Fall, 2009 Required Materials

Course Outline

Online Resources

Required Textbook: Biology:  8th edition, by Neil Campbell & Jane Reece et al.,   Benjamin Cummings, publisher.

 

 

Required Lab Manual: Custom lab manual for CCP

 

 

Required Equipment for the laboratory:

Students must purchase Safety Goggles and Gloves for the laboratory

 

A View of Life

I. Characteristics of Life

     A. Organization

           1. cell

           2. unicellular

           3. multicellular

                 a. tissue

                 b. organ

                 c. organ system

                 d. individual

                 e. population

                 f. community

                 g. ecosystem

                 h. emergent properties

     B. Metabolism = chemical reactions and energy transformations within cells

           1. homeostasis

     C. Response to stimuli = behavior

     D. Reproduction

           1. genes = DNA

           2. life cycle

     E. Evolution

           1. mutation

           2. species

           3. adaptation

           4. diversity

     F. Classification of organisms

           1. Five Kingdoms

                 a. Monera

                 b. Protists

                 c. Fungi

                 d. Plants

                 e. Animals

           2. scientific name

                 1. genus (e.g. Homo)

                 2. species (e.g. sapiens)

II. Ecosystems

     A. Environment

     B. Biosphere

     C. Population

 

Scientific Method

     I. Data

     II. Hypothesis

     III. Reasoning

           A. inductive

           B. deductive

     IV. Controlled experiment

           A. experimental variable

           B. dependent variable

           C. control group

           D. Results

     V. Theory and Principles

 

 

PART I: THE CELL AND CELLULAR CHEMISTRY

 

Basic Chemistry

I. Matter

     A. Elements ­ primarily C, H, O, N, P, S

II. Atoms

     A. Protons

           1. atomic number

     B. Neutrons

           1. atomic weight

           2. isotopes

     C. Electrons

           1. energy levels ­ shells

           2. electron configuration

                 a. octet rule

III. Compounds and Molecules

     A. Chemical bonds

           1. ionic

                 a. ions

                 b. salts

           2. covalent ­ single, double, triple

                 a. polar ­ electronegative and electropositive

                 b. non­polar

           3. hydrogen bonds (weak)

           4. hydrophobic and hydrophilic characteristics

           5. chemical reactions

                 a. reactants

                 b. products

                 c. oxidation ­ loss of electron or hydrogen atom

                 d. reduction ­ gain of electron or hydrogen atom

IV. Water

     A. Properties

           1. facilitates chemical reactions

           2. cohesive, adhesive

           3. resists change in temperature

           4. resists change in state

           5. solid water is less dense than liquid water

     B. Ionization

           1. acids

           2. bases

           3. pH scale

           4. Buffers

 

Molecules of Life

I. Diversity of organic molecules

     A. Carbon has a valence of 4

     B. Carbon can form covalent bonds to C, H, O, N, S

     C. Long or short chains of carbon atoms, branched carbon chains, cyclic carbon compounds

     D. Small organic molecules

           1. carbon backbone

           2. functional groups

           3. isomers

           4. hydrophilic

           5. hydrophobic

     E. Macromolecules

           1. monomer

           2. polymer

           3. condensation ­ synthesis (dehydration) and hydrolysis

II. Carbohydrates

     A. Monosaccharides

           1. pentoses ­ ribose and deoxyribose

           2. hexoses ­ glucose, fructose, galactose

     B. Disaccharides

           1. maltose

           2. sucrose

           3. lactose

     C. Polysaccharides

           1. starch and glycogen ­ energy storage

           2. cellulose and chitin ­ structural

III. Lipids

     A. Fatty acids ­ saturated and unsaturated

     B. Fats and oils ­ triglycerides ­ energy storage

           1. glycerol

     C. Waxes ­ structural

           1. long­chain alcohol

     D. Phospholipids ­ structural

     E. Steroids and cholesterol

IV. Proteins

     A. Amino acids

           1. structure

                 a. amino and carboxyl groups

                 b. side chain

                 c. chemical properties

     B. Peptides and polypeptides

           1. peptide bond

           2. hydrogen bond

     C. Protein structure

           1. primary

           2. secondary

                 a. alpha helix

                 b. beta sheet

           3. tertiary

                 a. ionic bonds

                 b. hydrogen bonds

                 c. covalent bond ­ disulfide bond

                 d. hydrophobic interactions

           4. quaternary

     D. Denaturation and renaturation

     E. Functions ­ enzymes, structural proteins

 

