Chapter 2: Chemical Context of Life Atoms and Molecules

Elements Organisms are composed of matter, which is anything that takes up space and has mass Matter is made up of elements, substances that cannot be broken down to other substances by chemical reactions 92 unique elements exist in nature More have been created in the lab

Periodic Table

Essential Elements of Life Essential elements Include carbon, hydrogen, oxygen, and nitrogen Make up 96% of living matter Essential elements Include carbon, hydrogen, oxygen, and nitrogen Make up 96% of living matter

A few other elements make up the remaining 4% of living matter

Each element Consists of a certain kind of atom that is different from those of other elements An atom Is the smallest unit of matter that still retains the properties of an element Elements

Subatomic Particles Atoms of each element are composed of even smaller parts called subatomic particles Relevant subatomic particles include Neutrons, which have no electrical charge Protons, which are positively charged Electrons, which are negatively charged Atoms of each element are composed of even smaller parts called subatomic particles Relevant subatomic particles include Neutrons, which have no electrical charge Protons, which are positively charged Electrons, which are negatively charged

Subatomic Particles Protons and neutrons Are found in the atomic nucleus Electrons Surround the nucleus in a “cloud” Protons and neutrons Are found in the atomic nucleus Electrons Surround the nucleus in a “cloud”

Nucleus (a) (b) In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus. Cloud of negative charge (2 electrons) Electrons This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron‘s position at one point in time. Simplified models of an atom

Atomic Number and Atomic Mass Atoms of the various elements Differ in their number of subatomic particles The atomic number of an element Is the number of protons Is unique to each element Is equal to the number of electrons for neutral atoms Atoms of the various elements Differ in their number of subatomic particles The atomic number of an element Is the number of protons Is unique to each element Is equal to the number of electrons for neutral atoms

Atomic Number and Atomic Mass The mass number of an element Is the sum of protons plus neutrons in the nucleus of an atom Is an approximation of the atomic mass of an atom The mass number of an element Is the sum of protons plus neutrons in the nucleus of an atom Is an approximation of the atomic mass of an atom

Atomic Number and Atomic Mass If you know some facts about an atom, you can figure out the rest For example, Boron (B) has an atomic number of 5 and a mass number of 11. How many protons does Boron have? How many neutrons? How many electrons? If you know some facts about an atom, you can figure out the rest For example, Boron (B) has an atomic number of 5 and a mass number of 11. How many protons does Boron have? How many neutrons? How many electrons?

Atomic Number and Atomic Mass Another example: Magnesium (Mg) has atomic number of 12 and mass number of 24. How many protons does Mg have? How many neutrons? How many electrons? Another example: Magnesium (Mg) has atomic number of 12 and mass number of 24. How many protons does Mg have? How many neutrons? How many electrons?

Isotopes Atoms of a given element may occur in different forms called isotopes

Isotopes Atoms of a given element may occur in different forms called isotopes Isotopes of a given element Differ in the number of neutrons in the atomic nucleus Have the same number of protons Atoms of a given element may occur in different forms called isotopes Isotopes of a given element Differ in the number of neutrons in the atomic nucleus Have the same number of protons

Isotopes Atoms of a given element may occur in different forms called Isotopes Isotopes of a given element Differ in the number of neutrons in the atomic nucleus Have the same number of protons Radioactive isotopes Spontaneously give off particles and energy Atoms of a given element may occur in different forms called Isotopes Isotopes of a given element Differ in the number of neutrons in the atomic nucleus Have the same number of protons Radioactive isotopes Spontaneously give off particles and energy

Isotopes of Hydrogen

Radioactive Dating Isotopes can be used to date biological samples In Carbon 14 dating, the ratio of C-12 and C-14 in a biological sample gives an estimate of when that organism died C-14 dating works for specimens less than 60,000 years old Isotopes can be used to date biological samples In Carbon 14 dating, the ratio of C-12 and C-14 in a biological sample gives an estimate of when that organism died C-14 dating works for specimens less than 60,000 years old

Energy Levels of Electrons An atom’s electrons Vary in the amount of energy they possess Energy Is defined as the capacity to cause change Potential energy Is the energy that matter possesses because of its location or structure

Energy Levels The electrons of an atom Differ in the amounts of potential energy they possess depending on their location

Electron Shells Energy levels Are represented by electron shells Third energy level (shell ) Second energy level (shell ) First energy level (shell) Energy absorbed Energy lost Atomic nucleus More potential energy to reside here Less potential energy to reside here

