Dr. Thomas Reeves




* The "core themes" of biology are presented in this unit. These include: (1) evolution, (2) hierarchy (levels) of organization, (3) relationships between structure and function, (4) scientific method (science as a way of knowing), and (5) the characteristics of life.  Taxonomy provides a means of scientifically organizing living things so that they may be analyzed and studied.


Taxonomy Purpose and History


Taxonomy - the science of classification


Aristotle - first taxonomic system


            Plants: trees, shrubs, and herbs

            Animals: air-dwellers, water-dwellers, land-dwellers


            * System flawed because scientifically valid characteristics (by modern standards) were often not used in determining the categories.


Carolus Linnaeus - father of modern taxonomy


            * Eliminated use of common names


            * Used Latin as a basis for nomenclature


* Created "binomial nomenclature" identifying each organism by their Genus and species, ex. Homo sapiens in which Homo is the genus and sapiens is the species.


* Created other taxa for classification purposes: kingdom, phylum, class, order, family, genus, species


            * Used morphological characteristics as a basis for classification


            * The Linnaean system of classification is still in use today.


* Linnaeus was devoutly religious, but his taxonomic system was later to be used to demonstrate the phylogenetic (evolutionary) relationships among living organisms.


            * Linnaeus Latinized his own name from Carl Line           

            * Five major kingdoms of life are currently recognized


Five Kingdoms of Life


1. Cell type:


            A. Prokaryotic (P) primitive, lack membrane-bound internal organelles

            B. Eukaryotic (E) - true nucleus, membrane-bound organelles


2. # Cells:  Unicellular (U), Colonial (C), Multicellular (M)


3. Nutrition:

            A. Autotrophic (A) - Source of carbon is simple, such as carbon dioxide (CO2)

B. Heterotrophic (H) - Source of carbon is complex, such as carbohydrates, proteins, lipids, or nucleic acids



    Kingdom  Organisms          Cell Type    # Cells     Nutrition  

(1) Monera    Bacteria                P                      U                      H

              Blue-green bacteria                             U, C                 A


(2) Protista  Protozoa                 E                      U                      H

              Algae                                                  U, C                 A

              Seaweeds                                           M                     A


(3) Fungi Mushrooms                 E                      M                     all H


              Yeasts                                                            U


(4) Plantae   Mosses                  E                      M                     all A



              Gymnosperms (Conifers)

              Angiosperms (Flowering plants)


(5) Animalia Sponges                 E                      M                     all H

              Cnidaria (Jellyfish)


              Arthropods (Insects, crustaceans)

              Mollusca (Clams, squid)

              Echinoderms (Sea star, sand dollar)

              Chordate (Fish, amphibians, reptiles, birds, mammals)                           


Common Threads that Connect All Life


* Life is diverse but there are common themes that all living things exhibit.


(1) Evolution is the core theme of biology.


Evolution - the process by which life on earth has changed over time.


Natural Selection - the theory proposed by Charles Darwin to explain how evolution has occurred.


1859 - On the Origin of Species by Natural Selection


* Natural selection emphasizes the variation that exists within and between species, the competition that occurs because of limited resources, and differential rates of survival and reproduction which result from this competition.


* The fossil record documents the evolution of species.


(2) Science is an active process for understanding life.


            Scientific method - processes by which scientists conduct investigations


* There is no one "scientific method". Scientists actually use a variety of techniques to learn more about the world around us. However, many experimental studies would recognize the following steps:


            A. Statement of the problem

            B. Hypothesis formation - An "educated guess"

            C. Experiment

                        1. experimental group

                        2. control group

            D. Collection of data

            E. Analysis of results

            F. Conclusion - Reject or accept the hypothesis

            G. Communication of findings


* Considerations pertaining to the scientific method:

            A. Hypothesis must be testable

            B. Sample size must be sufficiently large

            C. Experiment must have proper controls

            D. Experiment must be reproducible


(3) Life is organized at different levels.


chemical --- cellular --- tissues --- organs ---organ systems ---organisms --- population --- community --- ecosystem --- biome ---biosphere

(4) At every level of life's hierarchy, the whole is greater than the sum of its parts.

“Emergent properties” - special features or properties that result from a system's particular organization, do not exist without the organization


Emergent Properties that Define Life:


            A. organisms are highly structured (lower entropy)

            B. organisms can take in, transform, and use energy

            C. organisms respond to stimuli

            D. organisms grow and develop

            E. organisms reproduce

            F. organisms evolve


(5) Life's properties have a chemical basis.


* Living things are composed of inorganic and organic substances.          


Important inorganic substances - water, minerals, salts


Important organic substances - carbohydrates, proteins, lipids, nucleic acids


   ex. protein - keratin (hair, feathers, scales)

       DNA - genetic information

Gregor Mendel - Genetics

James Watson and Francis Crick - DNA

(6) All organisms are composed of cells.


            1838/ 1839 Schleiden and Schwann develop the cell theory


* All living things are composed of cells. They may be unicellular, colonial, or multicellular; and they may be prokaryotic or eukaryotic cells.


(7) All organisms demonstrate close connections between form (anatomy) and function (physiology).

            ex. dentition - herbivores, omnivores, carnivores

            plants - flower form related to pollination


(8) Organisms interact with their environments.


ecology - the branch of biology dealing with the relationships between organisms and their environments


photosynthesis and respiration


* Energy flows through ecosystems, while nutrients cycle.


food webs - interconnected feeding relationships within ecosystems


Biology is connected to our lives in many ways:


            Global warming

            Endangered species

            Genetic engineering

            Medical problems/ AIDS, Ebola


* Biology offers a deeper understanding of life on earth and offers solutions to problems that confront us.




* Many biological processes can only be understood by studying them at the chemical level. Biochemical processes are essential to life on earth.

            ex. photosynthesis

            cellular respiration


matter - anything that occupies space and has mass, matter is composed of various combinations of elements


element - a substance that cannot be broken down to other substances by ordinary chemical means


* 92 elements occur in nature, others have been synthesized in labs


* About 25 of these elements are essential to life


* Carbon (C), Hydrogen (H), Oxygen (O), and Nitrogen (N) make up about 96% of any living organism. The remaining 4% is made primarily of Calcium (Ca), Potassium (K), Phosphorus (P), and Sulfur (S).


Importance of Various Elements

Carbon - found in all organic molecules


Hydrogen - also found in all organic molecules, water


Oxygen - aerobic respiration, oxidation reactions, water


Nitrogen - constituent of amino acids, nucleic acids


Calcium - necessary for bone formation, muscle contraction


Potassium - electrolyte necessary for nerve impulses


Phosphorus - constituent of ATP, nucleic acids


Sulfur - found in certain amino acids


Sodium (Na) - necessary for nerve impulses


Chlorine (Cl) - constituent of gastric juice (hydrochloric acid)


Magnesium (Mg) - cofactor for certain enzymes


Trace elements (< .01%) - Boron (B), Chromium (Cr), Cobalt (Co), Copper (Cu), Fluorine (F), Iodine (I), Iron (Fe), Manganese (Mn), Molybdenum (Mo), Selenium (Se), Silicon (Si), Tin (Sn), Vanadium (V), and Zinc (Zn).


* Each element is composed of a unique type of atom. Each atom, in turn, is composed of a certain number of sub-atomic particles: protons, neutrons, and electrons


Comparison of Sub-Atomic Particles               

Particle     Charge       Size                Location in Atom       

proton      positive     1 AMU               nucleus

neutron     none         1 AMU               nucleus

electron    negative     1/1836 AMU      orbitals or shells       


Periodic Table - Provides information pertaining to the elements such as symbol, atomic number, and atomic weight


symbols - may represent the first letter of the element's name (Carbon - C), the first two letters (Calcium - Ca), or may be derived from the ancient name for the element (Sodium - Na, from the Latin natrium).


atomic number - the number of protons present in the nucleus of the atom

atomic mass (weight) - the number of protons and neutrons in the nucleus of the atom


* Elements are arranged on the Periodic Table based on increasing atomic number.

            ex. hydrogen (atomic number 1)

         helium (atomic number 2)


isotopes - variant forms of an atom that have the same number of protons and electrons, but different numbers of neutrons


* The weight of the various isotopes of a particular element are averaged to calculate an average atomic weight. This explains why the atomic weight values often include fractions.


radioisotopes  - an isotope in which the nucleus decays spontaneously giving off radiation

ex. carbon 12 (12C) which has 6 protons and 6 neutrons and carbon 14 (14C) which has 6 protons but 8 neutrons


* Radioisotopes are extremely important in medical and scientific research.


molecule - composed of two or more elements chemically combined

and held together by bonds



compound - composed of a single type of molecule



ionic bond - formed when atoms gain or lose electrons to form ions



covalent bond - formed when two or more atoms are a pair of electrons


* Electrons occur in orbitals or shells around the nucleus of the atom.


