AP/IB Biology Chapter 2 The Chemistry of Life Domains of Study Domain of BioMolecules Domain of Cells Domain of Organisms Domain of Populations Domain of Communities

Why are we studying chemistry? Chemistry is the foundation of biology. Biology is really chemistry in that most biological processes are chemical reactions.

Everything is made of matter Matter is made of atoms Hydrogen 1 proton 1 electron Oxygen 8 protons 8 neutrons 8 electrons Proton + Neutron Electron –

Different kinds of atoms =different elements The World of Elements H C N O Na Mg P S K Ca Different kinds of atoms =different elements

About 25 elements are essential for life Four elements make up 96% of living matter: • carbon (C) • hydrogen (H) • oxygen (O) • nitrogen (N) Five additional elements are important in living things: • phosphorus (P) • calcium (Ca) • sulfur (S) • iron (Fe) sodium (Na)

Essential Elements of Life Trace elements are those required by an organism in minute quantities. Missing essential elements can greatly affect living organisms. Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Figure 2.4 The effects of essential-element deficiencies Fig. 2-4a Figure 2.4 The effects of essential-element deficiencies (a) Nitrogen deficiency

Figure 2.4 The effects of essential-element deficiencies Fig. 2-4b Figure 2.4 The effects of essential-element deficiencies (b) Iodine deficiency

Role of some elements in living things: Sulfur In plants – In some amino acids In animals – In some amino acids In prokaryotes – In some amino acids Calcium In plants – Cofactor in some enzymes In animals – Cofactor in some enzymes and component of bones In prokaryotes – Cofactor in some enzymes

Role of some elements in living things: Phosphorous – In plants – Phosphate groups in ATP In animals – Phosphate groups in ATP In prokaryotes – Phosphate groups in ATP Iron – In plants – In cytochromes In animals – In cytochromes and in hemoglobin In prokaryotes – In cytochromes

Role of some elements in living things: Sodium – In plants – In membrane function In animals – In membrane function and sending nerve impulses In prokaryotes – In membrane function

How does this atom behave? Bonding properties Effect of electrons Electrons determine chemical behavior of an atom. Depends on number of electrons in atom’s outermost shell or energy level. (Add this)Valence shell is another name for outer shell. How does this atom behave?

How does this atom behave? How does this atom behave? Bonding properties Effect of electrons Atoms are stable when outer shell is full or has 8 electrons (Octet rule) Sulfur on the LEFT Magnesium on the RIGHT How does this atom behave? How does this atom behave?

Elements & their valence shells Elements in the same row have the same number of en. levels. Moving from left to right, each element has a sequential addition of electrons (& protons)

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

This tendency drives chemical reactions… and creates chemical bonds Chemical reactivity Atoms tend to complete a partially filled valence shell or empty a partially filled valence shell This tendency drives chemical reactions… and creates chemical bonds – –

Bonds in Biology Weak bonds Strong bonds Hydrogen bond hydrogen bonds H2O Weak bonds hydrogen bonds attraction between + and – hydrophobic & hydrophilic interactions van derWaals forces ionic bonds (sometimes weak) Strong bonds covalent bonds- share electrons ionic bonds - transfer electrons; (sometimes strong)

Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Covalent bonds Why is this a strong bond? Forms molecules Two atoms share a pair of electrons Both atoms holding onto the electrons Very stable Forms molecules H Oxygen – H O H — H H2 (hydrogen gas) H2O (water)

A compound is a combination of two or more different elements Covalent bonds can form between atoms of the same element or atoms of different elements A compound is a combination of two or more different elements Bonding capacity is called the atom’s valence Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

A molecule consists of two or more atoms held together by covalent bonds A single covalent bond, or single bond, is the sharing of one pair of valence electrons A double covalent bond, or double bond, is the sharing of two pairs of valence electrons Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Multiple covalent bonds 2 atoms can share >1 pair of electrons double bonds 2 pairs of electrons triple bonds 3 pairs of electrons Very strong bonds H H–C–H –

Polar covalent bonds Pair of electrons shared unequally by 2 atoms Water = O + H Oxygen has stronger “attraction” for the electrons than hydrogen Oxygen has higher electronegativity Water is a polar molecule “+” and “–” poles Leads to many interesting properties of water… + – H Oxygen – – – +

Electronegativity is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom, the more strongly it pulls shared electrons toward itself Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

In a nonpolar covalent bond, the atoms share the electron equally. In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 2-13  – O H H + + Figure 2.13 Polar covalent bonds in a water molecule H2O

Hydrogen bonding Polar water creates molecular attractions Weak bond Positive H atom in one H2O molecule is attracted to negative O in another H2O. Also can occur wherever an -OH exists in a larger molecule. Weak bond Typical strength of 5.0 kcal/mol, but it varies. APBio/TOPICS/Biochemistry/MoviesAP/03_02WaterStructure_A.swf Weak bonds are still important!

Oxygen – Significantly larger nucleus Greater charge (+8) Hydrogen – Smaller nucleus Charge of (+1) Electron pair found closer to the oxygen nucleus than the hydrogen nucleus. Oxygen carries a small negative dipole, and hydrogen carries a small positive dipole.

Molecular Shape and Function A molecule’s shape is usually very important to its function A molecule’s shape is determined by the positions of its atoms’ valence orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Hybridization of orbitals (a) Fig. 2-17a Four hybrid orbitals z s orbital Three p orbitals x y Tetrahedron Figure 2.17 Molecular shapes due to hybrid orbitals Hybridization of orbitals (a)

Molecules with similar shapes can have similar biological effects Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Structures of endorphin and morphine Fig. 2-18a Key Carbon Nitrogen Hydrogen Sulfur Natural endorphin Oxygen Morphine Figure 2.18 A molecular mimic (a) Structures of endorphin and morphine

Binding to endorphin receptors Fig. 2-18b Natural endorphin Morphine Endorphin receptors Brain cell Figure 2.18 A molecular mimic (b) Binding to endorphin receptors

Concept 2.4: Chemical reactions make and break chemical bonds Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Some chemical reactions go to completion: all reactants are converted to products Many chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction Chemical equilibrium is reached when the forward and reverse reaction rates are equal Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings