Properties of amino acids in proteins one of the primary roles of DNA (but far from the only one!!!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated in linear polymers We build ~20,000 different kinds, based on the number of identified genes in the human genome, ranging from small (29 aa) to large (34,000 aa)
Proteins are the workhorses of the cell Enzymes, signaling and transport, and structural support Eukaryotic cell (~10-30 µm) Proteins (~3-5 nm, or more) Trypsin - digests proteins (247 amino acids) Myoglobin - transports oxygen (154 amino acids) Titin - a muscle protein (34,000 amino acids!)
Proteins are made of amino acids Side chain (R group) α carbon Amino group Carboxyl group 3
Amino acids have chirality They are not identical to their mirror image, have two forms L-amino acids D-amino acids -all ribosome-synthesized proteins use L amino acids, most enzymes distinguish between L/D amino acids (D tastes sweet!), etc. - WHY? one hypothesis: circularly polarized radiation favors one enantiomer over the other in comet dust (more L-amino acids than D have been observed in meteorites!)
Diversity of amino acids Side-chains (R groups) give amino acids a wide range of properties humans use typically 20 amino acids, can synthesize many but others are essential (must come from diet) Essential: Phe, Val, Thr, Trp, Ile, Met, Leu, Lys, His Non-essential: Ala, Arg, Asp, Cys, Glu, Gln, Gly, Pro, Ser, Tyr, Asp
Nonpolar amino acids Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) 6
Polar amino acids Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) 7
Charged amino acids Acidic (negatively charged) Basic (positively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) 8
The Proton as an Ion Water dissociates very slightly 2 H2O H3O + + OH - Water Hydronium Hydroxide Correct van der Waals representation
Water is very good conductor: Proton hopping Grotthuss mechanism (proton hopping) The proton has a very high diffusion constant in water (D = 6 x 10-9 m 2 /s ) because it can move along the hydrogen bond connecting two water molecules without the water molecules moving. Hydronium cation Ice has a high electrical conductivity despite the fact that the water molecules may not translate in the solid.
Ionization states AH + B A - + BH + ph = - log10([h3o + ]) ph of pure water is 7 (~7.2 in cells) Ka = [H3O + ] [A - ] / [AH] pka = - log10 Ka ph = pka + log10 ([A - ] / [AH]) Henderson Hasselbalch equation - gives the ratio of protonated to deprotonated molecules as a function of the current ph and the molecule s pka
Ionization states ph = pka + log10 ([A - ] / [AH]) Glu - ph > pka - deprotonated Ionizable amino acids amino acid pka (model) Asp (D) 4.0 Glu (E) 4.4 Arg (R) 12.0 Lys (K) 10.4 His (H) 6.3 Cys (C) 9.5 Tyr (Y) 10.0 ph < pka - protonated Histidine is a special case! Glu
Calculating ionization states Empirical approaches - fast, use well-developed scoring function Ex: PROPKA http://propka.ki.ku.dk/ Poisson-Boltzmann equation solvers Ex: H++ http://biophysics.cs.vt.edu/ Free energy calculations - (relatively) expensive! pka = ph - ΔG/[kTln(10)]
Peptide bond formation -process takes place at the heart of the ribosome in its peptidyl transferase center (PTC) Ribosome (not to scale! more on this later)
Basic protein structure Backbone Side chain Amino acid (Phenylalanine) Polypeptide Surface representation Cartoon representation beta-sheet alpha-helix
From Primary to quaternary structure Primary structure Secondary structure Tertiary structure Quaternary structure α helix Hydrogen bond β pleated sheet β strand Hydrogen bond Transthyretin polypeptide Transthyretin protein forms from interactions along the backbone (contrast with RNA/DNA)
Single Mutation Disease Sickle-cell hemoglobin Normal hemoglobin Primary Structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Secondary and Tertiary Structures β subunit Exposed hydrophobic region β subunit α β α β Quaternary Structure Normal hemoglobin Sickle-cell hemoglobin β α β α Function Molecules do not associate with one another; each carries oxygen. Molecules crystallize into a fiber; capacity to carry oxygen is reduced. Red Blood Cell Shape 10 µm 10 µm 17