EH1008 Biomolecules Lecture 2: Inorganic and organic chemistry limian.zheng@ucc.ie 1 Inorganic & Organic Chemistry Inorganic Chemistry: generally, substances that do not contain carbon Inorganic molecules: lack C and H chains Exceptions: CO, CO 2, and HCO 3 - Often formed by ionic bonds, but not always e.g. H 2 O, O 2, CO 2, salts, acids, bases, calcium phosphate Organic Chemistry: study of carbon-containing substances. Those that are biologically active are called biochemicals. Organic molecules based on C and H chains structurally complex typically formed by covalent bonds e.g. sugars, amino acids, vitamins, etc. 2 Water Cells need a continuous supply of nutrients, removal of waste products. Living cells contain mostly water and GENERALLY interact with an aqueous environment: blood plasma (extracellular fluid ): 92% water 50% of female body weight and 60% of male Water is the vital SOLVENT:- a (liquid) substance in which SOLUTES are dissolved. inorganic salts (eg NaCl, KCl, nitrates, phosphates) small organic molecules (eg sugars, amino acids) dissolved gases (eg oxygen, carbon dioxide) 3
Weak hydrogen bonds form between the +ve charged H atoms of one H 2 O molecule and the ve charged O atoms of another H 2 O molecule. The attraction of one H 2 O molecule to another - Cohesion Hydrogen bonds organise H 2 O in to a lattice Adhesion: the same attractive force attracts other molecules Adhesion+ Cohesion hold cells together & movement fluid through body 4 Physical and Chemical Properties of Water Advantages of water: 1. Temperature Liquid @ body temperature (37 C) H-bonding resists rapid temp change high boiling point low freezing point very stable: stabilizes body temp 2.Protection Lubricant, tears protect surface of eyes Cushion cerebrospinal fluid protects brain 5 3. Chemical reactivity: Indirect - Many reactions take place in water Direct H 2 O participates in chemical reactions Polarity allows it to serve as reactant in many reactions: (i) Hydrolysis: decomposition using water ATP +H 2 O ADP + Pi + energy (ii) Dehydration synthesis: synthesis using water ADP + Pi ATP + H 2 O 6
4. Good solvent Water is considered as the universal solvent Polar and ionic substances dissociate easily in water to form solutions Solution: mixture of liquids, gasses, or solids that are uniformly distributed and chemically combined Solvent: that which dissolves the solute Solute: that which dissolves in the solvent Eg sweat is a salt solution: water is the solvent, salt (ionic substance) is the solute Water also dissolves certain organic substances e.g sugar and alcohols that do not dissociate into ions in solution but do have polar properties. Note water does NOT dissolve or dissolve in compounds that are completely nonpolar eg. fats and oils 7 Hydrophilic & Hydrophobic molecules Compounds that dissolve in H 2 O are hydrophilic, those that do not are hydrophobic Strict hydrophobic compounds do not mix well in H 2 O eg. lipids Some molecules have a hydrophobic and a hydrophilic end amphipathic polar and non-polar end Amphipathic substances make good emulsifiers they can attract hydrophilic and hydrophobic molecules to them, eg sodium oleate/soap 8 Properties of H 2 O Water also serves as a good mixing medium Mixture: substances physically but NOT chemically combined Solution: mixture of liquids, gases, or solids that are uniformly distributed and ARE chemically combined Suspension: is a mixture of materials that separate unless stirred. Eg Sand and water, Blood - Plasma and red blood cells Colloid: a mixture with properties between those of a solution and fine suspension. The dispersed (solute like) substance is distributed throughout a dispersing (solvent like) substance. Proteins are dispersed particles Proteins +H 2 O = Colloids 9
Solution Concentrations Concentration: measure of number of particles of solute per volume of solution Osmosis: movement of solvent along a concentration gradient across a semipermeable membrane. The cell membrane is semipermeable. Osmole (Osm): moles of solute contribute to the osmotic pressure of a solution. Osmolality (Osm/kg): the amount (osmole/osm) of particles dissolved in 1Kg of water Concentrations of particles in the human body: milliosmoles (mosm) 300 mosm is average in the human body 10 Circulatory system carries water and solutes to capillaries, where exchange with cells occurs. Solutes must cross capillary wall, interstitial space and cell membrane to reach cell. How? Diffusion: movement of molecules due to random, spontaneous thermal motion. Net movement occurs along a gradient (chemical ± electrical). Cell Membrane Diffusion: video Chemical potential: concentration gradient; charged particles Electrical potential: electrical gradient / potential. Electrochemical potential: energy driving movement due to combined effects of chemical and electrical gradients 11 Acids and Bases; Salts and Buffers Acid: molecules that DONATE protons in solution Base: molecules that ACCEPT protons in solution Water also tends to ionise acts as acid: OH - (hydroxyl anion) as base: forms H 3 O + (hydronium ion main form of protons in water) H O H O H H O - H + H H O H Salt: cation (but not H + ) and anion (but not OH - ) Formed by the interaction of an acid and a base: HCl + NaOH NaCl +H 2 O Buffer: Aqueous solution consisting of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid. ph of the solution changes very little when a small amount of strong acid or base is added to it 12 +
