Carbon and theCellular Respiration of Life The Organization andEarth and The Origin of Molecular Diversity and the

Gene Idea Mendel Early Control of Eukaryotic Ge An Introduction

Table of Contents

An Introduction to Metabolism Molecular Basis of Inheritance Origins of Eukaryotic Dive Cell Communi-cation The DNA Technology & Genomics The Body’s Defe The

A Tour of the Cell Cell Cycle The From Gene to Protein The Genetic Basis of Development Plants

PhotosynthesisMeiosis

The Genetics of Descent and Bacteria Viruses with Modification: Fungi

A Darwi

Index

Organic chemistry
 Biological thought:  Vitalism (life force outside
physical & chemical laws)

Berzelius  Mechanism (all natural
phenomena are governed by physical & chemical laws) Miller

 Carbon

tetravalence tetrahedron shape determines function

Hydrocarbons
 Only carbon & hydrogen
(petroleum; lipid ‘tails’)

 Covalent bonding; nonpolar  High energy storage  Isomers (same molecular
formula, but different structure & properties)  structural~differing covalent bonding arrangement

 geometric~differing spatial
arrangement

 enantiomers~mirror images
pharmacological industry (thalidomide)

Functional Groups, I
Attachments that

replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon Each has a unique property from one organic to another

Hydroxyl Group
H bonded to O; alcohols; polar (oxygen); solubility in water

Carbonyl Group
C double bond to O; At end of HC: aldehyde Otherwise: ketone

 Carboxyl Group

Functional Groups, II
O double bonded to C to hydroxyl; carboxylic acids; covalent bond between O and H; polar; dissociation, H ion

Sulfhydral Group
sulfur bonded to H; thiols

 Amino Group
amines;

N to 2 H atoms; acts as a base (+1)

Phosphate Group
phosphate ion; covalently attached by 1 of its O to the C skeleton;

Polymers
Covalent monomers Condensation reaction

(dehydration reaction):
One monomer provides a hydroxyl group while the other provides a hydrogen to form a water molecule

Hydrolysis:

bonds between monomers are broken by adding water (digestion)

Carbohydrates, I
Monosaccharides
√ CH2O formula; √ multiple hydroxyl (-OH) groups and 1 carbonyl (C=O) group: aldehyde (aldoses) sugar ketone sugar √ cellular respiration; √ raw material for amino acids and fatty acids

Carbohydrates, II
Disaccharides
√ glycosidic linkage (covalent bond) between 2 monosaccharides; √ covalent bond by dehydration reaction

Sucrose (table

sugar)

√ most common disaccharide

Disaccharides

Carbohydrates, III
 Polysaccharides
 Polysaccharides

Storage: Starch~ glucose monomers Plants: plastids Animals: glycogen

Structural: Cellulose~ most abundant organic compound; Chitin~ exoskeletons; cell walls of fungi; surgical thread

Lipids
 No polymers; glycerol and fatty acid  Fats, phospholipids, steroids  Hydrophobic; H bonds in water exclude fats  Carboxyl group = fatty acid  Non-polar C-H bonds in fatty acid ‘tails’  Ester linkage: 3 fatty acids to 1 glycerol

(dehydration formation)  Triacyglycerol (triglyceride)  Saturated vs. unsaturated fats; single vs. double bonds

Lipids, II

Phospholipids
2 fatty acids instead of

3 (phosphate group) ‘Tails’ hydrophobic; ‘heads’ hydrophilic Micelle (phospholipid droplet in water) Bilayer (double layer); cell membranes

Steroids
Lipids with 4 fused carbon

rings Ex: cholesterol: cell membranes; precursor for other steroids (sex hormones); atherosclerosis

Proteins Importance:

instrumental in nearly everything organisms do; 50% dry weight of cells; most structurally sophisticated molecules known carboxyl (COOH) group, amino group (NH2), H atom, variable group (R)…. polar (hydrophilic), nonpolar (hydrophobic), acid or base

Monomer: amino acids (there are 20) ~ Variable group characteristics:

Three-dimensional shape (conformation) Polypeptides (dehydration reaction):

peptide bonds~ covalent bond; carboxyl group to amino group (polar)

Primary Structure
Conformation:
Linear structure

Molecular Biology:
each type of protein has a unique primary structure of amino acids

Ex: lysozyme Amino acid

substitution:
sickle-cell anemia

hemoglobin;

Secondary Structure
Conformation:

coils & folds (hydrogen bonds) Alpha Helix: coiling; keratin Pleated Sheet: parallel; silk

Tertiary Structure
Conformation:

irregular contortions from R group bonding √hydrophobic √disulfide bridges √hydrogen bonds √ionic bonds

Quaternary Structure
Conformation:

2 or more polypeptide chains aggregated into 1 macromolecule √collagen (connective tissue) √hemoglobin

Nucleic Acids, I
 Deoxyribonucleic acid (DNA)  Ribonucleic acid (RNA)  DNA->RNA->protein  Polymers of nucleotides

(polynucleotide):
nitrogenous base pentose sugar phosphate group

 Nitrogenous bases:
pyrimidines~cytosine, thymine, uracil purines~adenine, guanine

Nucleic Acids, II
Pentoses:

√ribose (RNA)
√deoxyribose (DNA) √nucleoside (base + sugar)

Polynucleotide:

√phosphodiester
linkages (covalent); phosphate + sugar

Nucleic Acids, III
Inheritance based on

DNA replication Double helix (Watson & Crick - 1953)
H bonds~ between paired bases van der Waals~ between stacked bases

A to T; C to G pairing Complementary

Index

Metabolism/Bioenergetic s
Metabolism: The totality of an organism’s

chemical processes; managing the material and energy resources of the cell Catabolic pathways: degradative process such as cellular respiration; releases energy Anabolic pathways: building process such as protein synthesis; photosynthesis; consumes energy

Thermodynamics
 Energy (E)~ capacity to do work; Kinetic energy~ energy of motion;

Potential energy~ stored energy  Thermodynamics~ study of E transformations  1st Law: conservation of energy; E transferred/transformed, not created/destroyed  2nd Law: transformations increase entropy (disorder, randomness)

Combo: quantity of E is constant, quality is not

Free energy
Free energy: portion of system’s E that can perform work (at a constant

T) Exergonic reaction: net release of free E to surroundings Endergonic reaction: absorbs free E from surroundings

Energy Coupling & ATP
E coupling: use of

exergonic process to drive an endergonic one (ATP) Adenosine triphosphate ATP tail: high negative charge ATP hydrolysis: release of free E Phosphorylation (phosphorylated intermediate)~ enzymes

Enzymes
Catalytic proteins: change

the rate of reactions w/o being consumed Free E of activation (activation E): the E required to break bonds Substrate: enzyme reactant Active site: pocket or groove on enzyme that binds to substrate Induced fit model

Effects on Enzyme Activity
Temperature pH Cofactors:
inorganic, nonprotein helpers; ex.: zinc, iron, copper helpers; ex.: vitamins

Coenzymes: organic

Enzyme Inhibitors
Irreversible (covalent);

reversible (weak bonds) Competitive: competes for active site (reversible); mimics the substrate Noncompetitive: bind to another part of enzyme (allosteric site) altering its conformation (shape); poisons, antibiotics

Index

Cytology: science/study of cells
 Light microscopy •resolving power~ measure of clarity  Electron microscopy •TEM~ electron beam to study cell

ultrastructure •SEM~ electron beam to study cell surfaces  Cell fractionation~ cell separation; organelle study  Ultracentrifuges~ cell fractionation; 130,000 rpm

Cell Types: Prokaryotic
Nucleoid: DNA

concentration No organelles with membranes Ribosomes: protein synthesis Plasma membrane (all cells); semi-permeable Cytoplasm/cytosol (all cells)

Cell size
As cell size increases, the surface area

to volume ratio decreases Rates of chemical exchange may then be inadequate for cell size Cell size, therefore, remains small

Nucleus
Genetic material...

•chromatin •chromosomes •nucleolus: rRNA; ribosome synthesis Double membrane envelope with pores Protein synthesis (mRNA)

Ribosomes
Protein manufacture Free •cytosol; •protein function in cell Bound •endoplasmic reticulum; •membranes,

organelles, and export

Endomembrane system, I
 Endoplasmic reticulum (ER)  Continuous with nuclear

envelope  Smooth ER •no ribosomes; •synthesis of lipids, •metabolism of carbohydrates; •detoxification of drugs and poisons  Rough ER •with ribosomes; •synthesis of secretory proteins (glycoproteins), membrane production

Endomembrane system, II
Golgi apparatus•ER products are modified,

stored, and then shipped Cisternae: flattened membranous sacs trans face (shipping) & cis face (receiving) Transport vesicles

Endomembrane system, III
Lysosomes

•sac of hydrolytic enzymes; digestion of macromolecules Phagocytosis Autophagy: recycle cell’s own organic material Tay-Sachs disease~ lipid-digestion disorder

Endomembrane system, IV
Vacuoles

•membrane-bound sacs (larger than vesicles) Food (phagocytosis) Contractile (pump excess water) Central (storage in plants) •tonoplast membrane

Other membranous organelles, I
Mitochondria
• quantity in cell correlated with metabolic activity; •cellular respiration; •double membranous (phospholipid); •cristae/matrix; •intermembrane space; •contain own DNA

Other membranous organelles, II
Chloroplast
•type of plastid; •double membranous; •thylakoids (flattened disks); •grana (stacked thylakoids); •stroma; •own DNA

Peroxisomes
Single membrane Produce hydrogen

peroxide in cells Metabolism of fatty acids; detoxification of alcohol (liver) Hydrogen peroxide then converted to water

The Cytoskeleton
 Fibrous network in cytoplasm  Support, cell motility, biochemical

regulation  Microtubules: •thickest; •tubulin protein; •shape, support, transport, chromosome separation  Microfilaments : •thinnest; •actin protein filaments; •motility, cell division, shape  Intermediate filaments: middle diameter; •keratin; •shape, nucleus anchorage

Centrosomes/centrioles
Centrosome: region near nucleus Centrioles: 9 sets of triplet microtubules in a

ring; used in cell replication; only in animal cells

Cilia/flagella
Locomotive appendages Ultrastructure: “9+2”

•9 doublets of microtubules in a ring •2 single microtubules in center •connected by radial spokes •anchored by basal body •dynein protein

Cell surfaces & junctions
 Cell wall:

•not in animal cells •protection, shape, regulation  Plant cell: •primary cell wall produced first •middle lamella of pectin (polysaccharide); holds cells together •some plants, a secondary cell wall; strong durable matrix; wood (between plasma membrane and primary wall)

Extracellular matrix (ECM)
 Glycoproteins:

proteins covalently bonded to carbohydrate  Collagen (50% of protein in human body) •embedded in proteoglycan (another glycoprotein-95% carbohydrate)  Fibronectins •bind to receptor proteins in plasma membrane called integrins (cell communication?)

Intracellular junctions
 PLANTS:  Plasmodesmata:

cell wall perforations; water and solute passage in plants  ANIMALS:  Tight junctions~ fusion of neighboring cells; prevents leakage between cells  Desmosomes~ riveted, anchoring junction; strong sheets of cells  Gap junctions~ cytoplasmic channels; allows passage of materials or current between cells

Membrane traffic
Diffusion~ tendency of any

molecule to spread out into available space Concentration gradient Passive transport~ diffusion of a substance across a biological membrane Osmosis~ the diffusion of water across a selectively permeable membrane

Water balance
Osmoregulation~
control of water balance concentration of solutes

Hypertonic~ higher Hypotonic~ lower

concentration of solutes Isotonic~ equal concentrations of solutes

Cells with Walls: Turgid (very firm) Flaccid (limp) Plasmolysis~ plasma
membrane pulls away from cell wall

Specialized Transport
 Transport proteins  Facilitated diffusion~

passage of molecules and ions with transport proteins across a membrane down the concentration gradient  Active transport~ movement of a substance against its concentration gradient with the help of cellular energy

Types of Active Transport
Sodium-potassium pump Exocytosis~ secretion of
macromolecules by the fusion of vesicles with the plasma membrane macromolecules by forming new vesicles with the plasma membrane

Endocytosis~ import of

•phagocytosis •pinocytosis •receptor-mediated endocytosis (ligands)

Index

Photosynthesis in nature
 Autotrophs:

biotic producers; photoautotrophs; chemoautotrophs; obtains organic food without eating other organisms  Heterotrophs: biotic consumers; obtains organic food by eating other organisms or their by-products (includes decomposers)

The chloroplast
Sites of photosynthesis Pigment: chlorophyll Plant cell: mesophyll Gas exchange: stomata Double membrane Thylakoids, grana, stroma

Photosynthesis: an overview
 Redox process  H2O is split, e- (along w/ H+)

are transferred to CO2, reducing it to sugar  2 major steps: • light reactions (“photo”) √ NADP+ (electron acceptor) to NADPH √Photophosphorylation: ADP ---> ATP • Calvin cycle (“synthesis”) √ Carbon fixation: carbon into organics

Photosystems
 Light harvesting units of the

thylakoid membrane  Composed mainly of protein and pigment antenna complexes  Antenna pigment molecules are struck by photons  Energy is passed to reaction centers (redox location)  Excited e- from chlorophyll is trapped by a primary eacceptor

Noncyclic electron flow
 Photosystem II (P680):

photons excite chlorophyll e- to an acceptor √ e- are replaced by splitting of H2O (release of O2) √ e-’s travel to Photosystem I down an electron transport chain (Pq~cytochromes~Pc) √ as e- fall, ADP ---> ATP (noncyclic photophosphorylation)  Photosystem I (P700): √ ‘fallen’ e- replace excited e- to primary e- acceptor √ 2nd ETC ( Fd~NADP+ reductase) transfers e- to NADP+ ---> NADPH (...to Calvin cycle…)  These photosystems produce equal amounts of ATP and NADPH

The Calvin cycle
 3 molecules of CO2 are

‘fixed’ into glyceraldehyde 3-phosphate (G3P)  Phases: 1- Carbon fixation~ each CO2 is attached to RuBP (rubisco enzyme) 2- Reduction~ electrons from NADPH reduces to G3P; ATP used up 3Regeneration~ G3P rearranged to RuBP; ATP used; cycle continues

Calvin Cycle, net synthesis
For each G3P (and for 3 CO2)…….

