Amino Acids, Peptides, Proteins

Amino acids are the building blocks of proteins. They create the protein’s primary structure. There are 20 naturally occurring amino acids.2 When two amino acids join they form a peptide bond. An alpha-carbon is so named because it is the first carbon attached to a functional group. In the case of amino acids, the α-carbon is also the central carbon, making up the backbone in a polypeptide chain with a bond to an amino group (NH2) on one side and a carboxyl group (COOH) on the other. As a tetrahedral atom, an amino acid’s α-carbon holds bonds to four substituents (the NH2, the COOH, the H, and the R group), thereby making it a chiral center in all but one amino acid, glycine, whose R group is a second hydrogen atom. The spatial organization of substituents around the chiral α-carbon determines the absolute configuration of the amino acid. The absolute configuration distinguishes between the amino acid’s two stereoisomers, which are non-superimposable mirror images

In aqueous environments, the amino and carboxyl groups of an amino acid will be ionized. In an acidic environment (low pH), the amino acid will take a cationic form with an extra hydrogen on it amino group (NH3+) and the carboxyl group holding its hydrogen (COOH). In a basic environment (high pH), the amino acid will take an anionic form with its amino group in its neutral state (NH2) and the carboxyl group releasing its hydrogen (COO). At a neutral pH, the amino acid will exist as a neutral zwitterion or dipolar ion, holding a positive charge on its amino group (NH3+) and a negative charge on its carboxyl group (COO).

Amino acids can be classified in several ways. An amino acid will be acidic or basic if it has electrically charged side chains. As such, aspartic acid (aspartate as an anion) and glutamic acid (glutamate as an anion) are acidic amino acids because of the carboxyl group in their side chains, and arginine, histidine, and lysine are basic amino acids because of the amine in their side chains.2 Amino acids have a range of hydrophobicity (a measure of how soluble the amino acid is in water) based on their side chains. Side chains that are non-polar or mainly hydrocarbons are generally more hydrophobic. Side chains that are polar or with a group that participates in hydrogen bonding, such as a hydroxyl, a carboxyl, or an amine are generally more hydrophilic. Hydrophobic amino acids are generally found within the interior of a protein or exposed in a non-polar local environment such as a lipid membrane. Hydrophilic amino acids are readily found on the exterior of a protein, exposed to an aqueous environment.

A covalent disulfide bond can form between the sulfur containing R-groups (CH2SH) on two cysteine molecules, producing the amino acid cystine. Disulfide bonds between cysteine residues can affect protein folding and stability. Amino acids form polypeptide chains via peptide bonds, which are formed when the amine of one amino acid forms a covalent amide bond with the carbonyl carbon on a second amino acid, releasing a molecule of H20 in the process. Peptide bond formation is thus an example of a dehydration synthesis reaction because of the generation of water as a result of the linkage. Breaking a peptide bond requires the addition of a hydrogen to one amino acid’s amine group and a hydroxyl to the other amino acid’s carbonyl carbon (the breaking of water), thus classifying it as a hydrolysis. The function of the protein is determined by its structure, therefore each layer is dependent on the next. .

Strecker amino acid synthesis is an organic reaction used to convert an aldehyde or ketone and a primary amine or ammonia to an α-amino acid using a metal cyanide, acid catalyst, and water.2 The mechanism begins with the acid catalyzed reaction of the carbonyl with the amine to give the corresponding imine. The imine is then attacked by the cyanide to provide a nitrile intermediate. The nitrile gets protonated by the acid, is attacked by a molecule of water and after a series of proton transfer steps results in an amide intermediate. In the reaction’s acid conditions, the amide gets protonated and the amine group is displaced by water to eventually yield the carboxylic acid group and the final amino acid product. A simplified reaction of the overall processes is shown below:



The Gabriel synthesis is a chemical reaction that transforms primary alkyl halides into primary amines. Traditionally, the reaction uses potassium phthalimide. Potassium phthalimide is a NH2-synthon which allows the preparation of primary amines by reaction with alkyl halides. After alkylation, the phthalimid is not a nucleophile and does not react anymore. The product is cleaved by reaction with base or hydrazine, which leads to a stable cyclic product. A simplified reaction of the overall processes is shown below:





The primary structure of protein is the specific sequence of amino acids joined together by peptide bonds in a polypeptide chain. There are 20 different amino acids found in nature. The sequence of amino acids is determined by the DNA sequence that encodes for that particular protein. This is known as the gene. By convention a polypeptide starts on the end of the amino acid with its amine group exposed (the N-terminus) and finishes at the opposite end of the chain on the amino acid with its carboxyl group exposed (the C-terminus). The primary structure of proteins is read from the N-terminus to the C-terminus. The secondary structure of proteins is based on repetitive motifs formed by backbone interactions as a result of hydrogen bonding between the NH and C=O. The secondary structure is stabilised by hydrogen bonds between the C=O and H-N groups for the peptide backbone. This, in turn, allows the protein to have a hydrophobic core and a hydrophilic surface. Secondary structure is the first level of protein folding. The two most common secondary structures are α helices and β pleated sheets. The α helix is right-handed, with the R groups sticking outward and the β sheets, have their R groups sticking above and below the sheet. The tertiary structure of proteins refer to the 3D structure of proteins and it results from electrostatic side chain – side chain interactions.  Tertiary structure relates to the protein function.  If the tertiary structure is altered, then the protein is unlikely to function properly. Tertiary structure is held together by either hydrogen bonds or disulphide bridges depending on the amino acids present. Disulphide bridges are formed between the amino acid. The quaternary structure is made up of separate chains/subunits joining together and it is caused by covalent disulfide bonding of cysteine side chains. Two or more tertiary structures of protein linked together build up a quaternary structure. Quaternary structure can also refer to proteins with an inorganic prosthetic group attached, an example being haemoglobin, which consists of four myoglobin subunits and an iron-containing haem group. Two of the subunits are alpha, and two are beta. Isoelectric refers to the point at which the pH of molecule is neutral. Acidic amino acids and proteins with lots of acidic side chains have a lower isoelectric point while basic amino acids and proteins with lots of basic side chains have a higher isoelectric point.

