Biological Molecules Detailed Notes PDF

Chapter 2 Outcomes Biological Molecules Ms. Katie Alhodali  Lipids - Triglycerides and Phospholipids. Lipids: - Include triglycerides + phospholipids. - Molecules contain C, H, O atoms - Very small proportion of O. - Insoluble in water. 1. Triglyceri...

Chapter 2 Outcomes Biological Molecules Ms. Katie Alhodali  Lipids - Triglycerides and Phospholipids. Lipids: - Include triglycerides + phospholipids. - Molecules contain C, H, O atoms - Very small proportion of O. - Insoluble in water. 1. Triglycerides - Made of glycerol 'backbone', attached to 3 fatty acids by ester bonds. Fatty acids  Have long chains of C and H atoms.  Each C atom has 4 bonds: 2 to C atoms, 2 to H atoms.  Sometime, only 1 H atom attached --> C atom has a 'spare' bond, attached to the next-door C atom (also has 1 H bonded) ---> double bond.  Unsaturated fatty acids has ≥ 1 C-C double bonds (do not contain quite as much H).  Saturated fatty acids has no double bonds.  Lipids containing unsaturated fatty acids ---> unsaturated lipids (in plant)   Lipids containing completely saturated fatty acids ---> saturated lipids (in animal)  Unsaturated lipids tend to have lower melting points than saturated lipids. Triglycerides are insoluble in water ---> energy storage in plants, animals and fungi. They contain more energy per gram than polysaccharides. a. In mammals Triglyceride are build up beneath the skin in the form of adipose tissue:  It cells contain oil droplets of triglycerides;  Helps to insulate body against heat loss.  Relatively low density ---> ↑ buoyancy ---> useful for aquatic mammals living in cold water (whales, seals).  Forms a protective layer around organs (e.g. kidneys). b. In plants Triglycerides = major part of energy stores in seeds:  Cotyledons (sunflower seeds...)  Endosperm (castor beans...). 2. Phospholipids  Made of glycerol 'backbone', 2 fatty acids and 1 phosphate group.   Fatty acid chains are hydrophobic: no electrical charge ---> not attracted to H2O molecules.  Phosphate group is hydrophilic: has electrical charge ---> attracted to H2O molecules.  In H2O, phospholipid molecules arranges into a bilayer: hydrophilic heads facing outwards into the water + hydrophobic tails facing inwards, avoiding water.  This is the basic structure of a cell membrane. 3. Emulsion (Ethanol) test for lipids  Dissolve the substance by mixing it with absolute ethanol.  Decant the ethanol into water.  If lipids are present in the mixture, it will precipitates and forms an milky emulsion. A milky emulsion indicates the presence of lipid.  #09. Proteins - amino acids, peptid bonds Proteins are large molecules made of long chains of amino acids. Proteins are an extremely important class of macromolecule in living organisms. More than 50% of the dry mass of most cells is protein. Proteins have many important functions: All enzymes are proteins Proteins are essential components of cell Membranes Some hormones are proteins – for example, insulin and glucagon The oxygen-carrying pigments hemoglobin and myoglobin are proteins Antibodies, which attack and destroy invading microorganisms, are proteins Collagen is a protein that adds strength to many animal tissues – for example, bone and the walls of arteries, hair, nails and the surface layers of skin contain the protein keratin Actin and myosin are the proteins responsible for Muscle contraction Proteins may be storage products – for example, Casein in milk and ovalbumin in egg white. Despite their tremendous range of functions, all proteins are made from the same basic monomers. These are amino acids. 1. Amino acids All proteins have the same basic structure. They consist of an Amino Group (NH2), an Carboxyl group (COOH), and a Carbon in the middle which bonds with a Hydrogen atom and an 'R' group, which is specific to individual amino acids. There are 20 naturally occurring 'R' groups, making amino acids neutral, acidic, alkaline, aromatic (has a ring structure) or sulphur-containing). The 20 R groups corresponds to 20 different amino acids. Each different amino acid has a specific name. For example, Alanine's 'R' group consists of CH3. 2. Peptide bonds a. Condensation reaction: 2 amino acids are joined by a peptide bond ---> dipeptide + H2O. b. Hydrolysis reaction: Dipeptides are split into 2 amino acids by breaking the peptide bond using a molecule of H20.. Protein - Primary, Secondary, Tertiary and Quaternary structure Amino acids can be linked together in any order to form a long chain - polypeptide. Protein molecules can be made up of the same polypeptides or different polypeptides. 1. Primary structure: The sequence of amino acids in a polypeptide or protein molecule. The 3 letters in each circle are the first 3 letters of the amino acid. 2. Secondary structure: The way in which the primary structure of a polypeptide chain folds.  After synthesis, polypeptide chains are folded or pleated into different shapes: Alpha helix (regular 3D shape) and Beta-pleated sheet (twisted, pleated sheet)  The helix is hold by many Hydrogen bonds between amino acids at different places in the chain, giving the shape great stability. The typical Alpha helix is about 11 amino acids long. 3. Tertiary structure: The final 3D structure of a protein, involving coiling or pleating of the secondary structure. Tertiary structure. Tertiary structure is held by: 1. Hydrogen Bonds - formed between amino acids at different points in the chain. 2. Disulphide Bonds - a strong double bond (S=S) formed between the Sulphur atoms within the Cysteine monomers. 