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Amino acid,Protein structure Cheat Sheet by

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Amino Acids

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
Glycine
without a sidech­ain,It takes up so little space that it allows tight turns in a folded polype­ptide.
Proline
It is an IMINO acid, because the sidechain curls round to rejoin the main chain at the alpha carbon.
Cysteine
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.
 

Amino Acids

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.

Protein Structure

Primary structure
-Ala-G­lu-­Val­-Th­r-A­sp-­Pro­-Gly-
Secondary structure
alpha helix, beta sheet
Tertiary structure
each clump is called a domain
Quaternary structure
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.

Amino Acids

Peptide

 

Protein folding

 

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