the amino acids, peptide bonds, and the primary structure of proteins chem 333 week #1 9/10/01 -...
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The amino acids, peptide bonds, and the primary structure of
proteins
Chem 333 week #1
9/10/01 - 9/14/01
Protein structure is often discussed in terms of a hierarchy
Amino acids are the building blocks of proteins
• Three major parts: carboxyl group, amino group, and side chain.
• Central C atom called alpha carbon.
• Amino acids can differ in their side chains (R).
• The alpha carbon is a chiral center.
Two enatiomers possible for most amino acids
L-form found almost exclusively in naturally occurring proteins
The nonpolar amino acids
The charged amino acids
The polar amino acids
Glycine is pretty unique
• Smallest side chain
• No chiral center
• Neither very polar or nonpolar
Polarity can be hard to quantify
Review: acid-base chemistry
• Acid : Proton (hydrogen ion, H+) donor• Base: Proton (hydrogen ion, H+) acceptor
H Cl O
H
H Cl- O
H
HH+ +
+
Acid
Base Hydronium ion
The reaction when an acid is dissolved in water can written as an equilibrium:
HA (aq) + H2O (l) H3O+ (aq) + A- (aq)
acid base conjugate acid
conjugate base
The acid-base equilibrium is characterized by a constant Ka
HA (aq) + H2O (l) H3O+ (aq) + A- (aq)
Ka =[H3O
+][A−][HA]
=[H+][A−]
[HA]
HA (aq) H+ (aq) + A- (aq)
pKa = -log Ka
Some pKa facts
• The lower the pKa, the stronger the acid (smaller pKa--> larger Ka --> larger [H+])
• Acetic acid has pKa 4.8
– Ka = 10^-4.8 = 1.5 x 10-5
Henderson-Hasselbach equation relates pKa, pH, and [A-]/[HA]
pH=pKa +logA−
[ ]HA[ ]
⎛
⎝ ⎜ ⎜
⎞
⎠ ⎟ ⎟
Applications of the Henderson-Hasselbach Equation
• When pH = pKa, [A-] = [HA]
– Concentrations of protonated and unprotonated forms are equal
• If you know the pH and pKa, you can determine whether an amino acid is charged or uncharged
pKa’s can vary depending on environment
• Effect of solvent environment.
• Effect of specific local interactions.
Amino acids join together by forming peptide bonds
Proteins are chains of these peptide units (polypeptides)
Two backbone torsion angles : phi (and psi ()
Possible and angles are given in a Ramachandran plot
Cysteines can form disulfide bonds
Proteins are synthesized in vivo based on information encoded in genes
DNA--->RNA-->Protein
RNA is synthesized from a DNA template
Chromosomal DNA
Nascent RNA molecules
Protein synthesis occurs at ribosomes
The Genetic code
After translation, some proteins undergo further covalent modification
• Proteolytic processing• Phosphorylation: addition of a phosphate group
(PO43-) to a Ser or Tyr residue.
• Glycosylation: addition of sugar groups to Asn (N-glycosylation) or Ser (O-glycosylation).
• Alteration of chain termini– Removal of N-Met
– Acetylation and amidation
Preproinsulin is cleaved after translation to give insulin
Phosphorylation can modulate protein function
Proteins can be glycosylated at either Asn (N-linked) or Ser/Thr (O-linked)