Amino Acids & Peptide Bonds: Biochemistry Basics
Every peptide drug, every collagen supplement, every antimicrobial defense molecule in your immune system comes down to the same building blocks: amino acids linked by peptide bonds. These are the atomic-level fundamentals.
Every peptide drug, every collagen supplement, every antimicrobial defense molecule in your immune system comes down to the same building blocks: amino acids linked by peptide bonds. These are the atomic-level fundamentals. If you understand amino acids and how they connect, you understand the chemistry that makes semaglutide different from BPC-157, why some peptides survive your stomach acid and others don't, and how a chain of amino acids can fold into a molecule capable of lowering blood sugar or healing a wound.
This guide covers the biochemistry — the 20 standard amino acids, how peptide bonds form and break, how chains fold into functional shapes, and why structure determines everything about what a peptide does.
Table of Contents
- The 20 Standard Amino Acids
- Amino Acid Structure: The Common Core
- Side Chain Classification
- Essential vs. Non-Essential Amino Acids
- Peptide Bond Formation: Building the Chain
- Peptide Bond Properties
- Peptide Bond Hydrolysis: Breaking the Chain
- Primary Structure: The Sequence
- Secondary Structure: Local Folding Patterns
- Tertiary Structure: The 3D Shape
- Disulfide Bonds: Molecular Staples
- How Structure Determines Function
- Beyond the Standard 20
- FAQ
- The Bottom Line
- References
The 20 Standard Amino Acids
Your body uses 20 amino acids to build all of its peptides and proteins. These are called the "proteinogenic" or "coded" amino acids because they're the ones specified by the genetic code — each has one or more DNA codons that call for its insertion during protein synthesis.
From just these 20 building blocks, the diversity is staggering. A pentapeptide (5 amino acids long) can be arranged in 3.2 million different sequences. A 50-amino-acid peptide has more possible sequence combinations than there are atoms in the observable universe.
Here are all 20, organized by their side chain properties:
| Amino Acid | 3-Letter | 1-Letter | Essential? | Side Chain Type |
|---|---|---|---|---|
| Glycine | Gly | G | No | Nonpolar (simplest) |
| Alanine | Ala | A | No | Nonpolar |
| Valine | Val | V | Yes | Nonpolar, branched-chain |
| Leucine | Leu | L | Yes | Nonpolar, branched-chain |
| Isoleucine | Ile | I | Yes | Nonpolar, branched-chain |
| Proline | Pro | P | No | Nonpolar, cyclic |
| Methionine | Met | M | Yes | Nonpolar, sulfur-containing |
| Phenylalanine | Phe | F | Yes | Aromatic |
| Tryptophan | Trp | W | Yes | Aromatic (largest) |
| Tyrosine | Tyr | Y | Conditional | Aromatic, polar |
| Serine | Ser | S | Conditional | Polar, uncharged |
| Threonine | Thr | T | Yes | Polar, uncharged |
| Cysteine | Cys | C | Conditional | Polar, sulfhydryl |
| Asparagine | Asn | N | No | Polar, uncharged |
| Glutamine | Gln | Q | Conditional | Polar, uncharged |
| Aspartic Acid | Asp | D | No | Negatively charged |
| Glutamic Acid | Glu | E | No | Negatively charged |
| Lysine | Lys | K | Yes | Positively charged |
| Arginine | Arg | R | Conditional | Positively charged |
| Histidine | His | H | Yes | Positively charged |
Each amino acid has both a three-letter abbreviation (Gly, Ala, Val) and a one-letter code (G, A, V). You'll see both in scientific literature. One-letter codes are used for long sequences because they're more compact: the insulin B-chain written in one-letter code is FVNQHLCGSHLVEALYLVCGERGFFYTPKT.
