Table of Contents
- Introduction: The Central Dogma and the Role of Proteins
- What Are Amino Acids?
- Structural Fundamentals of Amino Acids
- Stereochemistry: L- and D-Amino Acids
- Acid-Base Properties and Ionisation
- The Isoelectric Point (pI)
- Titration Curves
- Classification of Amino Acids by R Group
- Essential, Non-Essential, and Conditional Amino Acids
- Uncommon and Modified Amino Acids
- Peptides and the Peptide Bond
- Properties of Peptides
- Classification of Peptides by Size
- Biologically and Clinically Important Peptides
- Conclusion and Key Takeaways
1. Introduction
The Central Dogma
Before diving into amino acids, it is essential to understand why they matter. The “Central Dogma” of molecular biology, first proposed in 1958 by Francis Crick, describes the flow of genetic information in living systems:
DNA → (Transcription) → RNA → (Translation) → Protein
↑
(DNA Replication)
- DNA replication: DNA is copied to produce more DNA.
- Transcription: DNA is used as a template to produce messenger RNA (mRNA).
- Translation: The mRNA sequence is read by ribosomes to assemble a chain of amino acids, producing a protein.
Proteins, therefore, are the final functional products of genetic information. They are built entirely from amino acids, and their sequence determines everything about their structure and biological activity.
This module focuses on the building blocks themselves: amino acids and peptides.
2. What Are Amino Acids?
Definition
Amino acids are small organic molecules that serve as the monomeric units (building blocks) of proteins. When amino acids are joined together in a chain, each one is called an amino acid residue, connected to its neighbours by a covalent amide bond known as a peptide bond.
Key Facts
- Proteins are polymers of amino acids. A protein may consist of thousands of amino acid residues and can have molecular weights of up to several million Daltons (Da).
- More than 500 amino acids have been found in nature, but only 20 are commonly used to build human proteins. Not all 500+ are constituents of proteins — many serve other biological functions.
- The sequence of amino acids within a protein is absolutely critical: it determines the protein’s three-dimensional structure and, by extension, its biological function.
Names and Abbreviations
All 20 common amino acids have:
- A full trivial (common) name — often derived from the source from which they were first isolated.
- A three-letter abbreviation (e.g., Ala, Gly, Lys).
- A one-letter symbol (e.g., A, G, K).
Some interesting naming histories:
- Asparagine — first isolated from asparagus.
- Glutamate — first isolated from wheat gluten.
- Tyrosine — from Greek tyros, meaning “cheese” (first isolated from cheese).
- Glycine — from Greek glykos, meaning “sweet” (named for its sweet taste).
Table: Three- and One-Letter Codes (partial list)
| Amino Acid | Three-letter code | One-letter code |
|---|---|---|
| Alanine | Ala | A |
| Arginine | Arg | R |
| Asparagine | Asn | N |
| Aspartic acid | Asp | D |
| Asparagine or Aspartic acid | Asx | B |
| Cysteine | Cys | C |
| Glutamine | Gln | Q |
| Glutamic acid | Glu | E |
| Glycine | Gly | G |
| Histidine | His | H |
| Isoleucine | Ile | I |
| Leucine | Leu | L |
| Lysine | Lys | K |
| Methionine | Met | M |
| Phenylalanine | Phe | F |
| Proline | Pro | P |
| Serine | Ser | S |
| Threonine | Thr | T |
| Tryptophan | Trp | W |
| Tyrosine | Tyr | Y |
| Valine | Val | V |
3. Structural Fundamentals
The General Structure of an α-Amino Acid
All 20 standard amino acids share the same basic “backbone” structure. They are α-amino acids, meaning that both the amino group (–NH₂) and the carboxyl group (–COOH) are attached to the same carbon atom, called the α-carbon (Cα).
The four groups bonded to the α-carbon are:
- An amino group (–NH₂, or –NH₃⁺ at physiological pH)
- A carboxyl group (–COOH, or –COO⁻ at physiological pH)
- A hydrogen atom (–H)
- A side chain, designated –R
COO⁻
|
H₃N⁺—Cα
|
R
Key Concept: At physiological pH (~7.4), the amino group is protonated (–NH₃⁺) and the carboxyl group is deprotonated (–COO⁻). Thus, amino acids exist as zwitterions — molecules carrying both a positive and a negative charge simultaneously, with an overall net charge that depends on the R group.