Consumption of 9 ATP’s & 6 NADPH (light reactions regenerate these molecules) G3P can then be used by the plant to make glucose and other organic compounds

Cyclic electron flow
Alternative cycle when ATP

is deficient Photosystem I used but not II; produces ATP but no NADPH Why? The Calvin cycle consumes more ATP than NADPH……. Cyclic photophosphorylation

Alternative carbon fixation methods, I
 Photorespiration: hot/dry

days; stomata close; CO2 decrease, O2 increase in leaves; O2 added to rubisco; no ATP or food generated  Two Solutions…..  1- C4 plants: 2 photosynthetic cells, bundlesheath & mesophyll; PEP carboxylase (instead of rubisco) fixes CO2 in mesophyll; new 4C molecule releases CO2 (grasses)

Alternative carbon fixation methods, II
2- CAM plants: open

stomata during night, close during day (crassulacean acid metabolism); cacti, pineapples, etc.

67of photosynthesis

Index

Principles of Energy Harvest
Catabolic pathway

√ Fermentation √Cellular Respiration
C6H12O6 + 6O2 ---> 6CO2 + 6H2O + E (ATP + heat)

Redox reactions
Oxidation-reduction OIL RIG (adding e- reduces +
charge)

Oxidation is e- loss;

reduction is e- gain Reducing agent: edonor Oxidizing agent: eacceptor

Oxidizing agent in respiration
NAD+ (nicotinamide

adenine dinucleotide) Removes electrons from food (series of reactions) NAD + is reduced to NADH Enzyme action: dehydrogenase Oxygen is the eventual e- acceptor

Electron transport chains
 Electron carrier molecules

(membrane proteins)  Shuttles electrons that release energy used to make ATP  Sequence of reactions that prevents energy release in 1 explosive step  Electron route: food---> NADH ---> electron transport chain ---> oxygen

Cellular respiration
Glycolysis: cytosol;

degrades glucose into pyruvate Kreb’s Cycle: mitochondrial matrix; pyruvate into carbon dioxide Electron Transport Chain: inner membrane of mitochondrion; electrons passed to oxygen

Glycolysis
 1 Glucose --->

2 pyruvate

molecules  Energy investment phase: cell uses ATP to phosphorylate fuel  Energy payoff phase: ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by food oxidation  Net energy yield per glucose molecule: 2 ATP plus 2 NADH; no CO2 is released; occurs aerobically or anaerobically

Kreb’s Cycle
 If molecular oxygen is present…….  Each pyruvate is converted into

acetyl CoA (begin w/ 2): CO2 is released; NAD+ ---> NADH; coenzyme A (from B vitamin), makes molecule very reactive  From this point, each turn 2 C atoms enter (pyruvate) and 2 exit (carbon dioxide)  Oxaloacetate is regenerated (the “cycle”)  For each pyruvate that enters: 3 NAD+ reduced to NADH; 1 FAD+ reduced to FADH2 (riboflavin, B vitamin); 1 ATP molecule

Electron transport chain
 Cytochromes carry electron

carrier molecules (NADH & FADH2) down to oxygen  Chemiosmosis: energy coupling mechanism  ATP synthase: produces ATP by using the H+ gradient (proton-motive force) pumped into the inner membrane space from the electron transport chain; this enzyme harnesses the flow of H+ back into the matrix to phosphorylate ADP to ATP (oxidative phosphorylation)

Review: Cellular Respiration
 Glycolysis:

2 ATP (substrate-level phosphorylation)

 Kreb’s Cycle:

2 ATP (substrate-level phosphorylation)  Electron transport & oxidative phosphorylation: 2 NADH (glycolysis) = 6ATP 2 NADH (acetyl CoA) = 6ATP 6 NADH (Kreb’s) = 18 ATP 2 FADH2 (Kreb’s) = 4 ATP  38 TOTAL ATP/glucose

Related metabolic processes
Fermentation:

alcohol~ pyruvate to ethanol lactic acid~ pyruvate to lactate Facultative anaerobes (yeast/bacteria) lipid Beta-oxidation catabolism

Index

Signal-transduction pathway
 Def: Signal on a cell’s surface is converted into a

specific cellular response  Local signaling (short distance): √ Paracrine (growth factors) √ Synaptic (neurotransmitters)  Long distance: hormones

Stages of cell signaling
 Sutherland (‘71)  Glycogen depolymerization by epinephrine  3 steps: •Reception: target cell detection

•Transduction: single-step or series of changes •Response: triggering of a specific cellular response

Protein phosphorylation
Protein activity regulation Adding phosphate from ATP to

a protein (activates proteins) Enzyme: protein kinases (1% of all our genes) Example: cell reproduction protein Reversal enzyme: phosphatases

Second messengers
 Non-protein signaling

pathway (  Example: cyclic AMP (cAMP)  Ex: Glycogen breakdown with epinephrine  Enzyme: adenylyl cyclase  G-protein-linked receptor in membrane (guanosine dior tri- phosphate)

Cellular responses to signals
Cytoplasmic

activity regulation Cell metabolism regulation Nuclear transcription regulation

Index

Cell Division: Key Roles
Genome: cell’s genetic information Somatic (body cells) cells Gametes (reproductive cells): sperm and egg cells  Chromosomes: DNA molecules  Diploid (2n): 2 sets of chromosomes  Haploid (1n): 1 set of chromosomes  Chromatin: DNA-protein complex  Chromatids: replicated strands of a chromosome  Centromere: narrowing “waist” of sister chromatids  Mitosis: nuclear division  Cytokinesis: cytoplasm division  Meiosis: gamete cell division
  

The Cell Cycle
Interphase
• G1 phase~ growth synthesis of DNA • G2 phase~ preparation for
(90% of cycle)

• S phase~ cell division

Mitotic phase • Mitosis~ nuclear division • Cytokinesis~ cytoplasm
division

Mitosis
Prophase Prometaphase Metaphase Anaphase Telophase

Prophase
Chromosomes visible Nucleoli disappear Sister chromatids Mitotic spindle forms Centrosomes move
QuickTime™ and a Cinepak decompressor are needed to see this picture.

Prometaphase
Nuclear membrane fragments Spindle interaction with chromosomes Kinetochore develops

Anaphase
Paired centromeres separate; sister chromatids liberated Chromosomes move to opposite poles Each pole now has a complete set of chromosomes

Telophase
Daughter nuclei form Nuclear envelopes arise Chromatin becomes less coiled Two new nuclei complete mitosis

Cytokinesis
Cytoplasmic division
Animals:

cleavage furrow Plants: cell plate

Cell Cycle regulation
Growth factors Density-dependent inhibition Anchorage dependence

Cancer
Transformation Tumor: benign or malignant Metastasis

Index

Heredity
 Heredity: the transmission of traits from   

one generation to the next Asexual reproduction: clones Sexual reproduction: variation Human life cycle: • 23 pairs of homologous chromosomes (46); • 1 pair of sex and 22 pairs of autosomes; • karyotype; • gametes are haploid (1N)/ all other cells are diploid (2N); •fertilization (syngamy) results in a zygote Meiosis: cell division to produce haploid gametes

Alternative life cycles
Fungi/some algae
•meiosis produces 1N cells that divide by mitosis to produce 1N adults (gametes by mitosis)

Plants/some algae
•Alternation of generations: 2N sporophyte, by meiosis, produces 1N spores; spore divides by mitosis to generate a 1N gametophyte; gametes then made by mitosis which then fertilize into 2N sporophyte

Meiosis
Preceded by

chromosome replication, but is followed by 2 cell divisions (Meiosis I & Meiosis II) 4 daughter cells; 1/2 chromosome number (1N); variation

Meiosis vs. mitosis
 Synapsis/tetrad/chiasmata

(prophase I)  Homologous vs. individual chromosomes (metaphase I)  Sister chromatids do not separate (anaphase I)  Meiosis I separates homologous pairs of chromosomes, not sister chromatids of individual chromosomes.

Origins of Genetic Variation, I
Independent assortment:

homologous pair of chromosomes position and orient randomly (metaphase I) and nonidentical sister chromatids during meiosis II Combinations possible: 2 ; with n the haploid number of the organism
n

Origins of Genetic Variation, II
 Crossing over (prophase I):

• the reciprocal exchange of genetic material between nonsister chromatids during synapsis of meiosis I (recombinant chromosomes)  Random fertilization: • 1 sperm (1 of 8 million possible chromosome combinations) x 1 ovum (1 of 8 million different possibilities) = 64 trillion diploid combinations!

Index

Mendelian genetics
 Character

(heritable feature, i.e.,

fur color)  Trait (variant for a character, i.e., brown)  True-bred (all offspring of same variety)  Hybridization (crossing of 2 different true-breds)  P generation (parents)  F1 generation (first filial generation)

Leading to the Law of Segregation
 Alternative versions of genes 

(alleles) account for variations in inherited characteristics For each character, an organism inherits 2 alleles, one from each parent If the two alleles differ, then one, the dominant allele, is fully expressed in the organism’s appearance; the other, the recessive allele, has no noticeable effect on the organism’s appearance The alleles for each character segregate (separate) during gamete production (meiosis). Mendel’s Law of Segregation

Genetic vocabulary…….
 Punnett square: predicts the

results of a genetic cross between individuals of known genotype  Homozygous: pair of identical alleles for a character  Heterozygous: two different alleles for a gene  Phenotype: an organism’s traits  Genotype: an organism’s genetic makeup  Testcross: breeding of a recessive homozygote X dominate phenotype (but unknown genotype)

The Law of Independent Assortment
Law of Segregation involves 1

character. What about 2 (or more) characters? Monohybrid cross vs. dihybrid cross The two pairs of alleles segregate independently of each other. Mendel’s Law of Independent Assortment

Non-single gene genetics, I
 Incomplete dominance:

appearance between the phenotypes of the 2 parents. Ex: snapdragons  Codominance: two alleles affect the phenotype in separate, distinguishable ways. Ex: Tay-Sachs disease  Multiple alleles: more than 2 possible alleles for a gene. Ex: human blood types

Index

The Chromosomal Theory of Inheritance
Genes have

specific loci on chromosomes and chromosomes undergo segregation and independent assortment

Chromosomal Linkage
 Morgan  Drosophilia melanogaster  XX (female) vs. XY (male)  Sex-linkage: genes located on

a sex chromosome  Linked genes: genes located on the same chromosome that tend to be inherited together

Genetic recombination
 Crossing over

Genes that DO NOT assort independently of each other  Genetic maps The further apart 2 genes are, the higher the probability that a crossover will occur between them and therefore the higher the recombination frequency  Linkage maps Genetic map based on recombination frequencies

Human sex-linkage
   

SRY gene: gene on Y chromosome that triggers the development of testes Fathers= pass X-linked alleles to all daughters only (but not to sons) Mothers= pass X-linked alleles to both sons & daughters Sex-Linked Disorders: Color-blindness; Duchenne muscular dystropy (MD); hemophilia (e.g., tortoiseshell gene gene in cats)

  X-inactivation: 2nd X chromosome in females condenses into a Barr body

Chromosomal errors, I
 Nondisjunction:

members of a pair of homologous chromosomes do not separate properly during meiosis I or sister chromatids fail to separate during meiosis II  Aneuploidy: chromosome number is abnormal • Monosomy~ missing chromosome • Trisomy ~ extra chromosome (Down syndrome) • Polyploidy~ extra sets of chromosomes

Chromosomal errors, II
 Alterations of chromosomal structure:  Deletion: removal of a chromosomal segment  Duplication: repeats a chromosomal segment  Inversion: segment reversal in a chromosome  Translocation: movement of a chromosomal segment to another

Genomic imprinting
Def: a parental effect on

gene expression Identical alleles may have different effects on offspring, depending on whether they arrive in the zygote via the ovum or via the sperm. Fragile X syndrome: higher prevalence of disorder and retardation in males

Index

Searching for Genetic Material, I
 Mendel: modes of heredity in pea plants  Morgan: genes located on chromosomes  Griffith: bacterial work; transformation: change in

genotype and phenotype due to assimilation of external substance (DNA) by a cell  Avery: transformation agent was DNA

Searching for Genetic Material, II
Hershey and Chase
√ bacteriophages (phages) √ DNA, not protein, is the hereditary material √ Expt: sulfur(S) is in protein, phosphorus (P) is in DNA; only P was found in host cell

DNA Structure
 Chargaff

ratio of nucleotide bases (A=T; C=G) (Wilkins,  Watson & Crick Franklin) √  The Double Helix nucleotides: nitrogenous base (thymine, adenine, cytosine, guanine); sugar deoxyribose; phosphate group  *Franklin died without knowing her contribution to DNA

DNA Bonding
Purines: ‘A’ & ‘G’ Pyrimidines: ‘C’ & ‘T’