V. Nucleic Acids ­ DNA and RNA

     A. Nucleotides

           1. pentose sugars ­ deoxyribose and ribose

           2. phosphate group

           3. nitrogenous base

                 a. purines

                       1) adenine

                       2) guanine

                 b. pyrimidines

                       1) thymine

                       2) cytosine

                       3) uracil

           4. ATP

     B. Single­stranded vs. double­stranded

     C. Complementary base pairing

     D. Functions ­ storage and transmission of genetic information

 

Cell Structure and Function

I. What is a Cell

      A. Significance of the size of cells

     B. The Cell Theory

II. Differences between Prokaryotic and Eukaryotic cells

III. Eukaryotic Cells

     A. Nucleus

           1. Nuclear membrane

           2. Chromatin

           3. Nucleolus

           4. Nucleoplasm

     B. Cytoplasm

           1. Ribosomes

           2. Endoplasmic Reticulum ­ "rough" and "smooth"

           3. Golgi Apparatus

           4. Lysosomes

           5. Vacuoles

           6. Plastids

                 a. chloroplasts

                 b. amyloplasts

                 c. chromoplasts

           7. Mitochondria

                 a. cristae

                 b. matrix

                 c. endosymbiotic hypothesis

           8. Microtubules: centrioles, cilia, and flagella

           9. Cell Wall

 

Cell Membrane Structure and Function

I. Fluid ­ Mosaic Model of Plasma Membrane

II. Cell Transport

     A. Diffusion

     B. Osmosis

           1. Hypertonic, Hypotonic, Isotonic solutions

           2. Dialysis

     C. Facilitated Diffusion

     D. Active Transport

     E. Endocytosis

           1. Phagocytosis

           2. Pinocytosis

     F. Exocytosis

 

Cellular Energy

I. Nature of energy

     A. definition

     B. types

     C. 1st, 2nd Law of Thermodynamics

     D. implication for living organisms

II. Enzymes

A. nature of catalysis

B. enzyme structure (active site, denaturation)

C. inhibition

D. regulation (effect of temperature, pH)

III. ATP

A. structure

B. function ­ energy of activation

C. formation

1. substrate ­ level phosphorylation

2. chemiosmotic phosphorylation

IV. Oxidation­Reduction reactions

A. role in energy transfer

B. role of coenzymes (from vitamins) (e.g. NAD+, NADP+, FAD)

Photosynthesis

I. Chloroplast structure and function

A. grana, thylakoids

B. stroma

II. Light Dependent Reactions: chlorophyll, carotenoids, photosystems

A. cyclic photophosphorylation (ATP formed)

B. non­cyclic photophosphorylation (NADPH and ATP formed)

C. water split; oxygen given off

III. Light­independent Reactions

A. Calvin cycle: carbon dioxide fixation and reduction

Glycolysis and Cellular Respiration ­ overview of glucose metabolism

I. Glycolysis ­ glucose to pyruvic acid

A. enzymes in cytosol

B. ATP produced by substrate­level phosphorylation

C. NADH produced

II. Fermentation ­ pyruvic acid to lactic acid or ethanol

A. enzymes in cytosol

III. Transition reaction (pyruvic acid to acetyl CoA): NADH produced

A. enzymes in matrix of mitochondria

IV. Krebs cycle (Citric acid cycle)

A. enzymes in matrix of mitochondria

B. NADH and FADH2 produced

C. ATP produced by substrate­level phosphorylation

V. Electron transport chain (cytochromes) in inner mitochondrial membrane (cristae): oxidative phosphorylation

VI. Comparison of energy yield from respiration (aerobic) and fermentation (anaerobic)

 

