Chapter 2: The Chemical Level of Organization. Chemistry = the science of the structure of matter Matter takes up space and has mass (weight)

Transcription

1 Chapter 2: The Chemical Level of Organization Chemistry = the science of the structure of matter Matter takes up space and has mass (weight) It can exist as a solid, liquid, or gas The smallest stable units of matter = atoms, which are made up of Protons in the nucleus; positively charged Neutrons in the nucleus; uncharged Electrons orbit the nucleus; negatively charged Elements An element is a pure substance composed of only one kind of atom Atoms are classified into elements by the number of protons they have (= the atomic number) Note that the atomic number of hydrogen is 1 Fig. 2-1, p. 27 1

2 FYI Elements found in the human body Table 2-1, p. 28 The basic structure of atoms Atoms have equal numbers of protons and electrons, so overall they are electrically neutral Up to 2 electrons can orbit in the first energy level (electron shell); up to 8 electrons can orbit in each of the higher-level energy levels The outermost electron shell determines an atom s reactivity with other atoms (i.e., an atom is stable only if its outermost electron shell is full) Fig. 2-2, p. 29 2

3 Atoms combine via chemical reactions, forming chemical bonds Molecule = a chemical substance made up of atoms of any elements held together by covalent bonds E.g. O 2 (oxygen gas), H 2 O (water), C 6 H 12 O 6 (glucose) Compound = a chemical substance made up of atoms of different elements, regardless of bond type E.g. NaCl (table salt), H 2 O, C 6 H 12 O 6 Types of bonds: 1. Ionic bonds 2. Covalent bonds 3. Hydrogen bonds Ionic bonds Ion = an atom that carries an electric charge (i.e., it has unequal protons and electrons) Cation = a positively charged ion Anion = a negatively charged ion Ions play many vital roles in our bodies (e.g. muscle/nerve function, osmotic water movement, etc.) Ionic bonds = the attraction between cations and anions (these can be fairly strong when solid/dry, but they also can dissolve in water) Fig. 2-3, p. 31 3

4 Electrons are shared between atoms; this is the strongest bond type Single covalent bond = one pair of electrons are shared Double covalent bond = two pairs of electrons are shared Nonpolar covalent bonds Electrons are shared equally between atoms Polar covalent bonds Electrons are shared unequally (see the next slide ) Covalent bonds Fig. 2-4, p. 32 Water: formed by polar covalent bonds Fig. 2-5, p. 33 O attracts H s electrons more strongly than H does The O becomes slightly/partially negative ( ) Each H becomes slightly/partially positive (+) Water is a polar molecule 4

5 Hydrogen bonds Occur between polar molecules The name is due to the fact that many polar molecules contain H atoms that have formed polar covalent bonds with another element (such as in H 2 O) H-bonds, then, are essentially the attractions between the partially positive (δ + ) and partially negative (δ - ) parts of neighboring polar molecules Are the weakest individual bonds (that we ll learn about, anyway) But lots of them working together can be strong cumulatively Help determine molecular shapes (e.g. proteins, DNA) and the properties of water (e.g. cohesion [surface tension], adhesion) Fig. 2-6, p. 33 Chemical reactions and energy Chemical reactions occur when bonds are broken, atoms are rearranged, and new bonds are formed Reactants = what go in Products = what come out Metabolism = the sum total of all the chemical reactions occurring in the body at any given moment Work = the movement of an object (matter) or change in its physical structure Energy = the capacity to perform work Kinetic energy = the energy of motion; i.e., energy that is doing work Potential energy = stored energy, due to the Position of matter (e.g. up high) Physical structure of matter (e.g. a compressed spring) Chemical structure of matter (in bonds) Chemical reactions convert energy from one form to another These energy conversions are not 100% efficient, resulting in the release of waste heat 5

6 Types of chemical reactions Decomposition or catabolic reactions = breaking molecules into smaller fragments (e.g. digestion) These often require water to break covalent bonds (hydrolysis), and release energy (exergonic) A-B + H 2 O A-H + B-OH + energy Synthesis or anabolic reactions = assembling smaller molecules into larger ones (e.g. muscle growth) These often remove water as covalent bonds are formed (dehydration or condensation), and require energy input (endergonic) A-H + B-OH + energy A-B + H 2 O Exchange reactions = shuffle parts of the reactants to make new products I.e., these are a combo of decomposition and synthesis reactions A-B + C-D A-C + B-D All reactions are theoretically reversible (e.g. A-B A + B) At equilibrium, the rates of the opposing reactions are equal (in balance) But how reversible? It depends on the activation energy requirements (see the next slide ) Reaction energetics and enzymes Activation energy = the amount of energy that is needed to start a reaction Enzyme = a protein that the rate of the reaction by the activation energy required Enzymes are catalysts (which accelerate reactions but are not permanently changed or consumed by them) Fig. 2-8, p. 37 6

