Proteins and enzymes

proteins roles (6)

structural support

communication w env

building other molecules

trasnport across membrane

catalysis of chemical reactions (enzymes)

signalling

AA structure, central A carbon attached to

carboxyl

amino group

hydrogen

R group

Body pH

7.4

at body pH, amino group (-NH2) grains

H+ becomes -NH3+

at body pH, carboxyl group (COOH) loses

H+ becomes COO-

So amino acids mostly exist as

NH3+ and COO-

r gourd gives amino acids

specific properties

4 types of R groups

hydrophobic

polar

charged

special

hydrophobic R groups dont interact w

water, usually non polar

hydrophobic R groups are

buries inside protein

hydrophobic R groups interactions

van der Waals

polar R groups have … sharing

unequal sharing of electrons

polar R groups have .. charge

partial (+) (-)

polar R groups found

outside, facing water

charged R groups on

outside folded proteins

charged R groups can form

ionic interaction with other charged molecule

basic R groups gains H+ —>

(+) charge

acidic R group loses H+ —>

(-) charge

special AA (3)

glycine

proline

cysteine

glycine s R groups is

hydrogen

glycine is

small, non polar, high flexibility

prolines r group linked back to

amino group —> restrict rotations, creates kink/ bend

peptide bonds are … bonds

covalent

peptide bonds between

carboxyl and amino gourd of 2 AA

peptide bond is a … reaction

dehydration

n terminus

free amino group

C terminus

free carboxyl group

primary structure

Amino acid sequence

primary structure doens’t tell u

how protein folds or what it would look like

seoncdary structure is the

local folding of backbone

seoncdary structure stabilized by

hydrogen bonds between backbone groups

2 types of secondary structure

a helix, B sheet

a helix is a

right handed coil

a helix has

2.6 Amino acids per turn

a helix stabilized by backbone hydrogen bonds —> carboxyl

groups of one aa hydrogen bodes with amide group of the AA 4 positions ahead

B sheet, peptide folds

back and forth, forms pleated sheet

b sheet stabilized by backbone hydrogen bonds between

neighbouring strands

in B sheet, R groups project

above and below sheet

parallel B sheet

neighbouring strands run in same direction, both strands

antiparallel B sheet

neighbouring strands run in opposite direction, strand 1 N—> C, strands 2 C—>N

tertiary structure is the

overall 3D shape of 1 polypeptide

tertiary structure mostly involves

R gourds interacting

tertiary structure important reactions (5)

hydrophobic effect

hydrogen bond

ionic interaction

van der waals

desulfide bonds

quaternary structure is

2+ polypeptide subunits tgth

each quaternary structure has

its own tertiary structure

quaternary structure subunits are either

idetical, different

not all proteins have quaternary structure, if made of 1 polypeptide, only

has primary to tertiary

primary bonds

peptide bond

secondary bonds

backbone h bonds

tertiary bonds

R group interactions : hydrophobic effect, hydrogen bonds, ionic interactions, van der waals, disulphide bonds

quaternary bonds

interaction between subunits

unfolded proteins can exist in

many possible arrangements

folded proteins have only

1 specific stable 3D conformation

most of protein stability comes from

many weak interactions added tgth

disulphide bonds add a

stronger covalent contribution

overall protein stability depends on

free energy difference between unfolded and folded states

a more stable protein has a more

favourable folded state

hydrophobic effect in protein folding 1

hydrophobic R groups exposed to water make water more organized around them

hydrophobic effect in protein folding 2

when they get buried inside —> less hydrophobic surface exposed oto water

hydrophobic effect in protein folding 3

water becomes less organized —> contributes to a more favorable folded state

change of 1 Amino acid can

change protein function

replacing hydrophobic interior with a charged one

charged R group would be buried inside (cant interact w surroundings)

hydrophobic and van der walls that held core tgth are lost

charged r group doesn’t like non polar env —> may disrupt fold/pull toward water

folded state becomes less stable, shape may change, function can be affected