Amino Acid Structure: The Common Core
Every amino acid shares the same backbone architecture:
- A central alpha-carbon (Cα) — the hub of the molecule
- An amino group (-NH₂) — the nitrogen-containing end
- A carboxyl group (-COOH) — the acid end
- A hydrogen atom
- A side chain (R-group) — the variable part that makes each amino acid unique
The amino group and carboxyl group are what form peptide bonds. The side chain determines the amino acid's chemical personality — whether it's attracted to water, repelled by it, electrically charged, or capable of special chemistry like forming disulfide bonds.
Chirality: L and D Forms
Because the alpha-carbon has four different groups attached to it (except in glycine, where the R-group is just a hydrogen), amino acids are chiral — they exist in two mirror-image forms, called L and D. Think of your hands: identical structures, but you can't superimpose one on the other.
Biology overwhelmingly uses L-amino acids. Nearly every natural peptide and protein is built from L-forms. D-amino acids are rare in nature but extremely useful in synthetic peptide design — because proteases have evolved to recognize L-amino acids, substituting D-forms makes a peptide resistant to enzymatic degradation. This is one strategy researchers use to extend the half-life of therapeutic peptides.
Side Chain Classification
The side chain is where the action is. It determines how each amino acid behaves in a peptide chain, how it interacts with water and other molecules, and what role it plays in protein folding and function.
Nonpolar (Hydrophobic) Side Chains
These amino acids have side chains made of carbon and hydrogen. They avoid water and pack into the interior of folded proteins.
Glycine (G) has the simplest side chain — just a hydrogen atom. It fits into tight spaces where nothing else can and is the only amino acid that's not chiral. Alanine (A) has a small methyl group and is the second most common amino acid in human proteins.
Valine (V), Leucine (L), and Isoleucine (I) — the branched-chain amino acids (BCAAs) — are all essential and abundant in muscle protein. Proline (P) is unique: its side chain loops back to the backbone nitrogen, creating a rigid ring that introduces kinks and bends. Proline is abundant in collagen. Methionine (M) contains a sulfur atom and is almost always the first amino acid in newly synthesized proteins (the start codon AUG codes for it).
Aromatic Side Chains
These have ring structures that absorb ultraviolet light. Phenylalanine (F) carries a benzene ring and is a precursor to dopamine and epinephrine. Tryptophan (W), the largest amino acid, has a double-ring indole group and is the precursor for serotonin and melatonin. Tyrosine (Y) has a hydroxyl-bearing phenol group that can be phosphorylated — making it central to cell signaling through receptor tyrosine kinases.
Polar, Uncharged Side Chains
Serine (S) and Threonine (T) have hydroxyl groups that can be phosphorylated by kinases, making them important in signaling pathways. Cysteine (C) has a sulfhydryl (-SH) group responsible for forming disulfide bonds — covalent S-S bonds that act as structural staples in peptides and proteins. Asparagine (N) and Glutamine (Q) have amide groups; asparagine is prone to deamidation, a common degradation reaction during peptide storage.
Charged Side Chains
Positively charged (basic): Lysine (K) participates in salt bridges and is a common site for post-translational modifications. Arginine (R) is a precursor for nitric oxide. Histidine (H) has an imidazole ring that can switch between charged and neutral states near physiological pH — useful in enzyme active sites.
Negatively charged (acidic): Aspartic acid (D) and Glutamic acid (E) carry negative charges and participate in enzyme catalysis and salt bridges. Glutamic acid is also a precursor for both GABA (inhibitory neurotransmitter) and glutamate (excitatory neurotransmitter).
Essential vs. Non-Essential Amino Acids
"Essential" means your body cannot synthesize the amino acid — you must get it from your diet.
Nine essential amino acids: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.
Eleven non-essential amino acids: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine.
Several non-essential amino acids are "conditionally essential" — your body can usually make enough, but during illness, stress, intense physical training, or at certain life stages, synthesis may not keep up with demand. Arginine, cysteine, glutamine, glycine, proline, serine, and tyrosine fall into this category.
For synthetic peptides (made in the lab), this distinction matters less. For your body's own peptide and protein production, essential amino acid deficiency can compromise synthesis.
