Biol 123

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Summer , 2012 Required Materials

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Required Textbook:

Campbell, Et Al., Biology, custom 9th Ed.

Required Lab Manual: Biology: Cellular and Molecular – BIOL 123, 3rd Custom Edition, Community College of Philadelphia, Biology, Department by Mader, Sylvia S. Laboratory Manual to Accompany Inquiry into Life, 13th edition, McGraw-Hill.

Required Lab Equipment: Students must purchase Safety Goggles and Gloves for the laboratory

I. INTRODUCTION TO BIOLOGY (chapter 1)

A. The Science of Biology

1. Characteristics of Life

a) Hierarchy of organization - correlation of structure and function

(1) complex biological molecules

(2) cell

(3) unicellular organism

(4) multicellular organism

(a) tissue

(b) organ

(d) individual – organism

(5) population

(6) community

(7) ecosystem - cycling of nutrients and flow of energy

(8) biosphere

b) Emergent properties

c) Respond to the environment

d) Growth and development

e) Reproduction

(1) heritable information as DNA = genes

(2) life cycle

f) Regulation/feedback and homeostasis

g) Process energy; metabolism = chemical reactions and energy transformations

in cells

h) Evolutionary adaptations - three domains of life (Bacteria, Archaea, Eukarya)

(1) mutation

(2) species

(3) adaptation

(4) diversity

B. Process of Science - scientific method

1. Observation, question

2. Hypothesis

3. Data

4. Reasoning - inductive and deductive

5. Controlled experiment

a) experimental and dependent variables

b) control group

c) results

6. Theory and Principles

II. CHEMICAL CONTEXT OF LIFE (chapter 2)

A. Elements and compounds

B. Atoms and molecules

C. Chemical bonds to form molecules

1. Covalent bond - nonpolar and polar

2. Ionic – salts (may also help to maintain molecular shape)

D. Weak chemical bonds

1. Hydrogen bonds

2. Van der Waals interactions

III. WATER AND THE FITNESS OF THE ENVIRONMENT (chapter 3)

A. Molecular structure

1. Polarity of water results in hydrogen bonding

2. Versatility as a solvent - facilitates chemical reactions

3. Hydrophobic and hydrophilic characteristics of molecules - hydrophobic interaction

4. Cohesion and adhesion

5. High specific heat - helps organisms resist change in temperature

6. High heat of vaporization - suitable for evaporative cooling

7. Insulation of bodies of water by floating ice

B. Dissociation of water molecules - acids, bases, pH scale, buffers

IV. CARBON AND THE MOLECULAR DIVERSITY OF LIFE (chapter 4)

A. Diversity of organic molecules

1. Carbon has a valence of 4

2. Carbon can form covalent bonds with C, H, O N, S, P

3. Variations in carbon skeleton

a) carbon backbone - long or short chains, branched chains, cyclic compounds

b) isomers - structural, geometric and enantiomers

4. Functional groups

V. THE STRUCTURE AND FUNCTION OF MACROMOLECULES (chapter 5)

A. Macromolecules

1. Monomer

2. Polymer

3. Dehydration reaction vs. hydrolysis - catalyzed by enzymes

B. Carbohydrates - structure and function

1. Monosaccharides - aldose vs. ketose

a) pentoses - ribose and deoxyribose

b) hexoses - glucose, fructose, galactose

2. Dissaccharides and the glycosidic linkage - maltose, sucrose, lactose

3. Polysaccharides

a) starch and glycogen - storage

b) cellulose and chitin - structure

C. Lipids - structure and function

1. Fats and oils (triacylglycerol) - energy storage

a) fatty acids - saturated vs. unsaturated

b) glycerol

2. Phospholipids (amphipathic) - structure

3. Waxes

4. Steroids

D. Proteins - simple vs. conjugated; oligomeric

1. Functions - enzymes, transport, defense, etc.

2. Amino acids - amphoteric

a) structure

(1) amino and carboxyl groups

(2) side chain

(3) chemical and physical properties

3. Peptides and polypeptides – peptide bond

4. Conformation and protein structure

a) primary

b) secondary

(1) alpha helix

(2) beta pleated sheet

c) tertiary

(1) ionic bonds

(2) hydrogen bonds

(3) disulfide bridges

(4) hydrophobic interaction and van der Waals interactions

d) quaternary

5. Denaturation and renaturation

E. Nucleic acids - DNA and RNA

1. Functions - storage & transmission of hereditary information

2. Nucleotides

a) pentose sugars - deoxyribose and ribose

b) phosphate group

c) nitrogenous base

