Proteins Learning objectiveLearning objective To be able to describe how bonds are made between amino acids forming polypeptidesTo be able to describe how bonds are made between amino acids forming polypeptides

Histidine Methionine Isoleucine Phenylalanine Leucine Tryptophan Lysine Valine

Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions.Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions. How many can you think of?How many can you think of?

Structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle)Structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle) Enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others)Enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others) Transport e.g. haemoglobin (oxygen), transferrin (iron)Transport e.g. haemoglobin (oxygen), transferrin (iron) Pumps e.g. Na+K+ pump in cell membranesPumps e.g. Na+K+ pump in cell membranes Motors e.g. myosin (muscle), kinesin (cilia)Motors e.g. myosin (muscle), kinesin (cilia) Hormones e.g. insulin, glucagonHormones e.g. insulin, glucagon Receptors e.g. rhodopsin (light receptor in retina)Receptors e.g. rhodopsin (light receptor in retina) Antibodies e.g. immunoglobulinsAntibodies e.g. immunoglobulins Storage e.g. albumins in eggs and blood, caesin in milkStorage e.g. albumins in eggs and blood, caesin in milk Blood clotting e.g. thrombin, fibrinBlood clotting e.g. thrombin, fibrin Lubrication e.g. glycoproteins in synovial fluidLubrication e.g. glycoproteins in synovial fluid Toxins e.g. diphtheria toxinToxins e.g. diphtheria toxin Antifreeze e.g. glycoproteins in arctic fleaAntifreeze e.g. glycoproteins in arctic flea and many more!and many more!

Proteins Proteins contain the elements C H O N & sometimes SProteins contain the elements C H O N & sometimes S They are made by condensation reactions between amino acids forming long polypeptide chains.They are made by condensation reactions between amino acids forming long polypeptide chains. The properties of each individual protein are determined by the aa sequenceThe properties of each individual protein are determined by the aa sequence There are 20 different R groups, and so 20 different amino acids e.g. There are 20 different R groups, and so 20 different amino acids e.g. Glycine R=HGlycine R=H Alanine R=CH3Alanine R=CH3 Since each R group is slightly different, each amino acid has different properties, and this in turn means that proteins can have a wide range of properties Since each R group is slightly different, each amino acid has different properties, and this in turn means that proteins can have a wide range of properties

H C H NC H H O O R Amino acids aminocarboxyl Draw the general structure of an amino acid molecule There is a central carbon atom (called the "alpha carbon"), with four different chemical groups attached to it: a hydrogen atom a basic amino group an acidic carboxyl group a variable "R" group (or side chain )

Amino acids are so-called because they have both amino groups and acid groups, which have opposite charges. At neutral pH (found in most living organisms), the groups are ionised, so there is a positive charge at one end of the molecule and a negative charge at the other end.

In a neutral solution and in a solid state amino acids exist as a dipolar ion.In a neutral solution and in a solid state amino acids exist as a dipolar ion. H 3 N + – CH 2 – COO -H 3 N + – CH 2 – COO - The ion is formed as a result of an internal acid base reaction the COOH group donates a proton to the NH 2 groupThe ion is formed as a result of an internal acid base reaction the COOH group donates a proton to the NH 2 group This kind of ion is called a zwitterionThis kind of ion is called a zwitterion Amino acids can therefore exist in three forms depending on the pHAmino acids can therefore exist in three forms depending on the pH

The charge on the amino acid changes with pH: low pH (acid) neutral pH high pH (alkali) It is these changes in charge with pH that explain the effect of pH on enzymes.

Proteins are said to be amphoteric and can act as buffersProteins are said to be amphoteric and can act as buffers An amphoteric substance can act as both an acid an a baseAn amphoteric substance can act as both an acid an a base Buffers resist changes in pHBuffers resist changes in pH

Polypeptides Amino acids are joined together by peptide bonds.Amino acids are joined together by peptide bonds. The reaction involves the formation of a molecule of water in another condensation polymerisation reactionThe reaction involves the formation of a molecule of water in another condensation polymerisation reaction

Peptide bonding H C H NC H H O O R H C H NC H H O O R

H C H NC H H O O R H C H NC H H O O R

H C H NC H H O O R H C H NC H H O O R

C H NC H H O R H C H NC H H O H O O R water Peptide bond A condensation reaction

Peptide bonding C H NC H H O R H C H NC H O O R A dipeptide

When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide. e.g.: +NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp —COO- In a polypeptide there is always one end with a free amino (NH 3 ) group, called the N-terminus, and one end with a free carboxyl (CO2) group, called the C-terminus.

In a protein the polypeptide chain may be hundreds of amino acids long.In a protein the polypeptide chain may be hundreds of amino acids long. Amino acid polymerisation to form polypeptides is part of protein synthesis.Amino acid polymerisation to form polypeptides is part of protein synthesis. It takes place in ribosomes, and is special because it requires an RNA template.It takes place in ribosomes, and is special because it requires an RNA template. The sequence of amino acids in a polypeptide chain is determined by the sequence of the genetic code in DNA.The sequence of amino acids in a polypeptide chain is determined by the sequence of the genetic code in DNA.

The diagram shows the structural formulae of two amino acids Name one chemical element found in all amino acids, but not in monosaccharides. Nitrogen / N (not N 2 ) (ii) What type of chemical reaction occurs to form a dipeptide? Condensation (iii) Draw around the amine group, the acid group and the R group for each amino acid and label them (iv) Draw the structural formula of the dipeptide formed when these two amino acids combine. Amine group Acid group R group