BIOLOGICAL CHEMISTRY. ATOMS AND MOLECULES. Atomic 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 .
Atomic structure determines the behavior of an element.
*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.
Atoms consist of 3 sub-atomic particles:
protons- pos. charge, located in the nucleus
Neutrons- neutral charge, located in the nucleus
Electrons- neg. charge, located in the orbitals
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%
*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
*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 nonpolarcovalent 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 polarcovalent bond. The unequal distribution of electrons have either a neg. or pos. charge (poles).
*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
*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.
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 Water1. Cohesive Behavior2. Ability to stabilize temperature3. its expansion upon freezing4. its versatility as a solvent
Ex. 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 another
Ex. 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 surface1. Cohesive Behavior of water
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.
(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.2. Ability to stabilize temperature
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
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 +)
*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
Acid- substance that increases the hydrogen ion concentration of a solution.Base- substance that reduces the hydrogen ion concentration of a solutionbuffers-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