Proteins are one of the four major types of biomolecules. They are linear, heterogeneous polymers made up of monomers called amino acids. Though amino acids share a basic structure, they have a variable group that determines their identity and properties. In this topic, we'll focus on how the structure of amino acids affect their properties.
Structure of amino acid
Amino acids are a family of organic compounds with the same fundamental structure. Each amino acid consists of a central, or alpha, carbon atom (C) bonded to an amino group (-NH2), a carboxylic group (-COOH), and a hydrogen atom (H). The fourth chemical bond connects the alpha carbon atom to the "R group", which is the variable side chain of the amino acid that can be a single atom or group of atoms. The R group is the only difference between more than 500 naturally occurring amino acids and determines their chemical properties. Thus, the basic chemical formula of an amino acid is NH2CHRCOOH. This is their electrochemically neutral form, but it is almost non-existent in our bodies!
Here is the thing. The amino group is basic, which means it can accept a positively-charged atom of hydrogen (H+). Simply put, the amino group can take a proton from its surroundings and become positive. The carboxylic group is acidic, which means it can donate, or give, a proton. Because they contain both positive and negative parts, amino acids are called amphoteric and can act as weak bases or weak acids depending on the environment. In pure water, which is neutral, functional groups of amino acid give and take protons. Gaining and losing the protons makes the functional groups of the amino acid charged, so its overall structure is NH3+CHRCOO−.
Amino acids are chiral molecules. This means that they exist in two alternative forms that are the mirror images of each other, just like our right and left hands. These forms are called L- and D-enantiomers. In living organisms, almost all amino acids have the L-configuration. The only exception are D-amino acids in some bacterial structures, but they are never present in proteins.
Amino acid groups
Of over 500 known amino acids, a subset of only 20 of them make up every protein contained in living organisms. Here you can see their structures. Let's take a closer look at them. Based on the chemical nature of the R group, these 20 amino acids can be classified into four general types.
Nonpolar amino acids have hydrophobic R groups. A polymer made of nonpolar amino acids will fold in such a way to cover these R groups from the water. Glycine, alanine, phenylalanine, valine, leucine, isoleucine, proline, methionine, and tryptophan are the nonpolar amino acids.
- Glycine (Gly/G) is the simplest amino acid; its R group is just a hydrogen atom. Thus, it is the only non-chiral amino acid because a single hydrogen atom does not cause any asymmetry. Since the R group of glycine is so small, it is soluble in both hydrophobic and hydrophilic environments.
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Alanine (Ala/A) is a little more complicated and has a methyl
(-CH3)R group. It is the second-most abundant amino acid found in proteins. -
Leucine (Leu/L) and isoleucine (Ile/I) have the same chemical formula but different structures, which makes them isomers. Along with valine (Val/V), they form a group of branched-chain amino acids.
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Methionine (Met/M) is one of two amino acids that contains a sulfur atom in its R group. It plays a crucial role in protein synthesis.
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Phenylalanine (Phe/ F) is exactly how its name sounds, consisting of a cyclic phenyl group attached to the alanine structure shown previously.
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Proline (Pro/P) stands out from the rest of the amino acids because its R group is bonded to its own amino group. This peculiar cyclic structure is very rigid, so proline causes kinks and bends in the amino acid chain.
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Tryptophan (Trp/W) is another variation on alanine, with an indole functional group attached to the alanine R group.
Polar, uncharged amino acids have hydrophilic R groups. Serine, cysteine, threonine, tyrosine, asparagine, and glutamine are in this group. Most of these amino acids have at least one atom (oxygen, nitrogen, or sulfur) that can interact with water.
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Serine (Ser/S) and threonine (Thr/T) contain hydroxyl
(-OH)group. -
Tyrosine (Tyr/Y) looks like phenylalanine, but one of the hydrogens on the phenyl ring is replaced with a hydroxyl group.
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Cysteine (Cys/C) contains a sulfur atom that is very chemically active, unlike the sulfur atom in methionine.
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Asparagine (Asn/N) and glutamine (Gln/Q) look similar. They both have amide R groups with oxygen and nitrogen atoms on their side chains.
Polar, negatively charged amino acids contain two carboxylic groups. There are two amino acids in this group: aspartate and glutamate. In aqueous (water-based) solutions like the cells that make up the human body, all three functional groups of these amino acids will be charged: the amino group takes a proton, getting a positive charge (+1), and the two carboxylic groups lose protons, making them negatively charged (-1x2). This gives an overall negative charge (-1).
Polar, positively charged amino acids have nitrogen atoms in their R groups that can take protons. Arginine, histidine, and lysine are in this group.
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Arginine (Arg/R) has a fixed positive charge.
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Lysine (Lys/K) takes a proton and becomes positively-charged in a neutral environment.
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Histidine (His/H) possesses a peculiar R group called an imidazole group with a five-membered ring with two nitrogen atoms, which allows it to exist in different charged states in physiological conditions. This unique quality makes histidine a key to many protein functions.
Essential and non-essential
All amino acids are necessary to build proteins, but not all of them are made in our bodies. Only 11 amino acids can be synthesized by human cells. They are termed non-essential amino acids. To get the other 9 essential or indispensable amino acids, you need to eat them. Here is the list of essential and non-essential amino acids. The division into these two groups depends little on their structure.
The set of essential amino acids varies from species to species. Plants, for example, can make all 20 amino acids by themselves.
Peptide bond
Two amino acids can be linked together by a peptide bond. In this chemical reaction, one amino acid loses an -OH from the carboxyl group, while the other loses a hydrogen (H) from the amino group, and the two amino acids become attached through a peptide bond (-CO-NH-). A molecule of water (H2O) is formed as a side product; in other words, dehydration (also called condensation) occurs.
Amino acids joined by a series of peptide bonds are referred to as amino acid residues. They make up a polymer called a peptide. If there are fewer than 50 amino acids in the polymer, it is called an oligopeptide. Larger polymers are called polypeptides. A protein molecule is a very long polypeptide built up from hundreds or even thousands of amino acid residues. Each protein has a distinctive shape and function that arise from both the proportions of the different amino acids and the order in which they are arranged.
Conclusion
All amino acids have the same general structure. They consist of a central carbon atom bonded to a hydrogen atom, an amino group, a carboxylic group, and an R group. The R group varies from one amino acid to another and determines if the amino acid is hydrophilic or hydrophobic, charged or uncharged. The amino group and the carboxylic group of two amino acids can react to form a peptide bond.
A protein consists of amino acids joined in a linear chain via peptide bonds. There are 20 different amino acids that make up proteins. The shape and the function of the protein depend on the number and the order of the amino acids.