Lecture 2: The Chemical Level of Organization PDF

13/01/2024 THE CHEMICAL LEVEL OF ORGANIZATION 1 Objectives o Basic Chemistry o Matter, Atoms and Elements o Chemical Bonding o Inorganic Compounds o Water o Acids and Bases o Buffers o...

13/01/2024 THE CHEMICAL LEVEL OF ORGANIZATION 1 Objectives o Basic Chemistry o Matter, Atoms and Elements o Chemical Bonding o Inorganic Compounds o Water o Acids and Bases o Buffers o Salts o Organic Compounds o Carbohydrates o Lipids o Nucleic Acids o Proteins 2 1  13/01/2024 Matter, Atoms & Elements 3 o Matter o Anything occupies space and has mass o Exists in three forms: Solid, liquid, gas o All matter is composed of atoms o Atom o smallest unit of matter o engage in chemical reactions o 3 types of subatomic particles o protons (yellow) = positive o neutrons (orange) = neutral o electrons (grey) = negative o protons and neutrons are in the nucleus o electrons are in the orbitals/shells around the nucleus 4 2  13/01/2024 o Element o any substance containing one type of atom o Cannot be broken down into simpler substances by chemical reactions o ~118 different elements 5 o 92 elements occur naturally o 25 of these are essential to humans o 4 of these (C,H,O,N) make up 96% of the weight of most cells 6 3  13/01/2024 Features of an Atom o Atomic number o number of protons o equals number of electrons o written as superscript o smaller of the two numbers o Mass (number) o sum of protons and neutrons o number of neutrons = 23-11=12 o written as subscript o larger of the two numbers 7 Electron Configuration – Bohr/Shell model o If there are 11 electrons: o first shell = 2 o second shell = 8 o third shell = 1 o therefore electronic configuration is written as 2)8)1 8 4  13/01/2024 9 Try These!!! o Atomic number o Atomic mass o # Protons o # Electrons o # Neutrons o Electron configuration 10 5  13/01/2024 Valence Electrons o Electrons contain energy in increasing amounts as one moves further from the nucleus o Electrons in the outermost ring have the most energy o Atom achieves stability when outermost (valence) shell is filled with electrons = Octet rule o Involved in chemical reactions 11 Chemical Bonding 12 6  13/01/2024 o Atoms react with one another so that they can have 8 electrons in the outer shell o one exception is Hydrogen – it is complete with electrons in outer shell. o Molecule o formed when 2 or more of the same atoms react with one another (e.g., O2 – oxygen molecule) o Strong and stable o Compound o combination of two or more different elements combined in a fixed ratio (e.g., water (H2O), salt (NaCl), methane (CH4)) 13 Types of Bonds 1. Ionic – atoms loose or gain electrons o occurs between metal and nonmetal o Not as strong as covalent bonds o Metal atoms with 1, 2 or 3 valence electrons will lose electrons becoming cations (positive) o Non-metal atoms with 5, 6 or 7 valence electrons will gain electrons becoming anions (negative) 14 7  13/01/2024 Common Ions in the Body 15 2. Covalent – share electrons o Electrons in bond are pulled evenly between (shared equally) o Occurs between nonmetals o Single, Double or triple bonds o Strongest type of bond 16 8  13/01/2024 3. Hydrogen –electrons are NOT shared o Result from the weak attraction between a positively charged H+ atoms in one compound and a negatively charged atom in another compound o In water, H-bonds provide water with strong cohesion = water molecules stick to one another because of the tendency of like particles to stay together, which ↑ surface tension = the force necessary to break the surface of a liquid 17 Try These!!! o Number of Valence Electrons for Atom 1 o Number of Valence Electrons for Atom 2 o Are valence electrons lost, gained or shared? o What type of bond is Formed? Carbon fluoride (CF4) Magnesium sulfate (MgS) Nitrogen gas (N2) 18 9  13/01/2024 Chemical Reactions 19 o occur when new bonds are formed, or old ones are broken o Reactants  Products o Reactants/substrates = starting substances o Products – ending substances o Metabolism o sum of all chemical activities in the body o Anabolic/synthetic (e.g., photosynthesis, dehydration reactions) o Catabolic/decomposition (e.g., cellular respiration, hydrolysis reactions) 20 10  13/01/2024 o Chemical reactions either require input of energy or release energy o endergonic = requires input of energy o exergonic = release energy o What is energy? o Capacity to do ‘work’ o Kilojoules (kJ) o 2 states of energy o potential = energy of position o kinetic = energy of motion o