3A_Biomolecules

= = **ENERGY, MATTER & ORGANISATION -** BIOMOLECULES //** Living systems are complex and highly organized, and they require matter and energy to maintain this organization. **//
 * 1) **Energy** is stored in the organization of matter.
 * E.g. Fats. Made up of carbon, hydrogen and oxygen.

2. Living organisms use matter and energy to build and maintain body structures.
 * E.g. Drinking milk helps to maintain the bone structure using calcium.
 * Eating Meat and soy products gives protein to help build muscles.
 * Snakes consume certain food, break them down, in order to build new skin after shedding their skin.

3. Living organisms obtain and process matter and energy.
 * E.g. Obtain Carbohydrates and process it to become energy or store as fats.

4. The structure of a molecule always dictates its function.

5. The structure and function of biological living systems obeys the laws of thermodynamics.

6. Communities of organisms depend on the cycling of matter and the flow of energy

7. The constant flow of energy and cycling of matter in the biosphere leads to a balanced or steady state.
 * Carbon circulates in the form of carbon cycle and cannot be created or destroyed.

This balance is achieved through various biogeochemical cycles and the processes of photosynthesis and cellular respiration - //focus is on ENERGY.

In order for us to understand this better, we will start by looking at biomolecules. The questions we ask about ourselves and the world around us: //
 * 1) Are we just chemicals?
 * 2) Are we what we eat?
 * 3) Why is the carbon molecule suitable for life as we know it?
 * Fourth most abundant element in the universe.
 * Four free electrons to bond itself to form many bonds, Single, Double or even Triple bonds. Can even form a bond of C6H12O6. (Glucose)
 * Can form bonds with not only others but also, itself. Important because we need the carbon backbone (C-C-C-C-C-C-C-C-C-C-C-C), form long chains of carbon=long chains of lipids, carbohydrates, proteins and DNA.
 * 1) Why is the chemistry of water suitable for life?
 * Many properties that make it important for life on earth. E.g. High Surface Tension
 * Universal Solvent.

In this unit you will need to know:
 * Understand and describe the properties of some important biological molecules; understand their roles, recall, recognize and identify the general formulae and structure of these molecules.
 * **Water**: understand its dipolar nature; understand formation of hydrogen bonds; understand the importance of water as a solvent; understand other roles of water related to its high latent heat of vapourisation, specific heat capacity, density and surface tension.
 * **Lipids**: understand the general nature of lipids as fats, oils and waxes; describe the roles of lipids as energy stores, and, in protection, waterproofing, insulation and buoyancy.
 * **Proteins**: understand the nature of amino acids as monomers in the formation of polypeptides and proteins; understand the meaning of the terms primary, secondary, tertiary and quaternary structure and their importance in the structure of enzymes; understand that condensation and hydrolysis reactions are involved in the synthesis of proteins; understand the nature and roles of fibrous and globular proteins as illustrated by collagen and (insulin?) hemoglobin.
 * **Carbohydrates**: understand that pentose and hexose’s are monosaccharide and have roles as monomers; understand that disaccharides and polysaccharides are composed of monomers joined by glycosidic bonds.; understand that condensation and hydrolysis reactions are involved in the synthesis and degradation of disaccharides and polysaccharides. Recall the structure and roles of basic carbohydrates.
 * **Vitamins and minerals**: understand their role and the effects of deficiency
 * **Enzymes**: understand the structure of enzymes as globular proteins, and the concept of active site and specifity; understand that enzymes are catalysts which reduce activation energy; understand how enzyme activity is affected by temperature, pH, substrate and enzyme concentrations; understand active site-directed and non-active site-directed inhibition of enzyme action; have an appreciation of the commercial uses of enzymes as illustrated by pectinases in food modification and proteases in biological detergents; discuss the advantages of immobalisation of commercial enzymes, as illustrated by lactase;

=Structure (molecule)= Chemically? =Role= What kind of role does it play? Thus, what can it's deficiency result in? =Form= What form does it take?

