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Chapter 2 – the chemistry of life Why is it important to have an understanding of chemistry to study anatomy? – All biological functions can be explained chemically What are the components of life? – Matter – Energy Nature of Matter: Atomic Structure – Nucleus—very small size compared to the entire atom, composed of a) protons (p+): have a positive electrical charge, have some mass, and b) neutrons (n0): have no electrical charge, have the same mass as a proton. – Electrons (e-): these orbit the nucleus, they have a negative electrical charge which is equal and opposite the charge of a proton, they have a negligible mass. – Atoms are usually electrically neutral—number of electrons = number of protons. Nature of Matter: Atomic Structure How can we tell one atom from another? What is the distinction? – Atomic Number — the number of protons in an atom. – Atomic Mass (weight) – mass of atom, which would include # of protons + # of neutrons Other Definitions – Element – matter composed of atoms of only one kind. » The number of protons in the nucleus of any given atom is always the same AND each element has a different number of protons in its nucleus – Molecules: A combination of atoms where electrons in the outermost orbital are either transferred or shared. – Compound: A molecule that has two or more kinds of atoms. – Chemical Formula: C6H12O6 http://wine1.sb.fsu.edu/chm1045/tables/period/PT_large.jpg Earth’s crust other 8% Human body other 7% hydrogen 10% oxygen 50% oxygen 65% silicon 26% aluminum 8% calcium 3% iron 5% carbon 18% Table. 2.2 Nature of Matter: Key Components of the Atom – Size - nucleus is much smaller than surrounding orbital and atoms are really, really tiny. – Identity – # of protons determines identity of atom. Neutrons only provide additional mass. – Charge - is determined by comparing the number of electrons to number of protons. If they are equal, then atom is electrically neutral. If they are not, then atom is existing in an ionic state. – Reactivity – is determined by the valence electrons in the outermost shell. The number of valence electrons really does make a difference in the way an atom will behave around other atoms. Some are stable; others are very reactive. – Lowest Energy State – all matter (atoms being the smallest particles of matter) always seek there lowest energy state, so they prefer to be neutral and they prefer to have their outermost energy shell full! – Isotopes – Most atoms exist in various isotopic forms. How can you tell? If number of neutrons is different from number of protons, atom is in an isotopic state. # of neutrons = atomic mass (weight) – atomic number. Radioactive Isotopes Medical Diagnosis Cancer Therapy Other Biological Uses – Radiometric Dating – Radioactive Labeling Chemical Bonding The goal of atoms is to find their lowest energy state! Types of bonds – Ionic Bonding – one atom loses an electron and one gains an electron. – Covalent Bonding – two atoms share a pair of electrons, sometimes equally/sometimes unequally. » Single Covalent Bond (one pair of electrons) » Double Covalent Bond (two pairs) » Triple Covalent Bond (three pairs) e- e- Hydrogen e- Helium ee- e- e- e- e- e- ee- e- e- Carbon e- e- e- Neon e- e- eee- e- e- ee- e- e- ee- e- Sodium unstable, very reactive e- e- e- ee- e- ee- e- e- ee- Argon e e- e- ee- stable, unreactive Sodium atom (Na) Chlorine atom (Cl) e- electron transfer e- Chlorine ion (Cl-) Ionic Compound (Na+ + Cl-) Salt crystals Polar vs. Non-polar Covalent Bonds Nonpolar Covalent Bonds – Neither nucleus exerts more attractive pull on shared electrons (equal electronegativity and equal sharing, like joint custody). Polar Covalent Bonds – H2O is most common example in the body – Oxygen has a greater atomic number than hydrogen. – Oxygen’s nucleus attracts the shared electrons with a greater electronegativity than hydrogen in a water molecule. – Unequal sharing results in polar charges on different parts of the molecule. O H H + – O O H + – – O O H – + H – + + H – H – H + – H + – H – + H + – O + H H