Chemical energy = potential energy stored as chemical bonds in food is released as kinetic energy for cell activities o Some energy released as heat (first law of thermodynamics) 21 o In the body, chemical reactions need a ‘push’ to get them going = Activation energy (Ea) o Enzymes function is to lower the Ea of a reaction o Have ‘active site’ where substrate/reactant fits into o Are extremely specific -> each enzyme catalyzes only one kind of substrate 22 11  13/01/2024 o Enzymes have shape that fosters binding of substrates (reactants) at a specific location; “lock and key” fit. o Induced fit model = enzyme's active site changes shape to ‘better fit’ the substrate 23 Types of Chemical Reactions 1. Synthesis/Anabolic (A + B  AB) 2. Decomposition/Catabolic (AB  A + B) 3. Exchange (AB + CD  AD + CB) o those in which cations and anions were partners in the reactants are interchanged in the products 4. Reversible (A + B ⇌ AB) 5. Oxidation-reduction o Oxidation – loss of electrons and energy release o Reduction – gain of electrons and energy gain 24 12  13/01/2024 LIVING ORGANISMS ARE MADE UP OF INORGANIC AND ORGANIC MOLECULES 25 Carbon dioxide Hydrochloric Acid DNA Inorganic Organic o Don’t usually contain o Always contain Carbon Carbon o Ionic bonding o Water is the most o Covalent bonding important and abundant o Usually do not inorganic compound in all dissolve easily in living things water o Soluble in water 26 13  13/01/2024 INORGANIC COMPOUNDS Lack Carbon 27 Water o Compound composed of 2 hydrogen and 1 oxygen atom o Linked via hydrogen bonds 28 14  13/01/2024 o Universal solvent – hydrophilic (polar) molecules and salts dissolve easily o Temperature stability - Stays liquid over wide range: 0 – 100°C 29 o Highest Heat Capacity of any liquid  amount of heat required to change temperature by 1°C = calorie (~4 Joules ) o It takes a lot of heat to increase the temperature of liquid water because some of the heat must be used to break hydrogen bonds between the molecules, thus temperature does not change much 30 15  13/01/2024 o Highest heat of vaporization  amount of heat needed to change one gram of a liquid to a gas o Again, many H-bonds in water therefore takes a lot of energy to turn water into vapour (540 cal/g at 100 °C) o As water molecules evaporate, the surface they evaporate from gets cooler = evaporative cooling. 31 o H-bonds provide water with strong cohesion = molecules stick to one another because their positive and negative regions are attracted to the oppositely-charged regions of nearby molecules o ↑ surface tension = the force necessary to break the surface of a liquid 32 16  13/01/2024 o Adhesion - polar nature allows for strong H-bonding with other substances (molecules/surfaces) too o Capillary forces = attraction of the surface of a liquid to the surface of a solid tends to pull molecules up against gravity result from both cohesion and adhesion (e.g., water traveling in the xylem of plants, meniscus in a graduated cylinder) 33 Acids & Bases o In liquid solutions, most of the water molecules are intact but some water molecules can break apart spontaneously into H+ (hydrogen ions) & OH- (hydroxide ions) o Acid o releases H+ into a solution (proton donor) o Sour taste o Neutralize bases o e.g., gastric juice, lemon juice, black coffee o Base/Alkali o accepts H+ (proton acceptor)and removes them from a solution – does this by releasing OH- when dissolved in water, which combines with H+ in solution o Bitter taste, feel slimy o Neutralize acids o e.g., Human Blood, Household Ammonia, Seawater 34 17  13/01/2024 o Strength of an acid (or base) measured using pH scale - a measure of the concentration of H+ in solution o 0 = most acidic o 14 = most basic o Each pH unit represents a tenfold change in the concentration of H+ o Stronger acids give up H+ more easily o Pure water is neutral (pH=7): equal amounts of H+ and OH- in solution Stomach acid (pH=2) is 100,000 times more acidic than water (pH=7) 35 Buffers o Buffers resist changes in pH when an acid or base is added o In the body, buffers are needed to maintain homeostasis o Narrow pH ranges crucial to many chemical reactions in the body o Bicarbonate buffer system 36 18  13/01/2024 Salts o When an acid reacts with a base, it neutralizes to form a salt and water o The H+ of the acid and the OH- of the base form water o The non-metallic ions of the acid and the metallic ions of the base form a salt o When the salt is dissolved in water it dissociates into cations (+ charged) and