Structure of Amino Acids and Proteins

What Are Proteins?

Proteins are among the three macronutrients that are essential for the structure and function of cells. They have various biological functions in the body including structure, storage, transportation, protection, hormone and enzyme activity. The smallest unit of a protein is called an amino acid. Two amino acids joined together is called a dipeptide, three is a tripeptide, four is a tetrapeptide, five is a pentapeptide and move than five is called a polypeptide. Polypeptides that are 50 amino acid units long or more is called a protein.

Know the 9 Essential Amino Acids

There are 20 amino acids that make up proteins. Nine of them are essential. The nine can be memorized using the mnemonic: “High protein intake left Larry’s muscles very tightly toned” i.e. –

1. High: Histidine
2. Protein: Phenylalanine
3. Intake: Isoleucine
4. Left: Leucine
5. Larry’s: Lysine
6. Muscles: Methionine
7. Very: Valine
8. Tightly: Threonine
9. Toned: Tryptophan

Know All 20 Amino Acids and their Abbreviations

The table below shows you a list of all 20 amino acids and their 3 and 1-letter abbreviations.

Notice that with the exception of tyrptophan, they end with the “ine” or “ic” (you may also see glutamic and aspartic acid given as glutamate and aspartate respectively). You should also notice that in most cases, the 3-letter abbreviations are the same as the first three letters of the amino acid e.g. alanine = ala. Similarly, in most cases, the one-letter abbreviation is the same as the first letter of the amino acid e.g. alanine = A. However, there are some exceptions, e.g. –

• Asparagine: Asn, N
• Memory tool: Remember that ends with an “N” sound
• Arginine: Arg, R
• Memory tool: The first two letters sounds like “R”
• Aspartic acid: Asp, D
• Memory tool: Pronounce it as “aspar-Dick” acid to remember the D
• Glutamic Acid: Glu, E
• Memory tool: The combined abbreviations spells “gluE”
• Glutamine: Gln, Q
• Memory tool: Pronounce it as “Q-tamin” with an “n” at the end
• Isoleucine: Ile, I
• Memory tool: “so” was isolated from “isole” leaving “Ile”
• Lysine: Lys, K
• Memory tool: “K” is next to “L”
• Phenylalanine: Phe, F
• Memory tool: The 1-letter abbreviation sounds like the first letter of the amino acid
• Tryptophan: Trp, W
• Pronounce it as “T-W-iptophan” to remember the W
• Tyrosine: Tyr, Y
• Memory tool: Think of the Y as resembling a “neck-tie” to remind you of “tyrosine”

Creating abbreviations for amino acids is necessary to simplify writing of amino acids sequences. For example a sequence of amino acids containing histidine, lysine, arginine, tryptophan and alanine would be written as: his-lys-arg-trp-ala, or H-K-R-W-A. consider if you had to write a sequence that was 20,000 amino acids long. Can you see how cumbersome writing out the entire name would be?

The Structure of Amino Acids

Now, let’s take a look at the structure of amino acids and proteins beginning with amino acids. An amino acid contains an amino group, a carboxylate group, an R group which distinguishes one amino acid from another, and a carbon called an alpha carbon on which a hydrogen and the R group is connected.

Amino acids are divided into basically two groups. They are either non-polar or polar. Non-polar amino acids are hydrophobic (water-hating) meaning that they cannot dissolve in water. Polar amino acids are are hydrophillic (water-loving) and can therefore dissolve in water. Polar amino acids may be one of three types, i.e. basic, acidic or neutral. Notice that this spells “BAN” to help you remember.

Of the 20 amino acids 9 are non-polar. The number nine should remind you of cats since they have “nine lives”. Also, remember that cats hate water to recall that these amino acids are hydrophobic. Three amino acids are polar-basic, two are polar-acidic and six are polar neutral. If you remember the time, three minutes to six (3-2-6), you will remember the amino acids that are “BAN”.

Non Polar Amino Acids

Note: The numbers at the bottom of each amino acid represents its isoelectric point. This is the pH at which the amino acid is neutral.

Memory tool: LIMP And Very Wet Grumpy Feline

Polar Basic Amino Acids

Polar basic amino acids have an extra amine group which is attached to the side chain. Since only one of the charged groups can be neutralized by the acid group, the amino acid is left with a net positive charge.

Memory tool: We get our basic training from Home, Kindergarten and Reality

Polar Acidic Amino Acids

Polar acidic amino acids are have an extra carbonyl group which is attached to the side chain. Since only one of the charged groups can be neutralized by the amino group, the amino acid is left with a net negative charge.