= = __**Carbohydrates**__

__Structure__

Contains elements C,H & O. C6H12O6 __Form__

Carbohydrates are either made from single monosaccharides monomers or several monosaccharides joined together. e.g. glucose (grape sugar and blood sugar), fructose (honey and fruit juices), galactose
 * 1) Monosaccharides (1 sugar)
 * 1) Trioses – C3H6O3 e.g. glyceraldehyde
 * 2) Pentoses – C5H10O5 e.g. deoxyribose
 * 3) Hexoses – C6H12O6 e.g. glucose, fructose

__Function__ Note: Often classified as reducing sugars. (Participate in reduction reactions.) e.g. sucrose, lactose, maltose (all have 12 carbon atoms with the general formula of C12H22O11.) Differences in the disaccharides are due to the different atomic arrangement within the molecule.
 * Used as primary energy source for fueling cell metabolism. (supporting structures)
 * Used as a source of energy. (glucose is the raw material needed for cellular respiration yielding ATP, the energy molecule.)
 * To be converted into other organic compounds such as amino acids and fats.
 * Formation of nucleic acids. (DNA)
 * Building blocks for larger molecules (e.g. DNA, Cellulose, starch, glycogen)
 * Source of respiratory energy (glucose)
 * To synthesis lubricants (e.g. mucus lining the respiratory system in Man traps dust)
 * To produce nectar in some flowers; Honey (Glucose) is used as bees food storage.
 * Attraction for the bees is flower nectarine and fruits. (fructose)
 * 1) Disaccharides (Made by compromising 2 monosaccharides together; sugars are joined together by glycosidic bond through condensation reaction and broken by hydrolysis)

Glucose + Fructose = Sucrose + Water (Transport compound in plantphloem) Glucose + Glucose = Maltose + Water (C6H22O11) Glucose + Galactose = Lactose + Water (Infant milk and Dairy products) Condensation is a chemical reaction whereby two simple molecules are joined together to form a larger molecule with the removal of one molecule of water. Disaccharides are split by treating them with heating with dilute acids at a suitable temperature or a suitable enzyme. They undergo a hydrolytic reaction or hydrolysis as a water molecule has been added to disaccharide. e.g. Starch, cellulose and glycogen.
 * Sucrose is a common transport form of sugar in plants.
 * Found in sweet fruits and sugar can stems.
 * Sucrose is not found in mammals.
 * Maltose is formed when starch is partially digested.
 * It is found in barley seeds which can be used during fermentation to produce beer.
 * It is found the milk of all mammals.
 * 1) Polysaccharides (More than 2 sugars combined together)
 * Process of condensing many smiliar molecules to form a large molecule is called polymerization.
 * 1) Other polysaccharides and polysaccharide derivatives eg pectins, chitin and mucopolysaccharides.

__Starch:__


 * Most important source of carbohydrates in our food.
 * Plentiful found in vegetable foods such as cereals, potatoes, tapioca. (Not formed or stored by animals)
 * Made up of large number of glucose molecules condensed together to form straight and branched chains of glucose chains.
 * A starch molecule may contain as many as 200 glucose units.
 * Can partially hydrolyse starch by using a suitable enzyme, amylase which digests the starch to the sugar maltose, and further broken down to glucose by maltase.

__Glycogen:__


 * “Animal Starch”.
 * Storage form of carbohydrate in animals and in fungi.
 * In humans, glycogen is stored in the liver and the muscles.
 * Glycogen and Starchs’ compactness provides an efficient way to store lots of glucose for future cellular respiration.
 * Their molecules have many side branches where glucose molecules can be removed from their tips (by enzymes).
 * Their insolubility stops them interfering with osmosis.

__Cellulose:__


 * Made from long, straight chains of glucose
 * Chains cross-linked by H-bonds which holds them tightly together (excludes water)
 * Chemically very inert and insoluble – few ‘tips’ on molecule make it difficult to digest
 * Many molecules form strong fibrils. (dietary fibre for humans)
 * Only some bacteria, fungi and a very small number of animals can secrete cellulase enzymes.
 * Not easily broken down, thus suitable as a biological structural material.

__Testing for Carbohydrates__ **Type of Carbohydrate** || **Example** || **Testing Reagent** || **Description** || Reducing Sugar || Glucose, Maltose, Lactose, Fructose || Benedict’s Solution || -Some sugars have reducing properties and will produce a red precipitate when boiled with Benedict’s solution. -BS contains copper (II) sulfate which is blue in colour. The salt is reduced to copper (I) oxide with red precipitate. -Green->Yellow->Orange->Brick Red Precipitate -Semi-quantitative. Only gives an approximate indication of how much reducing sugar is present. || Starch || - || Iodine Solution || -Add a few drops of iodine solution to the food sample. -A starch-polyiodide complex is formed during a positive test and the characteristics blue-black colouration appears. ||

__**Proteins**__

__Structure__

-Complex organic substances containing carbon, hydrogen, oxygen and nitrogen. Sulfur and phosphorus are usually present too. -Proteins are always present in protoplasm. -Proteins are the largest and the most complex out of all the good substances. -Every protein molecule is built up from simpler compounds known as amino acids, the basic units of proteins.

