The Proteins

Syllabus objectives (MOODLE)

Who needs proteins? Approx 18% of the body is protein. Proteins are found in all cells. Give some examples of where proteins are found in the body

Answer Plasma membranes – carrier proteins, channel proteins and glycoproteins. Enzymes – All enzymes are proteins. Hormones – chemical messengers. Made either form lipids or proteins. Proteins contain which elements?

Answer. Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N) and often Sulphur (S).

Structure of an amino acid The building blocks of proteins (or the monomer components) are called what? Label this diagram.

Labels Central carbon (C), or alpha carbon, to which are attached 4 different chemical groups. NH 2 Amino group. A basic group. Attached to the alpha carbon by a covalent bond. COOH Carboxyl group. An acidic group. H Hydrogen atom. R group Residual group.

R group= Residual group. This is different in each of the 20 amino acids. It could be as simple as a single hydrogen, (glycine), or more complex groups. Glycine: R is an H atom. Alanine: R is CH 3 Valine: R is C 3 H 7

Amino acids combine to make a polymer called a polypeptide. Polypeptides combine to form proteins.

3. How amino acids combine together. 2 amino acids combined form a dipeptide. 3 or more amino acids combine to form a polypeptide. Process = a condensation reaction = removal of a water molecule.

Complete the process....

↓ + H 2 O

Bond holding the 2amino acids together = Peptide bond This reaction can be reversed and the peptide bond can be broken to form 2 amino acids. This requires the addition of water = hydrolysis reaction. Many amino acids (sometimes 1000s), can be joined together in this way to form a polypeptide chain. The sequence (or order) of amino acids in a polypeptide chain = Primary structure of the protein.

Questions What type of bond links amino acids together? What type of reaction is involved in linking amino acids together? What 4 different components make up an amino acid?

Answers 1.Peptide bond. 2.Condensation. 3.Amine group, carboxyl group, residual group and hydrogen.

The secondary structure of proteins The primary structure of amino acids is too large and the incorrect shape, to function as a specific protein. In order to determine the specific 3D shape and therefore it’s correct function, it must be either folded, (into a β pleated sheet), or coiled, (as an α helix), into the secondary structure of the protein. Some proteins only have a secondary structure involving α helix secondary folding and some only have β pleated sheet folding. However many proteins have a combination of both α helix and β pleated sheet.

α helix. The sequence of amino acids, which makes up the primary structure of the protein, determines the 3-D shape of the protein. The polypeptide chain, (the primary structure of the protein), twists into a 3-D shape. It forms a coil. This coil is held together by many hydrogen bonds. The hydrogen bond forms between 2 amino acids in the same polypeptide chain, every 3 rd amino acid. A hydrogen bond is formed between the positive charge on the hydrogen of a NH 2 group, and the negative charge on the oxygen of a COOH group.

This coil is known as an α helix.

α helix. Hydrogen bonds are weak but there are many of them in each α helix, so overall the structure is strong. The formation of the hydrogen bonds between the amino acids causes the polypeptide chain to coil up. In this way it has a more compact shape and a very specific shape. This will determine the 3D shape of the whole protein.

Β pleated sheet A type of secondary folding is the β pleated sheet. Here polypeptide chains of amino acids, (the primary structure of the protein), lie parallel to each other but run in opposite directions. They are joined to each other by hydrogen bonds. The polypeptide chains are folded or pleated like a fan. This makes it a more complex shape. A hydrogen bond is formed between - The positive charge on the hydrogen of a NH 2 group, from one of the polypeptide chains. - And this bonds to the negative charge on the oxygen of a COOH group, from the other polypeptide chain, that it is lying opposite.

Β pleated sheet

The formation of the hydrogen bonds between opposite polypeptide chains (ANTI- PARALLEL) causes all the chains that are bonded together to fold up. In this way they have a more compact shape and a very specific shape. This will determine the 3D shape of the whole protein.

Question on secondary structure 4. Name the 2 bonds involved in holding together the primary structure of a protein. Identify where these bonds occur. 5. Name the bonds involved in holding together the secondary structure of a protein. Identify where these bonds occur in both the α helix and β pleated sheet. 6. What is the purpose of the secondary structure? 7. What causes the α helix to coil? 8. How often do the hydrogen bonds occur in the α helix? 9. What causes the β pleated sheet to fold? 10. Why do the polypeptide chains in β pleated sheet have to run in opposite directions? 11. How are the chains of polypeptides held together in the β pleated sheet?