* Each shell can only hold a certain number of electrons, which is 2, 8, and 8 for the first three shells respectively.


* Atoms will react in an attempt to fill their outermost electron shells. This can be accomplished by gaining, losing, or sharing electrons.   



Ionic and Covalent Compounds


* Sodium Chloride (NaCl) is an ionic compound whereas Methane (CH4) is a simple covalent compound.



Sodium Chloride (NaCl) - Sodium (atomic number 11/ electron configuration 2, 8, 1) will lose one electron to become a positively charged ion. Chlorine (atomic number 17/ electron configuration 2, 8, 7) will gain one electron and become a negatively charged ion. These opposite forces of attraction hold the sodium and chloride ions together in the ionic compound sodium chloride.


Methane (CH4) - Carbon (atomic number 6/ electron configuration 2, 4) will tend to share four electrons to form covalent bonds. Hydrogen (atomic number 1/ electron configuration 1) will either share or transfer one electron. It may form either covalent or ionic compounds.


polar covalent compounds - formed by two or more atoms sharing electrons, but the sharing is unequal. The electrons are held closer to one of the atoms in the compound than the other which results in partially positive and negative charges existing around the molecule.


* Water is an important polar covalent molecule.


* hydrogen bond - weak force of attraction between the slightly positive charge of the hydrogen of one molecule and the slightly negatively charged region of another molecule


* Hydrogen bonding occurs between adjacent water molecules. These hydrogen bonds contribute to most of the unique properties of the water molecule:


Properties of Water


1. Water molecules are cohesive. They are attracted to other water molecules. This contributes to water's high surface tension.


2. Water molecules are adhesive. They are attracted to other charged substances.


3. Water has a high specific heat. It takes a great deal of energy to heat or cool water.


4. Water has a high heat of vaporization. Water is therefore an excellent evaporative coolant.


5. Water is more dense as a liquid than as a solid. It reaches its greatest density at 4oC.


6. Water is an excellent solvent.


Acids and Bases


acid - a substance that donates hydrogen ions in a chemical reaction


            ex. hydrochloric acid      (HCl)

         sulfuric acid          (H2SO4)



base - a substance that donates hydroxide ions in a chemical reaction


            ex. sodium hydroxide       (NaOH)

         potassium hydroxide    (KOH)


* neutral solutions - have the same concentration of hydrogen and hydroxide ions, and are therefore neither acids nor bases


* The pH scale is used to measure whether a solution is acidic or basic. The pH scale runs from 0 to 14. 7.0 represents the point of neutrality.


            < 7.0 - a solution is increasingly acidic


            > 7.0 - a solution is increasingly basic


* Each unit represents a tenfold increase or decrease in acidity.


pH of Several Common Substances


2.0     lemon juice, gastric juice

4.0     tomato juice

7.0     distilled water

8.2     sea water

10.0    milk of magnesia

12.0    household bleach



chemical reaction - a process leading to changes in matter. Chemical equations attempt to demonstrate in a shorthand form what is taking place in the chemical reaction.


reactants - are indicated on the left side of the equation


products - are indicated on the right side of the equation


* The arrow indicates what is being produced and the direction the reaction is running. Often arrows will be drawn both ways indicating the reaction is reversible.

* Chemistry plays a critical role in the understanding of biology.



buffers - reversible chemical reactions designed to maintain pH levels




The Molecules of Cells



* Organic compounds are those that contain carbon. Four major groups of organic molecules that are important to biological systems are carbohydrates, lipids, proteins, and nucleic acids.



Properties of Carbon and Organic Molecules


1.  Each carbon atom forms four covalent bonds.

2.  Carbon may bond to other carbon atoms to form long chains.


3.  The carbon skeletons of organic molecules may vary in length.


4.  The carbon atoms on the skeleton may be single or double covalent bonds.


5.  The carbon skeletons may be arranged in rings.


isomers - molecules that have the same molecular formula but different structures.



* The unique properties of organic molecules depend not only on the nature of its carbon skeleton, but also on functional groups which may be attached.


functional groups - an assemblage of atoms that forms the chemically reactive part of an organic molecule


            examples - hydroxyl (-OH)    alcohols


                carbonyl (-CO-)   aldehydes  (terminal)


                ketones    (middle of chain)


                carboxyl (-COOH)  amino acids, nucleic acids


                amino    (-NH2)   amino acids


                   phosphate (PO4)    ATP, nucleic acids

* Monomers are the basic building blocks of organic molecules.  



* Monomers are linked together in a chemical reaction known as a dehydration synthesis or a condensation reaction to form more complicated polymers, long chains of the basic monomer unit.



* The polymers may be broken down in a process known as hydrolysis.



* Organic compounds are those that contain carbon. Four major groups of organic molecules that are important to biological systems are:


            1. carbohydrates

            2. lipids

            3. proteins

            4. nucleic acids.


* Each group can be compared based on molecular structure, major categories and examples, and functions in biological systems.






* Structure - Carbohydrates are a class of organic molecules which generally have the chemical formula (CH2O). The basic monomer is the monosaccharide.



* Categories and Examples


A. monosaccharides ("simple sugars") - generally contain five or six carbon atoms


            1. glucose  (C6H12O6)

            2. fructose

            3. galactose

            4. ribose

            5. deoxyribose





B. disaccharides - formed by joining two monosaccharides together in a dehydration synthesis


            1. sucrose (glucose + fructose)   "table sugar"

            2. maltose (glucose + glucose)    "malt sugar"

            3. lactose (glucose + galactose)  "milk sugar"


C. polysaccharides - formed by joining long chains of monosaccharides


            1. starch - plants

            2. glycogen - "animal starch"

            3. cellulose - plant cell walls

            4. chitin - arthropod exoskeletons


* Functions - Monosaccharides represent the main fuel for cellular respiration, which provides energy for the cell. In addition, ribose and deoxyribose are constituent parts of RNA and DNA respectively.


* An organism will store excess monosaccharides as the polysaccharide starch.  In addition, cellulose is a major constituent of the plant cell wall.  Chitin makes up the exoskeleton (outer skeleton) of an arthropod such as an insect or a crustacean.




* Structure - Lipids include all of the fats, oils, waxes; as well as, the steroids. Lipids are nonpolar molecules that generally are insoluble in water which is polar. The major categories of lipids have quite different structures.


* Categories and Examples


A. triglyceride - ("fats"), compose of glycerol and three "fatty acids", may be "saturated" if the carbon chain has only single bonds, or "unsaturated" if the carbon chain has some double bonds


* Corn and olive oils are unsaturated, while animal fats are saturated


B. phospholipids - one of the fatty acids is replaced by a phosphate group, phospholipids are a major constituent of cell membranes


C. waxes - a fatty acid linked to an alcohol, more hydrophobic than fats which makes them effective natural coatings as on the surface of pears and apples and on the exoskeleton of insects


D. steroids - lipids formed from four fused carbon rings


            1. cholesterol - cell membranes

            2. estrogen - primary female hormone

            3. testosterone - primary male hormone

            4. anabolic steroids




* Structure - Proteins consist of long chains of amino acids. Since their are twenty different amino acids, there is almost an infinite variety of proteins that can be synthesized.


amino acids - The basic monomer of a protein. Amino acids all contain an amine (amino) and a carboxyl (acid) functional group. Each of the twenty amino acids contain a different "R" group.


Examples of amino acids include lysine, serine, and phenylalanine.


The amino acids in a protein are held together by covalent bonds known as "peptide" bonds. Proteins may be made of more than 100 amino acids and are therefore complicated molecules.


Four Levels of Protein Structure


1. Primary Level - The sequence of amino acids


2. Secondary Level - Alpha helix, coiling due to hydrogen bonding


3. Tertiary Level - 3-D shape of a protein, due to covalent bonds between non-adjacent amino acids


4. Quaternary Level- Proteins consist of two or more polypeptide chains. For instance, insulin is composed of two polypeptide chains, while hemoglobin is composed of four


* Categories and Examples:  The complicated structure of proteins allows them to assume many roles in living systems.


