The amino acids, peptide bonds, and the primary structure of proteins Chem 333 week #1 9/10/01 -...
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Transcript of The amino acids, peptide bonds, and the primary structure of proteins Chem 333 week #1 9/10/01 -...
![Page 1: The amino acids, peptide bonds, and the primary structure of proteins Chem 333 week #1 9/10/01 - 9/14/01.](https://reader035.fdocuments.in/reader035/viewer/2022062407/56649d395503460f94a130c8/html5/thumbnails/1.jpg)
The amino acids, peptide bonds, and the primary structure of
proteins
Chem 333 week #1
9/10/01 - 9/14/01
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Protein structure is often discussed in terms of a hierarchy
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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.
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Two enatiomers possible for most amino acids
L-form found almost exclusively in naturally occurring proteins
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The nonpolar amino acids
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The charged amino acids
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The polar amino acids
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Glycine is pretty unique
• Smallest side chain
• No chiral center
• Neither very polar or nonpolar
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Polarity can be hard to quantify
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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
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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
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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
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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
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Henderson-Hasselbach equation relates pKa, pH, and [A-]/[HA]
pH=pKa +logA−
[ ]HA[ ]
⎛
⎝ ⎜ ⎜
⎞
⎠ ⎟ ⎟
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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
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pKa’s can vary depending on environment
• Effect of solvent environment.
• Effect of specific local interactions.
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Amino acids join together by forming peptide bonds
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Proteins are chains of these peptide units (polypeptides)
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Two backbone torsion angles : phi (and psi ()
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Possible and angles are given in a Ramachandran plot
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Cysteines can form disulfide bonds
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Proteins are synthesized in vivo based on information encoded in genes
DNA--->RNA-->Protein
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RNA is synthesized from a DNA template
Chromosomal DNA
Nascent RNA molecules
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Protein synthesis occurs at ribosomes
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The Genetic code
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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
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Preproinsulin is cleaved after translation to give insulin
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Phosphorylation can modulate protein function
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Proteins can be glycosylated at either Asn (N-linked) or Ser/Thr (O-linked)