__Amino Acids:__ All of the above are bonded to a central carbon atom. -Although there are only 22 naturally occurring amino acids, they can be combined in many different ways to form millions of different proteins molecules. -These amino acids link with one another to form long chains. When two amino acids link up, there is a removal of one molecule of water. (condensation reaction) -The bond formed between the two amino acids to form a dipeptide is strong and is known as peptide bond. -If three of more amino acids are linked up by peptide bonds, a polypeptide or peptone is formed. An average amino acid can contain up to 500 units. -The polypeptides join up to form long chains. These long chains will coil up to give the protein a distinctive three-dimensional structure. The coils are held in place by weak hydrogen bonds which are easily broken by heat, acids and alkalis. When these links are broken, the protein is said to be denatured. -Proteins are too large to pass through living membranes. They have to be broken down by enzymes in order to be absorbed as amino acids. These amino acids are link up again with the cells to form the protein the animal needs.
 * The building blocks of proteins.
 * Small molecules with a simple basic structure:
 * 1) An amino group (~NH2)
 * 2) A carboxyl group (~COOH)
 * 3) A Hydrogen atom (H)
 * 4) A functional group designated “R”.

__**Protein Structures**__
 * 1) Primary: order in which amino acids are linked to form a polypeptide chain
 * 2) Secondary: the way the polypeptide chain is coiled and folded, alpha-helix and beta-pleated
 * 3) Tertiary: large globular proteins formed by the coiling and folding the already coiled and folded chain eg enzymes
 * 4) Quaternary: proteins made from 2 more polypeptides eg haemoglobin

__Function__
 * Source of Energy: Proteins provide approximately 17Kj/g of energy when broken down.
 * Growth and repair of cells: Proteins are essential for the synthesis of protoplasm, growth and repair of worn tissues.
 * Globular Proteins: These proteins make up the thousands of enymes and antibodies that carry out the chemical reactions in our body and protect us from infection.
 * Structural Proteins: These proteins give structure to various parts of our bodies, for example, keratin in hair, actin and myosin in muscles, fibrin which aids in blood clotting.
 * Protein is the basic unit for hair nail and connective tissues. The triple helix of the collagen (a protein) gives our skin the elasticity. That is why it is injected under the sky in cosmetic surgery.

__Effects of protein deficiency:__

__-__Average adult 50g to 100g of proteins a day. -Deficiency of proteins in children may lead to kwashiorkor. (the children have swollen abdomens, their skin cracks and become scaly.)

__Test for proteins:__

The Biuret Test. To test for proteins: If protein is present, the substance will turn purple. The colour is due to the formation of a complex between nitrogen atoms in the peptide chain and Cu2+ ions in copper (II) sulfate. Thus testing for peptide bonds.
 * 1) Add 2cm3 of dilute sodium hydroxide solution and shake the mixture.
 * 2) Add a few drops of 1% copper sulfate solution and shake after each drop.

__**Lipids**__

__Structure__

-Fats are organic compounds made up of Carbon, Hydrogen and Oxygen. However, unlike carbohydrates, they contain lesser number of Oxygen atoms in proportion to Hydrogen atoms. (E.g. Tristearin C57H110O6)

-Formula: R-COOH or (CH3(CH2)nCOOH)

-Most fats contain more than 40 carbon atoms.

-e.g. Triglycerides (fats and oils)

Contains a glycerol and 3 fatty acids molecules which are joined together by ester bonds. Water is giving out through this condensation reaction.

Fats (solid at room temperature) contains saturated fatty acids chains.

Oils (liquid at room temperature) contains unsaturated fatty acids chains.

It is insoluble in water as it has no -OH group (hydrophobic).

__Role__

Fats are a good source of energy and are used as food storage. The more highly saturated the fat, the richer the energy as compared to the less saturated ones.

Fats can be hydrolysed to fatty acids and glycerol.

__**Types of Lipids**__

__1. Saturated fats__


 * Fatty acids have no double bonds (thus more closely packed and form immobile arrays)
 * Found in animal fat
 * Contain palmitic acid and stearic acid.

__2. Unsaturated fats__


 * Fatty acids have double bonds (Produce kinks and are not closely packed thus these fats are more fluid and mobile than the hard saturated fats)
 * Found in fish and plant oils
 * Contain oleic acid and linoleic acid.

__Function__


 * An efficient source and storage of energy. (providing approximately 38kJ/g)
 * As an insulating material, especially beneath the skin, to prevent excessive heat loss. (e.g. whales have blubber which is essentially fats, to keep them warm in the freezing ocean temperatures)
 * Solvent for fat soluble vitamins, A, D, E, K, and other hormones e.g. sex hormones
 * Means to restrict water loss form the surface of the skin.
 * Constituent of protoplasm, especially in membranes