7 Inorganic compounds Are not primarily composed of C and H Include Carbon dioxide (CO 2 ) a byproduct of cell metabolism Oxygen (O 2 ) an atmospheric gas required for important metabolic reactions Water (H 2 O) to be discussed next Inorganic acids, bases, and salts These are ionic inorganic compounds, and will be discussed later Water Makes up ~ 2/3 of total body weight Some important properties of water (many of which are due to H-bonding): Solubility water dissolves most charged or polar molecules Solvent = the medium (water in this case) Solutes = the dispersed molecules Solution = the uniform mixture of solvent and solutes Reactivity chemical reactions occur in water, and often water is a reactant in or a product of a reaction High heat capacity water will absorb (and release) a lot of energy (heat) before changing temperature Lubrication there is little friction between water molecules 7

8 Aqueous solutions I.e., solutions where water is the solvent Ionic compounds ionize/dissociate in water Polar molecules are hydrophilic (water-loving) and dissolve in water Molarity = the concentration of a solute in moles/l Mole = the weight (in grams) of a substance that is equal to its molecular weight Fig. 2-9, p. 39 Note: nonpolar molecules are hydrophobic (water-fearing) and do not dissolve in water ph Is a measurement of the acidity (or alkalinity/ basicness ) of a solution H 2 O H + + OH - H + = hydrogen ion (proton) OH - = hydroxide ion ph = -log[h + ] Fig. 2-10, p. 41 8

9 Acids and bases Acids release H + into a solution ( ph) Bases remove H + from a solution ( ph) Often by releasing OH - Strong acids and bases ionize completely E.g. HCl H + + Cl - Weak acids and bases do not completely ionize E.g. H 2 CO 3 H + + HCO 3 - Salts and buffers Salt = an ionic compound whose cation is not H + and whose anion is not OH - E.g. NaCl (table salt) Na + + Cl - Buffer = a compound that resists ph changes Buffer systems maintain the ph of body fluids They consist of a weak acid and its salt (a weak base) They release or remove hydrogen ions in solution, depending on what s needed to stabilize the ph E.g. the carbonic acid-bicarbonate buffer system H 2 CO 3 H + + HCO 3 - Carbonic acid functions as a weak acid» In solution, it releases H + Bicarbonate functions as a weak base» In solution, it removes H + 9

10 Organic compounds Are primarily composed of C and H, and usually O too Include: Carbohydrates (sugars, starches, glycogen, and cellulose) Lipids (fats, oils, waxes, etc.) Proteins Nucleic acids (DNA and RNA) High-energy compounds (e.g. ATP) Carbohydrates Have the general formula of (CH 2 O) n Are mainly hydrophilic/ water-soluble General functions: Quick energy source for metabolism (e.g. glucose, shown here) Energy reserve (e.g. glycogen) Others we ll discuss later Fig. 2-11, p

11 Classes of carbohydrates (see Table 2-4 for a summary) Monosaccharides (simple sugars) contain 3-7 carbons each E.g. glucose, fructose Disaccharides consist of 2 monosaccharide subunits bonded to each other E.g. sucrose, maltose, lactose Polysaccharides consist of many monosaccharide subunits bonded together E.g. glycogen (shown here), starches and cellulose/ fiber (in plants) Glycogen Fig. 2-13, p. 45 The formation and breakdown of complex sugars Fig. 2-12, p

12 Lipids fats, oils, waxes, etc. Contain C, H, and O, but significantly less O compared to carbohydrates Are mainly hydrophobic/insoluble in water General functions: Concentrated energy storage Cell membrane components Chemical messengers (hormones) 5 classes (summarized in Table 2-5): 1. Fatty acids 2. Eicosanoids 3. Glycerides 4. Steroids 5. Phospholipids and glycolipids Fatty acids E.g. lauric acid (shown here) Head = a carboxyl (--COOH) group Tail = a long hydrocarbon chain Saturated = all single covalent bonds; a straight chain Unsaturated = one or more double covalent bonds; kink(s) in the chain Monounsaturated = one double bond (kink) Polyunsaturated = multiple double bonds (kinks) Function: stored energy source (that can be mobilized if needed) Lipids are 2X as energy-dense as carbos Fig. 2-14, p