(Chargaff rules) ‘A’ H+ bonds (2) with ‘T’ and ‘C’ H+ bonds (3) with ‘G’ Van der Waals attractions between the stacked pairs

DNA Replication
 Watson & Crick

strands are complementary; nucleotides line up on template according to base pair rules (Watson)

 Meselson & Stahl

replication is semiconservative; densities of radioactive nitrogen

Expt: varying

DNA Replication: a closer look
 Origin of replication (“bubbles”): beginning of replication  Replication fork: ‘Y’-shaped region where new strands of

DNA are elongating  Helicase:catalyzes the untwisting of the DNA at the replication fork  DNA polymerase:catalyzes the elongation of new DNA

DNA Replication, II
Antiparallel nature:

sugar/phosphate backbone runs in opposite directions (Crick); • one strand runs 5’ to 3’, while the other runs 3’ to 5’; • DNA polymerase only adds nucleotides at the free 3’ end, forming new DNA strands in the 5’ to 3’ direction only

DNA Replication, III
 Leading strand:

synthesis toward the replication fork (only in a 5’ to 3’ direction from the 3’ to 5’ master strand)  Lagging strand: synthesis away from the replication fork (Okazaki fragments); joined by DNA ligase (must wait for 3’ end to open; again in a 5’ to 3’ direction)  Initiation: Primer (short RNA sequence~w/primase enzyme), begins the replication process

DNA Repair
Mismatch repair:

DNA polymerase Excision repair: Nuclease Telomere ends: telomerase

Index

Protein Synthesis: overview
 One gene-one enzyme

hypothesis (Beadle and Tatum)  One gene-one polypeptide (protein) hypothesis  Transcription: synthesis of RNA under the direction of DNA (mRNA)  Translation: actual synthesis of a polypeptide under the direction of mRNA

The Triplet Code
The genetic

instructions for a polypeptide chain are ‘written’ in the DNA as a series of 3-nucleotide ‘words’ Codons ‘U’ (uracil) replaces ‘T’ in RNA

Transcription, I
 RNA polymerase:

pries DNA apart and hooks RNA nucleotides together from the DNA code  Promoter region on DNA: where RNA polymerase attaches and where initiation of RNA begins  Terminator region: sequence that signals the end of transcription  Transcription unit: stretch of DNA transcribed into an RNA molecule

Transcription, II
 Initiation~ transcription

factors mediate the binding of RNA polymerase to an initiation sequence (TATA box)  Elongation~ RNA polymerase continues unwinding DNA and adding nucleotides to the 3’ end  Termination~ RNA polymerase reaches terminator sequence

mRNA modification

 1) 5’ cap: modified guanine; protection; recognition site for

ribosomes  2) 3’ tail: poly(A) tail (adenine); protection; recognition; transport  3) RNA splicing: exons (expressed sequences) kept,introns (intervening sequences) spliced out; spliceosome

Translation, I
mRNA from nucleus is

‘read’ along its codons by tRNA’s anticodons at the ribosome tRNA anticodon (nucleotide triplet); amino acid

Translation, II
rRNA
site of mRNA codon & tRNA anticodon coupling holds the tRNA carrying the growing polypeptide chain

P site

A site

holds the tRNA carrying the next amino acid to be added to the chain E site discharged tRNA’s

Translation, III
Initiation~
union of mRNA, tRNA, small ribosomal subunit; followed by large subunit •codon recognition •peptide bond formation •translocation ‘stop’ codon reaches ‘A’ site translation of mRNA by many ribosomes (many copies of a polypeptide very quickly)

Elongation~

Termination~

Polyribosomes:

Mutations: genetic material changes in a
cell
 Point mutations….  Changes in 1 or a few base pairs

in a single gene  Base-pair substitutions: •silent mutations no effect on protein •missense ∆ to a different amino acid (different protein) •nonsense ∆ to a stop codon and a nonfunctional protein  Base-pair insertions or deletions: additions or losses of nucleotide pairs in a gene; alters the ‘reading frame’ of triplets~frameshift mutation  Mutagens: physical and chemical agents that change DNA

Index

Viral structure
Virus: “poison”

(Latin); infectious particles consisting of a nucleic acid in a protein coat Capsid; (viral envelopes); DNA or RNA Bacteriophages (phages)

Viral reproduction: Lytic Cycle
 Host range: infection of a

limited range of host cells (receptor molecules on the surface of cells)  The lytic cycle: 1- attachment 2- injection 3- hydrolyzation 4- assembly 5- release  Results in death of host cell  Virulent virus (phage reproduction only by the lytic cycle)

Viral reproduction: Lysogenic Cycle
Genome replicated w/o

destroying the host cell Genetic material of virus becomes incorporated into the host cell DNA (prophage DNA) Temperate virus (phages capable of using the lytic and lysogenic cycles) May give rise to lytic cycle

RNA viruses
Retroviruses:

transcribe DNA from an RNA template (RNA--->DNA) Reverse transcriptase (catalyzing enzyme) HIV--->AIDS

Viroids and prions
Viroids: tiny, naked

circular RNA that infect plants; do not code for proteins, but use cellular enzymes to reproduce; stunt plant growth Prions: “infectious proteins”; “mad cow disease”; trigger chain reaction conversions; a transmissible protein

Bacterial genetics
Nucleoid:

region in bacterium densely packed with DNA (no membrane) Plasmids: small circles of DNA Reproduction: binary fission (asexual)

Bacterial DNA-transfer processes
 Transformation: genotype alteration

by the uptake of naked, foreign DNA from the environment (Griffith expt.)  Transduction: phages that carry bacterial genes from 1 host cell to another •generalized~ random transfer of host cell chromosome •specialized~ incorporation of prophage DNA into host chromosome  Conjugation: direct transfer of genetic material; cytoplasmic bridges; pili; sexual

Bacterial Plasmids
 Small, circular, self-replicating DNA separate from the bacterial

chromosome  F (fertility) Plasmid: codes for the production of sex pili (F+ or F-)  R (resistance) Plasmid: codes for antibiotic drug resistance  Transposons: transposable genetic element; piece of DNA that can move from location to another in a cell’s genome (chromosome to plasmid, plasmid to plasmid, etc.); “jumping genes”

Operons, I

Def: Unit of genetic function consisting of coordinately related clusters of genes with related functions (transcription unit)

 Repressible (trp operon):  tryptophan (a.a.) synthesis  promoter: RNA polymerase binding

site; begins transcription  operator: controls access of RNA polymerase to genes (tryptophan not present)
 repressor: protein that binds to

operator and prevents attachment of RNA polymerase ~ coded from a regulatory gene (tryptophan present ~ acts as a corepressor)  transcription is repressed when tryptophan binds to a regulatory protein

Operons, II
 Inducible (lac operon):  lactose metabolism  lactose not present:

Def: Unit of genetic function consisting of coordinately related clusters of genes with related functions (transcription unit)

repressor active, operon off; no transcription for lactose enzymes  lactose present: repressor inactive, operon on; inducer molecule inactivates protein repressor (allolactose)
 transcription is stimulated when

inducer binds to a regulatory protein

Index

Chromatin
 Def: complex of DNA and proteins  DNA Packing •histone protein (+

charged amino acids ~ phosphates of DNA are - charged)  Nucleosome •”beads on a string”; basic unit of DNA packing  Heterochromatin •highly condensed interphase DNA (can not be transcribed)  Euchromatin •less compacted interphase DNA (can be transcribed)

Molecular Biology of Cancer
 Oncogene •cancer-causing genes  Proto-oncogene •normal

cellular genes  How? 1-movement of DNA; chromosome fragments that have rejoined incorrectly 2-amplification; increases the number of copies of proto-oncogenes 3-proto-oncogene point mutation; protein product more active or more resistant to degradation  Tumor-suppressor genes •changes in genes that prevent uncontrolled cell growth (cancer growth stimulated by the absence of suppression)

Index

Recombinant DNA
 Def: DNA in which

genes from 2 different sources are linked  Genetic engineering: direct manipulation of genes for practical purposes  Biotechnology: manipulation of organisms or their components to perform practical tasks or provide useful products

DNA Cloning
 Restriction enzymes (endonucleases): in nature, these enzymes protect bacteria from intruding DNA; they cut up the DNA (restriction); very specific  Restriction site: recognition sequence for a particular restriction enzyme  Restriction fragments: segments of DNA cut by restriction enzymes in a reproducable way  Sticky end: short extensions of restriction fragments  DNA ligase: enzyme that can join the sticky ends of DNA fragments  Cloning vector: DNA molecule that can carry foreign DNA into a cell and replicate there (usually bacterial plasmids)

Steps for eukaryotic gene cloning
 Isolation of cloning vector

(bacterial plasmid) & genesource DNA (gene of interest)  Insertion of gene-source DNA into the cloning vector using the same restriction enzyme; bind the fragmented DNA with DNA ligase  Introduction of cloning vector into cells (transformation by bacterial cells)  Cloning of cells (and foreign genes)  Identification of cell clones carrying the gene of interest

DNA Analysis & Genomics
PCR (polymerase

chain reaction) Gel electrophoresis Restriction fragment analysis (RFLPs) Southern blotting DNA sequencing
Human genome

project

Polymerase chain reaction (PCR)
Amplification of any

piece of DNA without cells (in vitro) Materials: heat, DNA polymerase, nucleotides, singlestranded DNA primers Applications: fossils, forensics, prenatal diagnosis, etc.

DNA Analysis
 Gel electrophoresis: separates nucleic acids or proteins on the basis of size or electrical charge creating DNA bands

of the same length

Restriction fragment analysis
Restriction fragment length polymorphisms

(RFLPs) Southern blotting: process that reveals sequences and the RFLPs in a DNA sequence DNA Fingerprinting

DNA Sequencing
Determination of

nucleotide sequences (Sanger method, sequencing machine) Genomics: the study of genomes based on DNA sequences Human Genome Project

Practical DNA Technology Uses
 Diagnosis of disease  Human gene therapy  Pharmaceutical

products (vaccines)  Forensics  Animal husbandry (transgenic organisms)  Genetic engineering in plants  Ethical concerns?

Index

From fertilized egg to multicellular organism
 Cell Division:

increase in cell number  Differentiation: cells becoming specialized in structure and function  Morphogenesis; physical processes giving an organism shape

Morphogenesis: plants vs. animals
 Animals:  movements of cells and tissues are

necessary for 3-D form of the organism
 ongoing development in adults

restricted to differentiation of cells continually replenished throughout lifetime  Plants:  morphogenesis and growth of overall size occur throughout lifetime of plant; apical meristems (perpetually embryonic regions), responsible for plant’s continual growth

Differential gene expression
 Differences between cells come  

from differences in gene expression (genes turned on or off), not from differing genomes. Evidence: 1- Genomic equivalence: all the cells of an organism have the same genes 2- Totipotency: cells that can retain the zygote’s potential to form all parts of the mature organism (plant cells; cloning) 3- Determination: restriction of developmental potential causing the possible fate of each cell to become more limited as the embryo develops; noted by the appearance of mRNA

Determination-->Differentiation
 Determination: as the embryo

develops the possible fate of each cell becomes more limited  Differentiation: specialization of cells dependent on the control of gene expression  Induction: the ability of one group of embryonic cells to influence the development of another; cytoplasmic determinants that regulate gene expression  Homeotic genes: genes that control the overall body plan of animals by controlling the developmental fate of groups of cells

Genetic cell death
Apoptosis
programmed cell death (“suicide genes”)
 1. Programmed cell death is as

needed for proper development as mitosis is.  Ex: Reabsorption of the tadpole tail; formation of the fingers and toes of the fetus requires the removal of the tissue between them; sloughing off of the endometrium at the start of menstruation; formation of the proper connections (synapses) between neurons in the brain requires that surplus cells be eliminated.

Apoptosis, Pt. II
2. Programmed cell death is needed to destroy

cells that represent a threat to the integrity of the organism. Ex: Cells infected with viruses; waning cells of the immune system; cells with DNA damage; cancer cells

Index

Evolution
 Evolution:

the change over time of the genetic composition of populations  Natural selection: populations of organisms can change over the generations if individuals having certain heritable traits leave more offspring than others (differential reproductive success)  Evolutionary adaptations: a prevalence of inherited characteristics that enhance organisms’ survival and reproduction

November 24, 1859

Evolutionary history
 Linnaeus: taxonomy  Hutton: gradualism  Lamarck: evolution  Malthus: populations  Cuvier: paleontology  Lyell: uniformitarianism  Darwin: evolution  Mendel: inheritance  Wallace: evolution

Descent with Modification, I
5 observations: 1- Exponential fertility 2- Stable population size 3- Limited resources 4- Individuals vary 5- Heritable variation

Descent with Modification, II
3 Inferences: 1- Struggle for

existence 2- Non-random survival 3- Natural selection (differential success in reproduction)

Evolution evidence: Biogeography
Geographical

distribution of species Examples:
Islands vs. Mainland Australia Continents

Evolution evidence: The Fossil Record
Succession of

forms over time Transitional links Vertebrate descent

Evolution evidence: Comparative Anatomy
Homologous

structures (homology) Descent from a common ancestor Vestigial organs Ex: whale/snake hindlimbs; wings on flightless birds

Comparative Embryology

Pharyngeal

pouches, ‘tails’ as embryos

Evolution evidence: Molecular Biology

Similarities in

DNA, proteins, genes, and gene products Common genetic code

Final words…...
“Absence of

evidence is not evidence of absence.”

Index

Population genetics
Population:

a localized group of individuals belonging to the same species Species: a group of populations whose individuals have the potential to interbreed and produce fertile offspring the total aggregate of genes in a Gene pool: population at any one time Population genetics: the study of genetic changes in populations Modern synthesis/neo-Darwinism “Individuals are selected, but populations evolve.”

