Chemistry

Chemistry Notes

Principal Elements in the Human Body

Elements and Significance: (See Table 2-1)
- Oxygen (O): 65% of body weight; component of water and other compounds; essential for respiration.
- Carbon (C): 18.6% of body weight; found in all organic molecules.
- Hydrogen (H): 9.7% of body weight; component of water and most other compounds.
- Nitrogen (N): 3.2% of body weight; found in proteins and nucleic acids.
- Calcium (Ca): 1.8% of body weight; found in bones and teeth; important for membrane function, nerve impulses, muscle contraction, and blood clotting.
- Phosphorus (P): 1.0% of body weight; found in bones and teeth, nucleic acids, and high-energy compounds.
- Potassium (K): 0.4% of body weight; important for proper membrane function, nerve impulses, and muscle contraction.
- Sodium (Na): 0.2% of body weight; important for blood volume, membrane function, nerve impulses, and muscle contraction.
- Chlorine (Cl): 0.2% of body weight; important for blood volume, membrane function, and water absorption.
- Magnesium (Mg): 0.06% of body weight; a cofactor for many enzymes.
- Sulfur (S): 0.04% of body weight; found in many proteins.
- Iron (Fe): 0.007% of body weight; essential for oxygen transport and energy capture.
- Iodine (I): 0.0002% of body weight; a component of hormones of the thyroid gland.
- Trace Elements: Silicon (Si), Fluorine (F), Copper (Cu), Manganese (Mn), Zinc (Zn), Selenium (Se), Cobalt (Co), Molybdenum (Mo), Cadmium (Cd), Chromium (Cr), Tin (Sn), Aluminum (Al), Boron (B), and Vanadium (V). Some function as cofactors; the functions of many trace elements are poorly understood.
Other components mentioned:
- Water
- Glycogen
- Fat (12kg)
- Protein (12kg)

Chemical Bonds

Formed by atom interaction.
Ions:
- Formed when an atom either gives up or gains electrons.
- An atom with a positive or negative charge due to unequal numbers of protons and electrons.
Molecules/Compounds:
- Formed when two or more atoms share electrons.
Types of bonds:
- Ionic bond
- Covalent bond
- Hydrogen bond

Ionic Bonding

Forms when one atom gives up an electron and another atom gains an electron.
Creates ions:
- Cation: Positive ion
- Anion: Negative ion
Weak bonds
Process of Ionic Bond Formation (using Sodium Chloride as an example):
1. Formation of ions: A sodium (Na) atom gives up an electron, which is gained by a chlorine (Cl) atom.
2. Attraction between opposite charges: The sodium ion ( $Na^+$ ) and chloride ion ( $Cl^-$ ) have opposite charges, so they attract each other.
3. Formation of an ionic compound: Association of sodium and chloride ions forms sodium chloride (NaCl).

Covalent Bonding

Strong bonds involving shared electrons.
- One electron is donated by each atom to make the pair of electrons.
Sharing one pair of electrons is a single covalent bond.
Sharing two pairs of electrons is a double covalent bond.
Types of Covalent Bonds:
- Nonpolar covalent bonds: Equal sharing of electrons between atoms with equal pull on electrons.
- Polar covalent bonds: Unequal sharing of electrons because one atom has a disproportionately strong pull on the electrons.
  - Form polar molecules—like water.
  - In a water molecule, the oxygen atom holds electrons more tightly than hydrogen atoms, leading to slight negative charge on oxygen and slight positive charges on hydrogen atoms

Hydrogen Bonding

Weak polar bonds between adjacent molecules based on electrical attractions.
Involve attractions between a slight positive charge and a slight negative charge.
Hydrogen bonds between H2O molecules cause surface tension.

Chemical Reactions

Either new bonds are formed, or existing bonds are broken.
- Reactants: Materials going into a reaction.
- Products: Materials coming out of a reaction.
- Metabolism: All reactions occurring at one time.

Types of Chemical Reactions

Decomposition reaction (catabolism):
- Breaks chemical bonds.
- General form: $AB \rightarrow A + B$
- Hydrolysis reaction:
  - $AB + H_2O \rightarrow AH + BOH$
Synthesis reaction (anabolism):
- Forms chemical bonds.
- General form: $A + B \rightarrow AB$
- Dehydration synthesis (condensation) reaction:
  - $AH + BOH \rightarrow AB + H_2O$
Exchange reaction

Enzymes

Biochemical reactions in cells do not occur spontaneously.
Activation energy:
- The amount of energy needed to start a reaction.
Enzymes:
- Protein catalysts that lower the activation energy of reactions.

Inorganic and Organic Compounds

Inorganic compounds:
- Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts.
- Examples: NaCl, H2O
Organic compounds:
- Molecules containing carbon and hydrogen.
- Carbohydrates, proteins, lipids, and nucleic acids.
- Example: $C<em>6H</em>{12}O_6$ (glucose)

Properties of Water

Water ( $H_2O$ ) accounts for up to two-thirds of total body weight.
Produces solutions—uniform mixtures of two or more substances.
- A solution consists of a solvent (liquid) and solutes (dissolved substances).
Universal solvent: Many molecules are water soluble.
Reactivity: Water serves as a reactant in some reactions.
High heat capacity: Heat capacity is the heat required to raise the temperature of a unit mass of a substance 1°C.
Lubrication: To moisten and reduce friction.
Hydration spheres:
- Ionic compounds (e.g., sodium chloride) dissociate in water; polar water molecules break the ionic bonds.
- Each ion is surrounded by water molecules, creating hydration spheres.
Hydrophilic and hydrophobic compounds:
- Hydrophilic:
  - hydro- = water, -philos = loving
  - Includes ions and polar molecules.
  - Interact with water.
- Hydrophobic:
  - phobos = fear
  - Includes nonpolar molecules, fats, and oils.
  - Do not interact with water.