1. storage proteins - albumin


2. transport proteins - hemoglobin


3. signal protein - hormones (thyroxine, insulin)


4. structural proteins - keratin, hair, scales, feathers


5. contractile proteins - muscles, microtubules


6. defense proteins - antibodies


7. biological catalysts - enzymes (amylase, alcohol dehydrogenase)


Nucleic Acids


* Structure - Nucleic acids consist of long chains of nucleotides. Like proteins they have a helical shape. The two major types of nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).


nucleotide - The basic monomer of a nucleic acid, consisting of a sugar (deoxyribose or ribose), a phosphate group, and a nitrogen-containing base.


* Categories and Examples


DNA (deoxyribonucleic acid) contains encoded genetic information, while RNA (ribonucleic acid) translates that encoded information into some product, often a particular type of protein.


Comparison of DNA and RNA


1. DNA consists of a "double helix", while RNA consists of a single helix.


2. DNA contains the monosaccharide deoxyribose, while RNA contains the monosaccharide ribose.


3. DNA contains the nitrogenous bases adenine (A), guanine (G), cytosine (C), and thymine (T); while RNA replaces thymine with uracil (U).




* Cells are the smallest structural and functional unit of life.

Organisms may be unicellular or multicellular, but they are composed of cells.


History of Cell Biology


1665 - Robert Hooke (English scientist) First described and named cells while observing cork cells in lab.


1673     - Antonie van Leeuwenhoek (Dutch) Used simple microscopes to first observe unicellular organisms.


1838 - Matthias Schleiden (German) observes all plants to be composed of cells.


1839 - Theodore Schwann (German) observes all animals to be composed of cells.


* Cell Theory - All living things are composed of self-reproducing cells.


* Cells may either be prokaryotic or eukaryotic. Bacteria are composed of prokaryotic cells. Protists, fungi, plants, and animals are composed of eukaryotic cells.


Prokaryotic Cell Structure


* Prokaryotic cells are surrounded by a plasma (cell) membrane, but have no internal membrane-bound organelles or structures such as a nucleus. Many prokaryotic cells do have the following structures:


1. nuclear region - contains DNA, but no nuclear membrane


2. ribosomes - associated with protein synthesis


3. bacterial cell wall (differs from plants)


4. bacterial capsule - functions in protection


5. pili - functions in attachment and reproduction


6. flagellum - locomotion


Examples -  Streptococcus                       Escherichia coli (E. coli)

Eukaryotic Cell Structure


* Eukaryotic cells have numerous internal membrane-bound structures. All eukaryotic cells have:


1. plasma (cell) membrane

2. nucleus

3. cytoplasm


* Eukaryotic cells may also have the following structures:


1. nucleus - Control center of the cell; contains the chromosomes composed of DNA, the molecule of heredity.


            A. The nucleus is surrounded by a double membrane (nuclear membrane), containing many pores through which large molecules may pass.


            B. The nucleus may contain one or more nucleoli (nucleolus, sing.) which function in the synthesis of rRNA from which ribosomes are made.


2. rough endoplasmic reticulum - A folded membranous network to which ribosomes are attached.


            A. The rough ER functions in the synthesis and transport of proteins.


3. smooth endoplasmic reticulum - Similar to rough ER, but no ribosomes are attached.


            A. Smooth ER functions in the synthesis and transport of lipids. It also plays a critical role in the detoxification of certain drugs and other compounds.


* The nuclear membrane, rough ER, and smooth ER form a continuous membranous synthesis and transport network for the cell.



4. Golgi apparatus - Packaging plant for the cell.


            A. The Golgi apparatus can transform a variety of molecules and "package" them by surrounding them with membranes. These packaged substances may either be stored or secreted from the cell.



5. lysosomes - Contain hydrolytic (digestive) enzymes.


A. Lysosomes function in digestion within the cell, and in some cases defense and protection.


            Examples - Lysozymes secreted in tears.

                                     Macrophages (white blood cells) attacking bacteria.


6. vacuoles - Organelles that function in storage of various compounds.


Examples - Contractile vacuole of the Paramecium stores and regulates water balance in the organism.


            Central vacuoles in plants also store water.


7. mitochondrion - The "powerhouse" of the cell; center for cellular respiration, and the site of synthesis for most of the cell's ATP.


            A. The mitochondria provide energy (ATP) which cells need to perform various activities such as cell division and active transport.


8. chloroplast - Found in plant cells; serve as the site of photosynthesis.


* Mitochondria and chloroplast are thought to have originally been separate organisms; the mitochondrion a "bacteria-like" organism and the chloroplast an "alga-like" organism that developed a mutually beneficial relationship with cells.


9. cytoskeleton - The cytoskeleton is made of protein-based structures called microfilaments and larger microtubules.


            A. The cytoskeleton provides the cell with some support. Contractions of the protein fibers also keep the cytoplasm circulating. The microtubules found inside cilia and flagella contract to allow these structure to move.



10. centrioles - Structures composed of microtubules, which may help to organize the mitotic spindle for chromosome movement during mitosis.


Comparison of Plant and Animal Cells


1. Plant cells have cell walls, animal cells do not.


2. Plant cells have chloroplasts, animal cells do not.


3. Plant cells have large central vacuoles, animal cells have small or no vacuoles.


4. Animal cells contain centrioles, plant cells do not.



Junctions Found Between Animal Cells


1. tight junctions - bind cells tightly together to form a barrier, such as is found in the digestive tract


2. desmosome (anchoring junctions) - rivet adjacent cells together, substances can still flow between adjacent cells


3. gap (communicating junctions) - allow water and other molecules to flow through adjacent cells


* In plant cells, plasmodesmata function in a similar manner to gap junctions in animals, allowing water and other substances to pass from cell to cell.





Fluid-Mosaic Model of the Cell Membrane


* Cell membranes consist of a phospholipid bilayer (double layer), associated with a variety of proteins.


* The proteins may serve as signal molecules, transport molecules, receptor sites, or carrier molecules.


* Cell membranes are characterized by being "selectively permeable".


Transport Mechanisms


* Passive Transport Mechanisms:


1. diffusion

2. osmosis

3. facilitated diffusion


* Active Transport Mechanisms:

4. active transport

5. endocytosis (phagocytosis/pinocytosis)/ exocytosis



1. diffusion - the movement of molecules from an area of higher concentration to an area of lower concentration


* Diffusion works as a transport mechanism as long as the substance to be transported is small, and the concentration gradient is favorable (high to low concentration).


            examples - Gases such as O2 and CO2 diffuse easily through cell membranes.


2. osmosis - the diffusion of water through a selectively permeable membrane


* The direction water will flow toward is determined by the concentration of dissolved particles inside and outside of the cell. The following possibilities exist:


            A. hypotonic solution - has fewer dissolved particles than inside the cell, the net flow of water is into the cell, the cell increases in size as it absorbs water.


            B. hypertonic solution - has more dissolved particles than inside the cell, the net flow of water is out of the cell, the cell shrinks as it loses water.


            C. isotonic solution - has the same concentration of dissolved particles as inside the cell, there is no net change in the flow of water, the cell remains the same size.


osmoregulation - the control of water balance in living organisms


* Importance of osmosis (examples):


            1. turgor pressure in plants


            2. freshwater (hypotonic) and marine (hypertonic) environments


3. facilitated diffusion - carrier molecules (proteins) in the cell membrane assist with the transport of certain molecules


* Facilitated diffusion allows larger molecules to be transported across the cell membrane. This mechanism is still limited in that a favorable concentration gradient (high to low) must be maintained.


examples - most of the glucose that moves across our cell mebranes does so by facilitated diffusion


4. active transport - carrier molecules are utilized and the cell must use chemical energy in the form of ATP


* Active transport allows cells to move molecules from lower to higher concentrations. In doing so concentration gradients can be established.


            examples - Nerve cells concentrate high levels of sodium ions outside the nerve cell membrane by active transport (the "sodium potassium pump")



5. endocytosis (phagocytosis/ pinocytosis) exocytosis


* Endocytosis is a transport mechanism that allows certain cells to bring in extremely large substances by wrapping the cell membrane around the substance and forming a vacuole.


phagocytosis - involves the intake of substances as large as a bacterial cell, while


pinocytosis allows certain cells to form water vacuoles


exocytosis - a vacuole inside the cell fuses with the cell membrane and releases large molecules to the exterior


1. macrophages (white blood cells) kill bacteria in our bodies by engulfing them by phagocytosis. Lysosomes fuse with the vacuole and release their hydrolytic enzymes.


