Next Lesson - Protein Function in Oxygen Transport
Core
Proteins are found throughout the human body are play an important role in all biochemical processes:
- Catalysts - enzymes
- Transporters - haemoglobin for transport of oxygen
- Structural support - collagen
- Immune system - immunoglobins
- Ligands in cell signalling - hormones and neurotransmitters
- Ion channels and receptors - for hormones and neurotransmitters
Proteins are polypeptides, made up of covalently linked amino acids (monomers). The amino acid sequence of a protein is encoded by a gene. Therefore, the nucleotide sequence of a gene determines the sequence of amino acids in the protein. The final polypeptide chain folds into a highly-specific and intricate three-dimensional structure, which is determined by the sequence of amino acids.
There are different names to describe the sizes of peptides & proteins:
- Peptides or oligopeptides = relatively small polymers with a low number of amino acid residues.
- Polypeptides or proteins = large polymers with large numbers of amino acid residues.
Amino Acids Chemical Structure
Amino acids are the building blocks of proteins as the monomers that the final protein structure is made out of. They all have a general structure of central carbon atom covalently bonded to an amino group (NH2), carboxyl group (COOH), a hydrogen atom and distinctive R group (the side chain).
Diagram - The general structure of an amino acid
SimpleMed original by Dr. Peter Parkinson
Amino acids become ionised because the amino group can act as a base (proton acceptor) and the carboxyl group can act as an acid (proton donor). In aqueous solution, their protonation states are determined by acid-base equilibria with the surrounding environment. The amino group can act as a proton acceptor because the nitrogen ion has a pair of electrons in its outer shell that are not involved in bonding, which can bond to the proton. This means that the amino group goes from NH2 to NH3+, and the carboxyl group transitions from COOH to COO-.
Diagram - How the amino and carboxyl groups exchange a H+ ion to become charged
SimpleMed original by Dr. Peter Parkinson
When the amino acid has one negative charge and one positive charge, the net charge of the amino is zero and this is known as a zwitterion. Depending on the pH of the solution, the amino acid can exist as a cation (overall positive charge) or as an anion (overall negative charge).
Diagram - The structure of a zwitterion
SimpleMed original by Dr. Peter Parkinson
A peptide bond forms between individual amino acids to connect them. The remaining part of each amino acid now left in the amino acid chain is called the amino acid residue. The peptide bond is formed in a condensation reaction as a single molecule of H2O is produced with each peptide bond formed.
Diagram - The general appearance of an amino acid residue
SimpleMed original by Dr. Peter Parkinson
Amino acids are classified based on their R group which contributes to the overall function of the protein. The acid-base behaviour of the protein is determined by the R groups of the amino acids.
Chemical properties of amino acid:
- Polar (hydrophilic) - able to form hydrogen bonds and can be further classified into positive, negative or neutral charge
- Non-polar (hydrophobic)
- Acidic
- Basic
- Neutral
Physical properties of amino acid:
- Aliphatic - R group just contains carbon and hydrogen atoms
- Aromatic - R group with a cyclic, planar molecule which has great stability e.g. R group on phenylalanine
Diagram - The chemical structure of phenylalanine with its R group in red
SimpleMed original by Dr. Peter Parkinson
pKa and R Groups of Amino Acids
pKa is the pH at which an ionisable group is 50% protonated and 50% deprotonated, and is a measure used to indicate the strength of an acid. Whether an amino acid is positively or negatively charged, depends on the pKR (pK of the side group) value of the side group.
Positively charged R groups with pKR values:
- Lysine - 10.5
- Histidine - 6.0
- Arginine - 12.5
Negatively charged R with pKR values:
- Glutamate - 4.3
- Aspartate - 2.8
If the pH value of the solution < pKR value then the side group will be protonated (addition of hydrogen ions).
If the pH value of the solution > pKR value then the side group will be de-protonated (loss of hydrogen ions).
Examples:
- Lysine has a pKR of 10.5, therefore at physiological pH (7.4) the R group of lysine will be protonated.
- Aspartate has a pKR of 2.8, therefore at physiological pH (7.4), the R group of
aspartate will be de-protonated.
In summary: the amino acid wants to get the pH closer to its pKa - if the solution has a lower pH (meaning there are free protons) the amino acid will accept them and become protonated to try to raise the pH closer to its pKa. If the solution has a higher pH (meaning there are less free protons) the amino acid will donate its protons and become de-protonated to try to lower the pH closer to its pKa.
Definitions:
- Primary structure = linear amino acid sequence of polypeptide chain.
- Secondary structure = local folding of polypeptide backbone due to interactions between atoms of the backbone excluding R groups. These structures can either be alpha helix or beta-pleated sheet and are held in shape due to hydrogen bonds formed within the structure.
- Tertiary structure = the overall three-dimensional configuration of a protein. It forms based on the interaction between the R groups of the amino acids within the protein.
- Quaternary structure = the interaction between multiple polypeptides and prosthetic groups to form a multi-subunit protein, e.g. haemoglobin which is made up of multiple polypeptide chains and haem prosthetic groups containing iron atoms.
The bond formed by linking two amino acids together is called a peptide bond and the reaction to form this bond is a condensation reaction - removal of a molecule of water.
Diagram - The formation of a peptide bond by a condensation reaction
SimpleMed original by Dr. Peter Parkinson
Characteristics of the peptide bond include:
- Planar - the carbon, hydrogen, oxygen and nitrogen atoms all lie in the same plane.
- Rigid - the carbon-nitrogen bond in the peptide bond has partial double-bond characteristics causing the bond to be unable to rotate. This helps to contribute to the atoms being in the same plane.
- Exhibits a trans conformation - the carbon - R group bonds, of each amino acid residue are found on opposite sides of the peptide bond. The trans conformation reduces steric hindrance between side chains; flexibility of the polypeptide arises from rotation around bonds adjacent to the peptide bond.
The bonds either side of a peptide bond are able to rotate, allowing flexibility within the 3-D structure of the protein.
The way in which the polypeptide chain folds and the physical characteristic of the protein is determined by the sequence of the amino acids.
The overall structure of a protein determines the overall function of the protein.
Isoelectric point (pI) of a protein is the pH at which there is no overall net charge amongst the structure of the protein.
Basic proteins:
- pI > 7
- The protein contains many positively charged/basic amino acids - based on R groups and they will be protonated.
Acidic proteins:
- pI < 7
- The proteins contains many negatively charged/acidic amino acids.
Examples of proteins and their pI:
- Pepsin (protease found in the stomach) - pI of < 1.
- Haemoglobin (protein found in red blood cells that carries oxygen) - pI of 6.8.
- Cytochrome C (protein that carries electrons in the mitochondria in process of oxidative phosphorylation) - pI of 10.7.
Proteins can be covalently bonded to chemical components as well as amino acids. Examples:
- Lipoproteins - lipid non-covalently associated with protein. E.g. LDL and HDL.
- Glycoproteins - carbohydrate covalently linked to protein E.g. Immunoglobulin.
- Phosphoproteins - phosphate group covalently linked to protein. E.g. casein in milk.
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