Memory tool: The only amino acids ending with “ate” or “ic”.

Polar Neutral Amino Acids

These amino acids are polar (able to interact with water) due to differences in electronegativity in the OH, SH and C-O bonds. This happens because O and  S “hogs” electrons causing it to become negatively charged and the H positively charged. However, the groups are still neutral overall, since the atoms have an equal amount of electrons and protons.

Memory tool: Remember that water has a neutral taste. Therefore let’s use a mnemonic that has to do with water: Youthful Swimmers Never Quit Tough Competitions.

Forming Peptide Bonds

Amino acids join together to form long chains called polypeptide chains. Each amino acid is joined at a peptide bond. This is the result of a condensation reaction involving the loss of two hydrogen and an oxygen atom (H₂O).

The resulting peptide has an N-terminus at the amino end and a C-terminus at the carbonyl end. Amino acid sequences are written from left to right from the N to the C terminus.

Rigidity of Peptide Bonds

Peptide bonds are restricted to a single plane, that is, they are not able to rotate within the bond. Instead, rotation occurs at the alpha carbon. This restriction is due to the fact that electrons in the bond are delocalized (not restricted to a single bond) making it possible for the C-N bond to be a double bond and hence rigid, given the inflexible nature of double bonds.

How to Name Peptides

Drop the “ine” or “ate” and replace with “yl”. Leave the last (C-terminal) amino acid unchanged e.g.

1. Alanine-proline = alanylproline
2. Serine-histidine-glycine = serinylyhistidylglcyine
3. Lysine-methyonine-tyrosine-alanine = lysylmethyonyltyrosylalanine

Structure of Proteins

Proteins have four basic structural levels. These are primary, secondary, tertiary and quaternary. The structure of proteins play a key role in determining their functional properties. See my article on functional properties of proteins.

Primary

Secondary

Secondary structure of protein is the structure formed due to hydrogen bonding within the same peptide chain or across peptide chains. The two common types of secondary structures are alpha-helix and beta-pleated sheets. Structures that are neither alpha-helix or beta-pleated sheets are called random coils. Alpha helices have a spring-like appearance due to hydrogen bonding between the oxygen atom in the C=O bond and the hydrogen in the N-H bond four amino acids away.

Beta-pleated sheets consist of lengths of polypeptides running along side each other and connected by hydrogen bonds. The sheets can be caused by a bend in the same polypeptide chain or may be due to interaction across different polypeptide chains. Beta-sheets are so called because they form a zig-zag pleat-like structure.

The polypeptide strands may run in either a parallel or anti-parallel direction. You can tell the direction by looking at the ends to find the C and N-terminals. If the terminals of both strands line up, they are moving in an antiparallel direction. However, if they are on the opposite sides, they are parallel. You can also tell if the strands are running parallel or anti-parallel by counting the number of atoms in the hydrogen-bonded rings. Strands that are running parallel will have exactly 12 atoms in the rings while those that are running antiparallel will have 10 and 14 atoms alternating in the rings.

Tertiary

The tertiary structure of protein is caused by different forces of attraction and repulsion between amino acids in the polypeptide chain causing it to twist and bend resulting in a specific shape. These forces may be a combination of hydrophillic interaction with water, salt bridges (ionic bonds), disulfide bonds and hydrophobic interactions.

These bonds can be disrupted in a process called denaturation where the protein loses its shape. This can occur due to heat, agitation, and the presence of alcohol and acids. A good example of heat denaturation is seen when egg is fried. You can see denaturation occurring before your eyes as the transparent albumin turns white and the whole egg becomes solid. When we swab our hands with alcohol, we kill bacteria by denaturing proteins in the bacteria. When we whip egg-white it turns to a foam due to denaturation. An example of acid denaturation is seen in the production of cheese and yogurt. The presence of lactic acid produced by bacteria, causes the casein in the milk to coagulate.

Quaternary

Quaternary structures consist of two or more tertiary protein structures, called sub-units working together. They are held together by the same forces as required in tertiary structures. Most biologically active proteins are in the quaternary form. An example is hemoglobin shown in the image below. Hemoglobin consists of 4 different sub-units.

Big Ideas

1. Proteins are made up of amino acids
2. There are twenty amino acids, nine of which are essential
3. Amino acids are either polar or non-polar
4. Polar amino acids are either basic, acidic or neutral
5. Proteins consist of four structural levels – primary, secondary, tertiary and quaternary

Reference: Timberlake, KC. 2016. General, organic, and biological chemistry – Structures of life (5th edition). Boston, MA:Pearson Inc.