2. an amoeba ingests its food by phagocytosis


Membrane Disorders


cystic fibrosis




Binary Fission and Mitosis


* Living things are made of cells that are capable of reproducing. Prokaryotic cells divide by a process called binary fission; while eukaryotic cells divide by a process called mitosis.


* Unicellular organisms reproduce by cell division; while multicellular organisms grow and replace damaged cells by cell division.


* Binary fission involves replication (copying) of the bacterial chromosome followed by elongation and division of the original cell.


* Eukaryotic cell division (mitosis) also involves the replication of chromosomes followed by a series of nuclear divisions. A diploid cell divides to form two genetically identical diploid cells.


Terminology Needed for Mitosis:


1. mitosis - process by which a parent cell reproduces two identical daughter cells each identical to the parent cell.


2. diploid (2N) - a cell that has two of each type of chromosome.


3. haploid (N) - a cell that has only one of each type of chromosome.


4. chromosomes - structures composed of DNA and protein that contain the genetic information.


5. gene - a portion of a chromosome that contains a unit of heredity

6. homologous chromosomes - a similar pair of chromosomes that carry genes for the same traits, each of which was inherited from a single parent; the homologous chromosomes must be copied before mitosis can proceed. Humans have 23 pairs of homologous chromosomes.


7. sister chromatids - two identical copies of an original homologous chromosome produced after the DNA replicates.


8. cytokinesis - the division of the cytoplasm that follows mitosis, to form the two new cells.


9. centromere - an area where the sister chromatids are held together.


10. mitotic spindle - microtubule structure that directs chromosome movement during cell division.


11. centriole - an organelle that possible organizes the mitotic spindle during mitosis.



* The stages of cell division are Interphase, Prophase, Metaphase, Anaphase, and Telophase. Each stage plays a critical role in mitosis.


Interphase: Interphase is characterized by a high rate of cellular metabolic activity. Interphase may be divided into G1 (Gap 1), S (Synthesis), and G2 (Gap 2) phases. During the Gap phases of interphase the cell produces the substances (proteins, lipids, ATP) that it will need for cell division. During the S phase of interphase, the DNA of the chromosomes is copied (replicated).


Cell Appearance During Interphase


* Nuclear membrane is intact; and nucleus is quite visible.


* Centrioles are positioned on the same side of the nucleus.


* Chromosomes have replicated but are indistinct because the DNA is spread out and appears as chromatin.


* Nucleolus is visible inside the nucleus.

Prophase: During prophase the nuclear membrane disintegrates and the chromosomes shorten and thicken.


Cell Appearance During Prophase


* Nuclear membrane disintegrates.


* Chromosomes shorten and thicken and appear as pairs of sister chromatids held together by a centromere.


* Centrioles begin to migrate to opposite sides of the cell.


* The mitotic spindle fibers form and reach out toward the sister



Metaphase: Sister chromatids appear lined up along the metaphase plate (equator) of the cell.


Cell Appearance During Metaphase:


* Sister chromatids line up along the equator of the cell.


* Centrioles are positioned on opposite sides of the cell.


* Mitotic spindle fibers reach out from the centriole and join the centromere connecting the sister chromatids.



Anaphase: The centromere divides freeing the sister chromatids, which begin to move as separate chromosomes to opposite sides of the cell.


Cell Appearance During Anaphase:


* Centromere divides freeing the sister chromatids.


* Separate chromosomes begin to move toward opposite sides of the cell. Anaphase ends when the chromosomes have reached the opposite sides of the cell.


* Cytokinesis (division of the cytoplasm) may begin during late anaphase.



Telophase : cytokinesis divides the two identical sets of chromosomes to form two genetically identical cells.


Cell Appearance During Telophase:


* Cytokinesis divides the original diploid cell into two genetically identical diploid cells.


* In animal cells cytokinesis is accomplished by the formation of a cleavage furrow in which the sides of the cell pinch inward; whereas in plant cells which have a cell wall a cell plate forms to split the original cell in two.


* During late telophase, the nuclear membrane reforms in the two daughter cells, and the chromosomes once again stretch out and become indistinct.



* The rate of mitosis varies, but human cells are capable of dividing approximately every sixteen hours.



Cancer: Cancerous cells are characterized by extremely erratic mitotic divisions. Cells that are formed may not be genetically identical or even have the same number of chromosomes. Cancerous cells have also lost contact inhibition which means they do not stop dividing even when a certain cell number is reached. This is what results in a tumor forming.


* Radiation therapy - disrupts cell division of all cells, but because cancerous cells divide more often than normal may provide an effective treatment.


* Chemotherapy - various chemical have been found that will disrupt cell division.  Vinblastine is obtained from periwinkle growing in the rain forests of Madagascar; this drug interferes with the formation of spindle fibers. Taxol is obtained from the bark of the Pacific Yew in the northwestern United States; this drug immobilizes the microtubules. (The Pacific Yew is rare. Three trees are required to treat one patient, and it takes 100 years for the yew to reach maturity).


Cellular Energy



Energy - the capacity to do work


A. kinetic energy - energy of motion


B. potential energy - stored energy



1st Law of Thermodynamics (Conservation) - Energy can not be created or destroyed, but may be changed in form



2nd Law of Thermodynamics (Entropy) - Nature tends toward greater randomness or disorder (greater entropy)


* Living systems maintain the order only through the constant intake of energy



cell metabolism - the sum of all chemical reactions taking place in a cell


A. anabolic reactions - tend to store energy, form larger molecules


B. catabolic reactions - tend to release energy, break molecules


A. oxidation reactions - release energy


B. reduction reactions - store energy



phosphorylation - adds phosphate to a molecule, "energizes" the molecule


ATP (adenosine triphosphate) - a high energy molecule that the cell makes and can turn to as a source of chemical energy when needed


Enzymes - "biological catalysts" that speed up chemical reactions by lowering the activation energy required to get the reaction started


Properties of Enzymes:


1. Lower the activation energy required for the reaction


2. Are highly specific for a single type of substrate


3. Greatly speed up the rate of reaction (100,000 X or more)


4. May be used over and over again to catalyze the same reaction


* Enzymes are thought to work by the "induced-fit" method 



Factors Affecting Enzymes


1. pH 


* Most enzymes work within a very narrow pH range often near pH 7.0.


2. temperature


* Enzyme action increases with increasing temperature up to the point that the enzyme is denatured by the high temperatures



coenzymes - organic compounds necessary to make the enzyme work properly (examples - NAD, FAD)


cofactor - inorganic substances required to make enzymes work

(examples - Ca+2, Mg+2)





* Cellular respiration - is the process cells use to obtain energy from the food molecules that have been brought into the cell, this energy is then stored in the form of the molecule ATP.


* Cellular respiration occurs in three stages


1. Glycolysis

2. Kreb's Cycle

3. Electron transport chain



1. Glycolysis - glucose (a 6-carbon compound) is broken down into two molecules of pyruvic acid (a 3-carbon compound). This process occurs in the cytoplasm of the cell.



2. Kreb's Cycle - acetyl coenzyme A (produced from pyruvic acid) is further broken down, and the hydrogen is removed from the carbon skeleton. The hydrogens are picked up by the hydrogen carriers NAD and FAD and taken to the electron transport chain. Kreb's cycle occurs in the mitochondrion.



3. Electron Transport Chain - the hydrogen proton and electron are separated to form a chemical gradient. This provides the energy for the formation of ATP. Electron transport occurs in the mitochondrion.



Net Production of ATP


1. Glycolysis - 2 ATP molecules

2. Kreb's Cycle - 2 ATP molecules

3. Electron Transport Chain - 32 ATP molecules


TOTAL: 36 molecules of ATP from the respiration of 1 glucose




anaerobic respiration - fermentation





Electromagnetic Spectrum - UV, Infrared, Visible spectrum


            Visible Light - Violet - Blue - Green - Yellow - Orange - Red


* Blue and red wavelengths are selectively absorbed by the chlorophyll molecule


Photosynthesis - the process by which carbon dioxide is converted into more complex organic compounds such as glucose by plants. Photosynthesis occurs in two stages; the light reaction and the dark reaction.


