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Molecular Biology Molecules to Metabolism Topic 2.1 Molecular Biology • Relatively new science • Reductionism: the theory that every complex phenomenon, especially in biology or psychology, can be explained by analyzing the simplest, most basic physical mechanisms • Synthesis of Urea in 1720’s • Falsified the theory of vitalism Metabolism • The web of all the enzyme catalyzed reactions in a cell of an organism • Either synthesis or digestion Anabolism (synthesis) • Synthesis of complex molecules(macromolecules) from simpler molecules (monomers). • Condensation reaction (water is formed) Catabolism (digestion) • Breakdown of macromolecules into monomers. (complex→simple) • Hydrolysis reaction (water splits the molecule) Inorganic Compounds • Most inorganic compounds are compounds that do not contain carbon. They are usually small molecules(individual elements). Examples: – Carbon dioxide – Water Additional Necessary Elements for living organisms Element Role in plant or animal Sulfur Stabilizes protein structure via the formation of a sulfhydryl group. Calcium Needed to make the mineral that strengthens bone and teeth. (nerve transmission) Phosphorous Part of the phosphate group in ATP, and DNA molecules. (phospholipids) Iron Needed to make hemoglobin which is necessary for oxygen transport. (myoglobin) Sodium Used in Neurons for the transmission of impulses. (osmoregulation) Organic Compounds • Organic compounds are compounds that are found in living things that contain Carbon (C)and Hydrogen (H) . – Examples : • • • • Carbohydrates Lipids Proteins Nucleic acids Carbon based life • Carbon atoms can form 4 covalent bonds. • Strongest type of bond so molecules are very stable • Can form single and/or double bonds with more than one type of element Chemical Elements and Water Topic 2.2 Polarity • Definition: (Campbell) – A lack of symmetry, structural differences in opposite ends of an organism or structure, such as root end and shoot end of a plant. • Application to molecules: – Negative and positive poles Opposites Poles Attract Water Molecule = 2 Hydrogen's and 1 Oxygen Because of water’s opposite poles it is considered to be a dipole or a polar molecule Solvent Properties • Property: – Because of waters polarity is has the ability to dissolve both organic and inorganic particles • Example: (organic-glucose), (inorganic-sodium) • Significance to living organism: – This allows substances to be transferred via water in a dissolved state. • Example: sodium in blood, glucose in sap • Water (a.k.a. universal solvent) Cohesion • Property: – Water molecules attract to each other because of hydrogen bonds that form between them. – Surface tension is produced by the cohesion of water molecules. This makes breaking the surface of water difficult for small objects. Cohesion • Significance to living organism: – Transpiration, movement within plants – Many organisms use the surface of water as their habitat. Many organisms can remain afloat despite the fact that they are in fact more dense than the water. • Ex. Mosquito Larve – Buoyancy : supports organisms Thermal Properties: heat capacity • Property: – Large heat capacity. More energy needed to heat and more energy given off when cooled. • Significance to living organism: – Water temperature tends to be very stable. – Beneficial to aquatic organisms. – Heat transfer in mammals. Thermal Properties: boiling and freezing points • Property: – Boiling point = 100°C – Freezing point = 0°C – Becomes less dense as it freezes causing ice to form first on the surface • Significance to living organism: – Water rarely boils naturally – Ice that forms first acts as an insulator • Winter habitat Thermal Properties: Cooling effects of evaporation • Property: – Can evaporate at lower temperatures. Heat energy needed to break the hydrogen bond is taken from the liquid water cooling it down. • Significance to living organism: – Has useful cooling effects • Sweat Transparency • Property: – Light can pass through water • Significance to living organism: – Reach structures suspended within organisms. • chloroplast, • human eye – Necessary characteristic for survival of aquatic environments Practice Problem 1 • 1. Outline the significance to organisms of the different properties of water. • Total 5-8 marks Practice Problem 1 : Answer • • • • • • • • • water is transparent / allows light to pass through for photosynthesis cohesion of water molecules allow transport in plants solvent – chemical reactions take place in water many substances dissolve in water and can be transported high boiling point making liquid water available to organisms / water is liquid over a range of temperatures water is most dense at 4°C so ice floats over water providing winter habitat high specific heat capacity so stable environment (internal/external) high surface tension – supports (near) surface dwelling organisms coolant – absorbs heat when it evaporates / changes states; Carbohydrates • subunit = simple sugars • saccharides • Function: – Energy use (glucose) – Energy Storage (glycogen) –3 types found 3 Types of carbohydrates Monosaccharides: one sugar glucose, ribose and fructose Disaccharides: 2 sugars linked together maltose, lactose, sucrose Polysaccharides: 3 or more sugars linked together starch, glycogen, cellulose Glucose Ribose Sucrose Glycogen Condensation of Glucose and Fructose Condensation of Glucose Lipids • Subunit = fatty acids + glycerol • Functions of Lipids – Energy Storage (fat in animals, oil in plants) – Heat Insulation (subcutaneous fat) – Buoyancy (lipids are less dense than water) – Major component of cell membranes Fatty Acids Glycerol Triglycerides Triglyceride Condensation Reactions Continued Cis vs trans fat Energy Storage Comparison • Carbohydrates – Digest easier than lipids which makes releasing the energy stored in them more rapid – Soluble in water making these energy stores easier to transport – Short Term Energy Storage – Stored as Glycogen • Lipids – Lipids contain more energy per gram than carbohydrates so stores of lipids are lighter than stores of carbohydrates that contain the same amount of energy. – Insoluble in water so they do not cause problems with osmosis in cells. – Long Term Energy Storage – Stored as fat Proteins • Subunit = amino acids (20 found in nature) • Many different types of proteins found • Functions: enzymes (catalase) transport (hemoglobin) movement (actin/myosin in muscles) structural ( collagen) hormones (insulin) receptors immunity Amino Acids Amino acids Condensation Reactions • Condensation reactions always yield water. • This reaction is also called dehydration synthesis • Water is removed and creates new bonds Polypeptides • Most protein are made up of groups of polypeptides • Lysozyme (digests cell wall of bacteria) is made up of only one • Hemoglobin (transport of O2 and CO2) is made up of only 4 Polypeptides • Different species have a different number of polypeptides that they make • Fruitflies make 14,000 • Humans make 23,000 Protein Functions Rubisco: • Found in plants (leaves) • “fixes” atmospheric CO2 into a useable form for the plant. • Allows for photosynthesis Protein functions Insulin • Hormone that regulates blood sugar • Secreted by pancreas • Sends message to muscles and liver Protein Functions Immunoglobins • Antibodies that mark a foreign invader for destruction • Many different antibodies for different invaders Protein functions Rhodopsin • Pigment that absorbs light • Found in rod cells of eye • Light causes a change in shape of protein which sends a signal to the brain Protein Functions Collagen • Rope like proteins made up of 3 polypeptides • Connective tissue • Skin, blood vessels, ligaments Protein Functions • Spider silk • Protein in spider webs • Stronger than steel and tougher than Kevlar Proteins • Sensitive to pH and temperature • Most proteins have an optimum temperature or pH that they function best • Pepsin (stomach enzyme) works best at a pH of 1.5 • In the presence of high temperatures or extreme pH changes, a protein will denature (lose its shapes) Proteomes • All of the proteins made in a particular cell • Can be different for cells depending on their function • Genomes are all the genes in a cell; this is fixed (same) for every cell • Each person has a unique proteome