Biological Chemistry Topics                                                                                  

Peptides

Biomolecules and Water

Water can function as either an acid (proton donor) or a base (proton acceptor):

H2O     H+   +   OH-       or       2H2O     H3O+   +   OH-

The ionization of pure water can be expressed as an equilibrium constant:

Keq   =   [H+] [OH-]   =   1.8 x 10^-16 @ 25°C
                 [H2O]

Since the concentration of water is 55.5 M:

  [H+] [OH-]   =   1 x 10 ^-14 M^2

  [H+]   =   1 x 10 ^-7 M     and     [OH-]   =   1 x 10 ^-7 M

The pH scale is a way of expressing the hydronium (H+) concentration:

pH   =   -log[H+]

Since the pH scale is logarithmic, a change of one pH unit means a ten-fold change in the concentration of hydronium.

Weak acids and bases have acid dissociation constants:

HA    H+   +   A-       or       H2O   +   B    OH-  +   HB+

Ka   =   [H+] [A-]       or       Kb   =   [HB+]
              [HA]                               [B][H+]

Dissociation depends on pH. The dissociation constants can be expressed as:

pKa   =   -log Ka       or       pKb   =   -log Kb

which relates dissociation of H+ and OH- with pH. The pKa of a weak acid is the pH at which 50% of the H+ are dissociated.

Titration curves reveal the pKa for weak acids. When the acid is titrated with a strong base of known concentration, the pKa is the midpoint of the titration. The buffering capacity of an acid-base pair is about one pH unit above and below the pKa. The Henderson-Hasselbach equation relates pH, pKa, and acid-base (buffer) concentration:

pH   =   pKa + log [A-]
                          [HA]

Biological systems relay on constant pH, usually around 7. This is achieved by biological buffers: weak acid-base conjugate pairs with pKa near 7.0.

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Advance Topics: Distribution/Excretion (Medical Pharmacology)

Characteristics of Amino Acids

Amino acids are monomers of polypeptides and proteins with the same basic structure:

There are 20 standard amino acids used as building blocks of proteins. At physiological pH, the amino group gains a proton, while the carboxy group looses a proton. Under such conditions they exists as zwitterions, i.e. with one positively charged group and one negatively charged group.

All standard amino acids (except glycine) have a chiral a carbon, i.e. the first carbon in the chain has  four different groups around it. Chiral amino acids can exist as stereoisomers (same molecular formula, different spatial configuration). Amino acids which are mirror images of each other (enantiomers) are designated D (amino group on the right side) and L (amino group on the left side). All chiral standard amino acids occur naturally only in the L configuration.

            L- amino acid                     D-amino acid

The hydrophilicity of and amino acid is an important determinant of where it will be in a folded protein. There are five highly hydrophobic amino acids:

There are seven highly hydrophilic amino acids:

Important molecules are derived from amino acids, for example epinephrine is derived from tyrosine. Some amino acids are chemically modified after they are incorporated into polypeptides. For example, proline in collagen is oxidized to hydroxyproline.

Each standard amino has a 3 letter abbreviation and a one letter symbol:

Click on the names of the amino acids in the table above to study each one individually (may not be completed yet).

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Advance Topics: Amino Acids (Biochemistry)

Ionization of Amino Acids

Amino acids have up to three ionizable functional groups:

• carbonyl (pKa1 = 1.8 - 2.4, average = 2)
  COOH     COO-   +   H+ 
  
  
• amino (pKa2 = 8.8 - 10.7, average 6)
  NH3+     NH2   +   H+ 
  
  
• side chain (pKa3 = 3.65 - 12.48)

Seven standard amino acids have ionizable side chains:

The pH at which the net charge of an amino acid is zero is known as the isoelectric point or pI. For an amino acid without an ionizable side chain, the pI is the arithmetic mean of the pKa's for the carboxyl and amino groups.

pI = (pKa1 + pKa2) / 2

For an amino acid with an ionizable side chain, the pI is the arithmetic mean of the two pKa's between which lie the zero net charge of the amino acid.

Amino acids exist in their ionized form in the stomach (pH ~ 3) and will not be absorbed there. In the intestine, (pH ~ 8) amino acids are only partially ionized, thus available for absorption. 

In addition to the ionizable amino acids, eight amino acids have polar but uncharged side chains:

Three amino acids have positively charged (basic) side chains:

Two amino acids have negatively charged (acid) side chains:

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Advance Topics: Distribution/Excretion (Medical Pharmacology)

The Peptide Bond

Peptide bonds covalently link amino acids in a peptide chain. They are formed by linking the alpha carbon of one residue with the alpha amino of another via condensation reaction resulting in the release of water.

A peptide chain has an N-terminus and a C-terminus which retain the usual charges. The groups involved in the peptide bond carry no ionic charge but remain partially polar. There is electron delocalization (closer to the oxygen atom) and a partial C-N double bond which prevents free rotation. As a result, atoms involved in the peptide bond lie on  the same plane. 

<draw>

Since the peptide bond cannot rotate, it can only have two conformations: cis and trans.

<draw>

Interference between the side chains attached to the alpha carbons make the cis conformation less favorable than the extended trans conformation. Consequently, most peptide bonds in proteins are trans, except or bonds involving the amide nitrogen of proline, for which the cis conformation creates only slightly more interference than trans.

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Peptide Bond Configuration

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Peptides and Proteins

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Types of Proteins

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Continue to "Proteins" or take a test: [T1] [T2] [T3].

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