Hydrophobic interactions describe the relations between water and low water-soluble molecules. Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules. Hydrophobic Interactions are important for the folding of proteins. This is important in keeping a protein stable and biologically active, because it allow to the protein to decrease in surface are and reduce the undesirable interactions with water.

Protein folding is a consequence of intermolecular forces, including pure ionic interactions, dipole interactions, hydrogen bonds, van der Waals forces and hydrophobic interactions. To be biologically active, a protein must adopt and maintain a specific conformation under physiological conditions. Hydrophobic interactions utilize both repulsion and attraction to contribute to a protein’s conformational stability. The repulsion comes from the thermodynamically favorable shielding of hydrophobic residues afforded by their location inside the protein. The attraction results from van der Waals forces between nonpolar side chains on the polypeptide which are amplified in the close quarters of a hydrophobic core and produce a greater affect in larger proteins. The solvation layer (or shell) describes the structured organization of a solvent (e.g. water) around a solute. In the case of a protein which displays hydrophobic residues on its surface, the surrounding water will orient into a highly structured organization to optimize hydrogen bonding among water molecules, as hydrogen bonding with the presented hydrophobic side chains is not an option). This highly ordered rearrangement has a much lower entropy and is less favorable than if polar side chains were present on the surface of the protein. Thus, a conformation that buries its hydrophobic residues inside the protein leads to less disruption of water’s hydrogen bonding, allowing for less structure and higher entropy, which increases the protein’s conformational stability. Temperature is one factor that affects proteins as spontaneous rearrangement at its melting temperature will occur. This affects the secondary, tertiary and quaternary structure. Adverse pH conditions can disrupt the ionic bonds and hydrogen bonds of proteins and this affects the secondary, tertiary and quaternary structure. High salt concentration     causes the disruption of non-covalent interactions and this affects the secondary, tertiary and quaternary structure. Certain solvents will result in the disruption of hydrogen bonding in protein and this also affects the secondary, tertiary and quaternary structure. Certain enzymes can lead to the hydrolysis of peptide bonds, which only affects the primary structure.

One role a protein may play is as a biological catalyst, or enzyme, which assists in accelerating a chemical reaction by lowering the activation energy of the reaction. Enzymes are of incredible biological importance but the biological utility of proteins also extends into non-enzymatic functions, such as structure (e.g. collagen), transportation (e.g. hemoglobin), regulation (e.g. peptide hormones), movement (e.g. myosin), and immune defense (e.g. antibodies). A special feature of some proteins is the capability to bind other molecules with non-covalent interactions. Protein binding can be characterized by its affinity and specificity for the binding target. Affinity describes how readily the protein binds its target, and specificity refers to the preferential binding of the target over other entities. A change in the protein’s conformation can alter affinity and specificity as seen in the control of voltage-gated ion channels in cell membranes. The high degree of protein variability allows for a key feature of the adaptive (or acquired) immune system, which is the production of antibodies. An antibody is a type of protein that has a unique and very specific binding site that will readily bind its target, called an antigen, such that its target is inactivated or tagged for immune response. A motor protein can perform mechanical work by coupling exergonic (energy releasing) ATP hydrolysis to a conformational change that allows for interaction with the protein’s target substrate. Muscle contraction, for example, is achieved through a process of the motor protein myosin binding and releasing its microfilament (actin) substrate. Myosin also acts on microfilaments of the cytoskeleton to generate cellular movement.

Two other types of motor proteins, kinesins and dyneins, act on microtubules and play a role in transport within the cell. Kinesin walks microtubule tracks to deliver cellular cargo (e.g. chromosomes during mitosis), generally in an antegrade direction (center to periphery). Dynein is used in retrograde cargo transport in the axons of neurons, and is capable of sliding microtubules in relation to one another, generating the movement of cilia and flagella.



1) Bruce Alberts, A. J. (2007). Molecular Biology of the Cell.

2) Van Holde KE, M. C. (1996). Biochemistry. Menlo Park, California: Benjamin/Cummings Pub. Co., Inc.

3) NV, B. (2002). Medical Biochemistry. San Diego: Harcourt/Academic Press.

4) Suman Khowala, D. V. (2008, June 4). Biomolecules: (introduction, structure & function) . Retrieved from

5) H. M. Asif, M. A. (2011, January 21). Carbohydrates. Retrieved from International Research Journal of Biochemistry and Bioinformatics:


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