# Lecture 3: Amino Acids and Peptide Bonds
## Biochemistry
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## Learning Objectives
By the end of this lecture, students will be able to:
1. Draw the general structure of an amino acid and identify the alpha-carbon, amino group, carboxyl group, and R group
2. Classify the 20 standard amino acids by their side chain properties
3. Explain stereoisomerism in amino acids and why L-amino acids predominate in biology
4. Predict the ionization state of amino acids at different pH values
5. Describe the peptide bond and its properties
6. Identify non-standard and modified amino acids of biological importance
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## Lecture Content
### I. General Structure of Amino Acids
All 20 standard amino acids share a common backbone structure consisting of a central alpha-carbon bonded to four groups: an amino group (which is protonated to -NH3+ at physiological pH), a carboxyl group (which is deprotonated to -COO- at physiological pH), a hydrogen atom, and a variable R group (side chain) that defines each amino acid's unique identity. At physiological pH of approximately 7.4, amino acids exist as **zwitterions** in which the amino group carries a positive charge and the carboxyl group carries a negative charge. The net charge of the amino acid at any given pH depends on the nature of the R group.
### II. Stereochemistry of Amino Acids
The alpha-carbon is a chiral center in all amino acids except glycine, where the R group is simply a hydrogen atom. Two possible enantiomers exist, designated L and D based on their Fischer projection relative to L- and D-glyceraldehyde. **L-amino acids** are used almost exclusively in proteins, while D-amino acids appear in some bacterial cell walls and certain antibiotics. Enantiomers rotate plane-polarized light in opposite directions, receiving (+) or (-) designations for dextrorotatory or levorotatory rotation, but it is important to note that the L/D designation does not predict the direction of optical rotation.
### III. Classification of the 20 Standard Amino Acids
#### Nonpolar, Aliphatic R Groups
**Glycine (Gly, G)** is the smallest amino acid with R = H, giving it exceptional flexibility and the ability to fit into tight spaces within protein structures. **Alanine (Ala, A)** has a simple methyl group as its side chain. **Valine (Val, V)**, **Leucine (Leu, L)**, and **Isoleucine (Ile, I)** are branched-chain amino acids with hydrophobic isopropyl, isobutyl, and sec-butyl side chains, respectively. Isoleucine is notable for having two chiral centers. **Proline (Pro, P)** is unique because its cyclic side chain bonds to both the alpha-carbon and the amino group, making it technically an imino acid that introduces kinks in polypeptide chains. **Methionine (Met, M)** contains a thioether sulfur and often serves as the initiating amino acid in protein synthesis.
#### Aromatic R Groups
**Phenylalanine (Phe, F)** has a hydrophobic benzyl group and absorbs UV light at 257 nm. **Tyrosine (Tyr, Y)** carries a hydroxylated phenyl ring that can form hydrogen bonds, absorbs UV at 274 nm, and can be phosphorylated in cell signaling. **Tryptophan (Trp, W)** is the largest amino acid, featuring an indole ring system that absorbs UV light strongly at 280 nm; it is relatively rare in proteins.
#### Polar, Uncharged R Groups
**Serine (Ser, S)** and **Threonine (Thr, T)** both carry hydroxyl groups that can be phosphorylated; threonine also has two chiral centers. **Cysteine (Cys, C)** contains a thiol/sulfhydryl group with a pKa of approximately 8.3 and can form disulfide bonds with another cysteine to create cystine. **Asparagine (Asn, N)** is the amide of aspartate and is often the site of N-linked glycosylation. **Glutamine (Gln, Q)** is the amide of glutamate and serves as an important nitrogen carrier in metabolism.
#### Positively Charged R Groups (at pH 7.4)
**Lysine (Lys, K)** carries a primary amine with a pKa of approximately 10.5 and can be acetylated or methylated, particularly in histone modifications. **Arginine (Arg, R)** has a guanidinium group with a pKa of approximately 12.5, meaning it is almost always protonated at physiological pH. **Histidine (His, H)** contains an imidazole ring with a pKa of approximately 6.0, allowing it to be either protonated or unprotonated at physiological pH, which makes it particularly important in enzyme catalysis and buffering.
#### Negatively Charged R Groups (at pH 7.4)
**Aspartate (Asp, D)** has a carboxylate side chain with a pKa of approximately 3.65. **Glutamate (Glu, E)** also has a carboxylate side chain with a pKa of approximately 4.25 and serves as the major excitatory neurotransmitter in the brain.
A comprehensive table/chart of all 20 standard amino acids organized by side chain properties. Each amino acid is shown as its chemical structure at physiological pH with the side chain highlighted in color: blue for positively charged, red for negatively charged, green for polar uncharged, yellow for nonpolar aliphatic, and purple for aromatic. Three-letter and one-letter codes are listed beside each structure. A legend indicates the color coding for each category.
