Proteins

Proteins are a vital class of biological molecules, complex in structure and diverse in function, found in all living organisms and cells. Unlike lipids and carbohydrates, proteins contain the element nitrogen, and often sulfur, in addition to carbon, hydrogen, and oxygen.

What Proteins Are Made From: Amino Acids

The monomers of proteins are amino acids.

• All amino acids share the same general structure: a central carbon atom (also called the "alpha carbon") bonded to an amino (or amine) group (-NH2), a carboxyl (or carboxylic acid) group (-COOH), and a hydrogen atom.

• The distinguishing feature among the 20 common amino acids found in all organisms is their R group (or variable side group). This R group generally contains carbon, with glycine being an exception as its R group is just a single hydrogen atom. The unique R group of each amino acid gives it different properties.

Formation and Breakdown of Proteins

Amino acids link together through condensation reactions to form dipeptides (two amino acids) and polypeptides (more than two amino acids).

• During this reaction, a molecule of water is released.

• The bonds formed between amino acids are called peptide bonds.

• The reverse process, hydrolysis, breaks these peptide bonds by adding water, which occurs naturally during protein digestion in the stomach and small intestine.

• A polypeptide typically becomes a protein when it is about 50 amino acid molecules long. A functional protein may contain one or more polypeptides.

Levels of Protein Structure

Proteins are large, complex molecules whose structure can be described in four levels:

1. Primary Structure: This is the sequence of amino acids in the polypeptide chain. The DNA of a cell dictates this sequence, which in turn determines the protein's overall shape and function. Even a single amino acid change can significantly alter the protein's properties.

2. Secondary Structure: The polypeptide chain doesn't remain flat and straight. Hydrogen bonds form between the amino acids in the chain, causing it to coil into an alpha (α) helix or fold into a beta (β) pleated sheet. These shapes are stable due to the hydrogen bonds.

3. Tertiary Structure: The coiled or folded chain of amino acids often coils and folds further to form a precise, compact three-dimensional shape. This unique shape is held permanent by various bonds and interactions between different parts of the polypeptide chain, especially between the R groups of amino acids. These include:

   • Hydrogen bonds.

   • Ionic bonds (attractions between negative and positive charges).

   • Disulfide bridges (covalent bonds between sulfur atoms of two cysteine molecules). These are stronger than ionic and hydrogen bonds.

   • Hydrophobic interactions (between non-polar R groups).

   • For proteins made from a single polypeptide chain, the tertiary structure forms their final 3D structure. It also determines the shape of an enzyme's active site, making enzymes specific to their substrates.

4. Quaternary Structure: Some proteins are made of several different polypeptide chains (subunits) held together by bonds. For proteins with more than one polypeptide chain (e.g., haemoglobin, insulin, collagen), the quaternary structure is the protein's final 3D structure. Not all proteins have a quaternary structure.

Types and Functions of Proteins

Proteins have a vast array of functions in all living organisms, directly related to their specific 3D shapes.

• Globular Proteins:

  • Are generally soluble and have a roughly spherical (compact, round) three-dimensional shape.

  • Their polypeptide chains coil so that hydrophilic R groups are on the outside (interacting with water) and hydrophobic R groups face inwards. This makes them easily transported in fluids.

  • Examples include:

    • Enzymes: All enzymes are globular proteins, acting as biological catalysts to speed up metabolic reactions by lowering activation energy.

    • Haemoglobin: An oxygen-carrying pigment in red blood cells, composed of four polypeptide chains (two alpha and two beta globin chains), each with an iron-containing haem prosthetic group. It is soluble and transports oxygen around the body.

    • Hormones: Some hormones like insulin and glucagon are proteins.

    • Antibodies: Involved in immune response, made of two light and two heavy polypeptide chains with variable regions for antigen binding. They are globular glycoproteins.

    • Transport proteins: E.g., channel proteins and carrier proteins in cell membranes, transporting molecules and ions across membranes.

    • Storage proteins: E.g., casein in milk and ovalbumin in egg white.

• Fibrous Proteins:

  • Are physically strong, generally insoluble in water, and typically have structural roles.

  • Consist of long polypeptide chains lying parallel to each other with cross-links. They have little or no tertiary structure.

  • Examples include:

    • Collagen: Has three polypeptide chains tightly coiled together, making it strong; it's a major component of connective tissue in animals, like bone, skin, tendons, and cartilage.

    • Keratin: Found in hair and nails, provides waterproofing and structural strength.

    • Actin and Myosin: Responsible for muscle contraction.

Biochemical Test for Proteins

The presence of proteins can be tested using the Biuret test.

• First, the test solution needs to be alkaline, so a few drops of sodium hydroxide solution are added.

• Then, some copper(II) sulfate solution is added.

• If protein (peptide bonds) is present, the solution turns purple. If no protein is present, the solution will stay blue.

Related Concepts

• Protein Synthesis: Proteins are synthesized (made) using instructions in DNA through two main stages: transcription (DNA code copied into mRNA) and translation (mRNA code used to synthesize protein at ribosomes).

• Denaturation: This is the loss of a protein's three-dimensional (tertiary or quaternary) structure. It occurs when the bonds maintaining the shape are changed, often due to extreme temperatures or pH. Denaturation typically causes the protein to lose its function.

• Proteins in Cell Membranes: Proteins are essential components of cell membranes, fitting into and across the lipid bilayer. They have hydrophobic and hydrophilic regions, which determine their positioning within the membrane. Membrane proteins serve diverse roles, including transport (channel and carrier proteins), receptors for signaling, cell recognition (glycoproteins), enzymes, and maintaining cell shape.