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25/06/12 (Bio)Chemistry and Cytology BIOL241 Introduction or Recap of Cell Structure & chemistry INTERCONNECTEDNESS • Ma*er and Energy • Atoms, molecules, and chemical bonds • Importance of organic and inorganic nutrients and metabolites • Structure and funcBon of carbohydrates, lipids, proteins, and nucleic acids • Enzymes and ATP help run the metabolic reacBons of the body Energy • The capacity to do work (put matter into motion) • Types of energy – Kinetic – energy in action – Potential – energy of position; stored (inactive) energy: chemical energy • Energy is easily converted from one form to another • During conversion, some energy is “lost” as heat 1 25/06/12 Chemistry • Chemistry is the science that deals with matter • Matter is anything that takes up space and has mass • Smallest stable units of mass are atoms But I thought this was biology? • • • • MathemaBcs (the language of science) Physics (the structure of ma*er & energy) Chemistry (organic and inorganic structure) Biology: uses them all to understand Life. Atoms, Elements, Molecules • Elements are atoms of one particular type (see the periodic table) • Molecules are groups of atoms that (usually) contain more than one element è 2 25/06/12 Biologically significant elements • 13 principal elements – Carbon (C) – Oxygen (O) – Hydrogen (H) – Nitrogen (N) – Calcium (Ca), phosphorus (P), potassium (K), Sulphur (S), sodium (Na), chlorine (Cl), magnesium (Mg), iodine (I), and iron (Fe) • 13 trace elements – (e.g. zinc, manganese) Atoms with unfilled electron shells are reactive • Octet Rule • To become stable they form chemical bonds. • Three main types of chemical bonds – Intramolecular: • Ionic bonds (charged atoms resulBng from the gain or loss of electrons) • Covalent bonds (electrons are shared) – Intermolecular • Hydrogen bonds Covalent & Ionic Bonds • Molecules: atoms held together by covalent bonds • Salts: molecules held together by ionic bonds Q: What are the strongest type of bonds? 3 25/06/12 H 2O The body is mostly water (~2/3rd of total body weight) so all chemical reactions in the body occur in water Covalent bonds are much stronger than ionic bonds in water H2O – “Special” Properties • Water can dissolve organic and inorganic molecules making a solution • Water is needed for chemical reactions • Water absorbs and retains heat • Water is an effective lubricant H2O • What is it about water that makes it so special? • Water has all these amazing properBes due to its molecule’s ability to form hydrogen bonds 4 25/06/12 H-bonds b/t + & - charges Mixtures and Solutions • Mixtures – two or more components physically intermixed (not chemically bonded) – Solutions – homogeneous mixtures of components – Colloids (emulsions) – heterogeneous mixtures whose solutes do not settle out – Suspensions – heterogeneous mixtures with visible solutes that tend to settle out Essen5al Molecules • Nutrients: – essential molecules obtained from food (you have to eat them to get them) • Metabolites: – molecules made or broken down in the body 5 25/06/12 Organic vs. inorganic Organic molecules: • Always contain carbon with hydrogen, and someBmes oxygen • OUen soluble in water Inorganic: Electrolytes, minerals, and compounds that do not contain carbon with hydrogen. • Important examples: oxygen, carbon dioxide, water, inorganic acids and bases, salts Vitamins and Minerals • Vitamins and minerals are essenBal nutrients that are required in very small amounts for healthy growth and development. Examples? • They cannot be synthesized by the body and are essenBal components of the diet. Vitamins • Organic substances necessary for metabolism • There are 13 known vitamins (e.g. A, B1, D, K) • Some are fat soluble while others are water soluble • Are Coenzymes that help carry out the reacBons of metabolism 6 25/06/12 Minerals • Inorganic compound (oUen salts or elements) necessary for proper body funcBon • Can be bulk or trace minerals • Are Cofactors in metabolic reacBons Electrolytes • Inorganic ions (usually minerals) that conduct electricity in soluBon • Electrolyte balance is maintained in all body fluids; imbalance seriously disturbs vital body funcBons Electrolytes Table 2–3 7 25/06/12 Biological Macromolecules • Life depends on four types of organic macromolecules: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids Can you think of an example of each? 1. Carbohydrates • Contain carbon, hydrogen and oxygen in a raBo of 1:2:1 • Account for less that 1% of body weight • Used as energy source • Called saccharides (sugars, starches) Glucose is a monosaccharide 8 25/06/12 Disaccharides Sucrose Lactose Polysaccharides • Starch • Glycogen • Cellulose All are long strings of glucose molecules Difference lies in how they are bonded together Polysaccharides • Polysaccharides or polymers of simple sugars PLAY Polysaccharides Figure 2.14c 9 25/06/12 Polymers • A polymer is any molecule made up of several repeaBng units. Starch is a polymer of glucose. 2. Lipids • Contain carbon, hydrogen, and oxygen but the raBo of C:H is 1:2 (much less O) • May also contain other elements, phosphorous, nitrogen, and sulfur • Form essenBal structures in cells • Are important energy stores Lipids: Triglycerides (Fats and Oils) • Consist of 3 fa*y acids and glycerol – InsulaBon – Energy – protecBon Q: What’s the difference between saturated and unsaturated? 10 25/06/12 Lipids: Steroids and Cholesterol • All consist of a complex ring structure Lipids: Phospholipids Amphipathic 3. Proteins • Consist of chains of amino acids liked together by pepBde bonds • Enzymes are proteins 11 25/06/12 Protein Structure • Proteins are the most abundant and important organic molecules • Basic elements: – carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) • Basic building blocks: – 20 amino acids Protein Structure – 4 levels Primary: amino acid sequence Secondary: Hydrogen bonds form spirals or pleats (α-helix, β-sheet) TerBary: Secondary structure folds into a unique shape Quaternary: several terBary structures together: again: Shape!! Figure 2–20a Protein structure 12 25/06/12 Shape and Function • Protein funcBon is based on shape • Shape is based on sequence of amino acids • Denatura5on: – loss of shape and funcBon (due to heat, pH change or other factors) Protein FuncBons – support: • structural proteins – movement: • contracBle proteins – transport: • transport proteins – buffering: regulaBon of pH – metabolic regulaBon: • enzymes – coordinaBon and control: • hormones – defense: • anBbodies AcBvaBon Energy • Chemical reacBons in cells cannot start without help • AcBvaBon energy gets a reacBon started Figure 2–7 13 25/06/12 CharacterisBcs of Enzymes Figure 2.20 Energy In, Energy Out • Exergonic reacBons: – produce more energy than they use • Endergonic reacBons: – use more energy than they produce KEY CONCEPT • Most chemical reacBons that sustain life cannot occur unless the right enzymes are present 14 25/06/12 How Enzymes Work • Substrates: – reactants in enzymaBc reacBons • AcBve site: – a locaBon on an enzyme that fits a parBcular substrate Ac5ve site Amino acids + How Enzymes Work Enzyme (E) Substrates (S) Enzyme-‐substrate complex (E-‐S) H2O Free enzyme (E) Pep5de bond Internal rearrangements leading to catalysis DipepAde product (P) Figure 2–21 4. Nucleic acids • Contain C, H, O, N, and P • DNA and RNA are nucleic acids • Nucleotide consists of – Sugar – Phosphate group – Nitrogenous base 15 25/06/12 Structure of DNA Figure 2.22b A nucleoBde: ATP • Energy storage for cells • Many enzymes use ATP • Provides a way to run reactions that are otherwise endergonic (require energy) Membrane protein Pi P ATP is the energy currency of the cell Solute Solute transported (a) Transport work ADP + Pi ATP Relaxed smooth muscle cell Contracted smooth muscle cell (b) Mechanical work Pi X P X Y + Y Reactants Product made (c) Chemical work Figure 2.24 16 25/06/12 Compounds Important to Physiology Table 2–8 Summary • Energy and matter • Atoms, molecules, and chemical bonds • Importance of organic and inorganic nutrients and metabolites • Structure and function of carbohydrates, lipids, proteins, and nucleic acids • Enzymes and ATP help run the metabolic reactions of the body 17