1. BIOCHEMISTRY

2. 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

3. 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

5. 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

6. An element’s properties depend 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

7. 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

8. Cloud of negative charge (2 electrons) Electrons Nucleus (a) (b)
Fig. 2-5
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
Figure 2.5 Simplified models of a helium (He) atom
(a)
(b)

9. 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

10. Covalent Bonds
Lewis Dot
Structure &
Structural
Formula
Name and
Molecular
Formula
Electron-
distribution
Diagram
Space-
filling
Model
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
(a) Hydrogen (H2)
(b) Oxygen (O2)
(c) Water (H2O)
(d) Methane (CH4)
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

11. Double bonds: two pairs of shared electrons
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
Single
covalent bond
Double
covalent bond
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

12. 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

14. 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

16. 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.

17. Animation: Ionic/Covalent Bonds
In an ionic bond, cations and anions are linked by attraction of opposite charges Na Cl Na Cl Na Cl
Na+
Cl–
Sodium atom
Chlorine atom
Sodium ion
(a cation)
Chloride ion
(an anion)
Figure 2.14 Electron transfer and ionic bonding
Sodium chloride (NaCl)
Animation: Ionic/Covalent Bonds

19. Most biological molecules contain covalent bonds
Covalent bonds are stronger than ionic bonds but vary in their stability

20. 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

22. 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

23. 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 H2O
Reaction
Reactants
Products

24. Do atoms always have an equal number of protons, neutrons and electrons?
1. Yes.
2. No.

25. 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.

26. 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.

27. 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.

28. 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.

29. 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

30. 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

32. Organic Molecule Synthesis
All biological molecules fall into one of four categories
–Carbohydrates
–Lipids
–Proteins
–Nucleic Acids

33. 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

36. 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)

39. 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.