Atoms, Molecules, and Life

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Emma Hubbard
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1 1 Atoms, Molecules, and Life The Nature of Matter: Atoms and Molecules Elements All matter is composed of chemical elements, substances that cannot be broken down to other substances by ordinary chemical means There are 92 elements occurring in nature Of the 92 naturally occurring elements About 25 are essential to life Of these 25, four elements - oxygen (O), carbon (C), hydrogen (H), and nitrogen (N) - make up about 96% of the human body, which is typical of most living matter Calcium (Ca), phosphorus (P), potassium (K), sulfur (S), and a few other elements account for the remaining 4% There are a number of elements called trace elements that are essential to at least some organisms, but only in minute quantities Compounds Any substance that contains two or more elements is called a compound Atoms Each element consists of identical particles called atoms Atoms are composed of subatomic particles, including protons, electrons, and neutrons A neutron is a subatomic particle that is electrically neutral (no electric charge) A proton is a subatomic particle with a single positive electric charge (+) The neutrons and the protons are tightly packed in the atom's central core or nucleus An electron is a subatomic particle with a single negative electric charge (-) The smaller electrons orbit the nucleus - at about the speed of light Additional Information about Subatomic Particles The positive charge of a proton is equal to the negative charge of an electron An attraction between the negatively charged electrons and the positively charged protons keeps the electrons near the nucleus Electrons are very small subatomic particles - they have a mass that is 2000 times less than that of a proton or a neutron

2 2 Elements differ from one another in the number of subatomic particles in their atoms But, all atoms of a particular element have the same unique number of protons This is called the element's atomic number Sometimes information may be given about an atom's mass number - the sum of the numbers of protons and neutrons in its nucleus Isotopes Some elements have variant forms called isotopes The different isotopes of an element have the same number of protons and electrons but different numbers of neutrons A radioactive isotope is one in which the nucleus decays spontaneously, giving off particles and energy The Arrangement of Electrons Of the 3 subatomic particles, it is mainly the electrons that determine how an atom behaves when it encounters other atoms Electrons in atoms occur only at certain energy levels - these are called electron shells And depending on their atomic number, atoms may have 1, 2, or more electron shells, with the electrons in the outermost shell with the highest energy Also, each shell can accommodate a specific number of e- The inner most shell is full with only 2 e- So in atom's with more than 2 e-, the remainder are found in shells farther from the nucleus The outer most (high energy) shell can hold up to 8 e- Important: It is the number of electrons in the outer most shell that determines the chemical properties of an atom Atoms whose outer shell is not full tend to interact with other atoms Or participate in chemical reactions in ways that result in the filling of (or emptying of) a shell The configuration of electrons is only stable if the outer most occupied shell is full (He)

3 3 Q. How does a chemical reaction enable an atom to fill its outer electron shell? When 2 atoms with incomplete shells react, each atom gives up or acquires e- so that both partners end up with completed outer shells Atoms do this by either sharing or transferring outer e- These interactions typically result in atoms staying close together, held by attractions called chemical bonds 1. Ionic Bonds An ion - an atom (or a molecule) with an electric charge resulting from a gain or loss of one or more electrons Two ions with opposite charges attract one another When the attraction actually holds them together it is called an ionic bond 2. Covalent Bonds In a covalent bond, two atoms share one or more pairs of outer shell electrons There are 3 ways to chemically represent molecules: 1. The molecular formula 2. The electron configuration 3. The structural formula The number of single covalent bonds an atom can from is equal to the number of additional e- needed to fill its outer shell For some molecules each atom does not form two single bonds Instead, two atoms share two pairs of e- forming a double bond