The R Group (Side Chain)
The R group is what makes each of the 20 amino acids unique. It varies in:
- Structure (aliphatic, aromatic, contains sulfur, contains hydroxyl, etc.)
- Size (from a single hydrogen atom in glycine to complex ring structures)
- Charge at physiological pH (positive, negative, or neutral)
- Polarity (hydrophilic or hydrophobic)
These differences in R groups are the primary determinant of amino acid properties and, ultimately, protein structure and function.
Naming the Side Chain Carbons
In an amino acid R group, the carbons are designated with Greek letters proceeding outward from the α-carbon:
α-carbon → β-carbon → γ-carbon → δ-carbon → ε-carbon → ...
For example, in lysine, the terminal amino group (–NH₃⁺) sits on the ε-carbon, making it an ε-amino group.
4. Stereochemistry: L- and D-Amino Acids
Chirality
For all 20 standard amino acids except glycine, the α-carbon is bonded to four different groups. This makes it a chiral centre (also called a stereogenic centre or asymmetric carbon). Molecules with a chiral centre exist in two mirror-image forms called enantiomers, which are non-superimposable on each other.
All molecules with a chiral centre are optically active — they rotate the plane of plane-polarised light. (This is why you will sometimes see amino acids referred to as dextrorotatory ”+” or levorotatory ”–”, though these refer to the direction of light rotation, not the structural configuration.)
Glycine is the only amino acid that is NOT chiral — its R group is simply a hydrogen atom, making two of the four substituents on the α-carbon identical.
The Fischer Convention: L vs D
By Fischer’s convention, the spatial arrangement around the chiral carbon is compared to the reference molecule glyceraldehyde (a three-carbon sugar):
- L-configuration: the amino group (–NH₃⁺) is on the left in the Fischer projection.
- D-configuration: the amino group is on the right in the Fischer projection.
This is analogous to L- and D-glyceraldehyde, where the hydroxyl group is on the left (L) or right (D).
Biological Significance
The amino acid residues in all proteins are exclusively L-stereoisomers.
This is one of the most fundamental rules in biochemistry. D-amino acid residues have been found only in a very few, generally small peptides, including:
- Some peptides of bacterial cell walls (e.g., D-alanine in peptidoglycan).
- Certain peptide antibiotics (e.g., gramicidin).
The reason life uses only L-amino acids is thought to be due to an ancient evolutionary “choice” — once this preference was established, it was reinforced by the machinery of protein synthesis.
5. Acid-Base Properties and Ionisation
Amino Acids Are Amphoteric
Because amino acids contain both an acidic group (–COOH) and a basic group (–NH₂), they are called amphoteric — they can act as either an acid or a base depending on the pH of the solution.
Three Ionisation States
As pH changes, the ionisation state of an amino acid changes:
| pH Range | State | Net Charge |
|---|---|---|
| pH < ~3 | –COOH protonated, –NH₃⁺ protonated | +1 |
| ~3 < pH < ~9 | –COO⁻ deprotonated, –NH₃⁺ still protonated | 0 (zwitterion) |
| pH > ~9 | –COO⁻ deprotonated, –NH₂ deprotonated | –1 |
At physiological pH (~7.4), most amino acids exist in the zwitterionic form:
NH₃⁺
|
H — Cα — COO⁻
|
R
The transition between these states occurs at characteristic pH values called pKa values:
- pKa1 corresponds to the deprotonation of the α-carboxyl group (typically ~2.0–2.5).
- pKa2 corresponds to the deprotonation of the α-amino group (typically ~9.0–10.5).
- pKaR corresponds to the ionisation of the R group side chain (only present in amino acids with ionisable side chains).
6. The Isoelectric Point (pI)
Definition
For every amino acid, there is a specific pH at which it carries no net electrical charge (the molecule is in its zwitterionic form but the positive and negative charges cancel out). This pH is called the isoelectric point (pI).