Peptide Bond Formation: Building the Chain
A peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of the next, releasing a water molecule. This is a condensation (or dehydration) reaction.
The mechanics: the hydroxyl (-OH) from the carboxyl group and a hydrogen (-H) from the amino group depart as water (H₂O). What's left is a covalent CO-NH bond — the peptide bond — connecting the two amino acids.
Each amino acid in the resulting chain (except the two at the ends) has lost the equivalent of one water molecule. What remains is called an amino acid "residue." The number of peptide bonds is always one less than the number of residues: a pentapeptide has five residues and four peptide bonds.
In living cells, peptide bond formation is catalyzed by the ribosome and powered by GTP hydrolysis. The ribosome reads messenger RNA (mRNA) codon by codon, and for each codon, a transfer RNA (tRNA) carrying the appropriate amino acid adds it to the growing chain.
In the lab, peptides are built using solid-phase peptide synthesis (SPPS). The first amino acid is anchored to an insoluble bead, and subsequent amino acids are added one at a time using chemical coupling reactions. After the sequence is complete, the peptide is cleaved from the resin and purified. Robert Bruce Merrifield developed SPPS in 1963 and received the Nobel Prize for it in 1984.
Peptide Bond Properties
The peptide bond isn't just any chemical bond — it has several properties that shape the behavior of all peptides and proteins.
Partial double-bond character. Due to resonance between the carbonyl oxygen and the nitrogen, the peptide bond has about 40% double-bond character. This makes it shorter and stronger than a typical single bond, and it restricts rotation around the C-N axis.
Planarity. The six atoms involved in the peptide bond — the Cα of one residue, the C=O, the N-H, and the Cα of the next residue — lie approximately in a plane. This rigidity limits the backbone's conformational freedom and creates the angular geometry that drives secondary structure formation.
Trans configuration. In over 99% of peptide bonds in nature, the bond adopts a trans arrangement (the alpha carbons of adjacent residues are on opposite sides of the bond). The cis configuration is sterically unfavorable for most amino acids because the side chains would clash. The exception is proline, which has a measurable cis population (~5-6% of proline peptide bonds) because its cyclic side chain reduces the energy difference between cis and trans.
Polarity. The C=O and N-H groups of the peptide bond can form hydrogen bonds. These hydrogen bonds are the driving force behind secondary structures like alpha helices and beta sheets.
Peptide Bond Hydrolysis: Breaking the Chain
The reverse of peptide bond formation is hydrolysis — adding water across the bond to break it.
In purely chemical terms, peptide bonds are remarkably stable. At 25°C and neutral pH, the half-life for spontaneous hydrolysis of a peptide bond is 350 to 600 years. This stability is essential — it means your proteins don't fall apart on their own.
In the body, however, peptide bonds are broken quickly by enzymes called proteases (also called peptidases). Proteases position the peptide bond in an active site that lowers the activation energy for hydrolysis, speeding the reaction by factors of 10⁹ to 10¹² (a billion to a trillion times faster than the uncatalyzed reaction).
Proteases are classified by where they cut:
- Endopeptidases cut bonds in the middle of a chain (pepsin, trypsin, chymotrypsin)
- Exopeptidases cut from the ends — aminopeptidases from the N-terminus, carboxypeptidases from the C-terminus
- Dipeptidyl peptidases remove two amino acids at a time (DPP-4, the enzyme that degrades natural GLP-1)
Understanding protease specificity is central to peptide drug design. Trypsin cuts after lysine and arginine residues. Chymotrypsin prefers large hydrophobic residues like phenylalanine and tryptophan. DPP-4 cleaves after position 2 from the N-terminus. Knowing these preferences allows chemists to modify therapeutic peptides at vulnerable positions. For example, semaglutide has an Aib (2-aminoisobutyric acid) substitution at position 8, which sits in the DPP-4 cleavage site — this single change dramatically extends the peptide's half-life.