(1) purines - adenine and guanine

(2) pyrimidines - thymine, cytosine, and uracil

3. DNA structure: double helix (see pages 308 through 310)

a) Two polynucleotide stands

b) Deoxyribonucleotide will contain either of four nitrogenous bases: adenine,

guanine, cytosine, or thymine

c) Two strands held together by hydrogen bonds between adenine and thymine,

and between guanine and cytosine - complementary base pairing

4. RNA Structure: single-stranded molecule composed of ribonucleotides containing

either adenine, guanine, cytosine, or uracil

VI. CELL STRUCTURE (chapters 6)

A. What is a Cell?

1. Cell Theory

2. Significance of the size of cells

B. Prokaryotic and eukaryotic cells - importance of compartmentation

1. Prokaryotic cell - simple organization (see chapter 27 below - pages 556

through 560)

a) chromosome, nucleoid region, cell wall, capsule, pili, fimbriae,

flagella, plasmid, …

2. Eukaryotic cell

a) nucleus

(1) nuclear envelope / pore complex

(2) chromatin / chromosomes

(3) nucleolus

(4) nuclear lamina

b) cytoplasm

(1) ribosomes – bound vs. free

(2) endomembrane system

(3) endoplasmic reticulum

(a) rough - protein synthesis and membrane production

(b) smooth - synthesis of lipids, carbohydrate metabolism,

detoxification, storage

intracellular destinations

(4) Golgi apparatus

(5) polypeptide to functional protein (see pages 342 through 344)

(a) protein folding and posttranslational modification

(b) targeting polypeptides - signal peptide

(6) lysosomes - role in phagocytosis, autophagy, apoptosis (see

page 223)

(7) vacuoles, vesicles

(8) peroxisomes and glyoxysomes

(9) plastids

(a) amyloplasts

(b) chromoplasts

(10) mitochondria - cristae, matrix

c) cytoskeleton - support, mobility, maintenance of cell shape

(1) microtubules - tubulin; centrosome/microtubule organizing center, centriole, basal body, cilia, flagella

(2) microfilaments - actin; muscle contraction, cytoplasmic streaming

(3) intermediate filaments - anchors/supports nucleus

d) cell wall - prokaryotic vs. eukaryotic cell (extracellular matrix)

e) intercellular junctions

(1) tight

(2) anchoring - desmosome

(3) communicating – gap and plasmadesmata

VII. MEMBRANE STRUCTURE AND FUNCTION (chapter 7)

A. Model of plasma membrane - fluidity and asymmetry

1. Phospholipid bilayer with sterols

2. Integral and peripheral proteins

3. Carbohydrates and role in cell-cell recognition

B. Selectively permeable – permeability of lipid bilayer and transport proteins

1. Passive transport

a) diffusion

b) osmosis - hypertonic, hypotonic, and isotonic solutions

2. Transport proteins

a) facilitated diffusion – passive transport; channel and carrier proteins

b) active transport - carrier proteins

3. Membrane potential and electrochemical gradient

4. Cotransport

5. Bulk passage

a) endocytosis

(1) phagocytosis

(2) pinocytosis

(3) receptor-mediated

b) exocytosis

VIII. AN INTRODUCTION TO METABOLISM (chapter 8)

A. Metabolism - anabolic versus catabolic pathways; amphibolic pathways

B. Nature of energy

1. Definition

2. Forms

3. 1st and 2nd laws of Thermodynamics

4. Spontaneous changes - free energy, total energy, entropy

5. Exergonic and endergonic reactions, equilibrium

6. Implication for living organisms

7. ATP - structure and function

a) energy coupling and cellular work

b) formation and regeneration

C. Enzymes

1. Nature of catalysis - lowering of activation energy

2. Specificity - enzyme structure (active site) and substrate

3. Induced fit catalysis

4. Factors affecting enzyme activity

a) environment - temperature, pH

b) cofactors and coenzymes

c) inhibitors

(1) competitive

(2) noncompetitive

D. Control of Metabolism

1. Allosteric regulation

a) allosteric activators and inhibitors, coopertivity

b) feedback inhibition

IX. CELLULAR RESPIRATION: HARVESTING CHEMICAL ENERGY (chapter 9)

A. Catabolic pathways and production of ATP

1. fermentation - anaerobic

2. cellular respiration - aerobic

B. Redox reactions = oxidation-reduction reactions

1. Role in energy transfer

2. Role of coenzymes (from water-soluble vitamins); e.g. NAD+, FAD

C. Cellular Respiration

1. Glycolysis - glucose to pyruvate

a) enzymes in cytosol

b) ATP produced by substrate-level phosphorylation

c) substrate oxidized and NAD+ reduced

2. “Transition reactions”