At the pI:
- The molecule does not migrate in an electric field.
- Solubility is typically at its minimum.
Calculating pI
For a simple amino acid (no ionisable R group), the pI is the average of the two pKa values flanking the neutral species:
pI = (pKa1 + pKa2) / 2
For amino acids with ionisable R groups, the pI is calculated using the two pKa values on either side of the neutral (zero-charge) species:
- For acidic amino acids (e.g., Glu, Asp):
pI = (pKa1 + pKaR) / 2 - For basic amino acids (e.g., Lys, Arg, His):
pI = (pKa2 + pKaR) / 2
Isoelectric Points of the 20 Amino Acids
| Group | Amino Acid | pI |
|---|---|---|
| Non-polar chain | Alanine | 6.02 |
| Valine | 5.97 | |
| Leucine | 5.98 | |
| Isoleucine | 6.02 | |
| Phenylalanine | 5.98 | |
| Tryptophan | 5.88 | |
| Methionine | 5.75 | |
| Proline | 6.10 | |
| Polar chain | Glycine | 5.97 |
| Asparagine | 5.41 | |
| Glutamine | 5.65 | |
| Tyrosine | 5.65 | |
| Cysteine | 5.02 | |
| Serine | 5.68 | |
| Threonine | 6.53 | |
| Charged chain | Lysine | 9.74 |
| Histidine | 7.58 | |
| Arginine | 10.76 | |
| Aspartic acid | 2.87 | |
| Glutamic acid | 3.22 |
Clinical Importance
Differences in pI are exploited to separate amino acids and proteins using techniques such as:
- Isoelectric focusing (electrophoresis in a pH gradient)
- Ion-exchange chromatography
Acidic amino acids (Asp, Glu) have very low pI values because their side chain carboxyl groups ionise and carry negative charge, pulling the pI downward. Basic amino acids (Lys, Arg, His) have high pI values because their positively charged R groups shift the pI upward.
7. Titration Curves
Glycine as the Model: A Diprotic Amino Acid
Amino acids without ionisable R groups behave as diprotic acids (two ionisable protons). The titration curve for glycineillustrates this clearly:
- Starting point (very low pH): Glycine is fully protonated: ⁺H₃N–CH₂–COOH (net charge +1).
- First equivalence region (around pKa1 = 2.34): The carboxyl group loses its proton. At this midpoint, there are equimolar concentrations of proton donor and acceptor — this region is the best buffer around pH 2.34.
- Zwitterion plateau (pH ~5.97 = pI): Glycine has no net charge: ⁺H₃N–CH₂–COO⁻.
- Second equivalence region (around pKa2 = 9.60): The ammonium group loses its proton. At this midpoint, the buffering capacity is maximal around pH 9.60.
- Final state (high pH): Glycine is fully deprotonated: H₂N–CH₂–COO⁻ (net charge –1).
pI for glycine = (2.34 + 9.60) / 2 = 5.97
Glutamate: A Triprotic Acid (Acidic Side Chain)
Glutamate has three ionisable groups (two carboxyl + one amino), so it behaves as a triprotic acid. Its titration curve shows three transitions.
- pKa1 = 2.19 (α-carboxyl group)
- pKaR = 4.25 (γ-carboxyl group in the side chain)
- pKa2 = 9.67 (α-amino group)
pI for glutamate = (pKa1 + pKaR) / 2 = (2.19 + 4.25) / 2 = 3.22
The pI is very low because both acidic groups must be taken into account.
Lysine: A Triprotic Acid (Basic Side Chain)
Lysine also has three ionisable groups: one carboxyl + two amino groups.
- pKa1 = 2.2 (α-carboxyl group)
- pKa2 = 9.0 (α-amino group)
- pKa3 = 10.5 (ε-amino group of the R group)
pI for lysine = (pKa2 + pKa3) / 2 = (9.0 + 10.5) / 2 = 9.75
The pI is high because both amino groups must be protonated (positive) to reach the neutral species.
