Chapter 6 Chemistry in Biology

Section 6.1 Atoms, Elements, & Compounds

Matter! Matter is anything that occupies space and has mass. Will this astronaut occupy the same space on the moon as he does on Earth? Will this astronaut weigh the same on the moon as he does on the Earth? Mass and weight are not the same.

The Atom – The Simplest of Particles The atom is the simplest particle of an element that retains the properties of that element.

The Structure of an Atom Biology Class Notes - October 3, 2006 The Structure of an Atom Bohr Model – “planetary model” Proposed by Niels Bohr in 1915 A useful approximation of the structure of an atom. Consists of two parts: A central region, or nucleus Electron cloud – composed of orbitals or three-dimensional regions around a nucleus

Subatomic Particles Protons Positively (+) charged particles + Have mass (1 amu = 1 atomic mass unit) Located in the nucleus + Neutrons Neutral particles (No charge) Have mass (1 amu) Also located in the nucleus n Electrons Negatively (-) charged particles Mass is negligible (1/1840 amu) Remain in constant motion in orbitals

Biology Class Notes - October 3, 2006 The Bohr Model Below is a Bohr Model of a helium (He) atom. Nucleus 2 protons 2 neutrons n + Electron cloud Consists of orbitals where high-energy electrons orbit the nucleus

Elements Elements are substances that cannot be broken down chemically into simpler kinds of matter.

The Elemental Body -- The Major Elements Biology Class Notes - October 3, 2006 The Elemental Body -- The Major Elements A major element is any element that makes up more than 0.01% of your body mass. Rank Chemical Symbol Element % of human body* 1 O Oxygen 62 % 2 C Carbon 23 % 3 H Hydrogen 10 % 4 N Nitrogen 2.6 % 5 Ca Calcium 1.4 % 6 P Phosphorus 1.1 % 7 K Potassium 0.2 % 8 S Sulfur 9 Na Sodium 0.1% 10 Cl Chlorine 0.1 % 11 Mg Magnesium 0.02 % * Based on an average 70 kg (154 lbs.) person

The Elemental Body -- The Trace Elements Biology Class Notes - October 3, 2006 The Elemental Body -- The Trace Elements A trace element is any element that makes up less than 0.01% of your body mass, but is still critical to your health. Rank Chemical Symbol Element 12 Fe Iron 13 F Fluorine 14 Zn Zinc 15 Si Silicon 16 Cu Copper 17 I Iodine 18 Sn Tin Rank Chemical Symbol Element 19 B Boron 20 Se Selenium 21 Cr Chromium 22 Mn Manganese 23 Mo Molybdenum 24 Co Cobalt 25 V Vanadium

C The Periodic Table 6 12.011 Atomic Number Chemical Symbol Atomic Mass

Biology Class Notes - October 3, 2006 Atomically Speaking… The number of protons in an atom is called the atomic number. In an atom, the number of positive protons is balanced by an equal number of negative electrons. net electrical charge equals zero The Bohr model to the left represents an atom of which element? How many electrons must be in the electron cloud? = neutron = proton

Biology Class Notes - October 3, 2006 Atomically Speaking… The mass number of an atom is equal to the total number of protons and neutrons of the atom. What is the mass number of our carbon atom? = neutron = proton

Isotopes: Not All Atoms are Created Equal Biology Class Notes - October 3, 2006 Isotopes: Not All Atoms are Created Equal Isotopes are atoms of the same element that have different numbers of neutrons. therefore they will have different mass numbers this is the reason for the average atomic mass in the periodic table Click here to compare these two atoms. = neutron = proton These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another. Use this slide to explain why the average atomic mass is not always the same as the mass number. Explain to students that we assumed that the number of neutrons was the same as the protons, but that this is not always the case for all atoms of the same element. CLOSE

Biology Class Notes - October 3, 2006 Radioactive Isotopes Sometimes having too many neutrons can make the nucleus of an atom unstable. Unstable nuclei decay, or break apart. Particles (usually neutrons) and energy in the form of radiation are released. This radiation can be used to calculate the age of an object or it can be used in medical treatments such as radiation therapy.

A Few Words About Electrons Biology Class Notes - October 3, 2006 A Few Words About Electrons High energy particles Are attracted to (+)ve protons in the nucleus – keeps them close together Constant energy of motion prevents them from collapsing into nucleus Exact path of travel cannot be known An electron’s energy confines it to an energy level within the electron cloud Electrons with higher energy occupy energy levels farther from the nucleus

Biology Class Notes - October 3, 2006 Orbitals Energy levels contain orbitals which can only hold a certain number of electrons. Energy Level # of orbitals Maximum # of electrons 1 2 4 8 3 9 18

Expanding the Bohr Model Biology Class Notes - October 3, 2006 Expanding the Bohr Model Example: A carbon atom We know: From periodic table atomic number of carbon equals six; therefore the number of electrons equals six Why? From previous chart first energy level holds two electrons maximum second energy level holds eight electrons maximum

