#7- The Macromolecules of Life (III): Proteins

Now helping you understand the “sUsPiCiOuS cHeMiCaLs” listed on most of your food and supplement labels

Good job on keeping up with my posts! 👏🎉 I am happy that you enjoy reading them and find them helpful, be it for education or curiosity’s sake. Even if you understood only some of it, that’s okay because you are making an effort 🙌

This week’s post shall be on proteins, one of the crucial macromolecules needed for making all living organisms, going from your well-toned muscles to the capsids of viruses. I shall talk about, amino acids, structural basics, and their importance, but keeping it short as usual.

First stop! Amino acids.

Amino Acids: Proteins’ Monomers

Large molecules need smaller units to build them up, and that’s where amino acids come in to make the proteins.

Before going ahead, amino acids are called so because one amino acid molecule, for instance, alanine, has one amino group ( — NH2) and a carboxylic acid group ( — COOH).

Typical structure of an amino acid showing an amino group (left) and a carboxylic acid group (right) covalently bonding with the central alpha carbon (center). ‘R’ stands for any side chain. Source in caption.
Figure 1- A typical structure of an amino acid showing an amino group and a carboxylic acid group covalently bonding with the central α carbon. ‘R’ stands for any side chain. Source- Advanced Biology, by Kent, 2nd Edn.

You are not going to believe this! There are 500 amino acids found in nature, of which only 22 of them are found in the genetic code, where 20 amino acids are in the standard genetic code, and the other 2 are added via special translation mechanisms. To keep things nice and simple, we will just learn about the 20 amino acids. Know more about the codons on Post #6!

Interesting!: The amino acid asparagine, the first to be discovered in 1806, was named so since it originated from asparagus.

A concise table showing the 20 amino acids, their recognised abbreviations, and their side chains designated as ‘R’. Source in caption.
Table 1- A concise table showing the 20 amino acids, their recognised abbreviations, and their side chains designated as ‘R’. Source- Advanced Biology, by Kent, 2nd Edn.

The R groups in amino acids can vary from simple to complex side chains (See Table 1), and their properties range from non-polar and hydrophobic, or polar and hydrophilic.

One neat feature about them is the ability to have both an acidic and basic property when allowed to dissociate in water. Hence, they are amphoteric. This kind of quirk allows them to make an acidic solution have a neutral pH by accepting protons (H+ ions) through the amino group. The same can be said in the case of a basic solution going neutral, and this time the carboxylic acid group donates a proton. Figure 2 below explains this phenomenon.

It CaUsEs CaNcEr!: Monosodium glutamate (MSG), basically, glutamic acid + one sodium atom, doesn’t cause serious health issues like cancer, or anything nasty at all!! It just enhances the meaty and savoury flavour in many food items and snacks like your favourite bag of chips. It is also responsible for the fifth basic taste called umami, naturally present in tomatoes, cheese, and kombu seaweed. People do have some sort of allergic reaction to them though, but otherwise, nothing crazy, trust me 👌

Described in main text. Source in caption.
Figure 2- Depiction of the amphoteric nature in a typical amino acid molecule. Source- Advanced Biology, by Kent, 2nd Edn.

We’re not done yet because there is another trick an amino acid can pull off! When the pH reaches a specific point, which is different for each amino acid, the molecule will simultaneously become positively and negatively charged, forming a zwitterion (See Fig. 2). Overall, amino acids can be excellent buffers as they make sure body fluids are at their normal levels.

You must be familiar with how large chains of nucleic acids and carbohydrates are made by joining many monomeric units through special bonds. Here, amino acids bond with each other via the formation of peptide bonds due to condensation. This occurs between the carboxyl group of one amino acid and an amino group of the other (See Fig. 3). It can also be reversed by hydrolysis just like carbohydrates.

Description of figure in main text. Source in caption.
Figure 3- Formation of the peptide bond between two amino acids by condensation and reversed by hydrolysis reaction. Source- Advanced Biology, by Kent, 2nd Edn.

When a peptide bond is made with two amino acids, it is a dipeptide. Adding more amino acids one after the other will get you a polypeptide chain, and it won’t have any branching.

Point to Remember: The four elements needed to make an amino acid are carbon, oxygen, hydrogen, and nitrogen.

Now finally moving onto proteins!

Proteins, Proteins, and More Proteins

Ah, proteins, the important macromolecules that take part in many roles in many living beings. They make up a high percentage of the structures and biological functions categories. Did you know that approximately 18% of the human body has protein? Now that’s amazing!

Protein Factoid: The largest known protein in the human body is dystrophin, which is produced by muscle cells. The lack of it causes muscular dystrophy making the person undergo muscle wasting. It is coded by the largest gene in the human genome named DMD (Duchenne Muscular Dystrophy) gene.

Proteins are made of one or more polypeptide chains that later fold into a cool unique 3D structure with the help of other proteins in the cells’ cytoplasm. They can be simple, by only having amino acids, and others can be conjugated proteins that possess a non-amino acid accessory called a prosthetic group.

There are four different levels of protein structure — primary, secondary, tertiary, and quaternary. We shall look into each of them in a bit of detail.

Primary Structure: The Amino Acid String

This type of structure is a string or sequence of amino acids that make up the polypeptide chain or chains. If one amino acid is missing or got changed, the protein cannot carry out its work properly, resulting in seriously debilitating issues in the person.

The 153 amino acid-long sequence of the myoglobin polypeptide chain, found in muscle cells. It is a conjugated protein that holds an iron-containing prosthetic group (not shown). Source in caption.
Figure 4- The 153 amino acid-long sequence of a myoglobin polypeptide chain, found in muscle cells. A conjugated protein that holds an iron-containing prosthetic group (not shown). Source- Advanced Biology, by Kent, 2nd Edn.