Primary Structure: The Sequence
The primary structure of a peptide is simply its amino acid sequence, read from N-terminus to C-terminus. This sequence is the peptide's genetic instruction — it determines everything about the molecule's behavior.
Consider two peptides with identical amino acid compositions but different sequences:
- Ala-Gly-Ser (alanine-glycine-serine)
- Ser-Ala-Gly (serine-alanine-glycine)
Same building blocks, but different molecules with different properties. The sequence dictates which side chains are next to each other, how the chain can fold, and what the peptide does biologically.
Even a single amino acid change can transform a peptide's function. Natural GLP-1 has alanine at position 8 and a half-life of about 2 minutes. Replacing that alanine with Aib (a non-natural amino acid) — as done in semaglutide — blocks DPP-4 from recognizing the site and extends the half-life to roughly a week.
Secondary Structure: Local Folding Patterns
As a peptide chain is synthesized, it doesn't stay flat. Backbone hydrogen bonds between the C=O of one peptide bond and the N-H of another drive the formation of regular, repeating structures:
Alpha Helix (α-helix). The chain coils into a right-handed spiral, with hydrogen bonds forming between every fourth residue. Each turn contains 3.6 residues. Many peptide hormones adopt alpha-helical structures when binding their receptors — GLP-1 is one example. Alanine and leucine favor helix formation; proline and glycine tend to break helices.
Beta Sheet (β-sheet). Chain segments line up side by side, connected by hydrogen bonds between adjacent strands. Strands can run parallel or antiparallel. Beta sheets appear in structural proteins (silk is almost entirely beta sheet) and in amyloid fibrils — the misfolded aggregates linked to Alzheimer's disease.
Turns and loops. Short connecting segments, often containing proline and glycine. Loops frequently form the active sites of enzymes and binding surfaces of proteins.
Tertiary Structure: The 3D Shape
Tertiary structure is the overall three-dimensional arrangement, determined by long-range interactions between side chains. Four forces drive it: hydrophobic interactions (nonpolar residues clustering in the interior), hydrogen bonds (fine-tuning the structure), ionic bonds/salt bridges (between oppositely charged residues), and disulfide bonds (covalent links between cysteines — the strongest individual stabilizing interaction).
Most peptides under ~30 amino acids are too short to form stable tertiary structure in solution. Many peptide hormones only adopt their final shape upon binding their receptor — a process called "induced fit."
Disulfide Bonds: Molecular Staples
When two cysteine residues come near each other in a folded peptide, their sulfhydryl (-SH) groups can be oxidized to form a disulfide bond (S-S). This covalent bond is much stronger than the noncovalent interactions that drive most folding, locking structural elements in place.
Insulin has two peptide chains (A and B) held together by two interchain disulfide bonds, plus one intrachain bond within the A chain. Without these, the chains separate and insulin loses function. Oxytocin has one internal disulfide bond between residues 1 and 6, forming a ring essential for receptor binding.
Some disulfide bonds are "allosteric" — their formation or cleavage actively changes protein function, serving as regulatory switches. During storage, disulfide bonds can also undergo shuffling (rearrangement to incorrect pairings), leading to misfolded peptide — one reason proper peptide storage matters.
How Structure Determines Function
For peptides and proteins, there's a fundamental principle: sequence determines structure, and structure determines function.
The sequence dictates which side chains interact, where helices and sheets form, and how the molecule folds. The fold brings specific residues together to create receptor-binding sites, enzyme active sites, or structural interfaces. A peptide's biological activity depends on the spatial arrangement of its side chains — which depends on its three-dimensional structure, which depends on its sequence.
This has direct practical implications. When researchers design a new peptide drug, they're manipulating the sequence to achieve a specific three-dimensional shape that binds a target receptor with the right affinity and selectivity. When a certificate of analysis reports peptide purity, it's confirming the correct sequence — because the wrong sequence would produce the wrong structure and the wrong function.
Beyond the Standard 20
While the genetic code specifies 20 amino acids, others matter too.