Expanding the Bohr Model Biology Class Notes - October 3, 2006 Expanding the Bohr Model Putting it all together: Two of carbon’s electrons will be found in the first energy level of the electron cloud. The remaining four electrons will be found in the second energy level of the electron cloud. The second energy level of a carbon atom is not full. It can still accommodate four more electrons. = neutron = proton = electron

Compounds Compound – substance formed when two or more different elements combine Form a specific combination of elements in a fixed ratio Chemically and physically different from the elements that comprise them Cannot be broken down into simpler compounds or elements by physical means (can be broken down chemically)

Why Combine? Compounds form because most atoms are not stable in their natural state. A partially-filled outermost energy level is not as stable as an energy level that is completely filled with the maximum number of electrons it can hold. Is this carbon atom stable? = neutron = proton = electron

Two Ways to Bond Ionic Bonds Covalent Bonds

Chemical Bonds Ionic Bond Covalent Bond An atom can gain or lose an electron to make a stable energy level. This atom is called an ion and is now charged. An ionic bond is electrical attraction between two oppositely charged atoms. Example: sodium chloride A chemical bond that forms when electrons are SHARED Example: water

Achieving Stability Atoms become stable by attaining at least one of the following: They fill their outermost, or valence, energy level with the maximum amount of electrons that it will hold. OR They fill their outermost energy level with eight electrons. The ‘Rule of Eight’

There IS Another Way Atoms can also share one or more pairs of electrons. When two atoms share electrons, the shared electrons occupy orbitals around both of the atoms. The electrons move so quickly that it is difficult to predict which atom they are orbiting at any given time. So far we have investigated how atoms react when they have one or two electrons in their outermost energy levels. We have also discussed how atoms react when they have six or seven electrons in their outermost energy levels. But what happens when atoms have three, four, or even five electons in their outermost energy levels.

Water – A Model of Covalent Bonding Oxygen 8p 8n Hydrogen 1 p 0 n Hydrogen atom (atomic #: 1) Oxygen atom (atomic #: 8) How many valence electrons does each atom have? How many more electrons does each atom need to fill its outermost energy level?

Water – A Model of Covalent Bonding This is a molecule of water. It can also be referred to by its chemical formula, H2O. A shared pair of electrons can be considered to be part of the outermost energy level of both atoms that share them. How might each of these atoms fill its outermost energy level? Oxygen 8p 8n Oxygen 8p 8n Hydrogen 1 p 0 n Hydrogen 1 p 0 n Hydrogen 1 p 0 n If each hydrogen atom shares a pair of electrons with oxygen, how many valence electrons does each atom have?

Covalent Bond A covalent bond forms when two atoms share one or more pairs of electrons. A molecule is the simplest part of a substance that retains all the properties of that substance

Modeling Ionic Bonds Activity In your notes, draw a Bohr model of a sodium atom (atomic number 11). Next to the sodium atom draw a Bohr model of a chlorine atom (atomic number 17).

Activity 1. On the left, draw a neutral sodium atom with a mass number of 23 (atomic number 11). 2. On the right, draw a neutral chlorine atom with a mass number of 35 (atomic number 17).

The Sodium-Chlorine Ionic Bond 17 p 18 n Sodium 11 p 12 n Sodium atom (atomic #: 11) Chlorine atom (atomic #: 17) How many electrons does each atom have now? How does this affect the total charge of each atom?

The Sodium-Chlorine Ionic Bond These atoms are no longer electrically neutral. How many protons does sodium (Na) have? How many electrons does Na have now? What is the total charge of this atom of sodium? Chlorine 17 p 18 n Sodium 11 p 12 n These atoms are stable, but because of their opposite charges they now attract one another. Protons +11 Electrons -10 Charge +1 Protons +17 Electrons -18 Charge -1

The Sodium-Chlorine Ionic Bond An atom with an electrical charge is called an ion. As a result of their opposite charges, sodium ions and chlorine ions attract each other. Chlorine 17 p 18 n Sodium 11 p 12 n Chlorine ion -1 This new substance is a compound called sodium chloride. Sodium ion +1 An ionic bond is the chemical bond formed between ions with opposite charges.

Chapter 6.2 Chemical Reactions

Chemical Reactions Process by which atoms or groups of atoms in substances reorganize into different substances Chemical bonds are broken or formed For example – 4 Fe + 3 O2 2 Fe2O3

Reactants and Products Chemical Equation: C6H12O6 + O2 CO2 + H20 (Glucose and oxygen react to form carbon dioxide and water) Reactants (starting substances): C6H12O6 + O2 Products (substances formed): CO2 + H20

Balanced Equation According to the principle of conservation of mass, matter cannot be created or destroyed The number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side For example: 2 H2O2 2 H20 + O2 C6H12O6 + 6 O2 6 CO2 + 6 H20

Energy-Absorbing Reaction Energy-Releasing Reaction Products Activation energy Activation energy Reactants