Secondary Structure: Coils and Folds

Alpha-helix (top) and beta-pleated sheet (bottom) secondary structures. The hydrogen bonds shown as dotted orange lines retain the shape of the protein. Source in caption.
Figure 5- α-helix and β-pleated sheet secondary structures. Source- Advanced Biology, by Kent, 2nd Edn.

A polypeptide chain is not going to simply exist as a straight chain, it needs to get some shape. There are two basic shapes — α-helix coils and β-pleated sheet folds, which are formed by hydrogen bonds between — NH and — CO groups amongst the amino acids in different regions of the polypeptide (See Fig. 5).

You will notice that the hydrogen bonds in these shapes are efficiently spaced out to stabilise the structure. A single polypeptide can have both an α-helix and β-pleated sheet in some regions, and some are entirely made of just one or the other.

Tertiary Structure: Going 3D

It is the overall three-dimensional structure of a polypeptide chain. This is split into two categories:

  • Fibrous: Long parallel polypeptide chains form cross-links at intervals with each other to create sturdy fibres or sheets. They are usually insoluble in water and are pretty tough, hence you find them as structural proteins most of the time. Examples: Spider silk, keratin in hair and skin, etc.
  • Globular: Polypeptide chains are folded tightly into an almost spherical shape. Most of them do this to hide the hydrophobic regions and have only the hydrophilic portions exposed, making them soluble, like antibody proteins (See Fig. 6), hormones, etc.
A ribbon model of the actual tertiary structure of IgG antibody, a Y-shaped molecule where the two stretched arms help to bind to highly specific regions of the germ’s proteins. Source in caption.
Figure 6- A ribbon model of the tertiary structure of IgG antibody, a protein where the two stretched arms help to bind to highly specific regions of the germ’s proteins. Source- By Tokenzero — Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=95724189

The tertiary structure of a protein relies a lot on the primary structure because one mistake can result in the incorrect folding of the chain. Therefore, every detail on the protein, such as bumps, dents, twists, and coils should be absolutely 100% correct so it can do its job properly.

Molecular Assisstant Folders: Protein chains can fold on their own just fine, but molecular chaperones often show up to help the unfolded, or partially folded chains reach their perfectly folded forms more quickly, with less energy costs, and no damage to other proteins in the cramped cytoplasm.

The reason why the whole tertiary structure is perfectly shaped and not looking unstable is because of these awesome bonds:

Figure 7- The formation of a disulphide link by loss of a hydrogen molecule in cysteine’s side chain. Source- Advanced Biology, by Kent, 2nd Edn.
  • Hydrogen bonds
  • Disulphide bonds (See Fig. 7)
  • Ionic bonds
  • Hydrophobic interactions- Exists between hydrophobes 👀

The stinky smell of burning hair? That’s the disulphide bonds breaking, babe! It’s one of the strongest bonds that is broken by heat, which brings us to denaturation.

The denaturation event of proteins occurs through the change of pH, temperature, or salt concentration, thereby altering their shape. That’s why you can’t turn a boiled egg back into a raw egg! No take-backsies here…for most of the denaturation reactions.

Differences in denaturing (a) globular protein into an insoluble protein and (b) fibrous protein into a flimsy structure-less protein. Source in caption.
Figure 8- Differences in denaturing (a) globular protein and (b) fibrous protein. Source- Advanced Biology, by Kent, 2nd Edn.

Quaternary Structure: When One Polypeptide is Not Enough

This could be the final form of many proteins, like haemoglobin in red blood cells (RBCs), where more than one polypeptide are held together by chemical bonds.

The quaternary structure of haemoglobin showing two alpha chains (red) and two beta chains (blue) each having an iron-containing haem group (green) to carry oxygen. Source in caption.
Figure 9- A ribbon model of the quaternary structure of haemoglobin showing two α (red) and β chains (blue), each having an iron-containing haem group (green) to carry oxygen. There are 140 amino acids in each chain. Source- By Zephyris at the English-language Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=2300973

Amazing! You now know waaay too much about proteins (which is great 🙌) but this is just the beginning 👀 I really enjoyed doing this since I love looking at pretty protein structures as it reminds me of my time at university.

That’s all folks! You may subscribe/follow me for more simplified microbiology in your life 😊👍

Glossary

Capsids- Viruses that lack a lipid bilayer have a tough protein shell which comes in interesting and beautiful geometric shapes to contain their genome

Covalent bond- When two elements share a pair of electrons to form a bond

Translation- Production of proteins from a messenger RNA (mRNA) with help of many proteins, including ribosomes

Acidic- Ability of a molecule to donate one or more protons

Basic/Alkaline- Ability of a molecule to accept one or more protons

pH- The scale ranging from 0 to 14 to measure how acidic (low pH), basic (high pH) or neutral (pH 7) a substance is

Antibody- Y-shaped molecules produced by B-cells to fight off infections by recognising specific proteins from bad germs

IgG- Immunoglobulin G antibody which is part of the five types of antibodies we produce in our bodies

Ionic bond- Bond formation by the complete transfer of one or more electrons to the other to gain a positive charge and bind with the negatively charged element

Sources

  • Chapter 2: The Chemicals of Life, Section 2.9: Introduction to Proteins. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Chapter 2: The Chemicals of Life, Section 2.10: Protein Structure and Function. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Part I: INTRODUCTION TO THE CELL, Chapter 3: Proteins. From the textbook Molecular Biology of the Cell, by Alberts et al., 6th Edn.
  • Part II: BASIC GENETIC MECHANISMS, Chapter 6: How Cells Read the Genome: From DNA to Protein. From the textbook Molecular Biology of the Cell, by Alberts et al., 6th Edn.
  • Me remembering stuff from my school and university lectures

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