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The Chemistry of Life • Biology is a multidisciplinary science • Living organisms are subject to basic laws of physics and chemistry Matter consists of chemical elements and compounds • Matter is anything that takes up space and has mass ◦ Organisms are composed of matter • Matter exists in many form, each with its own characteristic • Matter is made up of elements Elements and Compounds • An element is a substance that cannot be broken down to other substances by chemical reactions • There are 92 naturally occuring elements • Each element has a unique symbol, usually the fist one or two letter of the name. some of the symbol are devived from Latin or German names . Elements and Compounds • A compound is a substance consisting of two or more elements in a fixed ratio • A compound has characterictics different from those of its elements LE 2-2 Sodium Chlorine Sodium chloride Essential Elements of Life • About 25 of the 92 elements are essential to life • Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter • Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur • Trace elements are those required by an organism in minute quantities The most common elements on Earth and Their distribution in the human body Element Atomic num er Percent of human body by weight Importance or function oxygen O 08 65.0 Necessary for cellular respiration; component of water Carbon C 06 18.5 Backbone of organic molecules Hydrogen H 01 9.5 Electron carrier, component of water and most organic molecules Nitrogen N 07 3.3 Component of all proteins and nucleic acids Calcium Ca 20 1.5 Component of bones and teeth trigger for muscle contraction Phosphorus P 19 1.0 Backbone of nucleic acids, important in energy transfer Potassium K 19 0.4 Principal positive ion in cell, important in nerve function Sulfur S 16 0.3 Component of most protein Chlorine Cl 17 0.2 Principal negative ion bathing cells Magnesium Mg 12 0.1 Critical component of many energy transferring enzymes Iron Fe 26 trace Critical component of hemoglobin in the blood zinc Zn 30 trace Key component of some enzymes Iodine I 53 trace Component of thyroid hormone Silicon Si 14 trace ---------------------------------------- Fluorine F 09 trace ---------------------------------------- LE 2-3 Nitrogen deficiency Iodine deficiency An element’s properties are determined by its atoms • Each element consists of unique atoms • An atom is the smallest unit of matter that still retains the properties of an element Subatomic Particles • Atoms are composed of subatomic particles • Relevant subatomic particles include: – Neutrons (no electrical charge) – Protons (positive charge) – Electrons (negative charge) • Neutrons and protons form the atomic nucleus • Electrons form a cloud around the nucleus LE 2-4 Cloud of negative charge (2 electrons) Electrons Nucleus • • • • • Atomic Number and Atomic Mass Atoms of the various elements differ in number of subatomic particles An element’s atomic number is the number of protons It is written as a subscript before the symbol for elements For example: 2He means that an atom of helium has 2 protons in nucleus An element’s mass number is the sum of protons plus neutrons in the nucleus (it is written as a superscript before an element’s symbol. For example 4He • Atomic mass, the atom’s total mass, can be approximated by the mass number Isotopes • Atoms of an element have the same number of protons but may differ in number of neutrons • Isotopes are two atoms of an element that differ in number of neutrons • Most isotopes are stable, but some are radioactive, giving off particles and energy 1. Some applications of radioactive isotopes in biological research: – Dating fossils – Tracing atoms through metabolic processes 2. Radioactive isotopes are also used to diagnose medical disorders _For example, a known quantity of a substance labeled with a radioactive isotope can be injected into the blood, and its rate of excretion in the urine can be measured _Also, radioactive tracers can be used with imaging instrument to monitor chemical processes in the body LE 2-6 Cancerous throat tissue The Energy Levels of Electrons • Electrons of atoms participate in reactions • Energy is the capacity to cause change • Potential energy is the energy that matter has because of its location or structure • The electrons of an atom differ in their amounts of potential energy • An electron’s state of potential energy is called its energy level, or electron shell LE 2-7b Third energy level (shell) Second energy level (shell) Energy absorbed First energy level (shell) Energy lost Atomic nucleus Electron Configuration and Chemical Properties • The chemical behavior of an atom is determined by the distribution of electrons in electron shells • The periodic table of the elements shows the electron distribution for each element LE 2-8 Hydrogen 1H 2 Atomic number He Atomic mass First shell 4.00 Helium 2He Element symbol Electron-shell diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Sodium 11Na Magnesium 12Mg Aluminum 12Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Third shell • Valence electrons are those in the outermost shell, or valence shell • The chemical behavior of an atom is mostly determined by the valence electrons Molecules form from chemical bonding between atoms • • • • Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms Chemical bonds is attraction between two atoms resulting from a sharing of outer shell electron or the presence of opposite charge on the atoms There are three basic chemical bonds: - covalent bonds - ionic bonds - hydrogen bonds The strongest chemical bonds are convalent bonds Covalent Bonds • A covalent bond is the sharing of a pair of valence electrons by two atoms • In a covalent bond, the shared electrons count as part of each atom’s valence shell • A molecule consists of two or more atoms held together by covalent bonds • A single covalent bond, or single bond, is the sharing of only one pair of valence electrons • A double covalent bond, or double bond, is the sharing of two pairs of valence electrons • The double bonds are stronger than single bonds • Covalent bonds can form between atoms of the same element or atoms of different elements LE 2-11b Name (molecular formula) Oxygen (O2) Electronshell diagram Structural formula Spacefilling model LE 2-11c Name (molecular formula) Water (H2O) Electronshell diagram Structural formula Spacefilling model LE 2-11d Name (molecular formula) Methane (CH4) Electronshell diagram Structural formula Spacefilling model • Electronegativity is an atom’s attraction for the electrons in a covalent bond • The more electronegative an atom, the more strongly it pulls shared electrons toward itself • In a nonpolar covalent bond, the atoms share the electron equally • A covalent bond between two atoms of the same element nonpolar :H-H ;Cl-Cl …. • A covalent bond between atoms that have similar electronegativities,the bond of CH4 are nonpolar • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally LE 2-12 – O H + H H2O + Ionic Bonds • An ionic bond is an attracted between ions of opposite charge in an ionic compound • An example is the transfer of an electron from sodium to chlorine • When sodium and chlorine interection with together.what’ll happen? • After the transfer of an electron, both atoms have charges • A charged atom (or molecule) is called an ion • An anion is a negatively charged ion • A cation is a positively charged ion • An ionic bond is an attraction between an anion and a cation LE 2-13 Na Cl Na+ Cl– Sodium atom (an uncharged atom) Chlorine atom (an uncharged atom) Sodium ion (a cation) Chlorine ion (an anion) Sodium chloride (NaCl) NaCl Na+ + Cl- • Compounds formed by ionic bonds are called ionic compounds, or salts • Salts, such as sodium chloride (table salt), are often found in nature as crystals LE 2-14 Na+ Cl– Weak Chemical Bonds • Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules • Within a cell,weak,brief bonds between molecules are important to a variety of processes • Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important • Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other Hydrogen Bonds • A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom • In living cells, the electronegative partners are usually oxygen or nitrogen atoms LE 2-15 – + Water (H2O) + Hydrogen bond – Ammonia (NH3) + + + Van der Waals Interactions • Molecules or atoms that are very close together can be attracted by temporary charge differences • These weak attractions are called van der Waals interactions • Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface Molecular Shape and Function • A molecule’s shape is usually very important to its function • A molecule’s shape is determined by the positions of its atoms’ valence orbitals • Biological molecules recognize and interact with each other with a specificity based on molecular shape • Molecules with similar shapes can have similar biological effects LE 2-17a Carbon Nitrogen Hydrogen Sulfur Natural endorphin Oxygen Morphine Structures of endorphin and morphine LE 2-17b Natural endorphin Brain cell Morphine Endorphin receptors Binding to endorphin receptors Chemical reactions make and break chemical bonds • Chemical reactions lead to new arrangements of atoms • The starting molecules of a chemical reaction are called reactants • The final molecules of a chemical reaction are called products LE 2-UN44 2 H2 O2 Reactants 2 H2O Reaction Products • Photosynthesis is an important chemical reaction • In photosynthesis, sunlight powers the conversion of CO2 and H20 to glucose (C6H12O6) and O2 6 CO2 + 6 H2O = C6H12O6 + 6 O2 • Some chemical reactions go to completion: All reactants are converted to products • Most chemical reactions are reversible: Products of the forward reaction become reactants for the reverse reaction • Chemical equilibrium is reached when the forward and reverse reaction rates are equal • 3H2 + N2 2NH3 • At equilibrium,products and reatants are continually being formed,but there is no net change in the concentrations of reactants and products At equilibrium,the concentrations of reactants and products are typically not equal,but their concentration have stabilized at a particular ratio excercise 1. How many atoms of hydrogen are able to bond with one atom of carbond ? a. only one b. two atoms of hydrogen c.three atoms hydrogen d. four atoms of hydrogen • A common isotope of phophorous is P31 a. A difference valence b. A difference atomic numer c. one less neutron d.one less proton e. oneless electron • if an atom of chlorine gains a neutron it becomes a (an) a. Cation b. molecule c. Isotope d. a different element e. anion