4 4 Water: A polar molecule A water molecule (H 2 O) consists of 2 H atoms covalently bonded to a single oxygen atom Atoms in this covalently bonded molecule are in a constant tug of war for the e- of their covalent bonds An atom's attraction for the shared e- of the bond is called electronegativity The more electronegative an atom is, the more strongly it pulls shared e- toward itself In molecules formed by only one element (e.g. O 2 and H 2 ) the two identical atoms exert an equal pull on the e- The covalent bonds in such molecules are said to be nonpolar because the e- are shared equally between the atoms Water is composed of atoms with very different electronegativities The O atom attracts the shared e- in the water molecule much more strongly than does H Thus, the shared e- are actually closer to the O atom than the H atoms This unequal sharing of e- produces what is called polarity or a polar covalent bond between the oxygen and each of the hydrogen atoms in the molecule Because of its polar covalent bonds water is a polar molecule - a slightly negative pole and two slightly positive poles Water and Hydrogen Bonding The polarity of water molecules makes them interact with one another The charged regions on each molecule are attracted to oppositely charged regions on neighboring molecules, actually forming weak bonds Since the positively charged region in this special type of bond is always an H atom, the bond is called a hydrogen bond Some other Properties of Water A. Hydrogen bonds make liquid water cohesive This tendency of like molecules to "stick" together is called cohesion - e.g., holding together molecules of the same substance

5 5 Water is also attracted to other charged substances - adhesion The cohesive and adhesive properties of water allow it to rise against the force of gravity = capillarity Surface tension - a measure of how difficult it is to stretch or break the surface of a liquid The hydrogen bonds of water give it very high surface tension - water almost behaves as if it were coated with an invisible film B Water's hydrogen bonds moderate temperature When water is heated, the heat energy first disrupts hydrogen bonds and then makes water molecules move faster So, initially when heat is applied to water it is absorbed as it breaks the H-bonds Water absorbs and stores a large volume of heat while warming up very little When it is cooled more H-bonds form Heat energy is released when the H-bonds form, slowing the cooling process Hydrogen bonds also decrease water's tendency to evaporate or vaporize Liquids such as water vaporize when some of their molecules move fast enough to overcome the attractions that keep the molecules close together C. Ice is less dense than liquid water The H-bonds in ice are fairly rigid (stable) and create an open lattice work that holds the water molecules farther apart In other words, the molecules in liquid water are much closer together than in ice Therefore, ice has fewer molecules than an equal volume of liquid water, making it less dense than liquid water D. Water is a versatile solvent Solution - is a liquid consisting of a homogeneous mixture of two or more substances The dissolving agent is called the solvent, and the substance that is dissolved is a solute Water dissolves an enormous variety of solutes, necessary for life (salt, aa,...) Water's versatility as a solvent results from the polarity of its molecules

6 6 E. Water Dissociation: acids and bases In the aqueous solutions of most organisms most of the water molecules are intact However, some of the water molecules actually break apart or dissociate into ions because of their polarity The ions formed are called H+ ions and hydroxide (OH-) ions H > H + + OH - There are some substances that when they dissolve in water, dissociate and release H+ ions By definition, an acid is any substance that gives of H+ ions when dissolved in water and thereby increases the H+ concentration of the solution A base is any substance that accepts H+ ions when dissociated in water Some bases such as sodium hydroxide (NaOH) do this by donating OH- ions; these combine with H+ to form H 2 0 ph Biologists measure H+ concentration on the ph scale (ph stands for the potential of hydrogen) The ph scale ranges from 1(most acidic) - 14 (most basic) Each ph unit represents a tenfold change in the concentration of H+ ions Even a slight change in ph can be harmful because the molecules in the cells are sensitive to H+ and OH- concentrations Most activities in cells must be carried out within a narrow ph range Fortunately, biological fluids contain substances called buffers, substances that resist changes in ph by accepting H+ ions when they are in excess and donating H+ ions when they are few

What Are Atoms? Chapter 2: Atoms, Molecules & Life

What Are Atoms? Chapter 2: Atoms, Molecules & Life Chapter 2: Atoms, Molecules & Life What Are Atoms? An atom are the smallest unit of matter. Atoms are composed of Electrons = negatively charged particles. Neutrons = particles with no charge (neutral).