The common plan of an amino acid

An amino acid is an organic molecule with an amine group and a carboxyl group attached to a central carbon atom. It also has a variable side chain, which gives the amino acid its particular chemical properties. Amino acids are the monomers that build polypeptides and proteins.

The central carbon is the alpha carbon. In a generalized amino acid, this carbon atom bonds to four different groups:

• an amine group, a nitrogen-containing group that can accept a hydrogen ion;
• a carboxyl group, a carbon-containing acidic group that can donate a hydrogen ion;
• a hydrogen atom;
• an R-group, the variable side chain that differs between amino acids.

When drawing the generalized amino acid, place the alpha carbon in the centre and join all four groups to it with single covalent bonds. A clear shorthand is H₂N–CH(R)–COOH, but in a diagram the amine group, carboxyl group, hydrogen and R-group should all be shown explicitly. The R-group isn’t a mysterious extra atom. It’s the part that changes from one amino acid to another.

Since the carboxyl group can act as an acid and the amine group can act as a base, amino acids respond to the pH around them. This matters later, because protein shape depends on charges and interactions within the molecule.

Making peptide bonds

A condensation reaction is a chemical reaction where two molecules become covalently linked and a small molecule, usually water, is released. Amino acids join in this way.

The word equation is:

amino acid + amino acid → dipeptide + water

A dipeptide is a molecule made of two amino acid residues joined by one peptide bond. A peptide bond is a covalent C–N bond between the carboxyl group of one amino acid and the amine group of another. The –OH from the carboxyl group and an –H from the amine group are removed, producing water.

Longer chains form as more amino acids are added by further condensation reactions:

peptide + amino acid → longer peptide + water

A polypeptide is a chain of many amino acid residues joined by peptide bonds. In cells, ribosomes catalyse peptide bond formation during translation. The chain has direction: one end has a free amine group, called the amino terminus, while the other has a free carboxyl group, called the carboxyl terminus.

What to show in a generalized dipeptide

When you draw a generalized dipeptide, focus on the backbone. Show the repeating N–C–C pattern, the peptide bond as C–N, and two R-groups projecting from the alpha carbons. In the middle of the molecule, the original amine and carboxyl groups are no longer both intact, because some of their atoms have been used to form the peptide bond and water.

A residue is the part of an amino acid that remains incorporated in a peptide chain after condensation has removed atoms to form water. The R-group belongs to an amino acid before it joins; once the amino acid is in the chain, the R-group is part of an amino acid residue.

Essential and non-essential amino acids

An essential amino acid is an amino acid that an organism cannot make in sufficient quantity, so it has to get it from food. A non-essential amino acid is an amino acid that an organism can make from other molecules, including other amino acids.

Humans use 20 amino acids to make ribosome-built polypeptides. Some have to come ready-made from the diet; others are made by metabolic pathways that alter molecules already in the body. Don’t mix up “essential” with “more important”. All 20 are required for protein synthesis. “Essential” just refers to whether that amino acid must be supplied in the diet.

Dietary protein is broken down into amino acids and small peptides. These are absorbed and then used to build the body’s own proteins. A food may contain plenty of total protein but still be low in one essential amino acid, so protein quality depends on the balance of amino acids, not just the number of grams of protein.

Vegan diets can supply the required amino acids, but they need some attention because plant foods differ in their amino acid profiles. The practical point is straightforward: a varied diet, using suitable combinations of plant protein sources, supplies all essential amino acids over time.

Why peptide variety is effectively enormous

The genetic code specifies 20 amino acids for protein synthesis. In principle, a ribosome can place any one of these amino acids at any position in a peptide chain. Some chains are very short. Others contain hundreds or thousands of amino acid residues, with the order able to change at every position.

Sequence possibilities rise extremely fast as chain length increases. For a chain of n amino acid residues, S = 20^n, where S is the number of possible amino acid sequences (dimensionless count) and n is the number of amino acid residue positions in the chain (dimensionless count). A dipeptide has 20² possible sequences; a tripeptide has 20³; a protein-length polypeptide gives a number so large that “effectively infinite” is fair classroom language.

There’s a useful distinction here: ribosomes do not make random chains just because many chains are possible. Genetic information determines the sequence. This links the genome, which is the complete set of genetic information in an organism, with the proteome, which is the complete set of proteins produced by a cell, tissue or organism under particular conditions.

