* 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

Mildews

Yeasts U

(4) Plantae Mosses E M all A

Liverworts

Ferns

Gymnosperms (Conifers)

Angiosperms (Flowering plants)

(5) Animalia Sponges E M all H

Cnidaria (Jellyfish)

Worms

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.

CHEMICAL BASIS OF LIFE

* 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 4^oC.

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

ORGANIC CHEMISTRY

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.

Carbohydrates

* 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.

Lipids

* 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

Proteins

* 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).

CELL BIOLOGY

* 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.

CELL MEMBRANES AND CELL TRANSPORT

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