Amino acids -> Peptide -> Protein
8 Hydrophobic amino acids
Hydrophobic effect: important for protein folding and ligand binding
Hydrophobic effect: maximizing contact with one another -> squeezing out the cage of water that were surrounding the both -> got rid of some waters, going to a HIGHER entropy situation
9 Hydrophilic amino acids
1.Got charge (basic, acidic) 2. Polar group (OH, NH2) (partial charge) (electronegative O and N)
H-bond not only in water, but also in OH group or nitrogen (h-bond donor)
Lots of interactions between polar compound and polar compound, or polar compound and water -> important in basic amino acids
All acidic residues and basic residues can be protonated
pKa: shorthand of showing protonation and deprotonation equilibrium (= -logKa)
If pKa = 4: that compound will be exactly 50% protonated and 50% deprotonated at pH = 4
All side chains will be negatively charged at pH = 7
Histidine is the weakest base among the three basic amino acids
Useful in enzyme catalytic site: to receive and donate protons
Special amino acids
without a sidechain,It takes up so little space that it allows tight turns in a folded polypeptide.
It is an IMINO acid, because the sidechain curls round to rejoin the main chain at the alpha carbon.
it's reactive –SH group offers a lot of chemistry and also the possibility of covalent disulphide links, especially in proteins that have to survive in a challenging environment – e.g. digestive enzymes.
Solubility: Amino acids are soluble in water, acids, alkalies, but sparingly soluble in organic solvents.
Color: Amino acids are colorless, white solids.
State: Amino acids are solid crystalline compounds.
Melting points: Amino acids have high melting points. Due to presence of basic and acidic groups in the same molecule, they may be regarded as salts and hence, most of them either possess higher melting point or melt with decomposition.
alpha helix, beta sheet
each clump is called a domain
These proteins are referred to as monomeric (1) or oligomeric (several), and more specifically in the case of haemoglobin, tetrameric (4).
Soluble proteins are often able to refold even in vitro.