Hardy-Weinberg Theorem
 Serves as a model for the

genetic structure of a nonevolving population (equilibrium)  5 conditions:  1- Very large population size;  2- No migration;  3- No net mutations;  4- Random mating;  5- No natural selection

Hardy-Weinberg Equation
p=frequency of one allele (A);

q=frequency of (p=1-q &

the other allele (a);

p+q=1.0

q=1-p) P2=frequency of AA genotype; 2pq=frequency of Aa plus aA genotype; q2=frequency of aa genotype;

p2 + 2pq + q2 = 1.0

Microevolution, I
A change in the

gene pool of a population over a succession of generations 1- Genetic drift: changes in the gene pool of a small population due to chance (usually reduces genetic variability)

Microevolution, II
The Bottleneck

Effect: type of
genetic drift resulting from a reduction in population (natural disaster) such that the surviving population is no longer genetically representative of the original population

Microevolution, III
Founder Effect:
a cause of genetic drift attributable to colonization by a limited number of individuals from a parent population

Microevolution, IV
2- Gene Flow:
genetic exchange due to the migration of fertile individuals or gametes between populations (reduces differences between populations)

Microevolution, V
3- Mutations:
a change in an organism’s DNA (gametes; many generations); original source of genetic variation (raw material for natural selection)

Microevolution, VI
4- Nonrandom

mating: inbreeding and assortive mating (both shift frequencies of different genotypes)

Microevolution, VII
5- Natural

Selection: differential success in reproduction; only form of microevolution that adapts a population to its environment

Population variation
Polymorphism:
coexistence of 2 or more distinct forms of individuals (morphs) within the same population

Geographical

variation:

differences in genetic structure between populations (cline)

Variation preservation
 Prevention of natural selection’s

reduction of variation 2nd set  Diploidy of chromosomes hides variation in the heterozygote 1 Balanced polymorphism heterozygote advantage (hybrid vigor; i.e., malaria/sickle-cell anemia); 2frequency dependent selection (survival & reproduction of any 1 morph declines if it becomes too common; i.e., parasite/host)

Natural selection
Fitness:

contribution an individual makes to the gene pool of the next generation 3 types: A. Directional B. Diversifying C. Stabilizing

Sexual selection
Sexual dimorphism:
secondary sex characteristic distinction

Sexual selection:
selection towards secondary sex characteristics that leads to sexual dimorphism

Index

Macroevolution: the origin of new taxonomic groups
Speciation: the origin of new

species 1- Anagenesis (phyletic evolution): accumulation of
heritable changes

2- Cladogenesis (branching

evolution): budding of new species
from a parent species that continues to exist (basis of biological diversity)

What is a species?
Biological species

concept (Mayr):

a

population or group of populations whose members have the potential to interbreed and produce viable, fertile offspring (genetic exchange is possible and that is genetically isolated from other populations)

Reproductive Isolation (isolation of gene pools), I
 Prezygotic barriers: impede mating

between species or hinder the fertilization of the ova  Habitat (snakes; water/terrestrial)  Behavioral (fireflies; mate signaling)  Temporal (salmon; seasonal mating)  Mechanical (flowers; pollination anatomy)  Gametic (frogs; egg coat receptors)

Reproductive Isolation, II
 Postzygotic barriers: fertilization

occurs, but the hybrid zygote does not develop into a viable, fertile adult  Reduced hybrid viability (frogs; zygotes fail to develop or reach sexual maturity)  Reduced hybrid fertility (mule; horse x donkey; cannot backbreed)  Hybrid breakdown (cotton; 2nd generation hybrids are sterile)

Modes of speciation
(based on how gene flow is interrupted)
Allopatric:
populations segregated by a geographical barrier; can result in adaptive radiation (island species) reproductively isolated subpopulation in the midst of its parent population (change in genome); polyploidy in plants; cichlid fishes

Sympatric:

Punctuated equilibria
Tempo of speciation:

gradual vs. divergence in rapid bursts; Niles Eldredge and Stephen Jay Gould (1972); helped explain the non-gradual appearance of species in the fossil record

Index

Phylogeny:
a species
Systematics:

the evolutionary history of

the study of biological diversity in an evolutionary context The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock Paleontologists

The fossil record
 Sedimentary rock: rock formed

from sand and mud that once settled on the bottom of seas, lakes, and marshes  Dating:  1- Relative~ geologic time scale; sequence of species  2- Absolute~ radiometric dating; age using half-lives of radioactive isotopes

Biogeography: the study of the past and present distribution of species
Pangaea-250 mya

Permian extinction Geographic isolation-180 mya √ African/South American reptile fossil similarities √ Australian marsupials

Mass extinction
Permian
(250 million years ago): 90% of marine animals; Pangea merge

Cretaceous
(65 million years ago): death of dinosaurs, 50% of marine species; low angle comet

Phylogenetics
The tracing of

evolutionary relationships (phylogenetic tree) Linnaeus Binomial Genus, specific epithet Homo sapiens Taxon (taxa)

Phylogenetic Trees
 Cladistic Analysis: taxonomic

  

approach that classifies organisms according to the order in time at which branches arise along a phylogenetic tree (cladogram) Clade: each evolutionary branch in a cladogram Types: 1- Monophyletic single ancestor that gives rise to all species in that taxon and to no species in any other taxon; legitimate cladogram 2- Polyphyletic members of a taxa are derived from 2 or more ancestral forms not common to all members; does not meet cladistic criterion 3- Paraphyletic lacks the common ancestor that would unite the species; does not meet cladistic criterion

Constructing a Cladogram
 Sorting homology vs. analogy...  Homology:

likenesses attributed to common ancestry  Analogy: likenesses attributed to similar ecological roles and natural selection  Convergent evolution: species from different evolutionary branches that resemble one another due to similar ecological roles

A Cladogram

Index

Early history of life
 Solar system~ 12 billion years

ago (bya)  Earth~ 4.5 bya  Life~ 3.5 to 4.0 bya  Prokaryotes~ 3.5 to 2.0 bya stromatolites  Oxygen accumulation~ 2.7 bya photosynthetic cyanobacteria  Eukaryotic life~ 2.1 bya  Muticelluar eukaryotes~ 1.2 bya  Animal diversity~ 543 mya  Land colonization~ 500 mya

The Origin of Life
Spontaneous generation vs.

biogenesis (Pasteur) The 4-stage Origin of life Hypothesis: 1- Abiotic synthesis of organic monomers 2- Polymer formation 3- Origin of Self-replicating molecules 4- Molecule packaging (“protobionts”)

Organic monomers/polymer synthesis (G.B.) Oparin (Rus.)/Haldane

hypothesis (primitive earth): volcanic vapors (reducing atmosphere) with lightning & UV radiation enhances complex molecule formation (no O2)  Miller/Urey experiment:  water, hydrogen, methane, ammonia  all 20 amino acids, nitrogen bases, & ATP formed  Fox proteinoid formation (abiotic polypeptides) from organic monomers dripped on hot sand, clay or rock  Oparin (coacervates) protobionts (aggregate macromolecules; abiotic) surrounded by a shell of H2O molecules coated by a protein membrane

Abiotic genetic replication
First genetic material Abiotic production of

ribonucleotides Ribozymes (RNA catalysts) RNA “cooperation” Formation of short polypeptides (replication enzyme?) RNA~ DNA template?

Index

Classification
Kingdom: Monera? Domain: Bacteria Domain: Archaea

Shape

•cocci (sphere) •bacilli (rod) •helical (spiral)

Structural characteristics
 Cell wall~ peptidoglycan

(sugars & proteins); √ Gram +: w/peptidoglycan penicillin action √ Gram -: little peptidoglycan, lipopolysaccharides; most pathogens; impede drug action  Capsule: adherence; protection  Pili: adherence; conjugation

Motility
1- Flagella 2- Helical shape

(spirochetes) 3- Slime 4-Taxis (movement away or toward a stimulus)

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Form & Function
 Nucleoid region (genophore: non-

eukaryotic chromosome)  Plasmids binary  Asexual reproduction: fission (not mitosis)  “Sexual” reproduction (not meiosis): transformation~ uptake of genes from surrounding environment conjugation~ direct gene transfer from 1 prokaryote to another transduction~ gene transfer by viruses  Endospore: resistant cells for harsh conditions (250 million years!)

Nutrition & Metabolism
 Photoautotrophs: photosynthetic; harness light   

 

to drive the synthesis of organics (cyanobacteria) Chemoautotrophs: oxidation of inorganics for energy; get carbon from CO2 Photoheterotrophs: use light to generate ATP but get carbon in an organic form Chemoheterotrophs: consume organic molecules for both energy and carbon saprobesdead organic matter decomposers parasites- absorb nutrients from living hosts Nitrogen fixation: conversion of atmospheric nitrogen (N2) to ammonium (NH4+) Oxygen relationships: obligate aerobes; facultative anaerobes; obligate anaerobes

Prokaryotic ecology
 Decomposers: unlock organics from

corpses and waste products •symbiont/host  Symbiosis~ •mutualism (+, +) •parasitism (+, -) •commensalism (+, 0) •opportunistic: normal  Disease residents of host; cause illness when defenses are weakened •Koch’s postulates: criteria for bacterial disease confirmation •exotoxins: bacterial proteins that can produce disease w/o the prokaryote present (botulism) •endotoxins: components of gram membranes (Salmonella)

Index

Protists
Ingestive

(animal-like); protozoa
Absorptive

(fungus-like)
Photosynthetic

(plant-like); alga

The Endosymbionic Theory
Mitochondria and chloroplasts were

formerly from small prokaryotes living within larger cells (Margulis)

Protist Systematics & Phylogeny, I
1- Groups lacking mitochondria;

early eukaryotic link; Giardia (human intestinal parasite; severe diarrhea); Trichomonas (human vaginal infection) 2- Euglenoids; autotrophic & heterotrophic flagellates; Trypanosoma (African sleeping sickness; tsetse fly)

Protist Systematics & Phylogeny, II
 Alveolata: membrane-

bound cavities (alveoli) under cell surfaces; dinoflagellates (phytoplankton); Plasmodium (malaria); ciliates (Paramecium)

Protist Systematics & Phylogeny, III
 Stamenophila: water molds/mildews and

heterokont (2 types of flagella) algae; numerous hair-like projections on the flagella; most molds are decomposers and mildews are parasites; algae include diatoms, golden, and brown forms

Protist Systematics & Phylogeny, IV
Rhodophyta: red

algae; no flagellated stages; phycobilin (red) pigment Chlorophyta: green algae; chloroplasts; gave rise to land plants; volvox, ulva

Protist Systematics & Phylogeny, V
 Affinity uncertain:  Rhizopods: unicellular

with pseudopodia; amoebas  Actinopods: ‘ray foot’ (slender pseudopodia; heliozoans, radiolarians

QuickTime™ and a Cinepak decompressor are needed to see this picture.

Protist Systematics & Phylogeny, VI
Mycetozoa: slime

molds (not true fungi); use pseudopodia for locomotion and feeding; plasmodial and cellular slime molds

QuickTime™ and a Cinepak decompressor are needed to see this picture.

Index

Plant Evolution
bryophytes (mosses),

pteridophytes (ferns), gymnosperms (pines and conifers); angiosperms (flowering plants) Plants: multicellular, eukaryotic, photosynthetic autotrophs Terrestrial colonization: Vascular tissue The seed The flower

Plant origins
Charophytes: green algae

(closest plant ancestor) Similarities:
 1-Homologous chloroplasts:

chlorophyll a & b  2- Biochemical similarity cellulose composition; peroxisomes  3- Cell division similarity mitosis; cytokinesis  4- Sperm similarity ultrastructure nuclear  5- Genetic relationship genes; rRNA

Characteristics that separate plants from algae ancestors
Apical meristems: localized

regions of cell division Multicellular, dependent embryos (embryophytes) Alternation of generations Walled spores produced in sporangia Multicellular gametangia

Other terrestrial adaptations
Cuticle Stomata Xylem and

phloem Secondary compounds

Bryophytes
 Mosses, liverworts, and

hornworts  1st to exhibit the embryonic condition (male = antheridium; female = archegonium)  Flagellated (water) sperm  No vascular tissue (imbibe water)  No lignin (short stature)  Haploid gametophyte is the dominant generation

Pteridophytes: seedless vascular plants
 Ferns, club ‘moss’, horsetails  True roots and leaves  Roots have lignified vascular tissue  Sporophyte-dominant life cycle  Homosporous plants: a single type

of spore….  Sporophyte---->Single type of spore ---->Bisexual gametophyte ---->Eggs; sperm (flagellated; damp locations)  Carboniferous period plants

Index

Seed Plant Reproductive Adaptations
 Reduction of the gametophyte: shift from haploid to diploid condition;

female gametophyte and embryo remain in sporangia (protection against drought and ionizing radiation on land?)  Advent of the seed multicellular sporophyte embryo with food supply and protective coat; heterosporous (two types of spores): megaspores--->female gametophyte--->eggs; microspores---> male gametophyte--->sperm  Evolution of pollen: develop from microspores which mature into the male gametophytes; resistant and airborne for a terrestrial environment; eliminated water (sporopollenin coats)

Gymnosperms
 Cone-bearing plants  Lack enclosed chambers

(ovaries) for seeds  Ovules and seeds develop on specialized leaves called sporophylls  Ginkgo, cycads, and conifers  All are “evergreens”  Needle-shaped leaves  Vascular tissue refinement: tracheids~ water conducting and supportive element of xylem

