Biological molecules: proteins

proteins

• Proteins are polymers (and macromolecules) made of monomers called amino acids

• The sequence, type and number of the amino acids within a protein determine its shape and therefore its function

• Proteins are essential in cells because they form all of the following:

  • Enzymes

  • Cell membrane proteins (e.g. carrier)

  • Hormones

  • Immunoproteins (e.g. immunoglobulins)

  • Transport proteins (e.g. haemoglobin)

  • Structural proteins (e.g. keratin, collagen)

  • Contractile proteins (e.g. myosin)

amino acids

• Amino acids are the monomers of proteins

• There are 20 amino acids found in proteins common to all living organisms

• The general structure of all amino acids is a central carbon atom bonded to:

  • an amine group -NH₂

  • a carboxylic acid group -COOH

  • a hydrogen atom

  • an R group (which is how each amino acid differs and why amino acid properties differ, e.g. whether they are acidic or basic or whether they are polar or non-polar)

peptide bonds

• To form a peptide bond, a hydroxyl (-OH) is lost from the carboxylic group of one amino acid, and a hydrogen atom is lost from the amine group of another amino acid

• The remaining carbon atom (with the double-bonded oxygen) from the first amino acid bonds to the nitrogen atom of the second amino acid

• This is a condensation reaction, so water is released

• Dipeptides are formed by the condensation of two amino acids

• Polypeptides are formed by the condensation of many (three or more) amino acids

• A protein may have only one polypeptide chain, or it may have multiple chains interacting with each other

• During hydrolysis reactions, the addition of water breaks the peptide bonds, resulting in polypeptides being broken down to amino acids

protein structure

• Proteins are macromolecules made from individual monomer units, amino acids

• There are four levels of structure in proteins

  • Three are related to a single polypeptide chain

  • The fourth level relates to a protein that has two or more polypeptide chains

• Protein molecules can have anywhere from three amino acids (Glutathione) to more than 34,000 amino acids (Titin) bonded together in chains

proteins - primary structure

• The sequence of amino acids bonded by peptide bonds is the primary structure of a protein

• DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence, during translation. This affects the shape and, therefore, the function of the protein

• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

proteins - secondary structure

• The secondary structure of a protein is held together by hydrogen bonds that form between the -NH region of one amino acid and the -C=O region of another

  • The hydrogen of -NH has an overall positive charge, while the oxygen of -C=O has an overall negative charge

• Hydrogen bonds are relatively weak, so they can be broken easily by high temperatures and pH changes

• Two shapes can form within proteins due to the hydrogen bonds:

  • α-helix

  • β-pleated sheet

• The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond

• The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other, enabling hydrogen bonds to form between the folded layers

proteins - tertiary structure

• Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)

• The additional bonds are:

  • hydrogen bonds between R groups

  • disulfide bonds between cysteine amino acids

  • ionic bonds between charged R groups

  • weak hydrophobic interactions between non-polar R groups

• This structure is common in globular proteins such as enzymes and antibodies

proteins - quaternary structure

• Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule, for example, haemoglobin

• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein

protein funciton

• Proteins perform a wide range of essential roles in all living organisms due to their diverse structures

• They are therefore vital for structure, transport, communication, defence, movement, and catalysis in all living cells:

  • Enzymes – biological catalysts that speed up metabolic reactions (e.g. amylase, DNA polymerase)

  • Transport proteins – carry substances (e.g. haemoglobin transports oxygen; channel proteins in membranes)

  • Structural proteins – provide support (e.g. collagen in connective tissues; keratin in hair and nails)

  • Hormones – regulate processes (e.g. insulin controls blood glucose levels)

  • Antibodies – part of the immune response, recognising and neutralising pathogens

  • Contractile proteins – enable movement (e.g. actin and myosin in muscles)

protein interactions

• A polypeptide chain will fold differently, into its tertiary structure, due to the interactions (and hence the bonds that form) between R groups

• Each of the twenty amino acids that make up proteins has a unique R group, and therefore, many different interactions can occur, creating a vast range of protein configurations and therefore functions

• Within tertiary structured proteins are the following bonds:

  • Strong covalent disulfide

  • Weak hydrophobic interactions

  • Weak hydrogen

  • Ionic

disulfide

• Disulfide bonds (also known as disulfide bridges) are strong covalent bonds that form between two cysteine R groups (this is the only amino acid with an available sulfur atom in its R group)

• These bonds are the strongest within a protein, but occur less frequently, and help stabilise the proteins

• They can be broken by reduction

• Disulfide bonds are common in proteins that are secreted from cells e.g. insulin

ionic

• Ionic bonds form between positively charged (amine group -NH₃⁺) and negatively charged (carboxylic acid -COO^-) R groups

• Ionic bonds are stronger than hydrogen bonds, but they are not common

• These bonds are broken by pH changes

hydrogen

• Hydrogen bonds form between strongly polar R groups

• These are the weakest bonds that form, but the most common, as they form between a wide variety of R groups