Histidine: Special Case
Histidine has a pI of 7.58, making it the only common amino acid with a pI near physiological pH (7.4). This means that histidine can switch between charged and uncharged forms at physiological pH — a property that makes it uniquely important in enzyme catalysis, where histidine residues frequently act as proton donors or acceptors.
pKa Reference Table
| Amino Acid | pKa α-COOH | pKa α-NH₃⁺ | pKa R group |
|---|---|---|---|
| Gly | 2.34 | 9.60 | — |
| Ala | 2.34 | 9.69 | — |
| Val | 2.32 | 9.62 | — |
| Leu | 2.36 | 9.68 | — |
| Ile | 2.36 | 9.68 | — |
| Ser | 2.21 | 9.15 | — |
| Thr | 2.63 | 10.43 | — |
| Met | 2.28 | 9.21 | — |
| Phe | 1.83 | 9.13 | — |
| Trp | 2.38 | 9.39 | — |
| Asn | 2.02 | 8.80 | — |
| Gln | 2.17 | 9.13 | — |
| Pro | 1.99 | 10.6 | — |
| Asp | 2.09 | 9.82 | 3.86* |
| Glu | 2.19 | 9.67 | 4.25* |
| His | 1.82 | 9.17 | 6.0* |
| Cys | 1.71 | 10.78 | 8.33* |
| Tyr | 2.20 | 9.11 | 10.07 |
| Lys | 2.18 | 8.95 | 10.53 |
| Arg | 2.17 | 9.04 | 12.48 |
*For these amino acids, the R group ionisation occurs before the α-NH₃⁺ ionisation.
8. Classification of Amino Acids
Amino acids are classified based on the chemical nature of their R groups, primarily considering:
- Polarity (hydrophobic vs hydrophilic)
- Charge at pH 7 (positive, negative, or neutral)
The simplest useful classification divides amino acids into three broad categories: Nonpolar, Neutral polar, and Charged polar.
8.1 Nonpolar (Hydrophobic) Amino Acids
These amino acids have R groups consisting only of carbon and hydrogen, making them water-insoluble (hydrophobic). They tend to cluster in the interior of proteins, away from the aqueous environment, stabilising protein structure through the hydrophobic effect.
Members: Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp), Methionine (Met)
Aliphatic Nonpolar (Gly, Ala, Val, Leu, Ile, Pro, Met)
- Glycine (Gly): Simplest amino acid (R = H). Not chiral. The tiny side chain makes no contribution to hydrophobic interactions. It is found on the surface of many proteins because its flexibility allows folding.
- Alanine, Valine, Leucine, Isoleucine: Progressive increase in side chain size and hydrophobicity (Gly < Ala < Val < Leu ≈ Ile). Their side chains cluster together inside proteins, stabilising protein structure.
- Methionine (Met): One of two sulfur-containing amino acids. Contains a thioether group (–S–CH₃) in its side chain. Slightly nonpolar. Notably, methionine is always the first amino acid incorporated during translation in eukaryotes (the “start” codon AUG codes for Met).
- Proline (Pro): Unique — its side chain forms a ring structure that connects back to the backbone nitrogen, creating an imino group (–NH–) rather than a primary amino group (–NH₂). This rigid pyrrolidine ring (also called a pyrrole ring) severely restricts backbone flexibility and can cause kinks in polypeptide chains. About 6% of proline-containing peptide bonds adopt the cis configuration (particularly in β-turns), unlike the >99.95% trans configuration seen elsewhere.
Aromatic Nonpolar (Phe, Trp)
- Phenylalanine (Phe): Contains a simple benzene ring. Relatively nonpolar; contributes to the hydrophobic effect.
- Tryptophan (Trp): Contains an indole ring (a fused bicyclic system containing a benzene ring and a pyrrole ring). More polar than phenylalanine because of the nitrogen in the ring. Still contributes to the hydrophobic effect.
Note: Tyrosine (Tyr) is sometimes grouped here, but it is more accurately classified as polar due to its hydroxyl group (see below).