Angiosperms
 Most diverse and geographically widespread of all plants  “Flowering plants”(Phy: Anthophyta)  Monocots: 1 embryonic seed leaf (lilies, palms, grasses, grain

crops)  Dicots: 2 embryonic seed leaves (roses, peas, sunflowers, oaks, maples)  Vascular tissue refinement: vessel elements/fiber cells

The flower: the defining structure of angiosperms
Reproductive structure:

pollen transfer; specialized shoot with modified leaves Sepals: enclose flower before it opens Petals: attract pollinators Stamens: male; anther (produces pollen), filament Carpels: female; stigma, style, ovary, ovules

Angiosperm life cycle
Fruit (mature ovary); seeds

from ovules Pollen grains: 2 haploid cells (immature male gametophytes) Ovules (female gametophyte~ embryo sac) Double fertilization: 1 sperm w/ egg = diploid zygote; other sperm w/ 2 nuclei in center of sac = triploid endosperm

Beginning of Plants

Index

Angiosperm structure
 Three basic organs:  Roots (root system)  fibrous: mat of thin roots  taproot: one large, vertical root  Stems (shoot system)  nodes: leave attachment  internodes: stem segments  axillary bud: dormant, vegetative

potential  terminal bud: apex of young shoot  apical dominance: inhibits axillary buds  Leaves (shoot system)  blade  petiole

Plant Organ Systems
 Dermal (epidermis): single layer

of cells for protection  cuticle  Vascular (material transport)  xylem: water and dissolved minerals roots to shoots  tracheids & vessel elements: xylem elongated cells dead at maturity  phloem: food from leaves to roots and fruits  sieve-tube members: phloem tubes alive at maturity capped by sieve plates; companion cells (nonconducting) connected by plasmodesmata  Ground (photosynthesis, storage, support): pith and cortex

Plant Tissue Cell Types
 Parenchyma primary walls thin and

flexible; no secondary walls; large central vacuole; most metabolic functions of plant (chloroplasts)  Collenchyma unevenly thick primary walls used for plant support (no secondary walls ; no lignin) support  Sclerenchyma element strengthened by secondary cell walls with lignin (may be dead; xylem cells); fibers and sclereids for support

Plant Growth
 Life Cycles  annuals: 1 year (wildflowers; food

crops)  biennials: 2 years (beets; carrots)  perennials: many years (trees; shrubs)  Meristems  apical: tips of roots and buds; primary growth  lateral: cylinders of dividing cells along length of roots and stems; secondary growth (wood)

Primary growth
 Roots  root cap~ protection of

meristem  zone of cell division~ primary (apical) meristem  zone of elongation~ cells elongate; pushes root tip  zone of maturation~ differentiation of cells (formation of 3 tissue systems)

Primary Tissues of Roots
 Stele~ the vascular bundle where both xylem and phloem

develop  Pith~ central core of stele in monocot; parenchyma cells  Cortex~ region of the root between the stele and epidermis (innermost layer: endodermis)  Lateral roots~ arise from pericycle (outermost layer of stele); just inside endodermis, cells that may become meristematic

Primary Tissues of Stems
Vascular bundles (xylem and phloem) Surrounded by ground tissue (xylem faces pith

and phloem faces cortex) Mostly parenchyma; some collenchyma and sclerenchyma for support

Primary Tissues of Leaves
 Epidermis/cuticle (protection; desiccation)  Stomata (tiny pores for gas exchange and

transpiration)/guard cells  Mesophyll: ground tissue between upper and lower epidermis (parenchyma with chloroplasts); palisade (most photosynthesis) and spongy (gas circulation)

Secondary Growth
 Two lateral meristems  vascular cambium ~

produces secondary xylem (wood) and secondary phloem (diameter increase; annual growth rings)  cork cambium ~ produces thick covering that replaces the epidermis; produces cork cells; cork plus cork cambium make up the periderm; lenticels (split regions of periderm) allow for gas exchange; bark~ all tissues external to vascular cambium (phloem plus periderm)

PRIMARY MERISTEMS

PRIMARY TISSUES

LATERAL MERISTEM

SECONDARY TISSUES

Protoderm Apical meristem of stem

Epidermis Primary phloem Vascular cambium

Secondary phloem Secondary xylem

Procambium Primary xylem Ground meristem

Ground Pith & tissue: Cortex

Periderm Cork cambium Cork

Index

Transport Overview
1- uptake and loss of water

and solutes by individual cells (root cells) 2- short-distance transport from cell to cell (sugar loading from leaves to phloem) 3- long-distance transport of sap within xylem and phloem in whole plant

 1- Roots absorb water and dissolved minerals

Whole Plant Transport

from soil  2- Water and minerals are transported upward from roots to shoots as xylem sap  3- Transpiration, the loss of water from leaves, creates a force that pulls xylem sap upwards  4- Leaves exchange CO2 and O2 through stomata  5- Sugar is produced by photosynthesis in leaves  6- Sugar is transported as phloem sap to roots and other parts of plant  7- Roots exchange gases with air spaces of soil (supports cellular respiration in roots)

 Water transport

Cellular Transport
√ Osmosis;

hyper-; hypo-; iso Cell wall creates physical pressure: √water potential solutes decrease; pressure increase  Water moves from high to low water potential  Flaccid (limp, iostonic);  Plasmolysis (cell loses water in a hypertonic environment; plasma membrane pulls away);  Turgor pressure (influx of water due to osmosis; hypotonic environment)

Transport within tissues/organs
 Tonoplast

vacuole

membrane  Plasmodesmata (components) cytosolic connection  Symplast route (lateral) cytoplasmic continuum  Apoplast route (lateral) continuum of cell walls  Bulk flow (long distance) movement of a fluid by pressure (xylem)

Transport of Xylem Sap
Transpiration: loss of water

vapor from leaves pulls water from roots (transpirational pull); cohesion and adhesion of water Root pressure: at night (low transpiration), roots cells continue to pump minerals into xylem; this generates pressure, pushing sap upwards; guttation

Transpirational Control
Photosynthesis-Transpiration compromise…. Guard cells control the size of the stomata Xerophytes (plants adapted to arid environments)~

thick cuticle; small spines for leaves

Translocation of Phloem Sap
 Translocation: food/phloem transport  Sugar source: sugar production organ (mature

leaves)  Sugar sink: sugar storage organ (growing roots, tips, stems, fruit)  1- loading of sugar into sieve tube at source reduces water potential inside; this causes tube to take up water from surroundings by osmosis  2- this absorption of water generates pressure that forces sap to flow alon tube  3- pressure gradient in tube is reinforced by unloading of sugar and consequent loss of water from tube at the sink  4- xylem then recycles water from sink to source

Index

Nutrients
 Essential: required for the plant life cycle  Macro- (large amounts) carbon, oxygen, hydrogen, nitrogen, sulfur,

phosphorus, potassium, calcium, magnesium  Micro- (small amounts; cofactors of enzyme action) chlorine, iron, boron, manganese, zinc, copper, molybdenum, nickel  Deficiency • chlorosis (lack of magnesium; chlorophyll production)

Soil
Determines plant growth &

variety (also climate) Composition/horizons: •topsoil (rock particles, living organisms, humus-partially decayed organic material) •loams (equal amounts of sand, silt, and clay)

Nitrogen Fixation
Atmosphere, 80% N2 Conversion to: ammonium (NH4+) or nitrate

(NO3-) Bacteria types: Ammonifying (humus decomposition); nitrogen-fixing (atmospheric N2); nitrifying (convert NH4+ to NO3-); denitrifying (convert NO3- to N2) Nitrogen fixation; crop rotation

Plant symbiosis, I
Rhizobium bacteria

(found in root nodules in the legume family) Mutualistic: legume receives fixed N2; bacteria receives carbohydrates & organic materials

Plant symbiosis, II
 Mycorrhizae (fungi); modified roots  Mutualistic: fungus receives sugar;

plant receives increased root surface area and increased phosphate uptake ectomycorrhizae •  Two types: ensheaths the root endomycorrhizae (90% of plants) •through cell wall but not cell membrane

Plant parasitism & predation
Mistletoe (parasite) Epiphytes Carnivorous plants
Q u ic k T im e ™ a n d a C in e p a k d e c o m p r e s s o r a r e n e e d e d t o s e e t h is p ic t u r e .

Index

Sexual Reproduction
 Alternation of generations:

haploid (n) and diploid (2n) generations take turns producing each other  Sporophyte (2n): produces haploid spores by meiosis; these spores divide by mitosis giving rise to male and female haploid plants called….  Gametophytes (n): develop and produce gametes

Floral variations
 Floral organs: sepals, petals,

stamens (male ), carpels (female)  •complete: all 4 floral organs  •incomplete: lacking 1 or more floral organs  •perfect: both stamens and carpels on 1 flower  •imperfect: lacking either a stamen or carpel  •monoecious: staminate and carpellate flowers on 1 plant)
 •dioecious: staminate and

carpellate flowers on separate plants

Gametophyte development
Male gametophyte:
microsporocyte (in pollen sacs of anther) divides by meiosis into 4-1N microspores; mitosis produces a generative cell (sperm) and a tube cell (pollen tube)= a pollen grain megasporocyte (in ovule) divides by meiosis to 4 cells, only 1 survives to a 1-N megaspore; 3 mitotic divisions forms the embryo sac; includes: 1 egg cell (female gamete) and 2 polar nuclei (synergids)

Female gametophyte:

Double fertilization
 Pollination (pollen grain

lands on a receptive stigma)  Tube cell (pollen tube produced down the style)  Generative cell (2 sperm by mitosis)  Enters ovary through micropyle  1 sperm fertilizes egg to form zygote; other sperm combines with 2 polar nuclei to form 3n endosperm (food-storing tissue)

The seed
From fertilized ovule….. The mature seed: •seed coat (protection) •cotyledons (seed leaves) •hypocotyl (lower

embryonic axis) •radicle (embryonic root) embryonic axis) •epicotyl (upper •plummule (shoot tip) embryonic •coleoptile (sheath for shoot)

The fruit
 From ovary….  Fruit protects seeds and aids in their dispersal  Pericarp (thickened wall of fruit from ovary wall)  Fruit types:  •simple (1 ovary/1 flower)~ cherry, soybean  •aggregate (1 flower with many carpels/ovaries)~ blackberry  •multiple (inflorescence; group of flowers/ovaries) ~ pineapple

Seed germination

Seed dormancy (low metabolic rate and

growth suspension) Imbibition (uptake of water) Radicle 1st, then shoot tip (hypocotyl); stimulated by light Germination

Index

Plant hormones
 Hormone: chemical signals that

coordinate parts of an organism; produced in one part of the body and then transported to other parts of the body; low concentrations  Tropism: movement toward or away from a stimulus  Went experiments (phototropism)  Hormone: auxin  Others: gravitropism, thigmotropism

Auxin
IAA (indoleacetic acid) Location: seed embryo; meristems of

apical buds and young leaves Function: stem elongation; root growth, differentiation, branching; fruit development; apical dominance; tropisms

Q ic T e a d a u k im ™ n C e a d c m re s r in p k e o p s o a n e e tos eth p tu . re e d d e is ic re

Cytokinins
Zeatin Location: roots (and actively growing

tissues) Function: root growth and differentiation; cell division and growth; germination; delay senescence (aging); apical dominance (w/ auxin)

Gibberellins GA3
Location: meristems of apical buds and

roots, young leaves, embryo Function: germination of seed and bud; stem elongation; leaf growth; flowering (bolting); fruit development; root growth and differentiation

Abscisic acid
ABA Location: leaves, stems, roots, green

fruit Function: inhibits growth; closes stomata during stress; counteracts breaking of dormancy

Ethylene
Gaseous hormone Location: ripening fruit tissue; stem

nodes; aging leaves and flowers Function: fruit ripening; oppositional to auxin (leaf abscission); promotes/inhibits: growth/development of roots, leaves, and flowers; senescence

Daily and Seasonal Responses
 Circadian rhythm (24 hour periodicity)  Photoperiodism (phytochromes)  Short-day plant: light period shorter than a critical length to flower

(flower in late summer, fall, or winter; poinsettias, chrysanthemums)  Long-day plant: light period longer than a critical length to flower (flower in late spring or early summer; spinach, radish, lettuce, iris)  Day-neutral plant: unaffected by photoperiod (tomatoes, rice, dandelions)  Critical night length controls flowering

Phytochromes
Plant pigment

that measures length of darkness in a photoperiod (red light) Pr (red absorbing) 660nm Pfr (far-red absorbing) 730nm

Index

Fungi
Heterotrophic by absorption

(exoenzymes) Decomposers (saprobes), parasites, mutualistic symbionts (lichens) Hyphae: body filaments •septate (cross walls) •coenocytic (no cross walls) Mycelium: network of hyphae Chitin cell walls (polysaccharide)

Fungi Diversity, I
Phy: Chytridiomycota

•aquatic fungi; chytrids •lineage closest to protists (flagella) Phy: Zygomycota •Rhizopus (food mold) •mycorrhizae: mutualistic with plant roots •zygosporangia: resistant structure (freezing and drying)

Fungi Diversity, II
Phy.: Ascomycota

•sac fungi • yeasts, truffles, morels, Sordaria •asci: sexual spores •conidia: asexual spores • club Phy.: Basidiomycota fungus •mushrooms, puffballs, shelf fungus, rusts •basidiocarps: produce sexual spores

Specialized Lifestyles, I
Molds

•only the asexual stage (asexual spores) •Penicillium (antibiotic, cheese)
Yeasts