4. Covalent bonds between the elements in the individual amino acids. Peptide bonds bonding the amino acids together. 5. Hydrogen bonds. In the α helix these occur every 3 rd amino acid between the positive charge on the hydrogen of a NH 2 group, and the negative charge on the oxygen of a COOH group, of the same polypeptide chain. In the β pleated sheet the hydrogen bond occurs between the positive charge on the hydrogen of a NH 2 group, from one of the polypeptide chains and the negative charge on the oxygen of a COOH group, from the other polypeptide chain, that it is lying opposite. 6. To fold the primary structure into a compact shape and to determine the 3D shape of the protein. 7. The formation of the hydrogen bonds. 8. Every 3 amino acids on the same polypeptide chain. 9. The formation of hydrogen bonds between anti-parallel polypeptide chains. 10. In order to form the hydrogen bonds. 11. By the hydrogen bonds between the anti-parallel polypeptide chains.

Tertiary structure of proteins. The α helices and/or the β pleated sheets can be twisted and folded even more to become complex unique 3-D shapes = tertiary structure. This forms a complex shape. Maintained by different bonds: Disulphide bonds = Some amino acids contain sulphur. Formed between 2 sulphur ions. Strong and not easily broken.

Ionic bonds = formed between any carboxyl and amine groups that are not already involved in forming peptide bonds. Weaker and easily broken, especially by changes in pH. Hydrogen bonds = between a hydrogen and an oxygen. Numerous and easily broken. 3-D shape is important as it determines its function. It also enables it to recognise and be recognised. Hydrophobic interactions = interactions between non- polar, water repellent groups in protein. Not a bond but an interaction.

Quaternary structure of proteins. This is formed when 2 or more polypeptide chains, (tertiary structures) are bonded together to form the final protein molecule. Proteins made simply of protein = simple proteins. Proteins are often associated with non-protein (prosthetic) groups. E.g. Haemoglobin has the iron containing haem group = conjugated proteins. Haemoglobin has 4 polypeptide chains bound together; 2 alpha (α) chains and 2 beta (β) chains, with 4 non=protein haem groups.

Collagen consists of 3 polypeptide chains wound together, like a rope.

Question 12. With reference to haemoglobin, distinguish between tertiary and quaternary structure.

12. Tertiary – as a globular protein the polypeptide chains are tightly folded to form a spherical shape. The precise 3D shape is further folded and this shape is maintained by ionic, hydrogen and disulphide bonds. Quaternary structure = 4 tertiary structures are bonded together to form the quaternary structure. There are 2 alpha and 2 beta polypeptide chains are chemically bonded together, with 4 non-protein haem, (iron) groups.

Summary of protein structure

Test for proteins. This detects peptide links. Place test solution in a test tube. Add equal volume of sodium hydroxide, (Biuret A) at room temp. Add few drops very dilute (0.05%) copper(II) sulphate solution, (Biuret B) and mix gently. Purple colouration = peptide bonds and so a protein. If it remains blue = no protein. (Can just cheat in an exam and say add Biuret reagent to test for protein.)

Protein shape and function There are 2 groups of proteins – fibrous and globular proteins. This is determined at the tertiary structure.

(i) Fibrous proteins. These have structural functions. They resemble a long string or fibre. All fibrous proteins form long chains which run parallel to one another. The chains are linked by cross bridges. So are stable. Usually insoluble in water and physically tough. E.g. keratin (found in skin and nails) and silk, (forms the threads of the spiders web), and collagen, found in bone, cartilage and tendons. Tendons join muscle to bones. When a muscle contracts the bone is pulled in the direction of the contraction.

Collagen Primary structure = repeating 3 compact amino acids in unbranched polypeptide chains. Secondary structure = α helix. Tertiary structure = chain twisted into a second helix. Quaternary structure =3 of these tertiary strucs wound together, like a rope. This is known as tropocollagen or a microfibril.

Collagen Each one of these quaternary structures is known as a microfibril. These group together to form fibrils. These join together to form collagen fibres.

Tropocollagen is exported by cells for extracellular assembly into fibrils.

Question 13. Explain why the quaternary structure of collagen makes it a suitable molecule for a tendon.

Answer 13. It has 3 polypeptide chains wound together to form a strong rope-like structure that has strength in the direction of the pull of the tendon.

The individual collagen polypeptide chains in the fibres are held together by cross linkages between amino acids of adjacent chains. Question 14. Suggest how the cross linkages between the amino acids of polypeptide chains increase the strength and stability of a collagen fibre.

Answer 14. It prevents the individual polypeptide chains from sliding past one another and so they gain strength cos they act as a single unit. The point where one collagen molecule ends and the next begins, are spread throughout the fibre (staggered) rather than all being in the same position along it.

Question 15. Explain why the arrangement of collagen molecules is necessary for the efficient functioning of a tendon.

Answer 15. The junctions between the adjacent collagen are points of weakness. If they were all at the same point in a fibre, then this would be a major weak point at which the fibre might break.