13 Eicosanoids Are derived from arachidonic acid (an essential fatty acid) E.g. prostaglandins (shown here) and leukotrienes Functions: Chemical messengers (local hormones) released by A prostaglandin Damaged tissues to cause pain (prostaglandins) The uterus to trigger labor contractions (prostaglandins) T lymphocytes for intercellular communication (leukotrienes) Fig. 2-14, p. 50 Triglycerides (neutral fats) = 1 glycerol + 3 fatty acids Functions: Concentrated stored energy Thermal insulation Protection (physical cushioning) Fig. 2-16, p

14 Steroids = cholesterol and its derivatives They have a relatively large, unique, 4-ring structure Functions: Hormones E.g. sex hormones, corticosteroids, calcitriol, etc. Membrane structure E.g. cholesterol Digestion E.g. bile Fig. 2-17, p. 48 Phospholipid = a diglyceride + a phosphate group + a nonlipid group E.g. lecithin (shown here) Glycolipid = a diglyceride + a carbohydrate Have hydrophilic heads and hydrophobic tails Functions: Form cell membranes Form micelles (droplets) in aqueous Phospholipids and glycolipids solutions Fig. 2-18, p

15 Proteins Are relatively large, 3-D molecules containing C, H, O, N, and sometimes S or P Their specific shapes are vital to performing specific, essential functions, such as: Support (structural proteins) e.g. collagen, keratin Movement (contractile proteins) e.g. actin, myosin Transport e.g. hemoglobin Buffering e.g. plasma proteins Metabolic regulation e.g. enzymes Coordination/control e.g. hormones Defense e.g. antibodies, clotting proteins Amino acid and peptide structure Protein = a long chain of amino acids (usually thousands) Amino acids contain a central C, an H, an amino group, a carboxyl group and a variable R group (or side chain ) Peptides = relatively short linear sequences of amino acids joined by peptide bonds Polypeptides of 100 or more amino acids are usually called proteins But they re not necessarily functional proteins yet Fig. 2-19, p. 50 Fig. 2-20, p

16 The four levels of protein structure 1. Primary structure = the linear sequence of amino acids in a polypeptide 2. Secondary structure = the local bending of parts of the polypeptide E.g. into an alpha helix or a pleated sheet 3. Tertiary structure = the coiling/folding of the entire molecule into an overall 3-D shape 4. Quaternary structure = the interactions between two or more polypeptides to form a larger protein complex E.g. globular proteins (like hemoglobin) and fibrous proteins (like keratin and collagen) Fig. 2-21, p. 52 The four levels of protein structure 16

17 More about enzymes Reactants called substrates bind to the enzyme s active site Enzymes: Are highly selective/specific Can be saturated Are sensitive to environmental conditions (e.g. ph, temperature) and may denature (= lose their shape and thus their function) Can be regulated at the active site or other sites by cofactors = ions or coenzymes Coenzymes = non-protein organic molecules such as many vitamins Fig. 2-22, p. 53 Nucleic acids Contain C, H, O, N, and P Store and process information inside cells at the molecular level Are made up of chains of nucleotides The chain has a sugar-phosphate backbone, with nitrogenous bases attached to the sugars There are 2 classes of nucleic acids: Ribonucleic acid (RNA) the machinery of protein synthesis It is typically single stranded There are 3 types of RNA: 1. Messenger RNA (mrna) 2. Transfer RNA (trna) 3. Ribosomal RNA (rrna) Deoxyribonucleic acid (DNA) the genetic code for protein synthesis and inherited characteristics It is double stranded with complementary base pairs (A-T, C-G) Fig. 2-24, p

18 Nucleotide structure Nucleotide = a pentose sugar + a phosphate group + a nitrogenous base Nitrogenous bases include purines (A, G) and pyrimidines (C, T, U) Fig. 2-23, p. 55 High-energy compounds Store cellular energy in highenergy bonds for quick release to meet immediate energy demands E.g. adenosine triphosphate (ATP) ATP is made by adding a phosphate group to adenosine diphosphate (ADP) This process is referred to as phosphorylation With help from the enzyme adensosine triphosphatase (ATPase), the reversible reaction is: ADP + P i + energy ATP + H 2 O Fig. 2-25, p