•unicellular, asexual budding •Saccharomyces (bread, alcohol)

Specialized Lifestyles, II
 Lichens

• symbiotic association held in a hyphae mesh •alga provides food, fungus provides physical environment •pioneer organisms •air pollution detection •root  Mycorrhizae and fungi mutualism •found in 95% of vascular plants •exchange of organic minerals •increases absorptive surface of roots

Index

Tissues: groups of cells with a common structure and function (4 types)
 Anatomy: structure  Physiology: function  1- Epithelial: outside of body and

lines organs and cavities; held together by tight junctions  basement membrane: dense mat of extracellular matrix  Simple: single layer of cells  Stratified: multiple tiers of cells  Cuboidal (like dice)  Columnar (like bricks on end)  Squamous (like floor tiles)  mucous membrane

Tissues, II
 2- Connective: bind and support other tissues; scattered cells through matrix; 3 kinds:  A-Collagenous fibers (collagen protein) B-Elastic fibers (elastin protein) C-Reticular fibers       

(thin branched collagen fibers) Loose connective tissue: binds epithelia to underlying tissue; holds organs 1-Fibroblasts- secretes extracellular proteins 2-Macrophages- amoeboid WBC’s; phagocytosis 3-Adipose tissue- fat storage; insulation Fibrous connective tissue: parallel bundles of cells 1-Tendons- muscles to bones 2-Ligaments- bones to bones; joints (BOBOLI) Cartilage: collagen in a rubbery matrix (chondroitin); flexible support Bone: mineralized tissue by osteoblasts Blood: liquid plasma matrix; erythrocytes (RBC’s) carry O2; leukocytes (WBC’s) immunity

Tissues, III
3-Nervous: senses stimuli and

transmits signals from 1 part of the animal to another Neuron: functional unit that transmits impulses Dendrites: transmit impulses from tips to rest of neuron Axons: transmit impulses toward another neuron or effector

Tissues, IV
 4- Muscle: capable of

contracting when stimulated by nerve impulses; myofibrils composed of proteins actin and myosin; 3 types:  A- Skeletal: voluntary movement (striated)  B- Cardiac: contractile wall of heart (branched striated)  C- Smooth: involuntary activities (no striations)

Organ systems
Organ: organization of

tissues Mesentaries: suspension of organs (connective tissue) Thoracic cavity (lungs and heart) Abdominal cavity (intestines) Diaphragm (respiration) Organ systems…...

 Digestive-food processing  Circulatory-internal distribution  Respiratory-gas exchange  Immune/Lymphatic-defense  Excretory-waste disposal;

osmoregulation  Endocrine-coordination of body activities  Reproductive-reproduction  Nervous-detection of stimuli  Integumentary-protection  Skeletal-support; protection  Muscular-movement; locomotion

Internal regulation
 Interstitial fluid: internal fluid

environment of vertebrates; exchanges nutrients and wastes  Homeostasis: “steady state” or internal balance  Negative feedback: change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation; i.e., body temperature  Positive feedback: physiological control mechanism in which a change in some variable triggers mechanisms that amplify the change; i.e., uterine contractions at childbirth

Metabolism: sum of all energy-requiring biochemical reactions
 Catabolic processes of cellular

respiration  Calorie; kilocalorie/C  Endotherms: bodies warmed by metabolic heat  Ectotherms: bodies warmed by environment  Basal Metabolic Rate (BMR): minimal rate powering basic functions of life (endotherms)  Standard Metabolic Rate (SMR): minimal rate powering basic functions of life (ectotherms)

Index

Embryonic development/fertilization
 Preformation~ until 18th century; miniature infant in sperm or egg  At fertilization/conception:  Acrosomal reaction~ hydrolytic enzyme action on egg jelly coat….  Fast block to polyspermy~ membrane depolarization prevents

multiple fertilizations….  Cortical reaction~ release of calcium causes hardening of egg outer layer and creates a...  Slow block to polyspermy and...  Egg activation~ increases metabolic activity; protein synthesis

The Fertilized Egg & Cleavage Blastomeres~

resultant cells of cleavage/mitosis

Yolk~ nutrients stored in the egg Vegetal pole~ side of egg with
high yolk concentration

Animal pole

~ side of egg with low yolk concentration

Morula~solid ball of cells Blastocoel~fluid-filled cavity in
morula

Blastula~hollow ball stage of
development

Gastrula~ 2 layered, cup-shaped
embryonic stage

Gastrulation

3 Embryonic germ layers:
 Ectoderm~ outer layer; epidermis;
nervous system, etc.

 Endoderm~ inner layer; digestive tract
and associated organs; respiratory, etc.

 Mesoderm~skeletal; muscular;
excretory, etc.

Invagination~ gastrula buckling
process to create the...

Archenteron~ primitive gut Blastopore~ open end of
archenteron

Organogenesis: organ formation
Blastodisc~ cap of
cells on top of yolk

Primitive streak~
invagination of blastodisc

Neural tube~
beginning of spinal cord

Somites~

vertebrae and skeletal muscles and muscles of skull

Neural crest~ bones

Amniote embryos
Extraembryonic

membranes: •yolk sac
(support; circulatory function)

•amnion
protection)

(fluid-filled sac;

•chorion •allantois

(placenta formation) (nitrogenous waste)

Index

Def: an•i•mal (n)
 Unique characteristics:  Heterotrophic eukaryotes; ingestion  Lack cell walls; collagen  Nervous & muscular tissue  Sexual; diploid; cleavage; blastula; gastrulation; larvae;

metamorphosis  Regulatory genes: Hox genes

Animal phylogeny & diversity, I
 Monophyletic; colonial flagellated

protist ancestor  1- Parazoa-Eumetazoa dichotomy: sponges (Parazoa)~ no true tissues; all other animals (Eumetazoa)~ true tissues  2- Radiata-Bilateria dichotomy: Cnidaria (hydra; ‘jellyfish’; sea anemones) & Ctenophora (comb jellies)~ radial body symmetry; all other animals~ bilateral body symmetry (also: cephalization)

Animal phylogeny & diversity, II
 3- Gastrulation: germ layer development;

ectoderm (outer), mesoderm (middle), endoderm (inner); radiata are diploblastic-2 layers; no mesoderm; bilateria are triploblastic-all 3 layers  4- Acoelomate, Pseudocoelomate, and Coelomate Grades: triploblastic animals~ solid body, no body cavity called acoelomates (Platyhelminthes-flatworms); body cavity, but not lined with mesoderm called pseudocoelomates (Rotifers); true coelom (body cavity) lined with mesoderm called coelomate

Animal phylogeny & diversity, III
 5- Protostome-Deuterostome

dichotomy among coelomates: protostomes (mollusks, annelids, arthropods); deuterostomes (echinoderms, chordates)  a) cleavage: protostomes~ spiral and determinate; deuterotomes~ radial and indeterminate  b) coelom formation: protostomes~ schizocoelous; deuterostomes~ enterocoelous  c) blastopore fate: protostomes~ mouth from blastopore; deuterostomes~ anus from blastopore

Index

Parazoa
Invertebrates: animals

without backbones Closest lineage to protists Loose federation of cells (unspecialized); no tissues Phy.: Porifera (sponges)

Phylum: Porifera
bearer”)
Sessile (attached to bottom) Spongocoel (central cavity)

(“pore

Osculum (large opening) Choanocytes (flagellated collar cells) Hermaphroditic (produce both sperm and eggs)

The Radiata, I
 Diploblastic  Radial symmetry  Phy: Cnidaria (hydra, jellies, sea

anemones, corals)  No mesoderm; GVC gastrovascular cavity (sac with a central digestive cavity)  Hydrostatic skeleton (fluid held under pressure)  Polyps and medusa  Cnidocytes (cells used for defense and prey capture)  Nematocysts (stinging capsule)

The Radiata, II
Phy: Ctenophora

(comb jellies) 8 rows of comblike plates of fused cilia (largest animals that use cilia for locomotion) Tentacles with colloblasts (adhesive structures that capture prey)

Eumetazoa: The Acoelomates
Phy: Platyhelminthes
(flatworms, flukes, tapeworms)

Bilateral; no body cavity Predators, scavengers,

parasites Triplobastic; mesoderm but, GVC with only one opening Some cephalization Many pathogens (Schistosoma, Cestodidias)

Eumetazoa: Pseudocoelomates, I
Body cavity partially

derived from mesodermally derived tissue Phy: Rotifera 1st with a complete digestive tract Hydrostatic skeleton Parthenogenesis: type of reproduction in which females produce offspring from unfertilized eggs

Eumetazoa: Pseudocoelomates, II
Phy: Nematoda
(roundworms)

 Very widespread group of

animals (900,000 sp. ?)  Cuticle (tough exoskeleton)  Decomposition and nutrient cycling  Complete digestive track; no circulatory system  Trichinella spiralis

The Coelomates: Protostomes, I
 Phylogenetics debated….  Phy: Nemertea (proboscis and

ribbon worms)  Complete digestion and closed circulatory system (blood)  Phy: the lophophorates (sea mats, tube worms, lamp shells)  Lophophore: Circular shaped body fold with ciliated tentacles around the mouth

The Coelomates: Protostomes, II
 Phy: Mollusca

(snails, slugs, squid, octopus, clams, oysters, chiton)  Soft body protected by a hard shell of calcium carbonate  Foot (movement), visceral mass (internal organs); mantle (secretes shell); radula (rasp-like scraping organ)  Ciliated trochophore larvae (related to Annelida?)

The Coelomates: Protostomes, III
 Phy: Annelida (earthworms,

leeches, marine worms)  True body segmentation (specialization of body regions)  Closed circulatory system  Metanephridia: excretory tubes  “Brainlike” cerebral ganglia  Hermaphrodites, but crossfertilize

QuickTime™ and a Cinepak decompressor are needed to see this picture.

The Coelomates: Protostomes, IV
 Phy: Arthropoda

trilobites (extinct); crustaceans (crabs, lobsters, shrimps); spiders, scorpions, ticks (arachnids); insects (entomology)  2 out of every 3 organisms (most successful of all phyla)  Segmentation, hard exoskeleton (cuticle)~ molting, jointed appendages; open circulatory system (hemolymph); extensive cephalization

Insect characteristics
 Outnumber all other forms of life

combined  Malpighian tubules: outpocketings of the digestive tract (excretion)  Tracheal system: branched tubes that infiltrate the body (gas exchange)  Metamorphosis…...  •incomplete: young resemble adults, then molt into adulthood (grasshoppers)  •complete: larval stages (looks different than adult); larva to adult through pupal stage

QuickTime™ and a Cinepak decompressor are needed to see this picture.

The Coelomates: Deuterostomes, I
 Phy: Echinodermata (sea stars,

sea urchins, sand dollars, sea lilies, sea cucumbers, sea daisies)  Spiny skin; sessile or slow moving  Often pentaradial  Water vascular system by hydraulic canals (tube feet)

QuickTime™ and a Cinepak decompressor are needed to see this picture.

Index

Chordates
 Notochord: longitudinal, flexible

rod located between the digestive and the nerve cord  Dorsal, hollow nerve cord; eventually develops into the brain and spinal cord  Pharyngeal slits; become modified for gas exchange, jaw support, and/or hearing  Muscular, postanal tail

Invertebrate chordates
 Both suspension feeders…..  Subphy: Urochordata (tunicates; sea squirt); mostly sessile & marine  Subphy: Cephalochordata (lancelets); marine, sand dwellers  Importance: vertebrates closest relatives; in the fossil record, appear

50 million years before first vertebrate  Paedogenesis: precocious development of sexual maturity in a larva (link with vertebrates?)

Subphylum: Vertebrata
 Retain chordate characteristics with

specializations….  Neural crest: group of embryonic cells near dorsal margins of closing neural tube  Pronounced cephalization: concentration of sensory and neural equipment in the head  Cranium and vertebral column  Closed circulatory system with a ventral chambered heart

Vertebrate diversity
Phy: Chordata Subphy: Vertebrata Superclass: Agnatha~
jawless vertebrates (hagfish, lampreys)

Superclass: Gnathostomata~
jawed vertebrates with 2 sets of paired appendages; including tetrapods (‘4-footed’) and amniotes (shelled egg)

Superclass Agnatha
Jawless vertebrates Most primitive, living

vertebrates Ostracoderms (extinct); lamprey and hagfish (extant) Lack paired appendages; cartilaginous skeleton; notochord throughout life; rasping mouth

Superclass Gnathostomata, I
 Placoderms (extinct): first with hinged jaws and paired appendages  Class: Chondrichthyes~ Sharks, skates, rays  Cartilaginous fishes; well developed jaws and paired fins; continual water

flow over gills (gas exchange); lateral line system (water pressure changes)  Life cycles:  Oviparous- eggs hatch outside mother’s body  Ovoviviparous- retain fertilized eggs; nourished by egg yolk; young born live  Viviparous- young develop within uterus; nourished by placenta

Superclass Gnathostomata, II
 Class: Osteichthyes  Ossified (bony) endoskeleton; scales operculum(gill covering);

swim bladder (buoyancy)  Most numerous vertebrate  Ray-fined (fins supported by long, flexible rays): bass, trout, perch, tuna, herring  Lobe-finned (fins supported by body skeleton extensions): coelocanth  Lungfishes (gills and lungs): Australian lungfish (aestivation)

III
 Class: Amphibia  1st tetrapods on land  Frogs, toads, salamanders, caecilians  Metamorphosis; lack shelled egg;

moist skin for gas exchange

Superclass Gnathostomata, IV
 Class: Reptilia  Lizards, snakes, turtles, and crocodilians  Amniote (shelled) egg with extraembryonic membranes (gas exchange,

waste storage, nutrient transfer); absence of feathers, hair, and mammary glands; ectothermic; scales with protein keratin (waterproof); lungs; ectothermic (dinosaurs endothermic?)