H O Hydrogen bond H O H Dissociation and Electrolytes Functional Groups (Handout) These are small groups of atoms that when attached to larger organic molecules will give those molecules predictable properties such as hydrophilic (polar) or hydrophobic (non-polar)/acid or base. a) Hydroxyl (R-OH): When attached to a hydrocarbon chain, it creates an alcohol. This group is found all over sugars. Because it contains a polar covalent bond, the Hydrogen atom is polar positive (+) and makes that part of the molecule hydrophilic and capable of forming H-bonds. b) Carbonyl (>C=O): It contains a polar covalent bond and the oxygen is therefore polar negative (-) which makes that part of the molecule hydrophilic and capable of forming H-bonds. There are two types of carbonyl: 1) Aldehyde: when the group is found at the end of a chain, and the 2) Ketone: when the group is found in the middle of a chain. Functional Groups, Continued c) d) e) f) Carboxyl (R-COOH): This group loses the H off of the hydroxyl group which forms both a negative charged Oxygen (- ion) and a Hydrogen ion (H+) is released into solution. This makes the molecule to which it is attached an acid. The polar charges and the ionic charges cause this part of a molecule to be highly hydrophilic. Amino (>NH2): This group tends to pick up H+ ions from the solution and causes the pH to rise. Therefore this group makes the molecule a base. The group becomes ionically charged (+) and this makes this part of the molecule highly hydrophilic. Phosphate (R-PO4): This group releases H+ into solution making the molecule to which it is attached both acidic and hydrophilic. Methyl (R-CH3): The nonpolar covalent bonds in this group make the part of the molecule to which it is attached hydrophobic. ACIDIC 100 10-1 battery acid 1 hydrochloric acid 10-2 2 lemon juice, gastric (stomach) juice 10-3 3 cola, beer, wine, vinegar 10-4 4 tomatoes 10-5 5 black coffee 10-6 6 urine NEUTRAL 10-7 7 pure water 10-8 human blood 8 seawater 10-9 9 baking soda 10-10 10 Great Salt Lake 10-11 11 10-12 10-13 BASIC 0 10-14 12 13 household ammonia household bleach oven cleaner 14 lye Chemical reactions 1. 2. 3. Types of chemical reactions: Synthesis reactions Decomposition reactions Exchange reactions – single or double replacement All metabolic pathways require energy at some point! – ATP/ADP Most biological reactions are reversible as well! Fig. 2.20 Chemical reactions, cont’d Reversible reactions - equilibrium In the body, reactants and products tend to react with one another back and forth until equilibrium is reached homeostasis Reaction Rates – what affects rate of rxn? – Concentration of reactants – Temperature – Enzymes (catalyst) biochemistry Inorganic Molecules – Molecules that do not contain carbon 1. Water – inorganic a. High Specific Heat, meaning water resists temperature changes which helps in maintaining body temperature. b. High Heat of Vaporization – Evaporative Cooling c. Effective lubricant – surface of the eye d. Necessary reactant in chemical reactions – digestion e. Universal Solvent – works for transport of nutrients throughout body Biochemistry, cont’d Macromolecules of Life (organic) – Molecules that contain carbon (Table 2.3 – page 31) Carbohydrates – mono, di and polysaccharides Lipids – fats, fatty acids, glycerol, triaglycerols/triglycerides – saturated and unsaturated fats Proteins – amino acids – Enzymes – activation energy Nucleic acids – DNA, RNA Fig. 2.11 Fig. 2.12 Fig. 2.13 Fig. 2.14 OH CH3 CH3 HC CH3 O CH3 CH2 CH2 testosterone CH3 CH2 HC OH CH3 CH3 CH3 cholesterol estrogen HO HO Fig. 2.16a Fig. 2.16b Fig. 2.19b The detailed structure of an animal cell’s plasma membrane, in cross section Enzyme Action Three-Dimensional Shape: Important in Biology – Compounds have very definite spatial configurations. – Shape determines how molecules can bind one another, a critical step in many activities. This is especially true where enzymes are concerned. – Throughout biology we see a complementarity of structure to function. This is easily seen throughout all of biology. Activation Energy & Enzymes