Protein Functions: catalyze reactions (enzymes) receptors (eg. pain receptors) transport (ions across membranes, oxygen in blood) molecular motors recognition (eg. antibodies) signals (eg. insulin) structural support

Protein structure chains of amino acids 4 levels of structure range of functional groups carb. acids amides amines hydroxyl thiol aromatic rings interact with other proteins: assemblies flexibility, movement (doors, hinges, levers, etc.)

Amino acids: 20 building blocks characterized by R group in nature, S (L) configuration

Notice: glycine is not chiral! Conformationally free Hydrophobic side-chains

Proline: side chain is bonded to main chain amine conformationally restricted - effect on structure

Aromatic planar

Hydroxyl

Thiol

Cysteine thiols can form disulfide linkages important for 3, 4 structure

Positively charged Lys: pKa ~ 10.8 Arg: pKa ~ 12.5 His: pKa ~ 6.0 Depends on environment!

Question: Why is Lys more acidic than Arg? Lys: pKa ~ 10.8 Arg: pKa ~ 12.5

Lys: pKa ~ 10.8 Arg: pKa ~ is stabilized in Arg “happier” with + Arg less like to give up proton Arg less acidic

Acids Amides pKa of acid ~ 4.1 amides not acidic or basic!

AA chain formed via peptide bonds - polypeptide Carbox acid + amine forms amide lose water

amino acids: protein <50 amino acids: peptide (eg. insulin, spider venom) primary structure: a.a. sequence

AA sequence is specific to each protein/peptide Sequence coded by DNA (gene): 3 base ‘codon’ encodes one amino acid, plus start/stop codons. eg: GAC = aspartate

Peptide bonds are planar: 6 atoms in a plane C , C, O, N, H, C 

Source of planarity: N is sp2 barrier to rotation about C-N bond free rotation between C-C , N-C  flexibility/rigidity

Notice: R group on opposite sides

Peptide bonds are trans: If cis, R groups clash

Free rotation, but only some angles possible due to steric clashes - limits possible folding patterns phi psi

Secondary structure: helices

R groups point out right handed/clockwise (alpha) found in proteins (energetically favorable) 3.6 residues per turn H-bonds between main chain O and N 4 aa’s down (next slide)

Ribbon form for depicting helices

Secondary structure: Beta sheet fully extended: parallel, anti-parallel H-bond between main-chain N and O R groups perpendicular

Ribbon depiction of Beta-sheets

hairpin turn

Tertiary structure (myoglobin) (oxygen carrier in muscle heme prosthetic group (contains iron)

Tertiary structure Beta-sheet rich many proteins have both helices and sheets Notice loops (no regular structure, but often still ordered (not random). Often act as doors or flaps

A: space-fill picture of myoglobin; blue = charged yellow - hydrophobic B : cross-section: hydrophilic outside hydrophobic inside When unfolded, most proteins are insoluble in water

Some proteins form distinct domains CD4 cell-surface protein: HIV virus attaches to this

Quaternary structure:  2  2 hemoglobin

F6P aldolase (use Jmol – 1L6W) Notice: Quaternary structure (homodecamer) ‘tails’ tie subunits together Beta barrel (conserved tert. structure motif)

Primary structure determines higher structure, function Classic study with ribonuclease (cuts RNA)

Enzyme loses function when denatured, reduced regains activity when dialized all the info necessary is contained in sequence (originally in DNA sequence!

Primary structure (sequence) is easy to determine: sequence DNA So shouldn’t we be able to predict structure from sequence? Yes, in theory - but haven’t figured out yet! Secondary structure prediction is somewhat accurate

We can predict structure, function by sequence alignment myoglobin: carries oxygen in muscle hemoglobin: carries oxygen in blood structure and function are related: sequences are similar

Protein structure is visualized by x-ray crystallography (Chapter 4) Static picture - but proteins are dynamic! Small peptides can be visualized by NMR - but complex!

Proteins are often post-translationally modified (in eukaryotes) expands repertoire of 20 aa’s eg. phosphorylation often turns proteins ‘on and off’