6CO2 + 6H2O --- C6H12O6 + 6 O2


Plant Anatomy - (Relevant to photosynthesis)


1. xylem - vascular tissue, conveys sap from roots to rest of plant


2. phloem - vascular tissue, conveys sugar from leaves to rest of plant


3. stomata - pores surrounded by guard cells on the epidermis of a plant leaf; water, carbon dioxide, and oxygen pass through these openings


4. guard cells - control the opening and closing of the stomata


5. chloroplast - organelle that is the site of photosynthesis


6. thylakoid - a disklike sac formed by the inner membrane of the chloroplast


7. granum - a stack of hollow disks formed of thylakoid membranes in a chloroplast.


8. mesophylll - cells found in the middle of a leaf containing large numbers of chloroplasts; these cells function actively in photosynthesis


9. photosystem - the "light-harvesting" unit of the chloroplast's thylakoid membrane; consists of several hundred chlorophyll molecules clustered in the thylakoid membrane


10. Upper and lower epidermis

* Photosynthesis consists of two major reactions; the light reaction and the dark reaction or Calvin Cycle.



Photosynthesis - light reaction - water is split to produce ATP, hydrogen, and electrons by light energy; these products will be used to "reduce" carbon dioxide in the dark reaction; the red and blue wavelengths of light seem to be most important


            1. Photosystem I


            2. Photosystem II


            3. Electron transport chain




Photosynthesis - dark reaction (Calvin Cycle) - carbon dioxide is reduced to produce organic molecules such as glucose


            1. PGA


            2. ATP


            3. Carbon dioxide



Autotroph - "producers"; are able to convert simple carbon sources such as carbon dioxide into complex organic molecules such as sugar


* Oxygen released as an end-product of photosynthesis has accumulated in the atmosphere to the current level of 21%



* Meiosis is the type of cell division that produces the sex cells or gametes.  During meiosis a diploid cell undergoes two sets of divisions to produce up to four haploid cell. Fertilization, which involves the joining of male and female gametes, restores the diploid number of chromosomes.


Comparison of Meiosis and Mitosis


1. Meiosis is the process by which sex cells or gametes are formed, while mitosis is the process by which all other cells of the body divide.


2. During meiosis a diploid cell divides to form up to four haploid cells; during mitosis a diploid cell divides to form two genetically identical diploid cells.


3. Meiosis involves two series of divisions each of which has a prophase, metaphase, anaphase, and telophase; while mitosis involves one series of divisions.


4. During prophase I of meiosis the four sister chromatids formed from the original pair of homologous chromosomes remain connected to form a tetrad; whereas in mitosis each pair of sister chromatids migrates to the metaphase plate independently of one another.


* Crossing-over of genetic information occurs when the sister chromatids are in the tetrad state. This increases genetic variability in the resulting cells.


5. The goal of meiosis is to produce genetically different cells that have half the number of chromosomes as the original cell; while the goal of mitosis is to produce two cells that are genetically identical to the parent cell.




* Genetics is the science of heredity. During the mid-1800's an Austrian monk named Gregor Mendel first discovered the basic principles of genetics working with pea plants. It was not until 1901 that the importance of Mendel's work was recognized by the scientific community.


Mendel's choice of pea plants as a test subject facilitated his discovery in several ways.


1. Pea plants self-pollinate in nature. Thus, Mendel could carefully control which pea plats were to be cross-fertilized.


2. Pea plants are easy to grow, produce many offspring (peas), and have a short life span. Thus, a great deal of genetic information can be collected quickly over a number of generations.


3. The pea characteristics (phenotypes) that he chose to study in were easy to observe and distinguish (tall or short plants, green or yellow peas).


Vocabulary of Genetics


1. P generation - the parental generation; the first breeding that takes place.


2. F1 - the "first filial" generation; the offspring resulting from the parental cross. Subsequent generations may be labelled F2, F3 ...


3. True-breeding - varieties that when crossed produce offspring identical to the parents.


4. Hybrids - offspring resulting from the cross of two different varieties.


5. monohybrid cross - a genetic cross that tracks the inheritance of a single trait.


6. dihybrid cross - a genetic cross that tracks the inheritance of two different traits.


7. gene - a portion of a chromosome that codes for a particular trait. There are many genes on a single chromosome.


8. allele - alternative forms of a particular gene that can affect the expression of a trait in different ways.


9. dominant allele - dominant alleles will be expressed as a certain trait even if only one member of a homologous pair is dominant.


10. recessive allele - recessive alleles require both members of the homologous pair to be recessive before they will be expressed as a certain trait.

11. homozygous - a pair of identical alleles; may be homozygous dominant (AA) or homozygous recessive (aa).


12. heterozygous - a pair of alleles in which one is dominant and the other recessive (Aa).


13. genotype  - the type of alleles in a certain pair (AA, aa, Aa).


14. phenotype - the expressed trait; the effect that a particular pair of alleles will have.


* With Mendel's pea plants a homozygous dominant genotype (TT) and a heterozygous genotype (Tt) both produced the tall phenotype.   


Mendel's Laws of Genetics


* Law of Dominance and Recessiveness - certain alleles (dominant) can mask or hide the effect of other alleles (recessive) when they occur in pairs. Dominant alleles will be expressed when only one is present in a gene pair, while recessive alleles are expressed only when they occur in pairs.


* Law of Segregation - gene pairs separate (segregate) during gamete formation (meiosis); fertilization restores the gene pair.


* Law of Independent Assortment - each pair of alleles separates independently during gamete formation (meiosis).



Types of Genetic Problems


1. monohybrid cross - a genetic cross that tracks a single trait.


2. testcross - an individual with an unknown genotype for a particular trait is crossed with a homozygous recessive individual


3. dihybrid cross - a genetic cross that tracks two traits.


4. incomplete dominance - a situation where two different alleles occurring in a pair are both expressed to some degree. This results in offspring that have intermediate phenotypes compared to the parents. For instance, a red flower crossed with a white flower produces pink-flowered offspring.


5. codominant - a situation where two different alleles occurring in a pair are both expressed. This results in both traits appearing in the offspring. For instance, with human blood groups an AB genotype will result in the presence of both the "A" protein and the "B" protein appearing on the red blood cell membrane.


6. pleiotropy - one gene affects many traits. An example would be the mutant sickle cell gene which in the homozygous condition may cause anemia, physical weakness, spleen damage, pain, fever, rheumatism, and kidney failure.


7. polygenic inheritance - a single trait is caused by many genes.  An example would be human skin color, which is determined by three sets of genes that are inherited separately.


8. linked genes - occur on the same chromosome, and are often inherited together.


9. sex-linked traits - genes affecting these traits occur on the same chromosome that determines the sex of the organism. Therefore, these traits often appear more often in one sex than the other. Fruit fly eye color was the first sex-linked trait discovered. Examples of sex-linked traits in humans would be hemophilia and color-blindness. In humans the XX genotype results in a female whereas the XY genotype results in a male.




* Many of the basic principles of genetics apply to all living things on earth, including humans.


Vocabulary for Human Genetics

1. genome - the genetic makeup of the organism.


2. karyotype - a method of organizing the chromosomes in a cell with respect to their appearance, number, and size.


3. nondisjunction - the failure of chromosomes to separate properly during meiosis.


4. pedigree charts - can be used to track genetic information over several generations.


Recessive Disorders in Humans


1. cystic fibrosis


2. sickle cell anemia


3. albinism


4. phenylketonuria (PKU)


5. Tay-Sachs disease



Dominant Disorders in Humans


1. achondroplasia


2. Huntington's disease


3. Alzheimer's disease


4. hypercholesteremia



Sex-linked Disorders in Humans


1. hemophilia


2. color-blindness



Chromosomal Abnormalities in Humans


1. Down's Syndrome (Trisomy-21)


2. Turner syndrome (XO)


3. Metafemale (XXX)


4. Klinefelter's syndrome (XXY)


5. Super male (XYY)




Detecting Fetal Abnormalities


1. ultrasound


2. amniocentesis


3. chorionic villi sampling




* DNA (deoxyribonucleic acid) - the compound that contains genetic information; the correct "double helix" structure of DNA was successfully sequenced by James Watson and Francis Crick in 1953.


Rosalind Franklin contributed x-ray crystallography pictures of DNA.

Erwin Chargaff determined the nucleotide base pairing sequences (adenine (A) to thymine (T); and guanine (G) to cytosine (C).


Structure of DNA - DNA is a double helix composed of long chains of nucleotides; each nucleotide consists of a (1) phosphate, (2) sugar (deoxyribose), and nitrogenous base (adenine, guanine, cytosine, or thymine).  If you straighten the DNA double helix and view the molecule as a long ladder; then the phosphates and the sugars form the sides of the ladder, and the paired bases (A-T or G-C) form the rungs of the ladder. DNA can make an exact copy of itself during a process known as replication; or the genetic code may direct the building of a protein through the processes of transcription and translation.