Examples of polypeptides help show the range. Some peptide hormones are short signalling molecules. Insulin is a small protein made from two polypeptide chains. Many enzymes are single polypeptides of several hundred residues. Some structural muscle proteins are enormous chains containing tens of thousands of residues. The same basic peptide-bond chemistry supports all of that variety.

Protein shape depends on weak interactions

A protein’s function usually depends on its three-dimensional shape. Interactions inside the molecule hold that shape in place, and many of these interactions are weak on their own. Temperature and pH are abiotic factors that can disturb them, which can change the molecule’s form.

Denaturation is a structural change in a protein where its normal three-dimensional shape is disrupted enough to reduce or destroy its function, without necessarily breaking the peptide bonds of the primary chain. So a denatured enzyme may still have the same amino acid sequence, but its active site may no longer have the right shape.

Temperature

As temperature rises, atoms and groups within a protein gain more kinetic energy. They move more, so the bonds and interactions holding the protein in shape experience more vibration and strain. Above a certain point, the protein unfolds or changes conformation. Many soluble proteins then become insoluble, because hydrophobic regions that were hidden inside become exposed to water.

Some proteins from organisms that live in very hot environments are unusually heat-stable, so don’t treat one temperature as a universal denaturation point. Even so, high temperature visibly denatures many familiar proteins: egg white turning opaque and solid is the kitchen version of the same principle.

pH

Changing pH changes the availability of hydrogen ions. It can alter the charges on acidic and basic groups in a protein, especially in R-groups. When charges change, ionic bonds may break, new attractions or repulsions may form, and the protein may change shape. Extreme acidity and extreme alkalinity can both denature proteins.

How temperature and pH changes can denature proteins.

One practical way to follow denaturation is to measure turbidity. A colorimeter is an instrument that measures how much selected light passes through or is absorbed by a sample. If albumen protein denatures and precipitates, the mixture becomes cloudier, so less light is transmitted and absorbance increases. In a temperature investigation, keep protein concentration and heating time controlled; in a pH investigation, use buffer solutions so that pH is the variable being tested.

R-groups make amino acids chemically different

After amino acids join to form a polypeptide, the repeating backbone stays broadly similar along the chain. Most of the chemical variation comes from the R-groups. Different R-groups create different local properties, and the pattern of those properties along the chain helps determine the final protein form and function.

A hydrophobic R-group is a non-polar side chain that tends to avoid contact with water. A hydrophilic R-group is a polar or charged side chain that can interact favourably with water. Hydrophilic R-groups may be uncharged but polar, or they may carry charge.

Acid-base behaviour is often used to describe charged R-groups. An acidic R-group is a side chain that can donate a hydrogen ion and become negatively charged. A basic R-group is a side chain that can accept a hydrogen ion and become positively charged. That is enough detail for the syllabus: you don’t need to memorize named R-group structures, but you do need to understand why a chain with different R-groups can fold and interact in many different ways.

This chemical diversity is why proteins can work as enzymes, receptors, structural fibres, transport molecules and signals. Same backbone idea; different R-group sequence; different properties.

Sequence determines shape

Primary structure is the linear sequence of amino acid residues in a polypeptide chain. It means the exact order and position of those amino acids from one end of the chain to the other, not just which amino acids are present.

Conformation is the three-dimensional arrangement of atoms in a protein or polypeptide. Most proteins fold into precise, repeatable conformations because the R-groups in the primary structure interact with each other and with the surrounding environment in predictable ways.

Here’s a key form-and-function link in biology. Change the primary structure, and you may change where hydrophobic groups cluster, where charged groups attract or repel, and where hydrogen bonds or disulfide bonds can form. Sometimes a small sequence change has little effect. Sometimes it alters the conformation enough to change function.

The genome-proteome relationship fits into this. DNA sequence determines the amino acid sequence during protein synthesis, and amino acid sequence helps determine protein conformation. Regulation of which genes are expressed matters too, because a cell’s proteome changes depending on which polypeptides it is making.

Regular folding patterns in the backbone

Secondary structure means a regular, local folding pattern in a polypeptide backbone, held in place by hydrogen bonds. These hydrogen bonds form at regular positions between the polar C=O and N–H groups of the peptide backbone, rather than mainly between R-groups.

