BIOLOGICAL CHEMISTRY

ATOMS AND MOLECULESAtomic structure

determines the behavior of an element.

Atoms combine by chemical bonding to form molecules.

Weak chemical bonds play important roles in the chemistry of life.

A molecule’s biological function is related to its shape.

Chemical reactions make and break chemical bonds.

ATOMS

*Atoms are the basic building blocks of matter that make up everyday objects.

*A desk, the air, even you are made up of atoms!

*There are 90 naturally occurring kinds of atoms.

*Scientists in labs have been able to make about 25 more.

ATOMSAtoms consist of 3 sub-atomic

particles:

a. protons- pos. charge, located in the nucleus b. Neutrons- neutral charge, located in the

nucleusc. Electrons- neg. charge, located in the

orbitals

Atomic # = the number of protons, which = the number of electrons

Atomic mass= the number of protons + the number of neutrons

25 CHEMICAL ELEMENTS REQUIRED FOR LIFE

•About 25 of 92 natural elements are known to be essential to life.

4 of these make up 96% of the body ( C, O, H, N)

•P, S, Ca, K, and a few others make up the other 4% of the organisms weight.

•Trace elements are required in only minute quantities. (Ex: Fe, I, F, Cu, Zn, etc.) Trace elements make up less than 0.01%

CHEMICAL BONDING*Atoms combine by chemical bonding to form molecules.

*Atoms with incomplete valence shells combine together to complete the shell.

• The strongest kinds of chemical bonds are ionic and covalent.

•Covalent bonds- sharing of electrons between molecules

•Ionic bonds- transferring of electrons from one molecule to another

COVALENT BONDS

*formed when electrons between atoms are shared• When 2 electrons are shared- single covalent bond• When 4 or 6 are shared- double or triple bond • When 2 atoms sharing electrons are exactly the

same, as in 02, the electrons are shared equally and the bond is a nonpolar covalent bond.

• When the atoms are different, H2O, the larger of the nucleus of the oxygen atom exerts a stronger pull on the shared electrons than does the single proton that makes up the hydrogen nucleus. This is called a polar covalent bond. The unequal distribution of electrons have either a neg. or pos. charge (poles).

Ionic Bonds

*form between 2 atoms when one or more electrons are completely transferred from one atom to the

other. • The atom that gains electrons has

an overall neg. charge.• The atom that donates electrons

has an overall pos. charge

Weak chemical bonds

• In living organisms- most of the strongest chemical bonds are covalent, which link together to form molecules.

• Weak bonds- ionic bonds and hydrogen bonds

• Advantage of weak bonding- contact between molecules can be brief, respond to each other, and then separate.

Function in relation to shape

*The precise shape of a molecule is very important to its’ function in the

living cell.*Linear, V-shaped, tear dropped,

tetrahedral.*It determines how molecules fit

together and transmit and receive information.

Chemical reactions making and breaking bonds

• Chemical reactions leads to the changes in the composition of matter.

• Examples: hydrogen and oxygen react to form water.

• In photosynthesis- carbon dioxide and water react to form sugar and oxygen.

Chemistry of water

First Cells Evolved in Water

1. All living things are about 70% water.2. Because water is a polar molecule, water molecules are hydrogen bonded to each other.3. Water is polar because opposite ends of the molecule have opposite charges.4. With hydrogen bonding, water is liquid between 0 C and 100 C which is critical for life.

Properties of Water

1. Cohesive Behavior2. Ability to stabilize temperature3. its expansion upon freezing4. its versatility as a solvent

1. COHESIVE BEHAVIOR OF WATER

*Cohesion- Bonding of like molecules by hydrogen bondsEx. Water transport in a plant against gravity: hydrogen bonds cause water molecules to tug on those below them to bring them up the vein of the plant.*Adhesion- Clinging of one substance to anotherEx. Adhesion of water to the walls of the vessels helps counteract the pull of gravity.*Surface Tension- a measure of how difficult it is to stretch or break the surface of a liquid.Ex. Makes water behave as if it has an invisible film. How many drops of water can you put on a penny?Skipping rocks on a pond; animals can walk, run, on water without breaking the surface

Water is a versatile solvent, facilitates chemical reactions both outside of and within living systems..a. Water is known as the universal solvent because it dissolves a great number of solutes.b. Ionized or polar molecules attracted to water are hydrophilic.c. Non-ionized and nonpolar molecules that cannot attract water are hydrophobic.

2. ABILITY TO STABILIZE TEMPERATURE• High specific heat- gives water the ability to stabilize

temperature(amount of heat absorbed or lost for 1g of that substance will change the temp. by 1 degree celsius.) When 2 objects of different temperatures come together: Heat is transferred from the warmer body to the cooler body until the temperature is equalized between the 2

• Heat of vaporation- the amount of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state. Ex. Puddles that slowly dry up, boiling water, evaporation

• Evaporative cooling- the “hottest” molecules are most likely to leave as a gas and cooler molecules are left behind to cool the body, or body of water. Ex. Sweating, transpiration in plants. Humidity prevents the evaporation of sweat.

3. Expansion upon Freezing-

*as water molecules cool they slow down and expand or stretch and then freeze. This process makes them less dense than liquid water and they become a solid (ice) and float.* Because of this ability to float, it makes life possible. If the ice sank the entire body of water would freeze and kill all life. The top layer of ice insulates the body of water for life to survive.

4. Waters versatility as a solvent

* Many polar compounds are dissolved in water of biological

fluids such as: blood, sap of plants, liquid within all cells.

*Surface of water has structure, think of skipping a rock, or insects that walk on water

*Water sticks to itself, this allows water to be moved from the roots to leaves in plants

*Water becomes less dense when it freezes, so it floats

*Water has an ability to stabilize temperature

* Water is a great solvent because of its polarity

Dissociation of Water Molecules• one of the hydrogen nuclei leaves its electron behind with the oxygen

atom to become a hydrogen ion

*the oxygen and other hydrogen atoms become a hydroxide ion.

• Since the hydrogen ion has no electron to neutralize the positive charge on its proton, it has a full unit of positive charge and is symbolized as H+.

• *The hydroxide ion retains the electron left behind and thus has a full unit of negative charge, symbolized by OH-.

*The hydrogen ion (proton) does not wander long by itself before it attaches to the oxygen atom of a second un-ionized water molecule to form a hydronium ion (H3O +)

Dissociation/Acids/Bases *Concentrations of H+ and OH- are equal in pure water.*Adding Acids and Bases changes the balance.*We use the pH scale to see the changes in the balance. More H+ ions More OH-ions

P=potentialH= Hydrogen

ACID- SUBSTANCE THAT INCREASES THE HYDROGEN ION CONCENTRATION OF A SOLUTION.

BASE- SUBSTANCE THAT REDUCES THE HYDROGEN ION CONCENTRATION OF A SOLUTION

BUFFERS-MINIMIZE CHANGES IN PH. ( EX. TUMS) INTERNAL PH OF MOST LIVING THINGS IS CLOSE TO 7. EVEN A SLIGHT CHANGE CAN BE HARMFUL. CELLS ARE VERY SENSITIVE TO HYDROGEN AND HYDROXIDE IONS.

*HUMAN BLOOD HAS A PH OF 7.4—A PERSON CANNOT SURVIVE IF PH DROPS BELOW 7 OR GOES HIGHER THAN 7.8

Acids and Bases