* The DNA genetic code is a "triplet code" in that three bases code for a particular amino acid. DNA passes the genetic code to messenger RNA (mRNA) in a process known as transcription, and mRNA directs the building of a particular polypeptide (protein) in a process known as translation. DNA polymerase is an enzyme that catalyzes replication, whereas RNA polymerase is a enzyme that catalyzes transcription.


* DNA replication and transcription take place in the nucleus; translation takes place in the cytoplasm of the cell. In addition to the mRNA the cell requires ribosomes and transfer RNA (tRNA) for the translation process to take. The tRNA brings the amino acids over to where the protein is being assembled. The ribosome brings the mRNA which has the building code in close proximity to the tRNA which has the amino acid.


mutation - any change in the genetic code; this may be as simple as a simple substitution of a single nitrogenous base or as complex as an extra chromosome


1. Point mutation



* recombinant DNA technology - techniques for combining genes from different sources in a test tube. Scientists have now genetically engineered bacteria that produce human insulin, erythropoietin, human growth factor and many other useful compounds.


restriction enzymes - isolated from bacteria, these are used to "cut" the DNA of a particular chromosome with the hope of isolating a particular gene


bacterial plasmids - bacterial chromosomes which will splice on genes that have been cut from another source of DNA




Stem cell research


Origin of Life on Earth


* Important Dates in Geological Time


4.5 billion years ago         -  Earth forms

4.0 - 3.0 billion years ago   -  * Origin of Life

3.5 billion years ago         -  Oldest prokaryotic organisms

1.5 billion years ago         -  Earliest eukaryotic organisms

0.5 billion years ago         -  Earliest animals


* How did life originate ?


1862 - Louis Pasteur (France) disproves the belief in "spontaneous generation"


1920 - Alexander Oparin (Russia) theorizes about the early atmosphere on earth during the time when life arose. Oparin believed the early atmosphere consisted of water vapor (H2O), hydrogen (H2), methane (CH4), and ammonia (NH3), but no molecular oxygen (O2). This represented an atmosphere that contained not only the four essential elements in biochemistry (carbon, nitrogen, hydrogen, and oxygen), but was also a "reducing atmosphere" that would favor the formation of more complex molecules (carbohydrates, lipids, proteins, and nucleic acids) necessary to form the first cells.


1953 - Stanley Miller (United States) performed experiments to test whether the atmospheric conditions that Oparin suggested would allow the formation of the molecules necessary to form cells. Miller discovered that Oparin's reducing atmosphere was conducive to the formation of carbohydrates, proteins, nucleic acids, and lipids.


Major Events Necessary to the Origin of Life on Earth


1. Atmosphere must contain sources of carbon, hydrogen, oxygen, and nitrogen.


2. Large molecules (carbohydrates, lipids, proteins, and nucleic acids) must form from the smaller compounds in the atmosphere and primitive seas.


3. Cell membranes must form from the large molecules.


4. Genetic machinery must be installed within a cell to control replication and other cell functions.


5. Eukaryotic cells must evolve from prokaryotic cells.

Proposed Early "Cells"


1. coacervates - first cells had lipid-based membranes as proposed by Oparin.


2. microspheres - first cells had protein-based membranes as proposed by Sidney Fox.


Origin of the Cell's Genetic Machinery


* Short strands of RNA most likely served as the first genes capable of replicating themselves. Certain proteins may have served as enzymes catalyzing the replication process, and the relationship between nucleic acids and proteins began. DNA would have formed much later to contain the genetic code, and to complete what we now think of as the "normal" genetic sequence in which DNA is transcribed into RNA, and RNA is then translated into a protein.


From Prokaryotic to Eukaryotic Cells


* Prokaryotic cells preceded eukaryotic cells. The present structure of the eukaryotic cell was formed by enfolding the cell membrane. The mitochondria and the chloroplasts present in cells evolved from a bacteria-like organism (mitochondrion) and an alga-like organism (chloroplast) that invaded early cells and developed a favorable (mutualistic) association.


Geological Time






65 million - present

Current era; dominant animals include mammals, dominant plants include flowering plants; modern man


248 - 65 million years ago

Dominant animals include the dinosaurs; dominant plants include conifers


590 - 248 million years ago

Dominant animals include amphibians and fish; first vascular plants


4.6 billion - 590 million years ago

No multicellular creatures; marine creature dominant; origin of prokaryotes and eukaryotes




*Evolution - the changes that have transformed life on earth from its earliest beginnings to the diversity that exists today. Evolutionary biology provides a cohesiveness to nature and allows us to "make sense" of the world that surrounds us.


*Natural Selection - the theory proposed by Charles Darwin to explain the process of evolution.



Historical Events that Preceded Darwin


Aristotle (384-322) Believed species to be fixed and permanent; living things could be arranged on a scale of complexity Scala naturae (scale of nature). Created a taxonomic (classification) system based on this ideology.


Carolus Linnaeus (1707-1778) Swedish physician and botanist; the "father of modern taxonomy"; created a taxonomic system based on morphological (form and structure) comparisons. Developed major taxa consisting of: kingdom, phylum, class, order, family, genus, and species; created binomial nomenclature and standardized the language of taxonomy through the use of Latin. Believed in the immutability of species, "God creates, Linnaeus arranges".

Georges Cuvier (1769-1832) French anatomist who developed the science of paleontology; developed theory of catastrophism a belief that the boundaries between various fossil assemblages could be explained by catastrophic events occurring in earth's past. Cuvier still was a staunch opponent of evolution. Believed that catastrophic events were confined to local geographical regions and fauna and flora would be repopulated through immigration.


Charles Lyell (1797-1875) English geologist who wrote Principles of Geology, theory of uniformitarianism which implied that geological processes are so uniform that their rates must balance out through time; implied an old age for the earth. Befriended Darwin but never fully accepted the idea of evolution.


Jean Baptiste Lamarck (1744-1829) French, believed that organisms evolved by a tendency toward greater complexity (perfection) through the use or disuse of various body parts (theory of use and disuse), and that traits, changes, and characteristics accumulated through an individual's lifetime could be acquired and passed to offspring (theory of inheritance of acquired characteristics). While the theories of use and disuse and acquired characteristics are now discredited, Lamarck emphasized (1) that evolution was the best way to explain what can be observed in the fossil record, (2) the great age of the earth, and (3) the important role the environment plays in the evolution of organisms.


Erasmus Darwin - Charles Darwin's grandfather who speculated about evolution as a process in Zoonomia (1794). His writings may have had some influence on his grandson's theories.


Reverend Thomas Malthus (1766-1834) - In 1798 wrote Essay on the Principles of Populations, Malthus believed much of human suffering due to overpopulation based on man's inherent potential to reproduce faster than food supplies and other resources. Darwin observed that this reproductive potential seemed to be true of all species.



Alfred Russell Wallace (1823-1913) - Independently developed a theory of evolution by a process nearly identical to what Darwin referred to as "natural selection".



Reverend John Henslow - professor of botany at Cambridge; recommended Charles Darwin to the captain of H.M.S Beagle.



Captain Robert Fitzroy - captain of H.M.S. Beagle; in 1831 invited Charles Darwin to join his crew for a five year voyage around the world. His interest in Darwin was to provide biological information that would support the Genesis version of creation. Fitzroy would later bitterly regret his decision to include Darwin on the voyage.



Thomas Huxley - English anatomist and physiologist; nicknamed "Darwin's Bulldog" due to his staunch defense of Darwin's view of evolution by natural selection.



Charles Darwin (1809-1882) Developed the theory of evolution by natural selection (gradualism); in 1859 published The Origin of Species.



Gregor Mendel - Austrian monk considered the "father of Genetics" due to his research in 1865, but his research was unknown to Wallace and Darwin.


Biographical Sketch of Charles Darwin


(1) Where and when did Darwin live?


(2) Darwin grew up in what type of family background?


(3) What was his grandfather’s name who also developed ideas about evolution?


(4) What was the name of the ship on which he sailed for five years and the dates of the voyage?


(5) What group of islands observed during his voyage greatly influenced Darwin’s thinking about evolution? Where are these islands located?


(6) Name three groups of animals that were observed on these islands that would later be referenced in Darwin’s work on evolution?


(7) Who did Darwin marry and what was her family background?