Hydrogen Ions in Body Fluids

Hydrogen ions ( $H^+$ ) are dangerous and reactive in solutions.
pH: The scale used to measure the concentration of hydrogen ions in solution.
Neutral pH: A balance of $H^+$ and $OH^-$ .
- Pure water = 7.0
pH of human blood: Ranges from 7.35 to 7.45.
Many body fluids must be maintained in a tight pH range, and most are around neutral.
pH Scale:
- Has an inverse relationship with $H^+$ concentration:
  - More $H^+$ ions mean lower pH, less $H^+$ ions mean higher pH.
Acids, Bases, and Salts:
- Acid (proton donor): A solute that adds hydrogen ions to a solution.
  - Strong acids dissociate completely in solution.
- Base (proton acceptor): A solute that removes hydrogen ions from a solution.
  - Strong bases dissociate completely in solution.
- Weak acids and weak bases: Fail to dissociate completely; help to balance the pH.
- Salt: Solute that dissociates into cations and anions other than hydrogen ions and hydroxide ions.
Buffers and pH control:
- Buffers stabilize pH of solutions.
  - Buffer systems often involve a weak acid and its related salt (weak base).
  - Neutralize strong acids or strong bases.
  - Carbonic acid–bicarbonate buffer system is very important in humans.
- Antacids: Use sodium bicarbonate to neutralize hydrochloric acid in the stomach.

Carbohydrates

Organic molecules containing C, H, and usually O in a 1:2:1 ratio.
Covalently bonded.
Energy sources that are catabolized.
Sugars & starches make up about half of the typical U.S. diet.
Monosaccharides:
- Simple sugars with three to seven carbon atoms.
- Examples: Glucose, fructose, galactose.
Disaccharides:
- Two monosaccharides condensed by dehydration synthesis.
- Examples: Sucrose, maltose, lactose.
Polysaccharides:
- Polymers of many sugars condensed by dehydration synthesis.
- Examples: Glycogen, starch.

Lipids

Mainly hydrophobic molecules such as fats, oils, and waxes.
Made mostly of carbon and hydrogen atoms.
Include:
- Fatty Acids
- Glycerides
- Steroids
- Phospholipids
Fatty acids may be
- Saturated with hydrogen, meaning there are no double bonds in the hydrocarbon tail
- Unsaturated, meaning there are one or more double bonds in the tail
- Both act as an energy source
Glycerides:
- Fatty acids attached to a glycerol molecule.
  - Monoglyceride: glycerol plus one fatty acid.
  - Diglyceride: glycerol plus two fatty acids.
  - Triglycerides: glycerol plus three fatty acids.
    1. Energy source
    2. Insulation
    3. Protection
Steroids:
- Four-ringed carbon structures with an assortment of functional groups.
  - Examples:
    - Cholesterol is a component of plasma (cell) membranes.
    - Sex hormones such as estrogen and testosterone.
Phospholipids and glycolipids:
- Both can be synthesized by our cells.
- Contain a diglyceride attached to either a phosphate group (phospholipid) or a sugar (glycolipid).
- Generally, both have hydrophilic heads and hydrophobic tails.
- Structural lipids—components of plasma membranes.
- When large numbers of phospholipids and glycolipids are in water, they form micelles, with the hydrophilic heads facing the water molecules, and the hydrophobic tails on the inside of each droplet.

Proteins

Are the most abundant and important organic molecules.
Contain basic elements: Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).
20 amino acids are monomers that combine to form proteins (polymers).
Seven major protein functions:
1. Support: Structural proteins
2. Movement: Contractile proteins
3. Transport: Transport (carrier) proteins
4. Buffering: Regulation of pH
5. Metabolic regulation: Enzymes
6. Coordination and control: Hormones
7. Defense: Antibodies
Linking two amino acids together:
- Requires dehydration synthesis between the amino group of one amino acid and the carboxyl group of another amino acid to form a peptide bond.
- The resulting molecule is a peptide.
- Polypeptides are tripeptides and larger peptides.
Protein function is based on shape and sequence of amino acids
Denaturation: Loss of shape and function.
- Hostile environments such as heat, acid, or salts will change a protein’s 3-D shape and destroy its ability to function.
Enzymes are catalysts:
- Proteins that lower the activation energy of a chemical reaction.
- Not changed or used up in the reaction.
- Substrates (reactants) bind to an active site on an enzyme.
- Enzymes exhibit:
  1. Specificity—catalyze only one type of reaction.
  2. Saturation limits—enzymes become saturated.
  3. Regulation—by other cellular chemicals.

Nucleic Acids

Large organic molecules found in the nucleus.
Store and process information.
Deoxyribonucleic acid (DNA):
- Determines inherited characteristics.
- Directs protein synthesis.
- Controls enzyme production.
- Controls metabolism.
Ribonucleic acid (RNA):
- Controls intermediate steps in protein synthesis.
- mRNA, tRNA, rRNA
A DNA molecule has a pair of nucleotide chains linked by hydrogen bonding between complementary base pairs.
An RNA molecule has a single nucleotide chain. Its shape is determined by the sequence of nucleotides and by the interactions among them.

High Energy Compounds

Nucleotides can be used to store energy.
- Adenosine diphosphate (ADP): Two phosphate groups; di- = 2
- Adenosine triphosphate (ATP): Three phosphate groups; tri- = 3
- Adding a phosphate group to ADP forms a HIGH ENERGY BOND …
  - $ADP + P = ATP$
- When broken, the bond releases energy that the cell can harness as energy.