3. Ionic Bonds - formed between 2 oppositely charged 'R' groups (+ and -) found close to each other. 4. Hydrophobic and Hydrophilic Interactions: amino acids may be hydrophobic or hydrophilic; in a water based environment, the hydrophobic parts of globular protein are orientated towards centre and the hydrophilic parts are towards edges. 4. Quaternary structure: ≥ 2 polypeptide chains join together to form a protein.  Some proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (e.g. a haem group in haemoglogin) called a Prosthetic Group. These proteins will only be able to function if all subunits are present.  The polypeptide chains are held by the same type of bonds as in the tertiary structure. The tertiary and quaternary structures of a protein, and its properties, are determined by its primary structure. Additional sources: Some parts of the note are taken from A level Notes  #11. Globular and fibrous proteins - haemoglobin and collagen Globular and Fibrous are 2 main types of proteins with a 3D structure. 1. Haemoglobin, a globular protein  Composed of 2 α + 2 β polypeptide chains + 1 inorganic prosthetic haem group. Hb's function: carry O2 from lungs to respiring tissues. 2. Collagen - a fibrous protein  Composed of 3 polypeptide chains wound around each other. Each chain is a coil itself of around 1000 amino acids.  Structure strength is increased by forming: - H bonds between the 3 polypeptide chains. - Collagen molecules wrapped around each other ---> Collagen Fibrils - Collagen Fibrils ---> Collagen Fibres. Collagen's function: support and elasticity in many animal tissues (human skin, bone and tendons). 3. Test for proteins The Biuret Test shows the presence of peptide bonds, which are the basis for the formation of proteins. These bonds will make the blue Biuret reagent turn purple. Add biuret solution. A purple colour indicates the presence of protein.  Water  Hydrogen Bonding A water molecule contains two hydrogen atoms and one oxygen atom held together by hydrogen bonds  Solvent Water is an effective solvent because of its polarity so that it can form electrostatic interactions with other polar molecules and ions Thus, it’s a transport medium and reagent for metabolic and other reactions in the cells of plants and animals  High surface tension and cohesion Cohesion refers to the attraction of one water molecule to the other Water molecules have strong, cohesive forces due to hydrogen bonds, thus having high surface tension  High specific heat capacity The amount of heat energy required to raise the temperature of 1 kg of water by 1 °C Water has high SPC due to its hydrogen bonds Temperature within organisms remains constant compared to external temperature, and water bodies also have a slow change in temperature, providing stable aquatic habitats.  High latent heat of vaporisation A measure of the heat energy needed to vaporise a liquid Water has a high LHV due to its high SPC, as H bonds need to be broken before water can be vaporised, cooling the surrounding environment. Sweating is a good cooling mechanism A large amount of energy can be lost for a small amount of water Thus, dehydration is prevented e.g. in transpiration.  Density and freezing properties Ice is less dense than water and floats on it, insulating water and preventing it from freezing, preserving aquatic life underneath it Changes in the density of water with temperature cause currents, which help to maintain the circulation of nutrients in the oceans. Answer the following Questions : State the property of water that allows each of the following (a, b and c) to take place. Explain the importance of a, b and c: a the cooling of skin during sweating anser b the transport of glucose and ions in a mammal c much smaller temperature fluctuations in lakes and oceans than in terrestrial (land-based) habitats. Dipoles and hydrogen bonds  unequal distribution of charges in a covalent bond is called a dipole  molecules which have groups with dipoles are polar  in water, oxygen atom gets more electrons due to it being more electronegative and therefore gets a small negative charge denoted by delta (𝛅-)  hydrogen atoms get less electrons and therefore get small positive charges (𝛅+)  negatively charged oxygen of one molecule is attracted to a positively charged hydrogen of another, this attraction is called a hydrogen bond Molecules which have groups with dipoles are polar  they’re attracted to H2O molecules as they also have dipoles and are considered to be hydrophilic (water-loving)  soluble in water  e.g., glucose, amino acids, NaCl Molecules which do not have dipoles are non-polar  they’re not attracted to water and hydrophobic (water-hating)  insoluble in water  e.g., oils, cholesterol Important Definitions Polypeptide: a long chain of amino acids formed by Condensation reactions between the individual amino Acids; proteins are made of one or more polypeptide Chains; Polysaccharide: a polymer whose subunits are Monosaccharides joined together by glycosidic bonds Monosaccharide: a molecule consisting of a single sugar Unit and with the general formula (CH2O)n Disaccharide: a sugar molecule consisting of two monosaccharides joined together by a glycosidic bond Monomer – one of many small molecules that combine to form a polymer, e.g. – monosaccharides, amino acids, nucleotides Polymer – large molecule made from many similar repeating subunits, e.g. – polysaccharides, proteins, nucleic acids Macromolecule – large molecule formed due to polymerisation of monomers, e.g. – polysaccharides, proteins (polypeptides), nucleic acids (polynucleotides