Introduction to Biochemistry

Living organisms operate within the same physical laws that apply to physics and chemistry:

Conservation of Mass, Energy Laws of Thermodynamics Laws of Chemical Kinetics Principles of Chemical Reactions

Living organisms are composed of lifeless molecules that conform to the physical laws of nature.

Electronegativity• nonpolar bond: electrons are shared equally

HCl:

• polar bond: electrons are shared unequally because of the difference in electronegativity.

H2,Cl2:

Bond PolarityA polar bond can be pictured using partial charges:

= 0.9

ElectronegativityDifference Bond Type

0 - 0.5 Nonpolar

0.5 - 2.0 Polar

2.0 Ionic

2.1 3.0

+

H Cl

MOLECULAR SHAPE

• When atoms form a covalent bond, the valence electron pairs arrange themselves to be as far away from each other as possible.

• This change to the orientation of the valence electrons is Hybridization.

• Symmetry of shape will also determine polarity of molecule or functional group.

Ammonia: NH3 – pyramidal shape – equal 107 angle between valence electrons; asymetrical shape – polar molecule

•Methane: CH4 – tetrahedral shape – equal 109.5 angle between valence electrons; symmetrical; nonpolar

To determine if a molecule is polar or nonpolar, must consider both electronegativity and shape

Which of the following is the essential characteristic of a polar molecule?

a. Contains double or triple bonds

b. Is formed at extremely low temperatures

c. Contains ions as part of the structure

d. Has an asymmetrical distribution of electrical charge

e. Contains the element oxygen

• intermolecular forces of attraction

Examples: London forces, dipole-dipole forces, hydrogen bonds

Van der Waals forces:

• London forces are weak because (1) partial charges are involved and (2) because they are temporary. They arise from the random movement of electrons in atoms and molecules.

a) small collection of nonpolar molecules

b) a nonpolar molecule may temporarily have a slight excess of electrons in one portion of the molecule

c) During the brief interval that these temporarily polar molecules exist, they are attracted to each other

LONDON FORCES

Hydrogen bonds: strongest intermolecular bonds

The Essential Role of Water

•H2O is the key to understanding the behavior of macromolecules. It is the solvent of life and all living transformations occur in an aqueous environment.

Water is a Polar Molecule

• The structure of water consists of two hydrogen atoms bonded to one oxygen.

• The hydrogen side of the water molecule has a slight positive charge. On the other side of the molecule a negative charge exists.

• Because of the polar structure, water molecules tend to form weak bonds with one another and with other substances which are charged.

• HYDROGEN BONDS are individually weak, but collectively strong.

Properties of water

• Water has a high specific heat. • Specific heat is the amount of energy required

to change the temperature of a substance.• Because water has a high specific heat, it can

absorb large amounts of heat energy before it begins to get hot. It also means that water releases heat energy slowly when situations cause it to cool.

• Water does not undergo changes in temperature easily.

• The temperature of the water within living organisms tends to change more slowly than does that of the surrounding air or soil, so that the living cells are protected against temperature fluctuations.

• This kind of protection is important because many biochemical reactions will take place only within a narrow range of temperatures.

• Water is a universal solvent. This feature also enables water to carry solvent nutrients in living organisms.

• Water is an unusually versatile solvent because its polar molecules are attracted to charged and polar substances. When ions or polar substances are surrounded by water molecules, they dissolve and are called solutes.

• Hydrophilic substances have an affinity for water. • Hydrophobic substances do not; they seem to

repel water.

• Water has a high surface tension.• This phenomenon also causes water to stick to

the sides of vertical structures despite gravity's downward pull.

• Water's high surface tension allows for the formation of water droplets and waves, allows plants to move water (and dissolved nutrients) from their roots to their leaves, and the movement of blood through tiny vessels in the bodies of some animals.

Cohesion and Adhesion

Acids, bases and pH

• Water can dissociate into H+ and OH- ions• Acids:(pH 0 to 6.9): high concentrations H+• Bases:(pH 7.1 to 14) high concentrations OH-• Human blood must be within range of 7.35-

7.45. Control of pH is very important.

Buffers

• A buffer is an aqueous solution that has a highly stable pH. If you add acid or base to a buffered solution, its pH will not change significantly.

• An acid-base buffer typically consists of a weak acid, and its conjugate base

• An acid donates a proton. The chemical that remains after the proton is donated is a base.

• HNO3 NO3-

Acid conjugate base

• When a base accepts a proton, it becomes an acid because it now has a proton that it can donate.

• The bicarbonate buffering system is an important buffer system in the acid-base homeostasis of living things, including humans.

• In this system, carbon dioxide (CO2) combines with water to form carbonic acid (H2CO3), which in turn rapidly dissociates to form hydrogen ion and bicarbonate (HCO3

- )

• When H+ are added to the solution, some of the base (HCO3

-) component of the buffer is converted to the weak-acid(H2CO3) component . This uses up most of the H+ added.

• When OH- are added to the solution, protons are dissociated from some of the weak-acid molecules of the buffer, converting them to the base of the buffer. This releases H+ ions.

Types of Reactions

• Dehydration synthesis

• Hydrolysis• Neutralization• Oxidation-Reduction

Dehydration synthesis

• aka Condensation reactions• Form a covalent bond between two molecules

by removing a water molecule• Anabolic reaction: creates bigger molecules

Hydrolysis

• Adds a water molecule to break a covalent bond

• Catabolic reaction: creates smaller molecules

Neutralization

• Acid + Base Salt + Water• Antacids are supposed to decrease the

amount of hydrochloric acid in the stomach by reacting with excess acid.

• Some of the ingredients in antacids are: milk of magnesia (Mg(OH)2, calcium carbonate (CaCO3), sodium bicarbonate (NaHCO3)

Oxidation -Reaction

• OIL RIG: Oxidation is loss (of electrons)Reduction is gain

• In biological systems, usually means gain or loss of H+ (protons)

• Coupled reactions are an important way to transfer energy (cellular respiration and photosynthesis)

Functional Groups

• Functional groups are clusters of atoms with characteristic structure and functions.

• Generally, they are polar covalent groups• They increase the solubility of a substance in

water.• The hydroxyl (OH) groups in glucose are what

make this sugar soluble