Chapter 2 The Chemical Context of Life The three subatomic particles and their significance. The types of bonds, how they form, and their relative strengths Domains of Study Domain of BioMolecules Domain of Cells Domain of Organisms Domain of Populations Domain of Communities

Overview Living organisms and the world they live in are subject to the basic laws of physics and chemistry. Biology is a multidisciplinary science, drawing on insights from other sciences. Life can be organized into a hierarchy of structural levels. At each successive level, additional emergent properties appear.

The Basics Everything is made of matter Matter is made of atoms Matter is anything that takes up space and has mass. Atoms are made of: protons + mass of 1 nucleus neutrons 0 mass of 1 nucleus electrons - mass <<1 orbits Different kinds of atoms = elements

The World of Elements

An element is a pure substance that cannot be broken down into other substances by chemical reactions. There are 92 naturally occurring elements. Each element has a unique symbol, usually the first one or two letters of the name. Some of the symbols are derived from Latin or German names.

A compound is a pure substance consisting of two or more elements in a fixed ratio. Table salt (sodium chloride or NaCl) is a compound with equal numbers of atoms of the elements chlorine and sodium.

Models of atoms Atoms have volume and mass. Mass of one proton or one neutron = atomic mass unit (amu) or 1 dalton, or 1.7 × 10–24 grams. Mass of one electron = 9 × 10–28—usually ignored

Atomic structure determines behavior The number of protons in an atom determines the element # of protons = atomic number this also tells you # of electrons, if neutral # of neutrons = atomic mass- atomic # All atoms of an element have same chemical properties all behave the same properties don’t change

Life requires ~25 chemical elements About 25 elements are essential for life Four elements make up 96% of living matter: • carbon (C) • hydrogen (H) • oxygen (O) • nitrogen (N) Four elements make up most of remaining 4%: • phosphorus (P) • calcium (Ca) • sulfur (S) • potassium (K)

Isotopes Isotopes: forms of an element with different numbers of neutrons, thus different mass numbers Example: 12C has 6 neutrons 13C has 7 neutrons 14C has 8 neutrons

Radioactive Isotopes Spontaneously give off particles and energy Alpha, beta, gamma radiation

How does this atom behave? Bonding properties Effect of electrons chemical behavior of an atom depends on its electron arrangement depends on the number of electrons in its outermost shell, the valence shell How does this atom behave?

The Energy Levels of Electrons Is defined as the capacity to cause change Potential energy Is the energy that matter possesses because of its location or structure A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between steps. (a) Figure 2.7A

How does this atom behave? How does this atom behave? Bonding properties Effect of electrons chemical behavior of an atom depends on number of electrons in its outermost shell How does this atom behave? How does this atom behave?

Elements & their valence shells Elements in the same row have the same number of shells

Elements & their valence shells Elements in the same column have the same valence & similar chemical properties Oxygen has medium electronegativity so doesn’t pull electrons all the way off hydrogen whereas chlorine would. So oxygen forms a polar covalent bond. Carbon has only a weak electronegativity so forms a nonpolar covalent bond

Elements & their valence shells Moving from left to right, each element has a sequential addition of electrons (and protons)

Chemical reactivity Atoms tend to Complete a partially filled outer (valence) electron shell or Empty a partially filled outer (valence) electron shell This tendency drives chemical reactions

Electron Configuration and Chemical Properties Orbitals occur in series called electron shells or energy levels. First shell: one orbital—s orbital Second shell: one s and three p orbitals (holds eight electrons) Third shell: one s and three p orbitals (holds eight electrons) Fourth & Fifth Shells: d orbitals added (10 more electrons) Seventh & Eighth Shells: f orbitals added (16 more electrons)

Ionic bonds

“Let’s go to the video tape!” Ionic bonds “Let’s go to the video tape!” Play Video Transfer of an electron Forms + & - ions + = cation – = anion Weak bond example: salt = dissolves easily in water

“Let’s go to the video tape!” Play Video Covalent bonds Two atoms need an electron Share a pair of electrons Strong bond both atoms holding onto the electrons Forms molecules example: water = takes energy to separate

Double covalent bonds Two atoms can share more than one pair of electrons double bonds (2 pairs of electrons) triple bonds (3 pairs of electrons) Very strong bonds

Multiple covalent bonds 1 atom can form covalent bonds with two or more other atoms forms larger molecules ex. carbon Methane Symmetrical molecule • leads to some of its properties • Charges are balanced • Leads to little attraction between different methane molecules • Therefore methane is a gas at room temperature

“Let’s go to the video tape!” Hydrogen bonds Positive H atom in 1 water molecule is attracted to negative O in another Can occur wherever an -OH exists in a larger molecule Weak bonds “Let’s go to the video tape!” Play Video

Polar covalent bonds Pair of electrons not shared equally by 2 atoms Water = O + H oxygen has stronger “attraction” for the shared electrons than hydrogen oxygen has higher electronegativity

Polar covalent bonds 2 hydrogens in the water molecule form an angle Water molecule is polar oxygen end is – hydrogen end is + Leads to many interesting properties of water….

Van der Waals Interactions Occur when transiently positive and negative regions of molecules attract each other

Strong and weak chemical bonds

Structure and Function run from large scale body systems through molecules and atoms. Structure and function are what Enzymes are all about Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Endorphin receptors Brain cell Figure 2.17

Chemical reactions make and break chemical bonds Convert reactants to products Reactants Reaction Product 2 H2 O2 2 H2O +

Life is the result of Chemical Reactions Photosynthesis Is an example of a chemical reaction Figure 2.18

Chemical Equilibrium Chemical equilibrium Is reached when the forward and reverse reaction rates are equal

Reductionist view of biology Matter is made of atoms Life requires ~25 chemical elements Atomic structure determines behavior of an element Atoms combine by chemical bonding to form molecules Weak chemical bonds play important roles in chemistry of life A molecule’s biological function is related to its shape Chemical reactions make & break chemical bonds