a) conversion of pyruvate to acetyl-coA in mitochondria

b) pyruvate decarboxylated

c) substrate oxidized and NAD+ reduced

3. Krebs cycle / citric acid cycle

a) enzymes in mitochondria

b) acetyl group decarboxylated

c) substrates oxidized and NAD+ and FAD reduced

d) ATP produced by substrate-level phosphorylation

4. Electron transport chain and oxidative phosphorylation

a) role of oxygen

b) cytochromes, iron-sulfur proteins, coenzyme Q

c) chemiosmosis - proton-motive force and ATP synthase complex

D. Fermentation - anaerobic

1. Glycolysis - enzymes in cytosol

2. Reduction of pyruvate to lactate or ethanol to regenerate cytosolic NAD+

E. Comparison of energy yield from cellular respiration and fermentation

F. Control of cellular respiration

G. Overview of catabolism of fats (b-oxidation) and proteins (deamination)

X. PHOTOSYNTHESIS (chapter 10)

A. Chloroplast structure and function

B. Light reactions

1. Photosynthetic pigments - chlorophyll and carotenoids

2. Photosystems and photophosphorylation (chemiosmosis - proton-motive force and

ATP synthase complex)

3. Linear (non-cyclic) electron flow (NADPH and ATP formed)

a) water split; oxygen given off

4. Cyclic electron flow (ATP formed)

C. Calvin cycle: carbon fixation (carboxylation) and its reduction to carbohydrate (glyceraldehyde-3-phosphate), and regeneration of ribulose biphosphate

D. Metabolic fate of glyceraldehyde-3-phosphate

E. Photorespiration - comparison of C3, C4 and CAM plants

XI. CELL COMMUNICATION (Chapter 11)

A. Cell signaling and communication

1. Signal reception - receptors

a) extracellular - in plasma membrane

(1) ligand-gated ion-channel

(2) receptor tyrosine-kinase

(3) G-protein coupled

b) intracellular - cytoplasmic

2. Signal transduction pathways

a) protein phosphorylation cascades – protein kinases, protein phosphatases

b) second messengers

(1) cyclic AMP

(2) calcium ions

(3) inositol triphosphate (lP3) and diacylglycerol (DAG)

3. Cellular response - regulation and signal amplification

XII. CEI.L CYCLE (chapter 12)

A. Cell division in prokaryotic organisms - binary fission

B. Eukaryotic chromosomes – structure (see chapter 16 below - pages 320 through 322)

C. Cell division in eukaryotic organisms

1. Cell cycle and control of cell cycle (see chapter 18 below - pages 373 through 375)

2. Mitosis in animal and plant cells: formation of two genetically-identical nuclei

3. Cytokinesis - division of cytoplasm

a) cleavage furrow (animals); cell plate (plants)

