Lesson 2 Nature of Molecules/Properties of Water September 1, 2015

Nature of an Atom Matter is defined as any substance that has mass and takes up space Mass vs. Weight All matter is comprised of various chemical elements An atom is the building block of an element. There is one atom for each corresponding element Each element is made of certain atoms that give it its unique characteristics The element, gold, is made of only gold atoms

Composition of an Atom Electron- particle that travels around the nucleus of an atom. Contains a negative charge Proton- particle located inside the nucleus of an atom. Contains a positive charge Neutron-particle located inside the nucleus of an atom. Contains no charge Mass measured in daltons or atomic mass units (amu)

Structure of an Atom Cloud of negative charge (2 electrons) Electrons Nucleus - - + + + + Figure 2.4 Simplified models of a helium (He) atom (a) (b) Helium (He)

Characteristics of an Atom The protons and neutrons of an atom are held together by a force called the nuclear binding energy Electrons orbit the nucleus due to the electrostatic forces b/w its negative charge and protons’ positive charge When an atom has the same number of electrons as protons it is electrically neutral (no charge)

Characteristics of an Atom Atoms are listed by their atomic number which is the number of protons in the nucleus. Unique to each element The sum of the masses of protons and neutrons in an atom is called the atomic mass Both neutrons and protons have approximately the same weight which is measured in daltons 1.7x10-24 grams = 1 dalton Neutrons and protons weigh roughly 2,000x the weight of the electron Weight of an electron does NOT contribute to Atomic Mass

Atomic number/Atomic mass Designation

Ions Electrons circle the nucleus of an atom in regions termed orbitals Strong forces can dislodge electrons from its orbital or cause the atom to gain electrons Atoms that contain more/less number of electrons than protons are called ions. Ions have a net charge (either + or -) Cation—atom that has lost an electron (+ charge) Anion—atom that has gained an electron (- charge) Examples Na+ = Cation Cl- = Anion

Isotopes Atoms of a single element that possess different number of neutrons are isotopes The number of protons remain the same Most elements in nature exist as a mixture of isotopes Some isotopes are very unstable (radioactive isotopes) Nucleus breaks apart giving off energy (radioactive decay)

Carbon Isotopes

Electrons determine how atoms interact B/c electrons are attracted to the protons of a nucleus, it requires energy to keep the e(-) in the orbital of that atom The greater the distance the electron is from the nucleus, the more energy is required This makes the electron LESS stable (More Reactive) Electrons within the atom have discrete energy levels and are denoted by rings Not to be confused with orbitals!!!!

Electron Configurations In atoms, electrons’ energy levels are denoted by electron shells Each electron shell has a different energy level The further the shell is from the nucleus, the higher the energy level The outermost shell (valence shell), because of its energy level, can readily accept or lose electrons The arrangement of an atom’s electrons in the electron shells is referred to as the electron configuration

Electron Shells Only for denoting the energy of the electron and not the location of the electron!!!!

*Each shell can hold a specific number of electrons* *Outermost shell is called the Valence Shell*

Can you Draw The Electron Configuration???? Lithium Atomic Number = 3 Oxygen Atomic Number = 8 Carbon Atomic Number = 6 Aluminum Atomic Number = 13

Section 2: Elements Found in Living Systems 92 elements occur naturally, each with a different number of protons and a different arrangement of electrons The most common elements in living organisms are Oxygen(65.0%), Carbon(18.5%), Hydrogen(9.5%), Nitrogen(3.3%), Phosphorus(1.0%), Sulfur(0.3%) When the elements are arranged in respect to their atomic numbers, they exhibit a certain pattern of chemical properties that repeats in groups of eight This is referred to as periodicity

Element Periodicity The eight-element periodicity is based on the interaction of the electrons in the outermost energy level of the different elements (valence electrons) For most atoms, the outermost energy level can contain no more than eight electrons

Element Periodicity Elements possessing a full outer shell are inert (non-reactive) Helium, Neon, Argon Elements possessing 7 electrons in its outer shell are highly reactive (readily accepts e-) Fluorine, Chlorine, Bromine Elements possessing 1 electron in its outer shell is also are highly reactive (readily loses e-) This concept of an atoms tendency to completely fill their outer shell is known as the octet rule

Molecular Bonding Atoms obtain their full complement of electrons in their valence shells by combining with other atoms to form molecules Molecules that contain atoms of more than one element are called compounds Molecules and compounds are held together through the attractive forces of their valence electrons. This force is called a chemical bond Covalent Bond Ionic Bond Hydrogen Bond Van der Waals Interactions

Covalent Bond Bond where the valence electrons are shared between two atoms Contains no net charge