(ii) Globular proteins Structure resembles globule or ball. Often folded so hydrophobic groups are on inside of molecule and hydrophilic are facing outwards, making them water soluble. Carry out metabolic functions, control cellular metabolism. E.g. enzymes, receptor proteins and haemoglobins, some hormones.

Question 16. Which class of proteins, fibrous or globular, has mainly structural functions?

Answer 16. Fibrous

Amino acids act as buffers Amino acids are amphoteric = have both acidic and basic properties when they dissociate in water. The acidic carboxyl group can donate a proton (positively charged hydrogen ion), so molecule becomes negatively charged. The basic amino group can take up a proton so molecule becomes positively charged in an acidic solution.

At a pH specific for each amino acid the molecule ionizes so different part of amino acid have positive and negative charged groups at same time. Ions like this = zwitterions. The positive and negative charges cancel each other out and so the molecule is electrically neutral.

Being able to donate or receive protons causes amino acids to behave as buffers. Buffer solutions resit changes to pH when an acid or base is added to it. Important in keeping the pH of blood and other body fluids within correct ranges.

Denaturation = breaking down the tertiary structure of proteins. Happens when bonds break. Primary structure retained but polypeptide chain unravels and loses specific shape. So protein can’t function correctly. Nearly always irreversible. Caused by changes in pH, salt concentration, or increase in temperature. E.g. boil an egg or fry it. Transparent area where yolk, (the egg white), solidifies and becomes white. Here tertiary structure unravelled, (irreversible here). If protein is soluble, denaturation makes it insoluble and the protein is inactivated. If protein is an insoluble fibrous protein, it loses its structural strength.

Question 17. What happens if a protein is exposed to excessive heat or extremes of pH?

Answer 17. The protein is denatured. The bonds holding the tertiary structure together break. The polypeptide chain unravels, and although the primary structure is maintained, the whole shape of the protein is changed and so it is unable to function.

3.2.4 The variety of life is extensive and this is reflected in similarities and differences in its biochemical basis and cellular organisation. Haemoglobin The haemoglobins are a group of chemically similar molecules found in many different organisms. Haemoglobin is a protein with a quaternary structure. The role of haemoglobin in the transport of oxygen. The loading, transport and unloading of oxygen in relation to the oxygen dissociation curve. The effects of carbon dioxide concentration.

Candidates should be aware that different organisms possess different types of haemoglobin with different oxygen transporting properties. They should be able to relate these to the environment and way of life of the organism concerned.

Haemoglobin (a) Structure of haemoglobin. There is a group of haemoglobins, all chemically similar. Same general structure. All conjugated proteins. Primary structure = 4 sequences of amino acids within 4 polypeptide chains. Secondary structure = α helix. Tertiary structure = each chain folded into a precise shape – relates to function. Quaternary structure = 2 pairs of polypeptides. 2α and 2β chains. All 4 polypeptide chains are linked to from an almost spherical shape. Each have a prosthetic group, which is a haem group associated with it, which contains a ferrous (Fe 2+ ) ion. Each Fe 2+ ion can combine with a single oxygen molecule (O 2 ). Process = oxygenation. In total 1 haemoglobin can combine with 4 O 2 molecules.

(b) The role of haemoglobin. = transport oxygen. To do this it must: Readily associate with oxygen at surface where gaseous exchange occurs. Readily dissociate from oxygen at those tissues requiring it.

Haemoglobin

Clever as haemoglobin can change its affinity for oxygen under different condition. Achieves this by changing shape in the presence of carbon dioxide. Different haemoglobins have slightly different sequences of amino acids and therefore slightly different shapes. Depending on the shape, haemoglobin molecules range from those with a high affinity to those with a low affinity for oxygen. In presence of carbon dioxide haemoglobin binds more loosely to oxygen, so haemoglobin releases its oxygen more easily.

Process of haemoglobin combines with oxygen = loading or associating. Happens in lungs. Process of haemoglobin releases its oxygen = unloading or dissociating. Happens in tissues.

Region of body Oxygen conc n Carbon dioxide conc n Affinity of haemoglobin for oxygen Result Gas exchange surface HighLowHigh Oxygen is attached or associated Respiring tissues LowHighLowOxygen is detached or dissociated

Questions 18. Describe the quaternary structure of haemoglobin. 19. Explain how DNA leads to different haemoglobin molecules having a different affinity for oxygen.

Answers pairs of polypeptides, (2α and 2β) link to form a spherical molecule, (globular protein). Each polypeptide has a haem group that contains a ferrous ion. 19. Different base sequences in DNA- different amino acid sequences (different primary structure) – and so get different tertiary/quaternary structures and shape – different affinities for oxygen.