimportant

• there are strong ionic attractions between z. ions • so very strong electrostatic forces of attraction. NOT imf • so solid other molecules of similar Mr would be liquid

will always have suffix of oic acid (unless main chain has 2 c acids, then dioic acid) because priority count longest chain length which C is amine group on relative to C1, the one in the c acid f group don’t forget side groups and any f groups in R group

chiral C in all but one amino acid (glycine because r group is a H) so could exist as two enantiomers however in nature only one enantiomer is presented !! the left handed thing that silly ps was saying!

HAS AN AMINE GROUP SO CAN - be protonated (acid base) - react with acyl chlorides or acid anhydrides to form n sub (2ndary) amides . nucleophilic addition elimination - n sub with h alkanes. amines are nucleophiles HAS A C ACID GROUP SO CAN - be deprotonated (acid base) - esterification with alcohols

two amino acids joined together in a condensation reaction to form one molecule. c acid OH and H from NH2 are removed, which forms the water (small molecule) released. several amino acids joined together into a condensation polymer (which is the polypeptide). water as other product. for n monomers, 2n-1 waters formed (?)

condensation reactions of amino acids reacting with water, hydrolysis. conditions 4M HCl and cook. acts as catalyst. forms the amino acids that was forming the dipeptide. they aren’t in no charge form, never are; they will be nh3+ because conc HCl (acidic, low pH)

unless its the same amino acid, there are two different options of dipeptides could form. because depends on, say for amino acid 1, whether its NH2 group or COO group reacts. shortcut for it: switch r groups

because amine (n in the amine group) is a nucleophile so attracted to delta +ve charge on C. not the OH in COOH, because although they do react with alcohols (lone pair on O; is a nucleophile) the COOH dissociates int COO- and then the negative charge is delocalised, making it more stable (like a benzene ring). so won’t do mechanism, because won’t disrupt delocalisation by doing addition

amide functional group CONH

• sequences of amino acids joined by peptide links • condensation polymers of amino acids • naturally occurring polymers • large complicated molecules, described by their structure

sequence of amino acids which are held together by covalent amide bonds

h bonding within an amino acid sequence (polypeptide) makes it non linear there is coiling into alpha helices and beta pleated sheets - a: more common. 3d arrangement - b: when there are antiparallel sections and h bonding between them - the N-H on one and the C=O on another. the delta +ve H and the delta -ve O

3D shape due to coiling and folding. H bonding, ionic interactions and S-S bridges between R groups (rather than the atoms in CONH for 2ndary) disulphide bridges form when the SH (thiol) R group in cysteine get close enough. the Ss are oxidised, losing e- and H+ S-S bridges stabilise structure

temp or pH. these affect h bonding, ionic bonding and the formation of disulphide bridges wider: S-S bridges only formed in ER not cytoplasm because needs oxidative envt and cytoplasm is reductive. so no ss bridges formed in cytoplasm, thiol groups remain in reduced form. good for keeping protein structure

• proteins • biological catalysts; can increase rate by a million or even billion trillion times ?! • have an active site wherein the Ea is much much lower. active site attracts substrate to it • can be inhibited by drugs • forms e-s complex then e-product complex then product is released • stereospecific

they are made of amino acids and therefore have chiral centres. which makes their active sites stereospecific, they only work with one enantiomer of substrate recall that enantiomers have the same chemical properties except with plane polarised light and with other enantiomeric molecules

hollow in the globular structure substrate binds with side chains through various interactions: VdW, H bonding, D-D, ionic interactions interaction needs to be strong enough that substrate is held for long enough so enzyme-catalysed reaction occurs, but weak enough for product to be released