Biology I Unit II: The Chemistry of Life Notes

Atoms

Atoms are the building blocks for all matter

Atoms are made of protons (positive), neutrons (neutral or no charge), and electrons (negative)

Protons and neutrons are in the nucleus at the center of an atom, electrons are in shells around the nucleus.  The number of protons and electrons are equal so the atom has no charge.

Atomic number: the number of protons in an atom.  Tells you what element it is.

Mass number: the number of protons and neutrons in an atom.  Tells you its mass.

Ions:  Formed when an atom gains or losses an electron and becomes charged (positive if it lost an electron, negative if it gained an electron).

Importance of ions:  Almost all reactions and processes in the body involve ions including the sending of message from the brain to the rest of the body and the movement of substances into and out of cells.

Types of Bonds

Molecule:  When two or more atoms are bonded together.

Chemical bond:  a process where the electrons furthest from the center of the atom are shared or transferred to another atom so that all the atoms have a full outer shell.

Ionic bonds: electrons are transferred between atoms to form ions.  The ions are attracted to each other to form the bond.  They both fill their own outer shells.  They can be identified because of the labeled charges on each of the ions.

Covalent bonds: electrons are shared between atoms and this forms the bond.  They both share their outer shells.  The can be identified by the overlap or sharing of the electrons.

Hydrogen bonds:  Formed between the partial positive charge of hydrogen in a polar compound and the partial negative charge in another atom it is bonded to.  Especially important in water.

Chemistry of Water

Water is made of 2 hydrogen atoms and 1 oxygen atom bonding through a polar covalent bond.

This makes it polar (one + end and one – end)à see picture above.

When 2 water molecules stick together they form a Hydrogen bond

Special Properties of Water because of its polar nature:

Universal solvent: because of its polarity, other polar and ionic compounds dissolve in it easily

Adhesion: water “sticking” to another surface

Cohesion: water “sticking” to water

High heat capacity: it takes a lot of heat/energy to change the temperature of water

Surface tension: caused by cohesion of water; makes it have a “surface”, bugs can walk on it

Expands when freezing:  unlike most substances which shrink when they freeze, water expands

pH

Acids are compounds that form H+ ions in a solution.  Bases are compounds that form OH- ions in a solution
The pH scale measures the concentration of H+ ions in solution

                                                1-6=acidic          7.0= neutral (pure water)        8-14= basic

Importance of acids/bases in the body-

                You must have a strong acid (pH 1.5) in the stomach to break down food into smaller pieces

                The pH of the blood must be 7.4.  If you get too much CO₂ in the blood, the blood will become too acidic

All organisms are designed to work at a specific pH-when they are put into environments with different pHs, they will no longer be able to function because the enzymes in their body would no longer work!

Neutralization:  when an acid and base mix, they will neutralize and create water.

Buffer:  a system that prevents change.  When acid is added, it will create a base to neutralize it.  When base is added, it will create an acid to neutralize it.

Four Major Organic Compounds

Organic compounds: compounds that are built around CARBON that is covalently bonded to other carbon atoms and to other elements (hydrogen, oxygen, nitrogen).  Chemistry of LIFE.

A. Carbohydrates:

Structure:  Made of C, H, and O

Monosaccharides: simple sugars.  Ex) glucose, fructose

Polysaccharides: chains of many sugars.  Ex)Glycogen, Starch  and Cellulose

Examples: bread, rice, pasta
Function: Provide short-term energy

B. Lipids:

Structure: triglycerides (glycerol backbone and 3 fatty acid chains)

Saturated:  no double bonds in the fatty acids

Unsaturated:  one or more double bonds in the fatty acid chains

Cholesterol: rings            Phospholipids:  two fatty acids and a phosphate group

Examples: fats & oils

Function: give lots of energy (long-term energy)

C.  Proteins:

Structure=chain of amino acids (carbon, hydrogen, oxygen, nitrogen)

Examples=meat, beans, and nuts

Function=structural (bone & muscle), enzymes

D. Nucleic acids:

Structure: chain of nucleotides (sugar, phosphate group, nitrogenous base)

Examples: DNA & RNA

Function: Store genetic information

Enzymes

Made of proteins.  Lowers the activation energy to increase the rate of a reaction.

Enzymes do not change in the course of the reaction-it gets reused over and over.

Activation energy: the energy required to make a reaction go

Substrate: the material that the enzyme acts on

Product: the results of the reaction, what the substrate turns into

Active site: this is the place the reaction occurs on the enzyme

Enzymes are incredibly specific.  Their shape determines what types of compounds they react with.  An enzyme and its substrate are like a lock and key-only the specific key will work for each lock.

Enzymes work best at specific pH, temperatures, and concentrations.

When it gets too cold, the enzyme does not interact with the substrates fast enough to help the reaction.  When it gets too hot for an enzyme, it will denature (fall apart like melting). 

If it gets too high or too low in pH, the enzyme will be destroyed.

The concentration of the enzyme and substrate is a balance-not enough of either and there will either be enzyme that is not interacting with a substrate or there will be substrate that will not be reacting.

ATP Structure and Function

ATP (Adenosine Triphosphate):  It stores energy needed for cells to undergo life processes.  It is made of adenine, ribose sugar, and three phosphates groups.  The energy is stored in the bonds between the phosphates-when you break the bonds, you release energy.  When you add a bond, you store energy.

ADP (Adenosine Diphosphate):  Is like ATP but is only has two phosphates which means less bonds and thus it stores less energy.  ADP is what we create when we use ATP by removing a phosphate.

 

ATP is the energy source for all cellular processes.  Whenever you are asked how a cell gets energy, it is using ATP and breaking the bonds to release the energy.  This is how it gets energy to build things in the cell and move things into and out of the cell.