XIII. MEIOSIS AND SEXUAL LIFE CYCLES (chapter 13)

A. Sexual reproduction versus asexual reproduction

B. Definition of homologous chromosomes and karyotypes

1. Sex chromosomes and autosomes

2. Gametes – haploid (n)

3. Somatic cells – diploid (2n)

C. Meiosis

1. Meiosis l

a) formation of tetrads and chiasmata/crossing over

b) separation of homologues

2. Meiosis II

a) separation of sister chromatids

b) formation of genetically non-identical haploid nuclei

D. Sources of genetic variation

1. Crossing-over

2. Independent assortment

3. Random fertilization

XIV. MENDEL AND THE GENE IDEA (chapter 14)

A. Dominant, recessive alleles of a gene

B. Genotype and phenotype

C. Monohybrid crosses: Mendel's Law of Segregation

D. Testcross

E. Extensions of Mendelian Genetics

1. Incomplete dominance and codominance

2. Multiple Alleles

F. Human Inheritance

1. Recessively-linked disorders – ex. cystic fibrosis, Sickle-Cell disease,

Tay-Sachs disease

2. Dominantly-linked disorders - ex. Huntingtons disease

G. Fetal testing - amniocentesis and chorionic villus sampling

XV. CHROMOSOMAL BASIS FOR INHERITANCE (chapter 15)

A. Chromosome theory of inheritance

B. Sex-linked inheritance

1. Chromosomal basis of sex

2. Unique patterns of inheritance

3. Sex-linked genes and disorders

4. Barr body - X inactivation in female mammals

C. Chromosome mutations

1. Alterations in chromosome number

a) polyploidy

b) aneuploidy (nondisjunction) - monosomy and trisomy

(1) ex. Down syndrome, Klinefelter syndrome, Turner syndrome

2. Alterations of chromosome structure

a) deletion ex. Cri-du-chat syndrome

b) duplication

c) inversion

d) translocation ex. chronic myelogenous leukemia

XVI. THE MOLECULAR BASIS OF INHERITANCE (chapter 16)

A. DNA: The genetic material of all cells, both prokaryotic & eukaryotic, and of some viruses

B. Evidence for DNA being the genetic material

1. Bacterial transformation

2. Viral infection

C. DNA structure (see chapter 5)

D. DNA replication

1. Each stand copied following base-pairing rules

2. New stands assembled by DNA Polymerase(s)

3. Numerous enzymes and other proteins involved - ex. DNA Ligase, Primase

4. Leading stand (continuous replication) vs. lagging strand (discontinuous replication);

Okazaki fragments

5. Replication shown to be semiconservative - each resulting DNA has one “old”

strand and one “new” stand

6. Proofreading and repair

7. Replicating ends of DNA molecules - telomeres

E. Eukaryotic chromosome structure (see chapter 12 above)

1. Histones

2. Nucleosomes à chromatin fiber à looped domains à chromosome

F. Heterochromatin and euchromatin

XVII. FROM GENE TO PROTEIN (chapters 17)

A. Definition of a gene

B. Gene expression - flow of genetic information:

DNA à RNA à Polypeptide

C. RNA (see chapter 5 above)

1. Transcription - synthesis of RNA from a DNA template - requires RNA

Polymerase(s); promoter, terminator, transcription factors, etc.

2. Three types involved in polypeptide synthesis in prokaryotes

a) messenger RNA (mRNA) - contains codons

(1) 61 codons encode for amino acids

(2) specific codons act as initiator and terminators

b) ribosomal RNA (rRNA) - structural component of ribosomes; some have

catalytic activity (ribozyme)

c) transfer RNA (tRNA) - has anticodon base triplet that will base-pair with the

RNA codon triplet

3. Several additional types in eukaryotes

a) primary transcript, small nuclear RNA (snRNA), signal recognition particle

RNA (SRP RNA), etc.

4. Processing in eukaryotes - post-transcriptional modification

a) RNA splicing: excision of introns and splicing together of exons

b) ribozymes

c) addition of 5' cap and 3' poly-A tail

D. Translation - synthesis of polypeptide

1. Initiation, elongation, and termination

E. Transcription and translation coupled in prokaryotes

F. Post-translational modification

G. Gene mutations / point mutations - chemical changes in nucleotide(s) in a gene

1. Substitution

2. Frame-shift - insertion and deletion

XVIII REGULATION OF GENE EXPRESSION (chapter 18)

A. Bacteria respond to environmental change by regulating transcription

1. Positive and negative gene regulation

B. Eukaryotic gene expression can be regulated at any stage

1. Regulation of chromatin structure

a) histone modifications

b) DNA methylation

C. Cancer results from genetic changes that affect cell cycle control - (see chapter 12 above)

1. Types of genes associated with cancer

a. proto-oncogenes and oncogenes

b. tumor-suppressor genes

2. Interference with normal cell signaling pathways

XIX VIRUSES (chapter 19)

A. Viruses

1. Structure – genome; capsid and envelope

2. Reproduction - infection: genome of virus enters host cell

a. reproductive cycle of bacteriophages

(1) lytic cycle and lysogenic cycle

b. reproductive cycle of animal viruses

(1) viral envelopes

(2) RNA as viral genetic material, retroviruses ex. human

immunodeficiency virus

XX. BIOTECHNOLOGY (chapter 20)

A. Gene manipulations and analysis

1. Gene cloning and recombinant DNA

a) restriction enzymes and DNA ligase

b) vectors - plasmid or virus

2. Gel electrophoresis

3. Southern Blotting and DNA probes

4. DNA microarray assays for gene expression levels

5. Complementary DNA (cDNA)

B. Applications of DNA technology

1. Diagnosis of diseases

2. Pharmaceutical products

3. Restriction fragment analysis

4. Restriction fragment length polymorphisms as genetic markers

5. Forensic evidence and DNA profiles – short tandem repeats

XXI. BACTERIA AND ARCHAEA (chapter 27)

A. Structural and functional adaptations (see chapter 5 above)

B. Rapid reproduction and mutation

C. Short generation span of bacteria

D. Gene transfer and genetic recombination

1. transformation

2. transduction

3. conjugation

4. plasmids - R plasmids and antibiotic resistance

Biol 123- Cellular & Molecular Biology

The CCP custom edition cover is different than shown above