Biology Notes

Unit 1 Chapter 2: Chemistry of Life

I. Matter
a. Atoms are the smallest unit of matter that cannot be divided chemically.
i. Three major components:
1. Neutrons [n0]
2. Electrons [e-]
a. electron clouds are the space that an electron may occupy at
any given time
3. Protons [p+]
ii. Relations
1. One proton is typically accompanied by one electron
2. neutrons amounts are most often but not always equal to the number
of protons and electrons
iii. Chemical Bonds
1. Covalent Bonds—two or more atoms sharing a pair of electron(s)
a. generates a molecule—atoms held together by covalent bonds
2. Hydrogen Bonds—weak chemical interaction between polar molecules
a. Polar molecules—two or more molecules having unequal
distribution of electrical charge
3. Ionic Bonds—interaction between ions of opposite charge
a. ions—atom or molecule that has gained or lost one or more
electrons
b. for ex. Na+ & CI- becomes NaCI
b. Elements are substances made of only one kind of atom, the simplest pure substance
i. Represented by one, two, or three letter symbol
ii. Elements are classified in accordance to the number of protons present
iii. Isotopes—atoms of the same amount of protons, but a differed neutron count
1. for ex. carbon has three isotopes (12, 13, and 14) but all have 6 protons
iv. Compounds are substances made of the joined atoms of two or more different
elements (the result of chemical bonds) in a certain ratio
1. common compounds include water (H 2O) and carbon dioxide (CO2)
2. compound identities differ from that of their original elements
II. Water and Solutions
a. Water is a major component of cells, and its properties make it vital for survival
i. More than 70% of your body is water
ii. Approximately 2/3 of the molecules in your body are water molecules
iii. Water aids the transition of nutrients and waste
b. Water stores heat efficiently, and helps cells maintain homeostasis
i. Water heats slowly, but retains the heat longer than many other substances
ii. Organisms release excess heat through water evaporation (humans—sweat)
c. Water bonds to itself and other substances
i. Water molecules
 1. Hydrogen bonds between molecules make some of water’s properties
possible
a. allows cohesion
i. Cohesion—attraction between identical substances
b. creates surface tension
i. Surface tension—the cohesive quality of liquid surface
2. Adhesion—attraction between different substances
a. Allows capillary action
i. capillary action—attraction of a liquid surface to a solid
d. Water dissolves many substances and allows substances to move within the body easily
i. The resulting mixture is referred to as a solution
1. Solution—mixture in which one or more substances are evenly
distributed in another
e. The polarity of water enables the dissolving of certain substances
i. Ionic compounds and polar molecules are more subject to dissolving
1. both are able to evenly distribute themselves amongst the water
ii. nonpolar molecules do not dissolve
1. water molecules have a stronger attraction between themselves, rather
than to the nonpolar molecules
2. nonpolar molecules will form clumps or beads in the water
f. Acids and Bases
i. tiny fractions of water molecules may at any given time lose their bonds
1. water molecules form a hydrogen ion, H+, and a hydroxide ion, OH-
a. H2O  H+ + OH-
2. pure water has an even amount of hydrogen and hydroxide ions
ii. compounds
1. acids—compounds that form hydrogen ions when dissolved in water
2. bases—compounds that reduce the concentration of hydrogen ions
when dissolved in water
a. many, but not all, bases form hydroxide ions
3. solvent – substance that is present in a greater amount
4.