Name and Molecular Formula Electron Distribution Diagram Lewis Dot Structure and Structural formula Space- Filling Model (a) Hydrogen (H2) H H (b) Oxygen (O2) O O (c) Water (H2O) O H H Figure 2.10 Covalent bonding in four molecules (d) Methane (CH4) H H C H H

Polar vs. Non-polar Covalent Bonds Atoms differ in their affinity for electrons. This is called electronegativity Electronegativity increases left to right across a row of the periodic table Electronegativity decreases down the column of the periodic table

Polar vs. Non-polar Covalent Bonds Electrons are more likely move closer to the atoms with a greater electronegativity This creates a region of partial negative charge near the more electronegative atom Negative charge is relatively small Molecules with similar atoms have no charge b/c atoms have same electronegativity (O2) Molecules containing atoms of different electronegativities exhibit a charge (H2O)

Ionic Bond Atoms have gained or lost their valence shell electrons Electronegativity between two atoms are so unequal that electrons are stripped The attraction b/w ions with opposite charges holds them together (ionic bonds) Na+ and Cl- The combination of these to atoms are termed ionic compounds or salts.

Figure 2.12-2 Na Cl Na Cl Na Sodium atom Cl Chlorine atom + - Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) Cl- Chloride ion (an anion) Figure 2.12-2 Electron transfer and ionic bonding (step 2) Sodium chloride (NaCl)

Figure 2.13 Na+ Figure 2.13 A sodium chloride (NaCl) crystal Cl-

Hydrogen Bond Bond where a hydrogen atom that is covalently bonded to oxygen or nitrogen is attracted another oxygen or nitrogen atom Results from atoms having different affinities for electrons. (electronegativity) Weakest of the three bonds

Van der Waals Interactions If electrons are distributed asymmetrically in molecules or atoms, they may accumulate by chance in one part of a molecule Van der Waals Interactions are attractions between molecules that are close together as a result of these charges

Section 3: Properties of Water One of the most important inorganic compounds is water. Water, on average, makes up 65-75% of every living cell. Water is the medium for most chemical rxns in the cell. Because of water’s polarity (direction of charge) it acts as a great solvent (dissolving medium) Stabilizes charges of substrates/intermediates Water is both cohesive (attracted to itself) and adhesive (attracted to other polar molecules)

How water stabilizes ions Sodium chloride crystal

Properties of Water Water has a high specific heat. It resists changes in temperatures Since most of our cells are composed of water, this helps us maintain a relatively constant internal temperature (homeostasis) Water has a high heat of vaporization, which is defined as the amount of energy required to change 1 gram of a substance from a liquid to a gas Many organisms dispose of excess body heat by evaporative cooling (sweating)

Section 4: Acids and Bases Acid– is a substance that dissociates into one or more hydrogen ions (H+) Also known as a proton donor Examples are HCl and HNO3 Base—is a substance that dissociates into one or more hydroxide ions (OH-) Proton acceptor Examples are NaOH and KOH The more H+ ions in a solution the more acidic it is and the more OH- ions in a solution the more basic it becomes

Measurements of Acidity A solutions acidity is measure by a logarithmic pH scale. pH scale range between 0-14. 0 is most acidic. 14 is most basic An increase of 1 on the scale represents a ten fold increase in H+ ions A solution at pH 5 contains 10X more H+ ions than a solution that is pH 6 Buffers are substances that minimizes the changes of H+ and OH-

Buffering Within Blood

Increasingly Acidic [H+] > [OH−] Increasingly Basic [H+] < [OH−] Figure 3.10 pH Scale 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Battery acid Gastric juice, lemon juice H+ H+ H+ Vinegar, wine, cola H+ OH– OH– H+ H+ Increasingly Acidic [H+] > [OH−] H+ H+ Acidic solution Tomato juice Beer Black coffee Rainwater Urine Saliva OH– OH– Neutral [H+] = [OH−] Pure water Human blood, tears H+ H+ OH– OH– OH– H+ H+ H+ Seawater Inside of small intestine Neutral solution Figure 3.10 The pH scale and pH values of some aqueous solutions Increasingly Basic [H+] < [OH−] Milk of magnesia OH– OH– OH– H+ OH– Household ammonia OH– OH– H+ OH– Basic solution Household bleach Oven cleaner

Critical Thinking People take antacids wherever they exhibit any sign of acid reflux The main ingredient in most antacids is Mg(OH)2. Therefore the chemical reaction that takes place in our digestive tract is: Mg(OH)2 + 2HCl MgCl2 + H2O Which is the acid? Which is the base?