anions (- charged) o These ions serve as electrolytes in body 37 K+ Na+ Cl- Mg2+ Ca2+ PO4- HCO3- 38 19  13/01/2024 ORGANIC COMPOUNDS 39 Carbon o Has the ability to join with several atoms at the same time o Can form up to four covalent bonds o may bond with nitrogen, oxygen, and phosphorus o Carbon comprised ~ 19% of the weight of an animal and ~ 12 % of a plant 40 20  13/01/2024 Macromolecules o Building blocks of life o Large carbon-based (organic) molecules needed by living organisms to help maintain homeostasis (a relatively constant internal environment) o Polymers constructed of monomers o built via dehydration synthesis (condensation reaction) o broken down via hydrolysis 41 Four Classes 42 21  13/01/2024 Functional Groups 43 1. Carbohydrates o 1:2:1 ratio of carbon, hydrogen, oxygen o Monomer = monosaccharide o End in “-ose” o C—H covalent bonds hold lots of energy o good source of short-term energy o any carbs not used will be stored as fat 44 22  13/01/2024 45 Monosaccharides o Simple carbs o Easily absorbed into the blood stream – no digestion needed o 3 -6 Carbon atoms o e.g., glucose, fructose, galactose, dextrose 46 23  13/01/2024 Disaccharides o two monosaccharides linked together via dehydration synthesis 47 o allows transport within an organism o used for energy storage o maltose (from grains) = glucose + glucose o lactose (milk sugar) = glucose + galactose o sucrose (table sugar) = fructose + glucose 48 24  13/01/2024 Polysaccharides o Long chains (3 or more) of monosaccharides bonded together 49 o Energy storage o plants use starch o animals use glycogen (stored in the liver – help regulates blood glucose levels) o Structural support o plants use cellulose – non digestible o arthropods and fungi use chitin 50 25  13/01/2024 2. Lipids o Loosely defined group of molecules that are insoluble in water (hydrophobic) o Contain C, H and O o Monomer = fatty acids and glycerol o Linked by an ester bond 51 Lipid Functions o Long term energy storage o Protection o Insulation o Shock absorber o Chemical messengers o Forming biological membranes 52 26  13/01/2024 Saturated vs. Unsaturated Fats 53 54 27  13/01/2024 Phospholipids o Found in cell membrane o Contains heads and tails 55 Steroids o Made from cholesterol, which is formed in the liver o e.g., sex hormones, corticosteroid hormones, bile salts 56 28  13/01/2024 Waxes o Solid at room temperature o Waterproof o Forms protective covering on plants, cuts down on water loss o Found in the ear (cerumen) o Honeybees produce wax to make honeycomb to store honey 57 3. Nucleic Acids o Contain C, H, O, N and P o Determines hereditary information o Monomer = nucleotide 58 29  13/01/2024 DNA = deoxyribonucleic acid o Double helix o Organic bases: Adenine, Guanine, Cytosine, Thymine o Sequence not right, can cause cancer or genetic defects 59 RNA = ribonucleic acid o Single strand o Three types: o mRNA o tRNA o rRNA o Organic bases: Adenine, Cytosine, Guanine and Uracil 60 30  13/01/2024 o ATP o Energy “currency” of cells o energy is released when the bond between two phosphates are broken 61 4. Proteins o Contain C, H, O, N and S o Monomer = amino acid o Linked by peptide bonds 62 31  13/01/2024 Functions Transport Enzymes (e.g., (e.g., lactase) hemoglobin) Defense Support (ligaments and (antibodies) tendons) Movement Receptors (motor proteins) 63 Amino Acids 64 32  13/01/2024 Protein Structure Amino acids  polypeptide  protein 65 Primary Structure o linear sequence of amino acids (joined by peptide bonds), e.g., glucagon, Insulin 66 33  13/01/2024 o spatial organization of parts of polypeptide Secondary Structure backbone (bonded by H- bonds) o Alpha-helix – coiling of polypeptide chain; chain held by weak hydrogen bonds making them elastic; found in wool, hair, skin, nails (keratin) o Beta-pleated sheet - polypeptide has a zig-zag pleated structure; does not stretch; e.g., silk, globular proteins (immunoglobulins) 67 Tertiary Structure o 3D structure created by interactions among the different R groups in the entire polypeptide chain (H-bonds, covalent disulfide bonds/bridges, ionic bonds, hydrophobic interactions) o hydrophobic amino acids orient towards the interior to allow the cell membrane to be suspended in water in the body 68 34  13/01/2024 Quaternary Structure o two or more polypeptide chains come together using the same types of interactions that produce secondary and tertiary structures, e.g., Hemoglobin, antibodies, collagen 69 Change in structure = change in function 70 35