iii. pH—measurement of the hydrogen ion concentration
1. most solutions have a pH between 0 and14
2. pure water has a pH value of 7; below 7 is acidic, and above 7 is basic
3. each whole number represents a factor of ten
a. for ex. 5 has 10x as many hydrogen ions as one with a pH of 6
4. stomach acid has a pH of 2, milk: 6.5, household ammonia: 12
III. Chemistry of Cells
a. Carbohydrates are organic compounds made of carbon, hydrogen, and oxygen atoms in
accordance to the ratio 1:2:1
i. Found in most foods as key energy source, and primarily in the following:
1. Fruits
2. vegetables
3. grains
ii. monosaccharides—building blocks of carbohydrates
1. examples include glucose, C(6)H(12)O(6), and fructose
a. glucose is a major source of energy in cells
 iii. disaccharides—double sugars, two conjoined monosaccharides
iv. polysaccharides—chains of three or more monosaccharides
1. made of hundreds of linked glucose molecules; considered a
macromolecule—large molecule made of many small molecules
2. stores energy from sugars
a. starch, plant form
b. glycogen, animal form
b. Lipids are nonpolar molecules that are not soluble in water, vital part of cell membrane
i. Examples include fats, phosolipids, steroids, chlorophyll pigment, and waxes
ii. Fats—lipids that store energy
1. Typical fat includes three fatty acids bound to a glycerol molecule
a. Glycerol—alcohol with three carbon atoms
b. Fatty acid—chain of carbon atoms bonded to either one or two
hydrogen atoms
2. Saturated fatty acid—all carbon atoms bonded to two hydrogen atoms
a. Straight molecules
b. Generally solid at room temperature
i. Includes butter, lard, grease, and other animal fats
3. Unsaturated fatty acid—all carbon atoms bonded to one hydrogen atom
a. Bent molecules through “double” covalent bonds
b. Generally liquid at room temperature
i. Excludes artificially hydrogenated plant and fish oils
c. Proteins are chains of amino acids folded into compact shapes
i. Amino acid—molecular building blocks of proteins
1. Twenty types: some polar or nonpolar, others electrically charged or not
ii. Proteins have many occupations throughout body:
1. Enzymes promote chemical reactions
2. Collagen is found in skin, bones, ligaments, and tendons
3. Fibrins aid blood clot
4. Hemoglobin carry oxygen
d. Nucleic Acid is a long chain of smaller molecules called nucleotides, macromolecule
i. Stores and transmits hereditary information
ii. Nucleotide—structural component of nucleic acids, three parts:
1. Sugar
2. Base
3. Phosphate group—phosphorus and oxygen atoms
iii. DNA—deoxyribonucleic acid, carries genetic information for producing proteins
1. Contained in chromosomes
2. two nucleotide strands held between bases by hydrogen bonds
iv. RNA—ribonucleic acid, several cell functions and manufactures proteins
1. Replaces DNA as genetic material in various viruses
2. One nucleic strand
3. Contains ribose
e. ATP—adenosine triphosphate, single nucleotide w/ two extra phosphate groups
i. Main energy currency
ii. Stores excess energy
IV. Energy and Chemical Reactions
a. Energy can be stored or released by chemical reactions
 i. Energy—the ability to move or change matter
ii. Chemical reaction—process in which chemical bonds between atoms are broken
and replaced, creating new substances
1. During reactions, energy is either released or absorbed
a. For ex. water releases heat energy when freezing, and absorbs
heat from environment when melting
iii. Reactantsproducts
iv. Metabolism—chemical reactions within the body
1. Construction of molecules using energy
2. Breakdown of molecules releasing energy
b. Starting a chemical reaction requires activation energy
i. Activation energy—energy required during the ignition of a chemical reaction
c. Enzymes speed up biochemical reactions by reducing activation energy of the reaction
i. Enzymes—substances increasing speed of chemical reactions
1. Classified as catalysts—substances reducing activation energy
ii. Biochemical reactions—chemical reactions occurring in cells
iii. Enzymes help organisms maintain homeostasis
1. Enzymes increase reaction rate 10 million times
2. Most enzyme-assisted activities are reversible
d. Enzymes bind only certain substrates
i. Substrate—substance upon which an enzyme acts during a chemical reaction
ii. For ex. amylase: starchglucose; catalase: hydrogen peroxidewater and
oxygen
iii. An enzyme’s active site shape determines its activity
1. Active site—reaction section of an enzyme
2. Thus, only the enzyme’s exact substrate can fit into the active site
e. Several factors affect enzyme activity
i. Temperature
1. Enzymes operate most efficiently within a certain range of temp.
2. Outside of temp: enzyme shape may break, enzyme shape may change
ii. pH value
1. enzymes operate most efficiently within a certain range of pH
2. outside of pH: enzyme may lose bonds, reducing effectiveness
iii. enzymes determine cell activity