8.2 Polar, Uncharged Amino Acids (Neutral Polar)
These R groups contain electronegative atoms (O, N, S) that can form hydrogen bonds with water, making these amino acids more hydrophilic. However, at physiological pH 7, the R groups carry no formal charge.
Members: Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), Glutamine (Gln), Tyrosine (Tyr)
Alcohols (Ser, Thr)
- Serine (Ser): Contains a hydroxyl group (–CH₂OH) on the β-carbon. Hydroxyl groups can form hydrogen bonds and are important sites for phosphorylation (a major post-translational modification involved in cell signalling).
- Threonine (Thr): Also contains a hydroxyl group (–CHOH–CH₃). Like serine, it is a common phosphorylation site.
Thiol (Cys)
- Cysteine (Cys): Contains a thiol group (–CH₂–SH). This is the second sulfur-containing amino acid. Key properties:
- The –SH group is a weak acid that can form hydrogen bonds with oxygen or nitrogen.
- Two cysteine residues can be oxidised to form a disulfide bond (also called a disulfide bridge or cystine): 2 Cys → Cys–S–S–Cys + 2H⁺ + 2e⁻. This covalent bond is very important for stabilising protein structure (e.g., in insulin, where disulfide bridges link the two polypeptide chains, even though the cysteines are far apart in the primary sequence).
Amides (Asn, Gln)
- Asparagine (Asn): The amide of aspartate. Contains –CH₂–CO–NH₂. The amide group provides polarity through hydrogen bonding.
- Glutamine (Gln): The amide of glutamate. Contains –(CH₂)₂–CO–NH₂. Like asparagine, it is polar and can form hydrogen bonds.
Aromatic Polar (Tyr)
- Tyrosine (Tyr): Contains a phenol ring (benzene ring with a hydroxyl group). The hydroxyl group makes Tyr significantly more polar than phenylalanine. It can form hydrogen bonds and is an important functional group in some enzymes (involved in active site catalysis). Tyr is also a precursor to the neurotransmitters dopamine and thyroid hormones.
8.3 Negatively Charged (Acidic) Amino Acids
These amino acids have R groups that contain a second carboxyl group (–COOH), which is fully deprotonated (–COO⁻) at physiological pH 7. This gives them a net negative charge at pH 7.
Members: Aspartate/Aspartic acid (Asp), Glutamate/Glutamic acid (Glu)
- Aspartate (Asp): Has a –CH₂–COO⁻ side chain. pI = 2.87.
- Glutamate (Glu): Has a –(CH₂)₂–COO⁻ side chain (one more CH₂ than Asp). pI = 3.22.
These amino acids confer negative charge on proteins. They are crucial for ionic interactions within proteins and at protein–protein interfaces. Glutamate (as glutamic acid) is famous for the disease sickle cell anaemia, where a single substitution of Glu to Val at position 6 of the β-globin chain causes haemoglobin to polymerise.
8.4 Positively Charged (Basic) Amino Acids
These amino acids have R groups with additional amino or nitrogen-containing groups that carry a positive charge at pH 7.
Members: Lysine (Lys), Arginine (Arg), Histidine (His)
- Lysine (Lys): Has a long aliphatic chain ending in a primary ε-amino group (–(CH₂)₄–NH₃⁺). pKaR ≈ 10.5, so it is always positively charged at neutral pH.
- Arginine (Arg): Has a guanidinium group (–(CH₂)₃–NH–C(=NH)–NH₂, with pKaR ≈ 12.5) — the most basic of all amino acids. It is essentially always positively charged under physiological conditions. pI = 10.76.
- Histidine (His): Has an imidazole ring as its R group. This is the only common amino acid with a pI near physiological pH (~7.58). With pKaR ≈ 6.0, histidine can be either uncharged or positively charged depending on its local microenvironment within a protein. This unique property makes histidine extremely important in enzyme catalysis — it is frequently found at enzyme active sites, where it shuttles protons during the catalytic mechanism. An example is the catalytic triad of serine proteases (Asp–His–Ser).
8.5 Polarity and Protein Location
The polarity of amino acids governs where they end up in the three-dimensional structure of proteins:
- Polar amino acids tend to be found on the surface of soluble proteins, where they interact with the aqueous environment.