### IV. Ionization of Amino Acids
Amino acids have at least two ionizable groups: the alpha-amino group (pKa approximately 9.0-9.5) and the alpha-carboxyl group (pKa approximately 2.0-2.5). Some amino acids have ionizable R groups that contribute a third pKa. The **isoelectric point (pI)** is the pH at which the amino acid has no net charge. For amino acids without an ionizable R group, the pI is calculated as the average of pKa1 and pKa2. For amino acids with an acidic R group, the pI is the average of the two lowest pKa values, and for those with a basic R group, the pI is the average of the two highest pKa values.
At a pH below the pI, the amino acid carries a net positive charge; at a pH above the pI, it carries a net negative charge; and at a pH equal to the pI, the amino acid has zero net charge and the zwitterion population is maximized.
A titration curve for a diprotic amino acid (such as alanine) and a triprotic amino acid (such as histidine) shown side by side. Panel A: Alanine titration curve showing two buffering regions at pKa1 (~2.3) and pKa2 (~9.7), with the isoelectric point labeled between them. The predominant ionic species is drawn at each region of the curve. Panel B: Histidine titration curve showing three buffering regions at pKa1 (~1.8), pKaR (~6.0), and pKa2 (~9.2), with the pI calculated as the average of pKaR and pKa2. The structure of histidine is drawn at each ionization state.
### V. The Peptide Bond
Amino acids are linked by **peptide bonds** (amide bonds), which are formed by a condensation reaction between the alpha-carboxyl group of one amino acid and the alpha-amino group of the next, releasing one molecule of water. This reaction is catalyzed by the ribosome during translation.
The peptide bond has several important properties. It exhibits **partial double bond character** due to resonance between the C=O and C-N bonds, with the lone pair on nitrogen delocalizing into the carbonyl. This makes the C-N bond shorter than a typical single bond (1.33 Angstroms versus 1.49 Angstroms). The six atoms of the peptide group (Calpha, C, O, N, H, Calpha) lie in a **plane**, and the **trans configuration** is strongly favored, occurring in more than 99.9% of peptide bonds. The exception is X-Pro bonds, which can adopt the cis configuration approximately 5-10% of the time due to proline's cyclic structure. Although the peptide bond itself **cannot rotate freely**, rotation is possible around the phi angle (N-Calpha bond) and the psi angle (Calpha-C bond), and these angles define the backbone conformation.
### VI. Peptides and the Polypeptide Chain
A dipeptide consists of two amino acids linked by one peptide bond, a tripeptide has three amino acids and two peptide bonds, an oligopeptide typically contains fewer than 20 residues, and a polypeptide has more than 20. By convention, peptides are written from the N-terminus (free amino group) to the C-terminus (free carboxyl group), which corresponds to the direction of synthesis.
Several biologically important peptides deserve mention. Glutathione (gamma-Glu-Cys-Gly) is a tripeptide antioxidant that contains an unusual gamma-peptide bond. Insulin, with 51 amino acids in two chains linked by disulfide bonds, regulates glucose metabolism. Oxytocin is a 9-amino acid peptide made cyclic by a disulfide bond.
### VII. Non-Standard and Modified Amino Acids
Beyond the standard 20, some additional amino acids are found in proteins. **Selenocysteine (Sec, U)**, considered the 21st amino acid, contains selenium in place of sulfur and is encoded by the UGA codon in conjunction with a specific mRNA structure called the SECIS element. **Pyrrolysine (Pyl, O)**, the 22nd amino acid, is found in some archaea and is encoded by the UAG codon.
Post-translational modifications greatly expand the chemical repertoire of proteins. **Phosphorylation** of serine, threonine, and tyrosine residues regulates enzyme activity and signaling. **Hydroxylation** of proline and lysine in collagen requires vitamin C, and its deficiency leads to scurvy. **Carboxylation** of glutamate residues in clotting factors produces gamma-carboxyglutamate and requires vitamin K. **Methylation** and **acetylation** of lysine and arginine residues in histones regulate gene expression epigenetically. **Glycosylation** can be N-linked (on asparagine) or O-linked (on serine or threonine). **Ubiquitination** of lysine residues tags proteins for degradation by the proteasome.
A diagram showing common post-translational modifications of amino acids. Each modification is illustrated with a before-and-after chemical structure: phosphorylation of serine (by a kinase, with ATP), hydroxylation of proline (by prolyl hydroxylase, requiring vitamin C and Fe2+), gamma-carboxylation of glutamate (requiring vitamin K), and acetylation of lysine. Arrows indicate the enzyme or cofactor required for each modification. Clinical consequences of deficiency are noted (scurvy for hydroxylation, bleeding disorders for carboxylation).
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