BIO. 4 Notes Inorganic Chemistry--Ch. 2,3
C. Shannon Su13 9th edition
Matter: Anything that has mass and occupies space.
Element: Substance that cannot be broken down into another substance by chemical
means.
-Elements CHON make up 96% of living matter.
-Periodic Table
Compound: 2 or more elements (ie. H2O)
I. Structure of the Atom
a. Atom: the smallest unit of an element that still has all the properties of that element.
Elements are things like carbon, hydrogen and oxygen. We use abbreviations for
elements that may or may not start with the first letter:
C = Carbon
P = Phosphorus
S = Sulfur
O = Oxygen Na = Sodium
Fe = Iron
H = Hydrogen Ca = Calcium
N = Nitrogen K = Potassium
b. The atom is made up of subatomic particles, examples would be: protons, neutrons and
electrons.
The atomic number is the number of protons in an atom.
The atomic weight is the number of protons + the number of neutrons.
A molecule = 2 or more atoms ie. O3
A compound = 2 or more elements ie. H2O
An isotope is a form of an atom which differs in the number of neutrons.
-radioactive
-tracers, date materials
-Chernobyl
Energy: Potential vs. Kinetic
II. Bonds
A. Ionic Bond: a bond formed by transferring electrons from one atom to another. When one
atom loses electrons (making it positively charged) and the other atom gains electrons
(making it negatively charged). Then the two atoms are held together by their opposite
charges.
An atom that loses or gains electrons and ends up being positively or negatively charged is
called an ion.
B. Covalent Bond: a bond formed when 2 atoms share electrons.
Very important bonds for living systems.
The sharing may be equal = nonpolar, or unequal = polar electronegative
C. Hydrogen Bond: a weak bond between a polar bonded hydrogen and
a polar bonded nitrogen or oxygen.
1
This type of bond holds water molecules together and it holds the double strands of DNA
together.
III. Important Inorganic Molecules
A. Water
makes up 70-95% of cells
present in solid, liquid and gas forms
hydrogen & polar covalent bonds
Important Properties of water (due to the above bonding):
1. Cohesion/Adhesion: water can travel up against gravity. ie. plant
2. Surface Tension: Measure of how difficult it is to stretch or break the surface of a liquid.
ie. Water Strider
3. High specific heat: resists temperature change
4. High heat of vaporization--so it absorbs much heat before evaporation. ie. evaporative
cooling
5. Lower density as a solid than a liquid--so ice floats
6. Good Solvent When water is used as the solvent in a solution it is called an "aqueous"
solution. Solute + Solvent = Solution
Hydrophilic, Hydrophobic (definitions)
B. Acids, Bases and Buffers
pH scale= measurement of hydrogen ion concentration.
acid = more hydrogen ion, less hydroxide
base = less hydrogen ion, more hydroxide
buffer = maintains a constant pH by absorbing hydrogen ion or releasing hydroxide.
acid precipitation can be in the form of rain, snow or fog
Acid precipitation is caused by sulfur and nitrogen oxides mostly from fossil fuels (by
factories and autos).
Normal rain pH = 5.6
Acid rain pH < 5.6 ie. pH = 2 or 3
What does it damage?--plants, animals, statues, buildings
Biggest effect in which season? --Spring Why?--snow melts and releases locked up acid into
lakes, and it is the reproductive season.
What can you do?--Decrease industrial and fossil fuel use: decrease electricity use, carpool,
watch car emissions (get car smogged)
Carbon--Ch. 4 All you have to know from Ch. 4 is:
Carbon can bond to itself to form long chains of atoms.
A molecule is "organic" that contains carbon chains.
A hydrocarbon is carbon and hydrogen bonds. A major component of fossil fuels.
2
There are 4 electrons in the outer shell of carbon. Carbon is the most common element in
living things.
Carbon can be complex with side groups and functional groups, see table 4.9.
Organic Chemistry--Ch. 5
I. Organic = carbon containing with carbon-hydrogen bonds
Organic molecules are macromolecules
A. Condensation Synthesis: two molecules are joined by removing water. A + B ---> AB +
H2O
B. Hydrolysis: two molecules are broken apart by adding water. AB + H2O ---> A + B
C. monomers = organic molecule building blocks
polymers = many monomers linked together (macromolecules)
D. Types of organic molecules
1. Carbohydrates: contain carbon, hydrogen and oxygen (1:2:1 ratio)
general formula = (CH2O)n
functions: energy conversion and storage, support, part of nucleic acids
monosaccharide = 1 sugar ie. glucose C6H12O6-- important in cellular respiration, major
nutrient for cells, can be stored as a disaccharide or polysaccharide.
disaccharide = 2 sugar units ie. sucrose (glucose + fructose)
or lactose (glucose + galactose)
polysaccharide = many sugars (more than 2) held together by covalent bonds--made from a
series of condensation reactions ie. starch, glycogen, cellulose
Storage polysaccharides:
1. Starch: used by plants for storage of extra sugar made from photosynthesis. (repeating
units of glucose)
2. Glycogen: used by animals to store excess glucose in the liver and muscles as glycogen.
(also repeating units of glucose)
3. Cellulose: also a polymer of glucose found in plants, but in a different configuration than
starch.
