💪Proteins 💪

• Peptides are polymers made up of amino acid molecules
• proteins consist on 1 or more polypeptides arranged a complex macromolecules
• proteins contain carbon, hydrogen, oxygen, and nitrogen
• Different R-groups result in different amino acids

  20 different amino acids are commonly found in cells:

  • 5 are said to be non-essential as our bodies are able to make them from other amino acids
  • 9 are essential a they can only be obtained from what we eat
  • 6 are said to be conditionally essential as they are only needed by infants and growing children
• Amino acids join when the amine group of one amino acid reacts with the carboxylic acid group of another amino acid.

  The hydroxyl in the carboxylic acid group reacts with a hydrogen in the amine group.

  A peptide bond is formed between the amino acids and water is produced

  The resulting compound is a dipeptide
• When many amino acids are joined by peptide bonds, they form a polypeptide

  This reaction is catalysed by the enzyme peptidyl transferase (found in the ribosomes)
• The different R-groups of the amino acids that make up a protein are able to interact with each other forming different types of bonds.

  This leads to polypeptides folding into complex structures (proteins).

  The presence of different sequences of amino acids lead to different proteins with different shapes being produced
• Amino acids can be separated using thin layer chromatography (TLC).

  This involves two phases: the stationary phase and the mobile phase (involves organic solvent).

  The mobile phase picks up the amino acids and moves through the stationary phase where the amino acids are separated
• In the stationary phase of TLC a thin layer of silica gel is applied to a rigid surface.

  The amino acids are then added to one side of the gel

  This end is then submerged in organic solvent
• In the mobile phase of TLC, the organic solvent moves through the silica gel.

  The rate at which the different amino acids in the organic solvent move through the silica depends on the interactions they have with the silica in the stationary phase and their solubility in the mobile phase

  This results in different amino acids moving different distances in the same amount of time so they separate out form each other.
• The primary structure of a protein is the sequence in which the amino acids are joined together.

  This is directed by the information carried within DNA

  The particular amino acids in the sequence influence how the polypeptide folds to give the protein's final shape (this in turn determines its function)

  The only bonds involved in the primary structure are peptide bonds.
• The secondary structure is formed by interactions of the oxygen, hydrogen, and nitrogen atoms of the basic repeating structure of the amino acids

  The R-groups are not involved yet
• In the secondary structure, hydrogen bonds can form within the amino acid chain, pulling it into a coil shape called an alpha helix.

  Polypeptide chains can also lie parallel to each other, joined by hydrogen bonds, to form a sheet-like structure called a beta pleated sheet
• The secondary structure consists of hydrogen bonds formed at regions along protein molecules depending on amino acid sequence
• The tertiary structure is the folding of a protein into its final shape.

  The folding/coiling that occurs in the secondary structure brings the different R-groups of amino acids close enough to interact and fold the protein further to form its tertiary structure
• The different types of interactions between R-groups include:

  • hydrophobic and hydrophilic interactions- weak interactions between polar and non-polar R-groups
  • hydrogen bonds- weakest of bonds formed
  • ionic bonds- stronger than hydrogen bonds and occur between oppositely charged R-groups
  • disulfide bonds (AKA disulfide bridges)- strongest of bonds formed. They are covalent bonds that only form between R-groups containing sulfur atoms
• The association of two or more individual proteins forms a quaternary structure.

  The individual proteins are called subunits

  The interactions between the subunits are the same as in the tertiary structure but in this case it is between individual protein molecules instead of within one.

  Protein subunits can be different or identical
• Proteases catalyse the hydrolysis of peptides

  A water molecule is used to break the peptide bond, reforming the amine and carboxylic acid groups
• There are two main types of proteins: globular and fibrous proteins
• Globular proteins form when proteins fold into their tertiary structure in such a way that the hydrophobic R-groups on the amino acids are kept away from the aqueous environment so the hydrophilic R-groups are on the outside of the protein

  This makes them soluble in water
• Globular proteins are:

  • compact
  • water soluble
  • roughly spherical
• Insulin is an example of a globular protein

  It is a hormone involved in the regulation of blood glucose concentration

  Hormones are transported in the bloodstream so need to be soluble

  They also have to fit into specific receptors on cell-surface membranes so need to be specific shapes
• Conjugated proteins are globular proteins that contain a non-protein component called a prosthetic group
• Proteins without prosthetic groups are called simple proteins
• Different types of prosthetic groups include:

  • lipids that form lipoproteins
  • Carbohydrates that form glycoproteins
  • metal ions and molecules derived from vitamins, e.g. haem groups conatain an iron (II) ion- Fe2+
• Heamoglobin is a globular protein

  It is the red, oxygen-carrying pigment in red blood cells.

  It is a quaternary protein made of four polypeptides, two alpha and two beta subunits

  Each subunit contains a prosthetic haem group

  The iron(II) ions in the heam groups are each able to combine reversibly with an oxygen molecule

  This is what enables heamoglobin to transport oxygen around the body
• Catalase is a globular protein that is an enzyme

  It is a quaternary protein with 4 haem prosthetic groups

  The Fe2+ ions allow catalase to interact with hydrogen peroxide and speed up its breakdown

  Hydrogen peroxide is a common product of metabolism but is damaging to cells if allowed to accumulate. Catalase prevents this
• Fibrous proteins are formed from molecules that are long and insoluble due to the presence of a high number of amino acids with hydrophobic R-groups in the primary structure

  They contain a limited range of amino acids usually with small R-groups

  This means they have a repetitive amino acid sequence in the primary structure

  This leads to organised structures that are strong and long
• Examples of fibrous proteins include: collagen, keratin, and elastin.
• Examples of globular proteins include: catalase, haemooglobin, and insulin
• Keratin is a group of fibrous proteins present in hair, skin, and nails.

  It has a large proportion of the sulfur-containing amino acid cysteine, resulting in many strong disulfide bonds

  This forms strong, inflexible and insoluble materials

  The degree of disulfide bonds determines flexibility e.g. hair contains fewer disulfide bonds than nails
• Elastin is a fibrous protein found in elastic fibres and is present in the walls of blood vessels and the alveoli of the lungs

  It is a quaternary protein made from many stretchy molecules called tropoelastin

  It gives structure the flexibility to expand when necessary but also return to normal size
• Collagen is a fibrous protein found in skin, tendons, ligaments and the nervous system

  It is mad of three polypeptide chains wound together in a long, strong, rope-like structure

  Like rope, collagen has flexibility