PART II: GENETIC BASIS OF LIFE

Cell Reproduction

I. Cell division in prokaryotic organisms ­ Binary Fission

II. Cell division in eukaryotic organisms

A. Cell cycle

B. Mitosis in animal and plant cells: identical offspring

C. Cytokinesis: cleavage furrow (animals); cell plate (plants)

Meiosis

I. Meiosis I

A. formation of tetrads, crossing over

B. separation of homologues

II. Meiosis II

A. formation of haploid nuclei, non­identical offspring

Mendelian Genetics

I. Dominant, Recessive alleles of a gene

II. Homozygous, Heterozygous genotypes

III. Phenotype: Expression of dominant allele(s)

IV. Monohybrid Crosses: Mendels's Law of Segregation

V. Dihybrid Crosses: Mendel's Law of Independent Assortment (Genes on Different Chromosomes)

 

Chromosomes and Genes

I. Chromosomal genetics

A. Degrees of dominance

1. incomplete dominance

2. codominance

B. Multiple alleles

C. Polygenic inheritance

D. Chromosomal sex determination

E. X­linked inheritance

II. Chromosomal Mutations

A. changes in chromosome number

1. polyploidy

2. monosomy and trisomy

B. changes in chromosome structure

1. deletion

2. inversion

3. duplication

4. translocation

Human Genetics

I. Chromosomal abnormalities

A. Autosomes: Trisomy­21 (Down Syndrome)

B. Sex chromosomes

1. trisomy (Klinefelter's Syndrome)

2. monosomy (Turner's Syndrome)

II. Chorionic villi sampling, amniocentesis, karyotypes

III. Autosomal recessive inheritance: Cystic Fibrosis, Tay­Sachs, Phenylketonuria

IV. Degrees of dominance: Sickle­Cell Disease

V. Polygenic inheritance: skin color and height

VI. Multiple alleles: ABO blood types

VII. X­linked inheritance: color­blindness, hemophilia

VIII. Sex­influenced traits

DNA ­ the genetic material of all cells, prokaryotic & eukaryotic, and of some viruses

I. Evidence for DNA being the genes

A. bacterial transformation

B. viral infection

II. Structure:

A. 2 strands

1. phosphate group

2. 5­carbon deoxyribose sugar

B. four nitrogenous bases

1. Adenine

2. Guanine

3. Cytosine

4. Thymine

C. 2 strands held together by hydrogen bonds between adenine and thymine, and between guanine and cytosine

III. DNA replication

A. Each strand copied following base­pairing rules

B. New strands assembled by enzyme DNA polymerase

C. Replication shown to be semiconservative (each resulting DNA has one "old" strand and one "new" strand)

IV. Mutations

A. Changes in the base sequence of replicated DNA

B. Inherited changes

Gene Activity: Protein Synthesis

I. RNA

A. Single­stranded molecule made up of phosphates, 5­carbon ribose sugars, and nitrogenous bases adenine, guanine, cytosine, and uracil

B. Synthesized copying a DNA base sequence using the enzyme RNA polymerase.

C. Three types involved in protein synthesis

1. Messenger RNA (mRNA): copy of gene containing information to make one specific protein (polypeptide.)

Codons: each 3 bases stand for 1 amino acid.

Specific mRNA codons act as initiators and terminators.

Synthesis of mRNA from DNA gene called transcription.

Polypeptide synthesis called translation.

Mutations may alter specific codons or may add or delete bases in the DNA sequences, changing many codons, and ultimately the gene product (polypeptide)

2. Ribosomal RNA (rRNA): in ribosomes, which serve as sites for protein synthesis.

Nonspecific: will make any protein

3. Transfer RNA (tRNA) ­ about 32 different molecules specific for the 20 different amino acids.

Has anticodon base triplet that will base­pair with the mRNA codon triplet.

Regulation of Gene Activity

 

I. Transcriptional control: genes turned on, off

II. Post­transcriptional control in eukaryotes; speed at which mRNA's leave nucleus

III. Translational control: lifespan of mRNA's

IV. Post­translational control: polypeptide to functional protein

V. Cancer as an example of failure to control cell division

Recombinant DNA and Biotechnology

I. genes transplanted into different organisms using Virus and Plasmid vectors

II. DNA probes