-every cell wall made of cellulose
-we can eat it but we don't have the enzyme to break it down -cows have bacteria in their
stomachs to break down cellulose
-termites have protozoans and bacteria to digest the cellulose in wood
-fungi can digest cellulose and are crucial in the food web as decomposers because of it
4. Chitin: used to make the exoskeleton of arthropods (insects, spiders, crayfish, lobster)--an
outer skeleton that allows little water loss.
2. Lipids: (fats, oils and waxes)
hydrophobic
functions: long term energy storage, insulation, protect organs, part of biological membranes.
examples:phospholipids (in the cell membrane), amphipathic
fatty acids: (saturated vs, unsaturated), atherosclerosis
3
3. Nucleic Acids (ie. ATP, DNA, RNA)
functions: carry genetic information, store and release energy, coenzymes, chemical
messengers.
monomer = nucleotide (a sugar, phosphate and nitrogen base)
Two types of nitrogenous bases:
pyrimidine: single ring (cytosine, thymine, uracil)
purine: double ring (adenine and guanine)
DNA held together by hydrogen bonds, in a double helix shape closely related species
share greater portion of their DNA: number of amino acid differences shows closest or
furthest relationships.
4. Proteins
contain C, H, O, N and usually S
functions: enzymes--speed up biochemical reactions,
structural-- in membranes and hair, part of some hormones ie. insulin, part of biological
membranes
monomer = amino acid R group or side chain is what makes one amino acid different
from another.
polymer = polypeptide or protein
peptide bond = a covalent bond between 2 amino acids conformation= shape, is important
to function
Levels of structure:
1. primary = chain or sequence of amino acids
-specific sequence of amino acids for each protein is determined by the DNA.
-if substitute the amino acid valine for glutamic acid (usually in hemoglobin) get sickle cell
anemia
2. secondary = helix, beta-pleated sheet
3. tertiary = 3-D folding into a globular shape
4. quaternary = more than one globular chain ie. hemoglobin
denaturation: irreversibly damage the 3-D structure of a protein (usually with heat). Makes
protein biologically inactive.
Bioenergetics/Enzymes
I. Enzymes
-proteins that serve as catalysts (most are proteins, but not all)
-regulate metabolic reactions (heat can speed reactions, but high temperature kills cells so
organisms use enzymes)
catalysts: speed reactions that would normally take place
(enzyme needed to make reaction go faster, not to occur in the first place)
A. The Structure and Characteristics of Enzymes
1. Enzymes are made of protein (with one exception) but not all proteins are enzymes.
-can have other molecules that assist them that are non-protein
coenzymes= organic enzyme helpers, like vitamins & NAD
cofactors= inorganic enzyme helpers, like minerals such as iron
2. Conformation or shape of the enzyme is important.
4
-remember levels of protein structure (primary, secondary, etc.)
3. Enzyme shape is dynamic.
-switches between catalyzing and non-catalyzing shapes
4. Enzymes may be free floating in the cytoplasm of the cell or in membranes.
5. Enzymes have an "active site" where the substrate binds. Substrate = Reactants
6. Enzymes are substrate specific.
The active site is very specific, will only fit with certain substrate(s).
Lock & key relationship.
The binding of the enzyme and substrate is called the "enzyme-substrate complex." These
two molecules fit together with induced fit.
7. Enzymes are macromolecules and are usually larger than their substrates.
8. Enzyme equation:
enzyme + substrate ---> enzyme-substrate ---> enzyme + product complex
9. Enzyme is recyclable. (Unchanged by reaction)
B. Function of Enzymes
Enzymes cannot change the free energy given off by a reaction. The way enzymes work is by
lowering the activation energy for a reaction. Activation Energy is the minimum amount of
energy needed to bring molecules together.
Enzymes lower activation energy by providing orientation and precise positioning in order to
lower the energy barrier between reactants and products.
C. Factors that Influence Enzymes
1. Temperature and pH
rate of activity of the enzyme tends to increase until a maximum (optimum) then falls off as
enzyme is denatured. When an enzyme is denatured the structure of the enzyme is
irreversibly changed, making it nonfunctional. What is optimum is different for different
enzymes.
2. Substrate Concentration
Enzyme activity increases until the amount of substrate added reaches of level of "saturation"
where the enzyme cannot process the substrate any faster. (All the active sites are full)
3. Coenzyme and cofactor concentration
4. Enzyme concentration
5. Inhibitors
D. Metabolic Regulation
Inhibition and activation of enzymes by molecules naturally present in the cell are
essential to metabolic control.
Negative Feedback Inhibition: product shuts off its own production
Regulatory Enzymes can set the reaction rate for an entire pathway. They have allosteric
sites where substances may bind and influence enzyme activity.
Inhibitors to enzymes can be competitive or noncompetitive:
Competitive Inhibitors: block the active site of the enzyme, thereby blocking the substrate
form binding with the enzyme.
Noncompetitive Inhibitors: attach to the enzyme somewhere other than the active site, and
change the shape of the enzyme, so the substrate no longer can bind with the enzyme.
5