(8) How many years after the Beagle voyage did it take for Darwin to publish         Origins?


(9) Name Darwin’s two great books dealing with the subject of evolution. In what year was the first book published?


(10) By what was Darwin’s theory of evolution known?


(11) Who was “Darwin’s bulldog”?


(12) Which scientist developed an idea very similar to that of Darwin, which encouraged Darwin to go ahead and publish?


(13) List five major points to Darwin’s theory of natural selection?


(14) What is meant by “fitness” in a Darwinian context? Would fitness necessarily mean the physically strongest organism?



“Industrial melanism” - English Pepper Moths - example of natural selection; darker moths were selected for survival as the industrail revolution wore on and   pollution became more pronounced



Evolution by Natural Selection (Charles Darwin)


(1) Population tend to exhibit exponential growth; there is a tremendous potential in nature for overproduction of offspring.


(2) Resources needed for survival are limited in nature, which leads to a struggle for survival.


(3) Individuals within populations vary. Some of these variations are more or less advantageous in the struggle for existence.


(4) The individuals with the best combination of characteristics will survive ("survival of the fittest").


(5) The survivors will have an opportunity to reproduce and pass the characteristics that gave them the survival edge on to their offspring.


Evidence that Evolution Has Occurred


(1) Fossil record - types of fossils include petrified remains, organisms trapped and preserved in amber, organisms trapped and preserved in tar pits, organisms trapped and preserved in ice, organism preserved in sedimentary rock, organisms preserved in acidic bogs, and casts

(2) Biogeography the distribution patterns of organisms


(3) Taxonomy - classification which implies descent


(4) Comparative anatomy


            a. homologous organs and structures

            b. vestigial structures


(5) Comparative embryology


(6) Molecular biology (biochemistry)




Population Genetics


1. microevolution


2. macroevolution


3. gene pool


Hardy-Weinberg equation - (p2 + 2pq + q2 = 1.0); used to measure changes in gene frequencies over time within a population


p2= frequency of the homozygous dominant genotype within gene pool


2pq= frequency of the heterozygous genotype within gene pool


q2= frequency of the homozygous recessive genotype within gene pool



* Hardy-Weinberg equation predicts that no change (evolution) will occur in a population if the following five conditions are met:


(1) The population is large.


(2) The population is isolated.


(3) Mutations do not alter the gene pool.


(4) Mating is random.

(5) All phenotypes (characteristics) are equally beneficial; natural selection does not occur.


* Some or all of these conditions are often not met in actual populations.


Agents of Evolutionary Change


(1) Genetic drift - a change in gene frequencies due to sampling error. In actual populations this may be due to the "founder effect" or after a disaster the "bottleneck effect".


(2) Gene flow - gain or loss of genes from a gene pool due to movement of individuals


(3) Mutations - changes in the genetic code


(4) Nonrandom mating - sexual selection


(5) Natural selection



Natural Selections Three Modes of Action


(1) stabilizing selection


(2) directional selection


(3) diversifying selection (disruptive selection)



species - a group of similar organisms who have the potential to interbreed to produce fertile offspring.



adaptive radiation - the emergence of numerous species from a common ancestor



Theory of Punctuated Equilibrium - proposed by Stephen Jay Gould and Niles Eldridge; suggests that evolution may be characterized by abrupt "starts and stops"; species may remain unchanged for long periods of time and then experience rapid evolution perhaps stimulated by catastrophic events; as opposed to Darwin's gradualistic model of evolution.


Scopes “Monkey Trial” - Tested a Tennessee statute that made the teaching of evolution illegal; Clarence Darrow defended Scopes (the teacher), while William Jennings Bryan prosecuted the case; later dramatized in the play and movie “Inherit the Wind”





Ecology and the Growth of the Environmental Science Movement


Before 1800      Exploitation of natural resources, frontier mentality.


Early 1800's      Natural theology


Mid-1850's        Literature, Henry David Thoreau - Walden, Ralph Waldo Emerson, Walt Whitman


1860-1900        Industrial Revolution; burning coal and other fossil fuels


1873                 National forest reserves in the United States


1880's               Ernst Haeckel coins term “ecology” defining this branch of the biological sciences


1905                 Theodore Roosevelt, established National Forest Service; National Park Service; and Wildlife Refuges; passed game management laws; “utilitarian conservation”


1916                 John Muir; 1st president of the Sierra Club; opposed utilitarian conservation; argued that nature deserves to exist for its own aesthetic and spiritual



1930's               Depression, massive environmental problems caused by poor agricultural practices


1940's               World War II; massive increase in industrialization with accompanying problems; development of nuclear energy and public awareness of dangers associated with this new energy source


1950's               Widespread use of new chemical pesticides (DDT) and herbicides; gradual awareness of environmental problems associated with the use of these



1962                 Silent Spring by Rachel Carson published and awakens the public to the threat of pollution and toxic chemicals; environmentalism


1960's               Hippy movement and environmentalism


1970's               Federal policies to protect the environment; EPA (Environmental Protection Agency); Clean Air and Water Act; Superfund        


1980's               Filtration of environmental awareness into school programs and daily lives; recycling centers


2000                 Earth’s human population at 6 billion with an expected doubling time of less than 25 years. 


Ecology - the branch of biology concerned with the relationships between organisms and their environment. Ecology examines the manner in which organisms affect their environment, and are in turn affected by their environment. Ecologist may study nature at various levels of organization including species, populations, communities, ecosystems, biomes, and the biosphere.


Species - a group of similar organisms that freely interbreed to produce fertile offspring


Populations - an interbreeding group of individuals of a particular species isolated from other groups


Community - all populations in a certain geographical area


Ecosystem - the living (biotic) and nonliving (abiotic) components interacting within a community. The biotic factors would include the various organisms present in the community; while the abiotic factors would include such variables as sunlight, air, water, nutrients, oxygen, wind, pH, and fire.


Biome - large biogeographical regions of the earth characterized by a certain climate and populated by characteristic assemblages of plants and animals. Some of the earth's major biomes include the tropical rain forest, temperate deciduous forest, northern coniferous forest (taiga), savanna, temperate grassland (prairie), tundra, and desert.


Biosphere - the narrow band around the earth within which life exists


Variables Within Populations


1. density - number of individuals per unit area



2. dispersion - the way individuals are spaced within their area


            a. clumped

            b. uniform

            c. random


3. growth rate


            a. biotic potential (r) - maximum inherent capacity for an organism to reproduce, the maximum growth rate, “r-selected species”


            b. carrying capacity (K) - the number of members of a population that an area can maintain with no increase or decrease, “K-selected species”


4. limitations of population growth


            a. density dependent factors - disease, starvation, predation

            b. density-independent - climate, natural disaster


5. survivorship curves - Types I, II, and III


6. age structure - human population growth


Communities and Ecosystems


Biological Community (characteristics)


1. diversity - variety of different types of organisms found within the community

2. prevalent vegetation - dominant plants


3. stability - ability to resist change and to return to its original species composition after being disturbed


4. trophic structure - the feeding relationships among the various species making up the community





1. mutualism       (+ +)


2. commensalism    (+ 0)


3. parasitism      (+ -)



Competition - interspecific and intraspecific


1. niche - an organism's functional role within an ecosystem


2. competitive exclusion principle - (Gause) only one organism can occupy a particular niche


3. predator-prey relationships


4. mimicry


            a. Batesian - mimic is harmless

            b. Mullerian - both mimic and model are harmful



Ecological succession - transition of the species composition of an ecosystem after a disturbance


1. primary succession


2. secondary succession




Trophic structures (Food chains and Food webs)

1. producers (autotrophs)


2. consumers (heterotrophs) primary, secondary, and tertiary consumers


3. pyramids of energy, biomass, numbers


Nutrient Cycles


1. water (hydrological) - evaporation and transpiration


2. carbon cycle - photosynthesis, cellular respiration, and combustion


3. nitrogen cycle - "nitrogen-fixing bacteria"


4. phosphorus cycle - no atmospheric phase


Biomes - the world's major biomes [the tropical rain forest, temperate deciduous forest, northern coniferous forest (taiga), savanna, temperate grassland (prairie), tundra, and desert] may be compared based on geographical location, climate, soil quality, annual rainfall, characteristic plants and animals; as well as, the environmental problems currently facing each biome. 