Superclass Gnathostomata, V
Class: Aves Birds Flight adaptations: wings

(honeycombed bone); feathers (keratin); toothless; one ovary Evolved from reptiles (amniote egg and leg scales); endothermic (4-chambered heart) Archaeopteryx (stemmed from an ancestor that gave rise to birds)

Superclass Gnathostomata, VI
Class: Mammalia Mammary glands; hair (keratin);

endothermic; 4-chambered heart; large brains; teeth differentiation Evolved from reptilian stock before birds Monotremes (egg-laying): platypus; echidna Marsupials (pouch): opossums, kangaroos, koalas Eutherian (placenta): all other mammals

Order: Primates (evolution)
 Characteristics: hands & feet for

grasping; large brains, short jaws, flat face; parental care and complex social behaviors  Suborder: Prosimii •lemurs, tarsiers  Suborder: Anthropoidea •monkeys, apes, humans (opposable thumb)  45-50 million years ago  Paleoanthropology: study of human origins  Hominoid: great apes & humans  Hominid (narrower classification): √ australopithecines (all extinct) √ genus Homo (only 1 exant, sapiens)

Human evolution Misconceptions:
1- Chimp ancestor (2 divergent branches) 2- Step-wise series (coexistence of human species) 3- Trait unison vs. mosaic evolution (bipedalism,

upright, enlarged brain)

The first humans
 Ape-human split (5-7 mya)  Australopithecus; “Lucy” (4.0 mya)  Homo habilis; “Handy Man” (2.5 mya)  Homo erectus; first to migrate (1.8

mya)  Neanderthals (200,000 ya)  Homo sapiens (1.0 mya?)  Multiregional model (parallel evolution)  “Out of Africa” (replacement evolution)

Regulatory systems
 Hormone~ chemical signal secreted

into body fluids (blood) communicating regulatory messages  Target cells~ body cells that respond to hormones  Endocrine system/glands~ hormone secreting system/glands (ductless); exocrine glands secrete chemicals (sweat, mucus, enzymes) through ducts  Neurosecretory cells~ actual cells that secrete hormones  Feedback mechanisms ~ negative and positive

Local regulators: cells adjacent to or near point of secretion
Growth factors ~

proteins for

cell proliferation Nitric oxide (NO) ~ neurotransmitter; cell destruction; vessel dilation Prostaglandins ~ modified fatty acids secreted by placenta and immune system; also found in semen

Mode of Action: Chemical Signaling
 1- Plasma membrane reception

• signal-transduction pathways (neurotransmitters, growth factors, most hormones)  2- Cell nucleus reception • steroid hormones, thyroid hormones, some local regulators

Vertebrate Endocrine System
 Tropic hormones ~

a hormone that has another endocrine gland as a target  Hypothalamus~pituitary  Pituitary gland  Pineal gland  Thyroid gland  Parathyroid glands  Thymus  Adrenal glands  Pancreas  Gonads (ovary, testis)

The hypothalamus & pituitary, I
 Releasing and inhibiting hormones  Anterior pituitary:  Growth (GH)~bones

√gigantism/dwarfism √acromegaly  Prolactin (PRL)~mammary glands; milk production  Follicle-stimulating (FSH) &  Luteinizing (LH)~ovaries/testes  Thyroid-stimulating (TSH)~ thyroid  Adrenocorticotropic (ACTH)~ adrenal cortex  Melanocyte-stimulating (MSH)  Endorphins~natural ‘opiates’; brain pain receptors

The pituitary, II
The posterior

pituitary: Oxytocin~
uterine and mammary gland cell contraction

Antidiuretic (ADH)~
retention of water by kidneys

The pineal, thyroid, & parathyroid
Melatonin~ pineal
gland; biological rhythms

Thyroid

hormones:
Calcitonin~ lowers blood calcium Thyroxine~ metabolic processes

Parathyroid

(PTH)~
calcium

raises blood

The pancreas
Islets of Langerhans •glucagon~ Alpha cells:
raises blood glucose levels

Beta cells:
•insulin~ lowers blood glucose levels

Type I diabetes mellitus
(insulin-dependent; autoimmune disorder)

Type II diabetes mellitus
(non-insulin-dependent; reduced responsiveness in insulin targets)

Adrenal medulla (catecholamines): •epinephrine &
norepinephrine~
pressure) increase basal metabolic rate (blood glucose and

The adrenal glands

Adrenal cortex (corticosteroids):

•glucocorticoids (cortisol)~ raise blood glucose •mineralocorticoids (aldosterone)~ reabsorption of Na+ and K+

The gonads
Steroid hormones:
precursor is cholesterol

androgens
(testosterone)~ sperm formation; male secondary sex characteristics; gonadotropin

estrogens
(estradiol)~uterine lining growth; female secondary sex characteristics; gonadotropin
Q u ic k Tim e™ an d a C in ep ak d ec om p ressor are n eed ed to see t h is p ic t u re.

progestins
(progesterone)~uterine lining growth

Steroid Hormone Action

QuickTime™ and a Cinepak decompressor are needed to see this picture.

Index

Overview
Asexual (one parent) fission (parent separation) budding (corals) gemmules (porifera) fragmentation &

regeneration (inverts) Sexual (fusion of haploid gametes) gametes (sex cells) zygote (fertilized egg) ovum (unfertilized egg) gamete) spermatozoon (male

Reproductive cycles
Parthenogenesis
unfertilized egg development; haploid, sterile adults (honeybees) both male & female reproductive systems; sessile & burrowing organisms (earthworms) reversal of gender during lifetime

Hermaphroditism

Sequential hermaphroditism

•protogynous (female 1st) •protandrous (male 1st)

Mechanisms of sexual reproduction
Fertilization
(union of sperm and egg)

• external • internal Pheromones
chemical signals that influence the behavior of others (mate attractants)

Mammalian reproduction, I
The Human Male
 Testes~ male gonads  Seminiferous tubules~ sperm
formation

 Leydig cells~ hormone production  Scrotum~ outside body temp.  Epididymis~ sperm development  Vas deferens~ sperm propulsion  Seminal vesicles~ semen  Prostate gland~ anticoagulant;
nutrients

 Bulbourethral glands~ acid
neutralizer

 Penis/urethra~ semen delivery

Mammalian reproduction, II
The Human Female Ovaries~ female gonads Follicle~ egg capsule Corpus luteum~ hormone
secretion

Oviduct~ fertilization Uterus/endometrium
~ womb/lining

Cervix/vagina~ sperm
receptacle

Spermatogenesis
 Puberty until death!  Seminiferous tubules~ location  Primordial germ cell (2N)~
differentiate into….

 Spermatogonium (2N)~ sperm
precursor

 Repeated mitosis into….  Primary spermatocyte (2N)  1st meiotic division  Secondary spermatocyte (1N)  2nd meiotic division  Spermatids (1N)~Sertoli cells….  Sperm cells (1N)

Oogenesis
 Ovaries  Primordial germ cells (2N)  Oogonium (2N)  Primary oocyte (2N)  Between birth & puberty;

 As embryo until menopause...

prophase I of meiosis  Puberty; FSH; completes meiosis I  Secondary oocyte (1N); polar body  Meiosis II; stimulated by fertilization  Ovum (1N); 2nd polar body

The female pattern
 Estrous cycles/estrus
(many mammals)

 Menstrual cycle (humans
and many other primates):

 Ovarian/Menstrual

cycles~ •follicular phase~follicle growth •ovulation~ oocyte release •luteal phase~
hormone release

Embryonic & fetal development
Gestation~ pregnancy 1st trimester: organogenesis fetus (week 8; all adult features) HCG hormone (menstruation
override; pregnancy test detection)

Parturition~birth Labor~uterine contractions Lactation~prolactin & oxytocin

Modern technologies

Index

Nutritional requirements
 Undernourishment: caloric deficiency  Overnourishment (obesity): excessive

food intake  Malnourishment: essential nutrient deficiency  Essential nutrients: materials that must be obtained in preassembled form  Essential amino acids: the 8 amino acids that must be obtained in the diet  Essential fatty acids: unsaturated fatty acids  Vitamins: organic coenzymes  Minerals: inorganic cofactors

Food types/feeding mechanisms
 Opportunistic  Herbivore: eat autotrophs  Carnivore: eat other animals  Omnivore: both  Feeding Adaptations  Suspension-feeders: sift food

from water (baleen whale)  Substrate-feeders: live in or on their food (leaf miner) (earthworm: deposit-feeder)  Fluid-feeders: suck fluids from a host (mosquito)  Bulk-feeders: eat large pieces of food (most animals)

Overview of food processing
 1-Ingestion: act of eating  2-Digestion: process of food break down  enzymatic hydrolysis  intracellular: breakdown within cells (sponges)  extracellular: breakdown outside cells (most animals)  alimentary canals (digestive tract)  3- Absorption: cells take up small molecules  4- Elimination: removal of undigested material

Mammalian digestion, I
 Peristalsis: rhythmic waves of contraction by smooth

muscle  Sphincters: ring-like valves that regulate passage of material  Accessory glands: salivary glands; pancreas; liver; gall bladder

Mammalian digestion, II
 Oral cavity

•salivary amylase •bolus  Pharynx •epiglottis  Esophagus  Stomach •gastric juice •pepsin/pepsinogen (HCl) •acid chyme •pyloric sphincter

 Small intestine •duodenum •bile  Intestinal digestion: a-carbohydrate b-protein c-

Mammalian digestion, III
nucleic acid d-fat

Mammalian digestion, IV
 Villi / microvilli  Lacteal (lymphatic)  Chylomicrons (fats mixed with cholesterol)  Hepatic portal vessel

Mammalian digestion, V
 Hormonal Action:  Gastrin food---> stomach wall

---> gastric juice  Enterogastrones (duodenum)  1-Secretin acidic chyme---> pancreas to release bicarbonate  2-Cholecystokinin (CCK) amino/fatty acids---> pancreas to release enzymes and gall bladder to release bile

 Large intestine (colon)  Cecum  Appendix  Feces  Rectum/anus

Dentition: an animal’s assortment of

Evolutionary adaptations

teeth Digestive system length Symbiosis Ruminants

Overview of Mammalian Digestive Enzymes

Index

 Gastrovascular cavity (cnidarians, flatworms)  Open circulatory •hemolymph (blood & interstitial fluid)

Circulation system evolution, I

•sinuses (spaces surrounding organs)  Closed circulatory: blood confined to vessels  Cardiovascular system •heart (atria/ventricles) •blood vessels (arteries, arterioles, capillary beds, venules, veins) •blood (circulatory fluid)

Fish: 2-chambered heart; single circuit of blood flow Amphibians: 3-chambered heart; 2 circuits of blood flow-

Circulation system evolution, II

pulmocutaneous (lungs and skin); systemic (some mixing) Mammals: 4-chambered heart; double circulation; complete separation between oxygen-rich and oxygen poor blood

Double circulation
 From right ventricle to lungs via

pulmonary arteries through semilunar valve (pulmonary circulation)  Capillary beds in lungs to left atrium via pulmonary veins  Left atrium to left ventricle (through atrioventricular valve) to aorta  Aorta to coronary arteries; then systemic circulation  Back to heart via two venae cavae (superior and inferior); right atrium

The mammalian heart
 Cardiac cycle:

sequence of

filling and pumping  Systole- contraction  Diastole- relaxation  Cardiac output: volume of blood per minute  Heart rate- number of beats per minute  Stroke volume- amount of blood pumped with each contraction  Pulse: rhythmic stretching of arteries by heart contraction

The heartbeat
 Sinoatrial (SA) node (“pacemaker”): sets rate and timing

of cardiac contraction by generating electrical signals  Atrioventricular (AV) node: relay point (0.1 second delay) spreading impulse to walls of ventricles  Electrocardiogram (ECG or EKG)

Blood vessel structural differences
Capillaries
•endothelium; basement membrane

Arteries •thick connective
tissue; thick smooth muscle; endothelium; basement membrane

Veins

•thin connective tissue; thin smooth muscle; endothelium; basement membrane

The lymphatic system
 Lymphatic system: system

of vessels and lymph nodes, separate from the circulatory system, that returns fluid and protein to blood  Lymph: colorless fluid, derived from interstitial fluid  Lymph nodes: filter lymph and help attack viruses and bacteria  Body defense / immunity

 Plasma: liquid matrix of blood in which cells are suspended (90%

Blood

water)  Erythrocytes (RBCs): transport O2 via hemoglobin  Leukocytes (WBCs): defense and immunity  Platelets: clotting  Stem cells: pluripotent cells in the red marrow of bones  Blood clotting: fibrinogen (inactive)/ fibrin (active); hemophilia; thrombus (clot)

Cardiovascular disease
 Cardiovascular disease (>50% of

all deaths)  Heart attack- death of cardiac tissue due to coronary blockage  Stroke- death of nervous tissue in brain due to arterial blockage  Atherosclerosis: arterial plaques deposits  Arteriosclerosis: plaque hardening by calcium deposits  Hypertension: high blood pressure  Hypercholesterolemia: LDL, HDL

Gas exchange
CO2 <---> O2 Aquatic: •gills •ventilation
exchange •countercurrent

Terrestrial:

•tracheal systems •lungs

Mammalian respiratory systems
 Larynx (upper part of

respiratory tract)  Vocal cords (sound production)  Trachea (windpipe)