Selenocysteine — the 21st genetically encoded amino acid — contains selenium instead of sulfur and appears in about 25 human proteins, including the antioxidant enzymes glutathione peroxidase and thioredoxin reductase. Post-translational modifications expand the repertoire further: hydroxyproline stabilizes collagen, and phosphoserine/phosphotyrosine drive cell signaling.
For peptide drug design, non-natural amino acids are game-changers. 2-aminoisobutyric acid (Aib) — used in semaglutide at position 8 — resists DPP-4 cleavage because the enzyme's active site can't accommodate the extra methyl group. D-amino acids resist most proteases. N-methylated amino acids block endopeptidases. These modifications are fundamental tools for extending peptide half-life and improving drug-like properties.
FAQ
Why are peptide bonds so stable without enzymes?
The partial double-bond character of the C-N bond makes it stronger than a typical single bond, and the thermodynamic barrier for hydrolysis is high. At 25°C, a peptide bond has a half-life of 350-600 years. Proteases accelerate this by a factor of 10⁹ to 10¹², which is why biological degradation happens in seconds to minutes.
What happens if one amino acid in a peptide changes?
It depends on the position. Some spots tolerate substitution — swapping leucine for isoleucine in a buried core may have minimal effect. Other positions are critical. A single change in hemoglobin's beta chain (glutamic acid to valine at position 6) causes sickle cell disease. In drug design, strategic substitutions can improve stability — as with the Aib substitution at position 8 in semaglutide that extends its half-life from minutes to about a week.
What are disulfide bonds?
Covalent bonds between the sulfur atoms of two cysteine residues. They act as molecular staples. Insulin has three (holding its two chains together). Oxytocin has one (forming its ring). Without them, these peptides lose biological activity.
How does structure relate to function?
Sequence determines folding. Folding determines 3D shape. Shape determines receptor binding and biological effects. This chain — sequence → structure → function — is the central principle of peptide science.
How do D-amino acids improve peptide stability?
Proteases have active sites shaped to recognize L-amino acids (the natural form). D-amino acids are the mirror image and don't fit properly, so substituting them at vulnerable positions makes a peptide resistant to enzymatic breakdown.
The Bottom Line
Amino acids and peptide bonds are where peptide science begins. The 20 standard amino acids — each with a unique side chain — combine through peptide bonds to create chains that fold into specific three-dimensional shapes. Those shapes determine function: which receptors a peptide can bind, what cellular responses it triggers, and ultimately what therapeutic effects it can produce.
Understanding this chemistry gives you a foundation for everything else on PeptideJournal.org. When you read about semaglutide's mechanism of action, you'll understand why a single amino acid substitution extends its half-life from minutes to a week. When you learn about GHK-Cu's effects on skin, you'll understand how a tripeptide's structure allows it to carry copper to target cells. When you compare different growth hormone peptides, you'll understand why sequence differences lead to different receptor specificities and clinical profiles.
For the vocabulary to navigate peptide literature, see our peptide glossary. For how these structural principles translate into biological signaling, read how peptides work. And for a broader introduction to the field, start with what are peptides.
References
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- Merrifield RB. "Solid Phase Peptide Synthesis. I. The Synthesis of a Tetrapeptide." Journal of the American Chemical Society. 1963;85(14):2149-2154. https://pubmed.ncbi.nlm.nih.gov/14044142/
- Bachem. "Peptides & Amino Acids for Beginners." https://www.bachem.com/knowledge-center/peptide-guide/peptides-and-amino-acids-for-beginners/
- Sanger F, Thompson EOP. "The amino-acid sequence in the glycyl chain of insulin." Biochemical Journal. 1953;53(3):353-374. https://pmc.ncbi.nlm.nih.gov/articles/PMC1198157/
- Western Oregon University Chemistry. "Chapter 2: Protein Structure." https://wou.edu/chemistry/courses/online-chemistry-textbooks/ch450-and-ch451-biochemistry-defining-life-at-the-molecular-level/chapter-2-protein-structure/
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