Forested Biomes:


1. tropical rain forest

2. temperate deciduous forest

3. northern coniferous forest (taiga)




4. savanna

5. temperate grassland (prairie)


Treeless Biomes:


6. tundra

7. desert


1. tropical rain forest


a. geographical location


b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems



2. temperate deciduous forest


a. geographical location


b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems


3. northern coniferous forest (taiga)


a. geographical location

b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems


4. savanna


a. geographical location


b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems


5. temperate grasslands (prairie)


a. geographical location


b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems


6. tundra


a. geographical location


b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems


7. desert


a. geographical location


b. climate (average temperature and annual rainfall)


c. soil quality


d. characteristic or unique species


e. environmental problems


Biology 101                                           Objectives

Final Exam


Unit 1   Introduction and Chemistry


(1) Give examples and describe the structure and role of the following molecules: (a) carbohydrates (monosaccharides, disaccharides, polysaccharides); lipids (triglycerides and steroids); proteins; nucleic acids (DNA and RNA).


(2) Describe the structure of the water molecule and relate the polar covalent nature of water to the following properties: cohesion, adhesion, high specific heat, excellent evaporative coolant, excellent solvent.


(3) Define taxonomy and compare the five major kingdoms (Monera, Protista, Fungi, Plant, and Animal) based on nutrition (heterotroph/ autotroph), cell type (prokaryotic/ eukaryotic), and types of organisms.


(4) Describe the improvements made by Carolus Linnaeus to the existing taxonomic system.


(5) Define atomic number and atomic weight and use these to predict the electron configuration and type of ion for a given atom


(6) Define ionic, covalent, and hydrogen bonds and give examples of several molecules formed from each


Unit 2   Cell Biology, Photosynthesis, Respiration


(1) Differentiate between a prokaryotic and a eukaryotic cell giving examples of each.


(2) Describe the structure and function of the following cell organelles and structures: nucleus, mitochondrion, chloroplast, lysosomes, rough and smooth endoplasmic reticulum, vacuoles, Golgi apparatus, nucleus, ribosomes, cytoskeleton, cell membrane.


(3) Describe the structure of the cell membrane based on the fluid-mosaic model.


(4) Describe the major steps and products of the light and light-independent (Calvin Cycle) reactions of photosynthesis.


(5) Give the reactants and products in a summarized equation fro photosynthesis.

(6) State the number of ATP molecules produced in Glycolysis, Kreb’s Cycle, and Electron Transport Chain and state where each reaction takes place in the cell.


(7) Describe the following type of cell transport: diffusion, osmosis, facilitated diffusion, active transport, phagocystosis (endocytosis).


(8) List three differences between plant and animal cells.


(9) Describe the major events taking place in each stage of mitosis: interphase, prophase, metaphase, anaphase, telophase.


(10) Define enzyme and give five characteristics of enzymes.


Unit 3  Genetics and Protein Synthesis


(1) Perform genetics problems related to monohybrid, dihybrid, sex-linked traits, and incomplete dominance.


(2) Describe the dominant, recessive, and sex-linked human genetic disorders listed in the Study Guide.


(3) Given a portion of DNA transcribe the mRNA sequence and determine the amino acid sequence from a codon chart. Define transcription, translation, replication.


(4) Describe the role of  DNA, mRNA, tRNA,  rRNA, ribosomes, amino acids in protein synthesis.


(5) Describe the structure of DNA including the structure of the nucleotide.


(6) Describe the contributions of  Gregor Mendel, James Watson and Francis Crick, Rosalind Franklin.


Unit 4 Evolution


(1) Describe five points to Charles Darwin’s theory of natural selection.


2) List and describe five sources of evidence that support the idea that evolution has occurred.


(3) Define: genetic drift, gene flow, natural and sexual selection.


(4) Describe the importance of Jean Lamarck, Charles Darwin, Alfred Wallace, Thomas Huxley, Charles Lyell, Oparin, Stanley Miller, Stephen Jay Gould

(5) Describe five ways that fossils can form.


(6) List the four geological eras in order.


(7) Describe the contribution of Oparin and Stanley Miller to ideas about the origin of life on earth.


(8) Define coacervates and microspheres.


Unit 5  Ecology


(1) Compare and contrast the following biomes: tropical rain forest, temperate deciduous forest, desert, tundra, temperate grassland, northern coniferous forest, savanna.


(2) List and describe three type of symbiosis (mutualism, commensalism, parasitism).


(3) List and describe the major steps (trophic levels) in a food chain: producer, consumer.


(4) Define the following: density, dispersion, diversity, limiting factors. biotic potential, carrying capacity.





Biology 101                                                      Study Guide                Name                                        

Rachel Carson    Silent Spring


1. Describe Rachel Carson’s early background.





2. Discuss the evidence that began to accumulate which focused Rachel Carson’s attention on the DDT issue.








3. Why was DDT initially viewed as a positive technological advancement?







4. Which group of animals were soon affected in a harmful way by DDT?








5. What harmful effects did DDT have in the environment? What were some of the major problems with this pesticide?












State Museum Field Trip


Research the following topics, write a synopsis of your answer, and prepare a brief presentation for lab next week.


(1) Describe the geological changes that have occurred in South Carolina during the past 200 million years. Be specific as to when various events occurred and what South Carolina would have been like during various periods of geological time. Describe the role that continental drift has played over the past 4.5 billion years in shaping the face of the earth. Include the terms "pangaea" and "Gondwanaland" in your answer.


(2) Describe 5 ways in which fossils can be formed and give an example of each.


(3) Describe when the last ice age occurred in South Carolina. Discuss eight animals that inhabited South Carolina during the last ice age but are now extinct. Include in your answer possible causes of their extinction.


(4) Compare and contrast the following three habitats that are found in South Carolina: mountain cove, sandhill, salt marsh/ sand dune community based on (a) the types of plants and animals found in each community, (b) the quality of soil, (c) the availability of water, (d) unique problems that each habitat presents which must be overcome if various endemic organisms are to survive,

(e) adaptations that have evolved to allow various organisms to survive in the respective habitats. Answers may be found by reading the information presented at each diorama, and through your own observations. 




BIO 101                  Field Trip


"Ecology of the Temperate Deciduous Forest"




(1)  Describe the prevailing climate and fauna and flora in the temperature deciduous forest.


(2)  Define "ecosystem" and "biome".


(3)  Describe three layers of forest structure (canopy, understory, ground cover).


(4)  Name the dominant trees in the temperate decidous forest.


(5)   Describe the major abiotic factors that influence the structure and diversity of the temperate deciduous forest.


(6)  Estimate the percent of ground cover in a representative forest and relate this to availability of light.


(7)  Estimate the percent canopy cover in a representative forest.


(8)  Compare the following groups of plants in terms of the presence or absence of vascular tissue;  seed or spore-producing

reproductive strategies, and the presence or absence of flowers:

bryophytes, tracheophytes, pteridophytes, gymnosperms, angiosperms.


(9)  Describe the role of water and light in terms of the distribution patterns observed among bryophytes and tracheophytes.


(10)  Define epiphyte and give an example found in the temperature

deciduous forest.


(11)  Describe the mutualism exemplified by a lichen.


(12)  Define the following terms related to sampling techniques in plant ecology: DHB, frequency, abundance, dominance.


(13)  Name ten  (10)  common trees and ten (10) common herbaceous species found in the temperature deciduous forest.


(14)  Different the terms trees, shrubs, and herbs; giving an example of each.


(15)  Describe the plant tissue that makes a plant "woody".

(16)  Compare "hardwoods" to "softwoods" in terms of the types of trees represented by each class, and in terms of the niche occupied by each type in the temperature deciduous forest.


(17)  Distinguish between primary and secondary succession.


(18)  Describe the stages of secondary that occur in a temperature deciduous forest by naming some common successional species.  Describe what is meant by "old field succession".    







1.         Introduction                                                                   1


2.         Chemical Basis of Life                                                   7


3.         Organic Chemistry                                                         12


4.         Cell Biology                                                                   17


5.         Cell Membranes and Cell Transport                                 21


6.         Cell Reproduction: Binary Fission and Mitosis                  24


7.         Cell Energy                                                                   28


8.         Cellular Respiration                                                        30


9.         Photosynthesis                                                              31


10.       Meiosis                                                                         33


11.       Genetics: Mendelian                                                      34


12.       Genetics: Human                                                           36


13.       DNA and Protein Synthesis                                            39


14.       Origin of Life                                                                 41


15.       Evolution                                                                       43


16.       Ecology                                                                        49


Final Exam Objectives                                                                57