ph Scale ph: potential of Hydrogen -logarithmic expression of amount of H + in solutions: -log10 [H + ] Log scale = 10 fold change ph calculated as log10 [H + ] in moles/liter (scale 0-14) 13 The ph Scale Refers to the hydrogen ion concentration in a solution Neutral: ph of 7 [H + ] = [OH - ] Acidic: higher [H + ], ph < 7 Alkaline or basic: higher [OH - ], ph > 7 Physiologic ph is 7.4 14 Acids bases and buffers in the body The body contains many acids and bases which alter body function by releasing and binding protons Most organisms grow best around neutral ph The normal ph range for human blood is 7.35 to 7.45 Blood < 7.35 Acidosis depressed nervous system disorientated Blood >7.45 Alkalosis overexcited nervous system convulsions 15
Acids bases and buffers in the body Chemical behaviour of many molecules changes as the ph of the solution in which they are dissolved changes. Maintaining a normal range of H + and OH - ions is necessary for most biological processes Enzymes work best within a narrow range of ph Homeostatic mechanisms: i. Respiratory system ii. Kidneys iii. Buffers are used in living things to absorb H + ions released during metabolism to keep the ph from changing. Eg. bicarbonate, phosphates, amino acids and proteins. 16 Oxygen and Carbon Dioxide Oxygen (O 2 ): Inorganic molecule 21% atmosphere is O 2 Essential for most living organisms required in the final step in the series of reactions used to extract energy from food. Carbon dioxide (CO 2 ): produced during the catabolism of organic compounds eg glucose. Metabolic waste product. Exhaled during respiration Combines with water in plasma and forms H + thus affecting acid/base balance CO 2 + H 2 O H 2 CO 3 H + + HCO 3-17 Molecules & Macromolecules Molecular weight < 1000 = small molecule Molecular weight > 1000 = large or macromolecule One role of small molecules is to serve as material for construction of larger molecules Remember from Lecture 1, some macromolecules are polymers, formed from smaller molecules, or monomers 18
Importance of Carbon Organic chemicals contain carbon Carbon atoms bound together by covalent bonds constitute the backbone of many large molecules Carbon s ability to form covalent bonds with other atoms allows the formation of the large, diverse complicated molecules necessary for life 19 Diversity of Life A wide variety of molecules are available due to: Variation in length of the carbon chains Different combinations of atoms 20 Molecules & Macromolecules: fall in to one of 4 main families Small molecules Sugars Fatty acids Amino acids Nucleotides Macromolecules Carbohydrates Lipids Proteins Nucleic acids 21
Composed mainly of: Carbon Hydrogen Oxygen Lipids Some lipids contain small amounts of other elements, e.g. Phosphorous Nitrogen 22 Lipids High ratio of carbon and hydrogen to oxygen and other elements Poorly soluble in water Dissolve in nonpolar organic solvents 23 Fats Phospholipids Eicosanoids Steroids Fat-soluble vitamins Types of Lipids 24
Role of Lipids in the Body Role Protection Insulation Regulation Vitamins Structure Energy Example Fat surrounds and pads organs Fat under skin prevents heat loss Steroid hormones regulate many physiological processes: oestrogen/testosterone responsible for many female/male differences Fat-soluble vitamins provide a variety of functions: vitamin E promotes wound healing Phospholipids and cholesterol important components of cell membranes Lipids can be stored and broken down later for energy 25 Fats ingested from food Fats Broken down in cells to release energy for those cells If more fat is ingested than is needed it can be stored in the body as fat for later use Triglycerides make up 95% of the fats in humans 26 Triglycerides 2 building blocks: Glycerol x 1 Fatty acid x 3 Fatty Acids saturated unsaturated 27
Fatty Acids Saturated only single covalent bonds between carbon atoms Beef, milk, cheese, butter, eggs Monounsaturated 1 double covalent bond Olive oil Polyunsaturated 2 double covalent bonds Fish oils 28 Saturated vs. Unsaturated Saturated fats contribute to cardiovascular disease Unsaturated fats do not (less rigid, so do not stick to blood vessel walls) Trans fats are unsaturated fats, chemically altered to make them more saturated (longer shelf-life) by the addition of hydrogen Even greater factor than saturated fats in the risk for cardiovascular disease 29 Triglycerides 30
Phospholipids Similar to triglycerides, except that 1 fatty acid is replaced by a molecule containing phosphate and, usually, nitrogen video 31 Phospholipids Polar (hydrophilic) at one end; nonpolar (hydrophobic) at other Function: important structural component of cell membranes 32 Steroids Composed of carbon atoms bound together into 4 ringlike structures 33
Steroids Cholesterol, bile salts, oestrogen, progesterone, testosterone Component of cell membranes; physiological regulators High levels of cholesterol in blood increase risk for cardiovascular disease, certain amount is vital for normal function 34 Fat-soluble vitamins Essential for many normal body functions, eg. Vitamin A D E K Function Forms retinol; necessary for seeing in the dark Promotes calcium uptake Promotes wound healing Necessary for synthesis of proteins responsible for blood clotting 35