Electron Configuration and Chemical Properties Valence electrons Are those in the outermost, or valence shell Determine the chemical behavior of an atom The valence number of an atom is the number of unpaired electrons in its valence shell This valence number determines the number of bonds the atom can form

Periodic Table The periodic table of the elements Shows the electron distribution for all the elements Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 5 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar

Orbitals An orbital Is the three-dimensional space where an electron is found 90% of the time

Orbitals Each electron shell Consists of a specific number of orbitals Electron orbitals. Each orbital holds up to two electrons. 1 s orbital2 s orbitalThree 2 p orbitals 1 s, 2 s, and 2 p orbitals (a) First shell (maximum 2 electrons ) (b) Second shell (maximum 8 electrons ) (c) Neon, with two filled shells (10 electrons) Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. x Z Y

Combining Atoms into Bigger Structures: Molecules & Compounds A molecule consists of two or more atoms held together by chemical bonds A compound is specifically 2 more more different kinds of atoms held together by chemical bonds

Examples of Molecules: Specifically compounds

Types of Chemical Bonds Chemical bonds form because atoms “desire” to complete their valence shell Atoms can get full valence shells by different methods: Sharing electrons Losing/gaining electrons Note: Inert elements already have complete valence shells and thus do not form bonds with other atoms (Ex. Helium)

Covalent Bonds A covalent bond (co- = sharing) Is the sharing of a pair of valence electrons between 2 atoms Each atom involved appears to have a complete valence shell therefore A single bond Is the sharing of one pair of valence electrons A double bond Is the sharing of two pairs of valence electrons Covalent bonds are strong, stable bonds Create the diverse molecules of biology

Formation of a covalent bond 2 Hydrogen atoms (2 H) 1 Hydrogen molecule (H 2 )

Name (molecular formula) Electron- shell diagram Structural formula Space- filling model Hydrogen (H 2 ). Two hydrogen atoms can form a single bond. Oxygen (O 2 ). Two oxygen atoms share two pairs of electrons to form a double bond. HH O O Single and Double Covalent bonds

Name (molecular formula) Electron- shell diagram Structural formula Space- filling model Methane (CH 4 ). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. Water (H 2 O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. H O H HH H H C Covalent Bonding in Molecules

Electronegativity Is the attraction a particular kind of atom has for the electrons in a covalent bond The more electronegative an atom The more strongly it pulls shared electrons toward itself Electronegativity Is the attraction a particular kind of atom has for the electrons in a covalent bond The more electronegative an atom The more strongly it pulls shared electrons toward itself

Electronegativity Electronegativity values can vary between elements causing different types of covalent bonds In a nonpolar covalent bond: The atoms have similar electronegativities Share the electrons equally In a polar covalent bond: One of the atoms has a higher electronegativity value than the other atom The shared electrons are pulled towards the atom with the higher value Electronegativity values can vary between elements causing different types of covalent bonds In a nonpolar covalent bond: The atoms have similar electronegativities Share the electrons equally In a polar covalent bond: One of the atoms has a higher electronegativity value than the other atom The shared electrons are pulled towards the atom with the higher value

Polar vs. Nonpolar Covalent Bonds

Ionic Bonds In some cases, atoms don’t share but strip electrons away from their bonding partners This will also create complete valence shells of the atoms involved Electron transfer between two atoms creates ions Ions Are atoms with more or fewer electrons than usual (charged atoms) In some cases, atoms don’t share but strip electrons away from their bonding partners This will also create complete valence shells of the atoms involved Electron transfer between two atoms creates ions Ions Are atoms with more or fewer electrons than usual (charged atoms)

Ions An anion Atom that gains electrons Is negatively charged A cation Atom that lost electrons Is positively charged An anion Atom that gains electrons Is negatively charged A cation Atom that lost electrons Is positively charged

Ionic Bonds Cl – Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium on (a cation) Sodium chloride (NaCl) An ionic bond Is an attraction between anions and cations

Ionic Bonds In ions, the number of protons and electrons will be unequal For example: Cl has an atomic number of 17 Regular Cl would have 17 protons and 17 electrons The Cl anion still has 17 protons but will have 18 electrons making it Cl - In ions, the number of protons and electrons will be unequal For example: Cl has an atomic number of 17 Regular Cl would have 17 protons and 17 electrons The Cl anion still has 17 protons but will have 18 electrons making it Cl -

Ionic Bonds Na + Cl – Ionic compounds Are often called salts, which may form crystals

SodiumChlorine Sodium Chloride + Reminder of Emergent Properties Concept