- Non-polar amino acids tend to be buried in the hydrophobic core of soluble proteins.
- Non-polar amino acids are also found embedded in the hydrophobic interior of biological membranes (e.g., transmembrane helices of membrane proteins pass through the lipid bilayer).
9. Essential, Non-Essential, and Conditional Amino Acids
From a nutritional standpoint, amino acids are classified based on whether the human body can synthesise them:
Essential Amino Acids (9 total)
These cannot be synthesised by the human body in sufficient amounts and must be obtained from the diet:
His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val
A useful mnemonic: PVT TIM HaLL (Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine)
Non-Essential Amino Acids
These can be synthesised by the body from other metabolic intermediates:
Alanine, Asparagine, Aspartic acid, Glutamic acid
Conditional Amino Acids
These are usually non-essential, but become essential during illness, stress, rapid growth, or specific physiological states (e.g., infancy):
Arginine, Cysteine, Glutamine, Glycine, Ornithine, Proline, Serine, Tyrosine
10. Uncommon and Modified Amino Acids
Selenocysteine: The 21st Amino Acid
Selenocysteine is sometimes called the “21st amino acid.” It is structurally identical to cysteine, except that the sulfur atom is replaced by selenium (–Se–H instead of –S–H). It is derived from serine.
Selenocysteine is found in the active sites of specific enzymes involved in oxidation–reduction reactions, including:
- Glutathione peroxidase
- Thioredoxin reductase
- Iodothyronine deiodinase
It is incorporated into proteins via a special re-coding of the UGA stop codon.
Post-Translationally Modified Amino Acids
In addition to the 20 standard amino acids, proteins may contain residues created by chemical modification of standard amino acids after the polypeptide chain has been synthesised — a process called post-translational modification. Examples include:
- 4-Hydroxyproline: A derivative of proline, formed by hydroxylation. Found abundantly in collagen (the most abundant protein in the human body; provides structural support to connective tissue). Essential for the stability of collagen’s triple helix structure.
- 5-Hydroxylysine: Derived from lysine by hydroxylation. Also found in collagen and involved in cross-link formation.
- 6-N-Methyllysine: Found in myosin, the contractile protein of muscle.
- γ-Carboxyglutamate: Found in the blood-clotting protein prothrombin and other proteins that bind Ca²⁺ as part of their biological function. Requires vitamin K for its synthesis — this is the target of anticoagulant drugs like warfarin.
Non-Protein Amino Acids with Biological Functions
Many amino acids are not incorporated into proteins but serve important biological roles:
- Ornithine and citrulline: Intermediates in the urea cycle, which is the pathway for nitrogen excretion in the liver.
- Taurine: Used for the synthesis of bile salts, which emulsify fats during digestion.
- Histamine: Derived from histidine; a mediator of allergic and inflammatory reactions. Released by mast cells during allergic responses.
- Dopamine: Derived from tyrosine; an important neurotransmitter in the central nervous system.
11. Peptides and the Peptide Bond
What Is a Peptide?
A peptide is a molecule in which two or more amino acids are joined by peptide bonds. A peptide bond is a special type of amide bond that links the α-amino group of one amino acid to the α-carboxyl group of another.
Formation of the Peptide Bond
Peptide bond formation is a condensation (dehydration) reaction — a molecule of water is removed for each peptide bond formed:
H₂N–CHR¹–COOH + H₂N–CHR²–COOH → H₂N–CHR¹–CO–NH–CHR²–COOH + H₂O
(amino acid 1) (amino acid 2) (dipeptide)
The reaction involves:
- The α-carboxyl group of amino acid 1 reacting with
- The α-amino group of amino acid 2
This produces a dipeptide with a free N-terminal (amino) end and a free C-terminal (carboxyl) end.
The Chemical Nature of the Peptide Bond
The peptide bond can be represented by two resonance structures:
- The “standard” form: C–N single bond, C=O double bond.
- The “resonance” form: C=N double bond, C–O single bond.
