BIOCHEMISTRY

Elements and Compounds

• An element is a substance that cannot be broken down to other substances by chemical reactions (pure)

– Carbon

– Oxygen

• A compound is a substance consisting of two or more elements in a fixed ratio

– Sodium chloride

Essential Elements of Life

• About 25 of the 92 elements are essential to life

• Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

• Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur

• Trace elements are those required by an organism in minute quantities

Trace elements are elements that are necessary, but present

in very small quantities• Sulphur: an important element in some

amino acids.

• Calcium: used during nerve impulses

• Iron: found in hemoglobin (oxygen transport protein)

• Sodium: needed for a nerve impulse

• Phosphorus: in cell membrane structures and DNA

An element’s propertiesdepend on the structure of its

atoms• Each element

consists of unique atoms

• An atom is the smallest unit of matter that still retains the properties of an element

Subatomic Particles• Atoms are composed of subatomic

particles• Relevant subatomic particles include:

– Neutrons (no electrical charge)– Protons (positive charge)– Electrons (negative charge)

• # protons = atomic number• # protons + # neutrons = mass number• # protons = # electrons• Electrons form a cloud around the nucleus

Cloud of negativecharge (2 electrons)

Fig. 2-5Fig. 2-5

Nucleus

Electrons

(b)(a)

The formation and function of molecules depend on chemical

bonding between atoms

• Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

• These interactions usually result in atoms staying close together, held by attractions called chemical bonds

Covalent Bonds

• A covalent bond is the sharing of a pair of valence electrons by two atoms

• A covalent bond hold together two atoms that share one or more pair of electrons

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(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure & Structural Formula

Space-fillingModel

• A molecule consists of two or more atoms held together by covalent bonds

• Double bonds: two pairs of shared electrons

• Triple bonds: three pairs of shared electrons

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Singlecovalent bond

Doublecovalent bond

Electrons in a covalent bond may be equally or unequally shared between the atoms

• Non-polar covalent bond: atoms share electrons evenly

• Polar covalent bond: atoms share electrons unequally, so there is a slight difference in charge between the two poles of the bond

Polar Covalent Bond

• A molecule with polar bonds may be polar overall

• H2O is a polar molecule

• The (slightly) positively charged pole is around each hydrogen

• The (slightly) negatively charged pole is around the oxygen

Ionic Bonds

• When atom loses or gains an electron, it becomes an positively or negatively charged ION

• Cations are positively charged (because they have fewer electrons than protons). They are giving away their electrons.

• Anions are negatively charged (because they have more electrons than protons) They are receiving the electrons.

Na Cl Na Cl

NaSodium atom Chlorine atom

Cl Na+

Sodium ion(a cation)

Cl–Chloride ion

(an anion)

Sodium chloride (NaCl)

Animation: Ionic/Covalent BondsIonic/Covalent Bonds

In an ionic bond, cations and anions are linked by attraction of opposite charges

• Most biological molecules contain covalent bonds

• Covalent bonds are stronger than ionic bonds but vary in their stability

Hydrogen Bonds• Polar molecules like water have

partially charged atoms at their ends

• Hydrogen bonds form when partial opposite charges in different molecules attract each other– The partially positive hydrogens of one

water molecule are attracted to the partially negative oxygen on another

Hydrogen Bonds…

• Weak bond that is easily broken because no electrons are shared

• Important in stabilizing the 3D shape of large molecules like proteins and DNA

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

2 H2 O2 2 H2OReactants Reaction Products

Do atoms always have an equal number of protons, neutrons and electrons?

1. Yes.

2. No.

A chemical bond is formed through:

1. The gaining, losing, or sharing of protons.

2. The gaining, losing, or sharing of neutrons.

3. The gaining, losing, or sharing of electrons.

4. The gaining, losing, or sharing of isotopes.

5. The gaining, losing, or sharing of ions.

After sodium loses an electron, it is:

1. A positive ion.

2. A negative ion.

3. A neutral ion.

4. An isotope.

5. A compound.

After chlorine gains an electron, it is:

1. A positive ion.

2. A negative ion.

3. A neutral ion.

4. An isotope.

5. A compound.

What is the difference between a nonpolar covalent bond and a

polar covalent bond?1. A polar covalent bond results when there is unequal sharing of electrons in a molecule, whereas electrons are shared equally in a nonpolar covalent bond.

2. A polar covalent bond has two equal sides and a nonpolar covalent bond has two different sides.

3. A nonpolar covalent bond is positively charged and a polar covalent bond is negatively charged.

4. A polar covalent bond is positively charged and a nonpolar covalent bond is negatively charged.

Why Is Carbon So Important?

• Organic vs. Inorganic in Chemistry

• Organic refers to molecules containing a carbon skeleton

• Inorganic refers to carbon dioxide and all molecules without carbon

• Carbon atoms are versatile and can form up to four bonds (single, double, or triple) and rings

• Functional groups in organic molecules confer chemical reactivity and other characteristics

– Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules

Organic Molecule Synthesis

• All biological molecules fall into one of four categories

–Carbohydrates

–Lipids

–Proteins

–Nucleic Acids

Organic Molecule Synthesis• Biomolecules are polymers(chains) of

subunits called monomers

Polymer Monomer

polysaccharide (complex carbohydrate)

monosaccharide (simple sugar)

fat (a lipid) glycerol, fatty acid

protein amino acid

nucleic acid nucleotide

Organic Molecule Synthesis

• Monomers are joined together through condensation reactions.

• An H and an OH are removed, resulting in the loss of a water molecule (H2O)

• Also called dehydration synthesis (but IB uses the word condensation)

Organic Molecule Synthesis

• Polymers are broken apart through hydrolysis (“water cutting”)

• Water is broken into H and OH and used to break the bond between monomers

• Hydrolysis is the reverse of condensation: one molecule is split by the addition of H+ and OH- (from water) to the components.