An alpha helix is a secondary structure where the polypeptide backbone coils into a spiral. Hydrogen bonds between nearby turns of the coil stabilize it. The R-groups point outward from the helix, so they can still interact with the surroundings or with other parts of the protein.

A beta-pleated sheet is a secondary structure where extended sections of polypeptide lie next to one another, with hydrogen bonds holding the sections together. It looks “pleated” because the bond angles in the backbone create a folded, zigzag shape, not a flat ribbon.

Don’t treat secondary structure as the whole protein shape. A protein may contain several alpha helices, several beta-pleated sheets, both, or neither. These regular regions are smaller building features within the larger three-dimensional structure.

Folding the whole polypeptide

Tertiary structure is the overall three-dimensional folding of a single polypeptide chain. It comes from interactions between R-groups that may sit far apart in the primary sequence, then end up close together once the chain folds.

Four interaction types matter especially here:

• A hydrogen bond is an attraction in which a hydrogen atom covalently bonded to an electronegative atom is attracted to another electronegative atom. In tertiary structure, hydrogen bonds can form between polar R-groups.
• An ionic bond is an electrostatic attraction between oppositely charged groups. In proteins, these bonds can form between positively and negatively charged R-groups.
• A disulfide bond is a covalent bond between sulfur atoms in two cysteine residues. It is stronger than the other interactions listed here and can hold parts of a polypeptide, or different polypeptides, together firmly.
• A hydrophobic interaction is the clustering of non-polar groups away from water. It is not a single bond in the same sense as a covalent bond; instead, hydrophobic R-groups tend to pack together when water is present.

pH matters because it changes charge. Amine groups in R-groups can accept hydrogen ions and become positively charged. Carboxyl groups in R-groups can release hydrogen ions and become negatively charged. Once these groups are charged, they can take part in ionic bonding. If pH changes, the pattern of charges can change, so tertiary structure can change too.

Many proteins include secondary structures within their tertiary structure, so the levels of structure are not separate boxes in a real molecule. The final shape comes from the amino acid sequence, backbone folding and R-group interactions together.

Water-soluble proteins and membrane proteins fold differently

A polar amino acid is an amino acid with an R-group that has an uneven distribution of charge and can interact with water. A non-polar amino acid is an amino acid with an R-group that lacks strong charge separation and tends to avoid water.

In water-soluble globular proteins, hydrophobic amino acids usually pack into the protein’s core, away from water. Hydrophilic amino acids are more often found on the surface, where they can form hydrogen bonds or ionic interactions with water and dissolved ions. This makes the folded protein more stable in an aqueous environment such as cytoplasm or blood plasma.

Integral membrane proteins deal with a different chemical environment. The middle of a phospholipid bilayer is hydrophobic, so the parts of an integral protein that sit inside the membrane have many hydrophobic amino acids on the outer surface of that region. That helps the protein stay embedded in the membrane.

A transmembrane channel protein shows how neatly this works. The outer surface touching the membrane core is hydrophobic, while the channel lining can be hydrophilic, allowing polar molecules or ions to pass through a route that the hydrophobic membrane interior would otherwise block.

Proteins with more than one part

Quaternary structure is the three-dimensional arrangement of more than one subunit in a protein. These subunits may be polypeptide chains; in some proteins, non-polypeptide components are present as well.

A non-conjugated protein contains only polypeptide subunits. Insulin is non-conjugated because it has two polypeptide chains held together, including by disulfide bonds. Collagen is non-conjugated too: three polypeptide chains wind around one another to form a strong rope-like structure.

A conjugated protein includes one or more non-polypeptide components as well as its polypeptide chains. Haemoglobin is the main example. It has four polypeptide subunits, each associated with a haem group. The haem group contains iron and binds oxygen, making this non-polypeptide component essential to haemoglobin’s transport function.

Technology and seeing protein structure

Protein molecules are much smaller than the unaided eye can see, and many are too small for ordinary light microscopy. Cryogenic electron microscopy rapidly freezes biological molecules and images them with electrons, allowing scientists to study very small protein structures and protein interactions.

This works well as a Nature of Science example: technology changes what counts as observable. When scientists can image single protein molecules and their interactions, they can link structure to function much more directly, including changes in conformation during molecular activity.