The true structure is a hybrid of these two resonance forms, giving the C–N bond partial double-bond character (bond length ~1.32 Å, intermediate between a pure C–N single bond of 1.49 Å and a C=N double bond of 1.27 Å). This has profound structural consequences:
The six atoms of the peptide group (Cα–CO–NH–Cα) are coplanar. They form a rigid, planar unit called the peptide plane.
This rigidity significantly reduces the number of possible backbone conformations.
Bond Rotation and Protein Conformation
Within the peptide backbone, three bonds are relevant:
- N–Cα bond (rotation angle = Φ, phi) — free to rotate (in principle)
- Cα–C bond (rotation angle = Ψ, psi) — free to rotate (in principle)
- C–N peptide bond — rigid due to partial double-bond character; rotation NOT freely allowed
Because the Φ and Ψ angles can theoretically rotate freely (but are limited in practice by steric clashes between R groups), proteins can adopt a vast number of three-dimensional arrangements called conformations. The allowed combinations of Φ and Ψ are summarised in a Ramachandran plot.
Trans vs. Cis Peptide Bonds
For essentially all peptide bonds (>99.95%), the two Cα atoms flanking the bond are on opposite sides — this is the trans configuration. The trans form is strongly preferred because the cis form causes severe steric clashing between the R groups.
Exception: For peptide bonds involving the imino nitrogen of proline, about 6% are in the cis configuration (found in β-turns). Proline is the only amino acid that can adopt the cis conformation with reasonable frequency because its cyclic side chain reduces the steric penalty.
12. Properties of Peptides
Naming Peptides
When writing a peptide sequence:
- The residue at the N-terminal end (free α-amino group) is placed on the left and named with an “-yl” suffix for all residues except the last.
- The residue at the C-terminal end (free α-carboxyl group) is placed on the right and retains its full name.
For example, the pentapeptide Ser–Gly–Tyr–Ala–Leu (written in one-letter code: SGYAL) has:
- Serine at the N-terminus (free –NH₃⁺)
- Leucine at the C-terminus (free –COO⁻)
Stability of Peptide Bonds
Hydrolysis of a peptide bond (breaking the bond by adding water) is thermodynamically favourable (exergonic). However, it occurs very slowly in the absence of a catalyst because the reaction has a high activation energy. As a result, peptide bonds in proteins are remarkably stable, with an average half-life of approximately 7 years under typical intracellular conditions.
In living cells, proteases (proteolytic enzymes) are needed to catalyse peptide bond hydrolysis at a biologically useful rate.
Thermodynamics of Peptide Bond Hydrolysis
The overall free energy change for peptide bond hydrolysis can be broken into two contributions:
- ΔGₘ (free energy of hydrolysis of the amide bond to uncharged products) — positive (endergonic step)
- ΔGᵢ (free energy of ionisation of the resulting carboxyl and amino groups at physiological pH) — negative(exergonic step)
The total ΔGₕ = ΔGₘ + ΔGᵢ is negative (net exergonic), which is why hydrolysis is thermodynamically favourable overall.
Acid-Base Properties of Peptides
The ionisation behaviour of a peptide depends on:
- Its free α-amino group (at the N-terminus)
- Its free α-carboxyl group (at the C-terminus)
- The ionisable R groups of all residues within the chain
For example, a tetrapeptide containing Ala, Glu, Gly, and Lys has:
- 1 free α-amino group (N-terminal)
- 1 free α-carboxyl group (C-terminal)
- 1 negatively charged side chain (Glu: –COO⁻)
- 1 positively charged side chain (Lys: –NH₃⁺)
At pH 7.4, all four of these groups are ionised.
13. Classification by Size
| Term | Definition | Molecular Weight |
|---|---|---|
| Oligopeptide | Short chain of amino acids joined by peptide bonds (tripeptide = 3 aa; tetrapeptide = 4 aa; pentapeptide = 5 aa, etc.) | Varies (small) |
| Polypeptide | Longer chain of amino acids | Generally < 10,000 Da |
| Protein | Long polypeptide chain(s) with defined structure and function | Generally > 10,000 Da |
Estimating the Number of Amino Acid Residues
The average molecular weight of an amino acid is approximately 128 Da. However, each peptide bond formation removes one water molecule (MW = 18 Da), so the average molecular weight of an amino acid residue in a protein is approximately:
128 – 18 = 110 Da
Therefore, to estimate the approximate number of residues in a protein:
Number of residues ≈ Molecular Weight / 110
For example, a protein with a molecular weight of 55,000 Da contains approximately 500 amino acid residues.
14. Biologically Important Peptides
Even very short peptides can have profound biological effects. Here are some notable examples:
Aspartame (Dipeptide)
- Structure: L-aspartyl-L-phenylalanine methyl ester
- Function: Artificial sweetener, approximately 200 times sweeter than sucrose. Commercially synthesised.
Oxytocin (Nonapeptide — 9 amino acids)
- Structure: A cyclic peptide (the cysteine residues at positions 1 and 6 are connected by a disulfide bridge)
- Function: Secreted by the posterior pituitary gland. Stimulates uterine contractions during labour and milk ejection during breastfeeding. Also plays roles in social bonding.
α-Amanitin (Cyclic Nonapeptide)
- Structure: A cyclic peptide containing 9 amino acids (some unusual), isolated from the deadly _Amanita phalloides_mushroom (“death cap”).
- Function: Potent toxin — it inhibits RNA polymerase II, blocking transcription in eukaryotic cells. Even very small amounts are lethal.
Bioactive Peptides in Medicine and Food Science
Bioactive peptides are commercially available in several forms:
- Supplements: Antihypertensive peptides (e.g., LKPNM from bonito fish, VY from sardine) — these inhibit angiotensin-converting enzyme (ACE) and are marketed as natural blood pressure lowering agents.
- Drugs: Neuropeptides for neurological research, antibiotics (e.g., vancomycin — a glycopeptide antibiotic used against MRSA).
- Food products: Peptides derived from milk (IPP, VPP) are incorporated into functional foods with antihypertensive properties.
15. Conclusion and Key Takeaways
Summary
This lesson covered the fundamentals of amino acids and peptides, which are the building blocks of proteins — the functional products of gene expression.
Amino acids:
- All 20 standard amino acids are α-amino acids, with a carboxyl group, amino group, hydrogen, and a variable R group all attached to the α-carbon.
- With the exception of glycine, all are chiral and exist exclusively as L-stereoisomers in proteins.
- They are amphoteric (zwitterionic), possessing both acidic and basic properties. Each has a characteristic pI at which it carries no net charge.
- They are classified by R group polarity: nonpolar/hydrophobic, polar uncharged, negatively charged (acidic), or positively charged (basic).
- 9 essential amino acids must be obtained from the diet.
Peptide bonds:
- Formed by a condensation reaction between the α-carboxyl group of one amino acid and the α-amino group of another.
- The C–N bond has partial double-bond character, making the peptide group planar and rigid.
- Backbone rotation occurs around the Φ (N–Cα) and Ψ (Cα–C) angles.
- Nearly all peptide bonds are in the trans configuration; cis is seen mainly at proline residues (~6%).
- Peptide bonds are kinetically stable (long half-life) but thermodynamically susceptible to hydrolysis.
Peptides:
- Range from dipeptides to large polypeptides.
- The chain is read from the N-terminus (left) to the C-terminus (right).
- Even small peptides have powerful biological activities (e.g., oxytocin, amanitin, aspartame).
Connections to Upcoming Topics
Understanding amino acid structure, properties, and peptide bond chemistry is foundational for studying:
- Protein structure (primary, secondary, tertiary, quaternary)
- Haemoglobin and myoglobin (oxygen-binding proteins)
- Enzyme mechanisms (especially the role of active-site residues like His, Ser, Asp, Cys)
- Post-translational modifications and diseases caused by mutations (e.g., sickle cell anaemia)
This lesson note was prepared based on the General Biochemistry Module 1 lectures at the Università di Bologna (Alma Mater Studiorum). For visual diagrams of molecular structures, refer to the original lecture slides.