 Bronchi (tube to lungs)  Bronchioles  Alveoli (air sacs)  Diaphragm (breathing

muscle)

 Positive pressure breathing: pushes air into lungs (frog)  Negative pressure breathing: pulls air into lungs (mammals)  Inhalation: diaphragm contraction; Exhalation: diaphragm

Breathing

relaxation  Tidal volume: amount of air inhaled and exhaled with each breath (500ml)  Vital capacity: maximum tidal volume during forced breathing (4L)  Regulation: CO2 concentration in blood (medulla oblongata)

Respiratory pigments: gas transport
 Oxygen transport Hemocyanin: found in hemolymph

of arthropods and mollusks (Cu)  Hemoglobin: vertebrates (Fe)  Carbon dioxide transport Blood plasma (7%)  Hemoglobin (23%)  Bicarbonate ions (70%)  Deep-diving air-breathers Myoglobin: oxygen storing protein

Index

Lines of Defense

Nonspecific Defense Mechanisms……

Phagocytic and Natural Killer Cells
 Neutrophils 60-70% WBCs; engulf and destroy microbes at infected tissue  Monocytes 5% WBCs; develop into….  Macrophages destroy microbes
enzymatically

 Eosinophils 1.5% WBCs; destroy large parasitic invaders (blood flukes)  Natural killer (NK) cells destroy virus-infected body cells & abnormal cells

The Inflammatory Response
 1- Tissue injury; release of chemical signals~

• histamine (basophils/mast cells): causes Step 2... • prostaglandins: increases blood flow & vessel permeability • chemokines: secreted by blood vessel endothelial cells mediates  2/3- Dilation and increased permeability of capillary~ phagocytotic migration of WBCs • fever & pyrogens: leukocyte-released molecules increase body temperature  4- Phagocytosis of pathogens~

Lymphocyctes •pluripotent stem
cells... • B Cells (bone marrow) • T Cells (thymus)

Specific Immunity
elicits a response by lymphocytes (virus, bacteria, fungus, protozoa, parasitic worms)

Antigen: a foreign molecule that

Antibodies: antigen-binding
immunoglobulin, produced by B cells

Antigen receptors: plasma
membrane receptors on b and T cells

Clonal selection
 Effector cells: short-lived cells that

combat the antigen  Memory cells: long-lived cells that bear receptors for the antigen  Clonal selection: antigen-driven cloning of lymphocytes
 “Each antigen, by binding to

specific receptors, selectively activates a tiny fraction of cells from the body’s diverse pool of lymphocytes; this relatively small number of selected cells gives rise to clones of thousands of cells, all specific for and dedicated to eliminating the antigen.”

Induction of Immune Responses Primary immune response:

lymphocyte proliferation and differentiation the 1st time the body is exposed to an antigen

Plasma cells: antibody-producing effector B-cells Secondary immune response: immune response if the
individual is exposed to the same antigen at some later time~ Immunological memory

Self/Nonself Recognition
 Self-tolerance: capacity to distinguish self from non-self  Autoimmune diseases: failure of self-tolerance; multiple sclerosis, lupus,

rheumatoid arthritis, insulin-dependent diabetes mellitus  Major Histocompatability Complex (MHC): body cell surface antigens coded by a family of genes  Class I MHC molecules: found on all nucleated cells  Class II MHC molecules: found on macrophages, B cells, and activated T cells  Antigen presentation: process by which an MHC molecule “presents’ an intracellular protein to an antigen receptor on a nearby T cell  Cytotoxic T cells (TC): bind to protein fragments displayed on class I MHC molecules  Helper T cells (TH): bind to proteins displayed by class II MHC molecules

Types of immune responses
 Humoral immunity  B cell activation  Production of antibodies  Defend against bacteria,

toxins, and viruses free in the lymph and blood plasma  Cell-mediated immunity  T cell activation  Binds to and/or lyses cells  Defend against cells infected with bacteria, viruses, fungi, protozoa, and parasites; nonself interaction

 Function in both humoral & cell-mediated immunity  Stimulated by antigen presenting cells (APCs)  T cell surface protein CD4 enhances activation  Cytokines secreted (stimulate other lymphocytes):

Helper T lymphocytes
a) interleukin-2 (IL-2): activates B cells and cytotoxic T cells b) interleukin-1 (IL-1): activates helper T cell to produce IL-2

 Destroy cells infected by intracellular pathogens and cancer cells  Class I MHC molecules (nucleated body cells) expose foreign proteins  Activity enhanced by CD8 surface protein present on most cytotoxic T cells

Cell-mediated: cytotoxic T cells

(similar to CD4 and class II MHC)  TC cell releases perforin, a protein that forms pores in the target cell membrane; cell lysis and pathogen exposure to circulating antibodies

Humoral response: B cells
Stimulated by T-dependent

antigens (help from TH cells) Macrophage (APCs) with class II MHC proteins Helper T cell (CD4 protein) Activated T cell secretes IL-2 (cytokines) that activate B cell B cell differentiates into memory and plasma cells (antibodies)

Antibody Structure & Function
Epitope: region on antigen surface recognized by

antibodies 2 heavy chains and 2 light chains joined by disulfide bridges Antigen-binding site (variable region)

5 classes of Immunoglobins
 IgM: 1st to circulate; indicates

infection; too large to cross placenta  IgG: most abundant; crosses walls of blood vessels and placenta; protects against bacteria, viruses, & toxins; activates complement  IgA: produced by cells in mucous membranes; prevent attachment of viruses/bacteria to epithelial surfaces; also found in saliva, tears, and perspiration  IgD: do not activate complement and cannot cross placenta; found on surfaces of B cells; probably help differentiation of B cells into plasma and memory cells  IgE: very large; small quantity; releases histamines-allergic reaction

Antibody-mediated Antigen Disposal
 Neutralization (opsonization): antibody binds to and blocks antigen

activity  Agglutination: antigen clumping  Precipitation: cross-linking of soluble antigens  Complement fixation: activation of 20 serum proteins, through cascading action, lyse viruses and pathogenic cells

Immunity in Health & Disease
 Active immunity/natural: conferred

immunity by recovering from disease  Active immunity/artificial: immunization and vaccination; produces a primary response  Passive immunity: transfer of immunity from one individual to another • natural: mother to fetus; breast milk • artificial: rabies antibodies  ABO blood groups (antigen presence)  Rh factor (blood cell antigen); Rh- mother vs. an Rh+ fetus (inherited from father)

function
 Allergies (anaphylactic shock): hypersensitive responses to

environmental antigens (allergens); causes dilation and blood vessel permeability (antihistamines); epinephrine  Autoimmune disease: multiple sclerosis, lupus, rheumatoid arthritis, insulin-dependent diabetes mellitus  Immunodeficiency disease: SCIDS (bubble-boy); A.I.D.S.

Overview of Human Immune System Function

Index

Homeostasis: regulation of internal environment
Thermoregulation
internal temperature

Osmoregulation
solute and water balance

Excretion
nitrogen containing waste

Regulation of body temperature
 Thermoregulation  4 physical processes:  Conduction~transfer of heat between molecules of body and environment  Convection~transfer of heat as water/air move across body surface  Radiation~transfer of heat produced by organisms  Evaporation~loss of heat from liquid to gas  Sources of body heat:  Ectothermic: determined by environment  Endothermic: high metabolic rate generates high body heat

Regulation during environmental extremes 
Torpor~ low activity; decrease in metabolic rate
 1- Hibernation

long term or winter torpor (winter cold and food scarcity); bears, squirrels  2- Estivation short term or summer torpor (high temperatures and water scarcity); fish, amphibians, reptiles  Both often triggered by length of daylight

Water balance and waste disposal
 Osmoregulation:

management of the body’s water content and solute composition  Nitrogenous wastes: breakdown products of proteins and nucleic acids; ammonia-very toxic  Deamination~  Ammonia: most aquatic animals, many fish  Urea: mammals, most amphibians, sharks, bony fish (in liver; combo of NH3 and CO2)  Uric acid: birds, insects, many reptiles, land snails

Osmoregulators
 Osmoconformer: no active adjustment of internal

osmolarity (marine animals); isoosmotic to environment  Osmoregulator: adjust internal osmolarity (freshwater, marine, terrestrial)  Freshwater fishes (hyperosmotic)- gains water, loses; excretes large amounts of urine salt vs. marine fishes (hypoosmotic)- loses water, gains salt; drinks large amount of saltwater

Excretory Systems
 Production of urine by 2 steps: • Filtration (nonselective) •

Reabsorption (secretion of solutes)  Protonephridia ~ flatworms (“flame-bulb” systems)  Metanephridia ~ annelids (ciliated funnel system)  Malpighian tubules ~ insects (tubes in digestive tract)  Kidneys ~ vertebrates

Kidney Functional Units
 Renal artery/vein: kidney blood flow  Ureter: urine excretory duct  Urinary bladder: urine storage  Urethra: urine elimination tube  Renal cortex (outer region)  Renal medulla (inner region)  Nephron: functional unit of kidney  Cortical nephrons (cortex; 80%)  Juxtamedullary nephrons (medulla;

20%)

hormones
 Antidiuretic hormone (ADH) ~ secretion

increases permeability of distal tubules and collecting ducts to water (H2O back to body); inhibited by alcohol and coffee  Juxtaglomerular apparatus (JGA) ~ reduced salt intake--->enzyme renin initiates conversion of angiotension (plasma protein) to angiotension II (peptide); increase blood pressure and blood volume by constricting capillaries  Angiotension II also stimulates adrenal glands to secrete aldosterone; acts on distal tubules to reabsorb more sodium, thereby increasing blood pressure (renin-angiotensionaldosterone system; RAAS)  Atrial natriuretic factor (ANF) ~ walls of atria; inhibits release of renin, salt reabsorption, and aldosterone release

Overview of Mammalian Nephron Function

Index

Nervous systems
Effector cells~
muscle or gland cells

Nerves~

bundles of neurons wrapped in connective tissue

Central nervous

system (CNS)~
and spinal cord

brain

Peripheral nervous

system (PNS)~
sensory and motor neurons

Structural Unit of Nervous System
 Neuron~ structural and functional unit  Cell body~ nucelus and organelles  Dendrites~ impulses from tips to neuron  Axons~ impulses toward tips  Myelin sheath~ supporting, insulating layer  Schwann cells~PNS support cells  Synaptic terminals~ neurotransmitter releaser  Synapse~ neuron junction

Simple Nerve Circuit
 Sensory neuron: convey information

to spinal cord  Interneurons: information integration  Motor neurons: convey signals to effector cell (muscle or gland)  Reflex: simple response; sensory to motor neurons  Ganglion (ganglia): cluster of nerve cell bodies in the PNS  Supporting cells/glia: nonconductiong cell that provides support, insulation, and protection

Neural signaling, I
 Membrane potential (voltage differences across the plasma membrane)  Intracellular/extracellular ionic concentration difference  K+ diffuses out (Na+ in); large anions cannot follow….selective

permeability of the plasma membrane  Net negative charge of about -70mV

Neural signaling, II
 Excitable cells~ cells that can change membrane potentials (neurons, muscle)  Resting potential~ the unexcited state of excitable cells  Gated ion channels (open/close response to stimuli): photoreceptors; vibrations in air

(sound receptors); chemical (neurotransmitters) & voltage (membrane potential changes)  Graded Potentials (depend on strength of stimulus):  1- Hyperpolarization (outflow of K+); increase in electrical gradient; cell becomes more negative  2- Depolarization (inflow of Na+); reduction in electrical gradient; cell becomes less negative

Neural signaling, III
 Threshold potential: if stimulus reaches a     

 

certain voltage (-50 to -55 mV)…. The action potential is triggered…. Voltage-gated ion channels (Na+; K+) 1-Resting state •both channels closed 2-Threshold •a stimulus opens some Na+ channels 3-Depolarization •action potential generated •Na+ channels open; cell becomes positive (K+ channels closed) 4-Repolarization •Na+ channels close, K+ channels open; K+ leaves •cell becomes negative 5-Undershoot •both gates close, but K+ channel is slow; resting state restored Refractory period~ insensitive to depolarization due to closing of Na+ gates

Neural signaling, IV
 “Travel” of the action potential is self-propagating  Regeneration of “new” action potentials only after refractory

period  Forward direction only  Action potential speed:  1-Axon diameter (larger = faster; 100m/sec)  2-Nodes of Ranvier (concentration of ion channels); saltatory conduction; 150m/sec

Synaptic communication
 Presynaptic cell: transmitting cell  Postsynaptic cell: receiving cell  Synaptic cleft: separation gap  Synaptic vesicles:

neurotransmitter releasers  Ca+ influx: caused by action potential; vesicles fuse with presynaptic membrane and release….  Neurotransmitter

Neurotransmitters
Acetylcholine (most common) •skeletal muscle Biogenic amines (derived from amino acids)

•norepinephrine Amino acids Neuropeptides •endorphin

•dopamine

•serotonin

(short chains of amino acids)

Vertebrate PNS
Cranial nerves (brain origin) Spinal nerves (spine origin) Sensory division Motor division

•somatic system
voluntary, conscious control

•autonomic system √parasympathetic
conservation of energy

√sympathetic
increase energy consumption

The Vertebrate Brain
 Forebrain •cerebrum~memory, learning,
emotion •cerebral cortex~sensory and motor nerve cell bodies •corpus callosum~connects left and right hemispheres

•thalamus; hypothalamus •inferior (auditory) and  Midbrain superior (visual) colliculi •cerebellum~coordination of  Hindbrain movement •medulla oblongata/ pons~autonomic, homeostatic functions

Index

Vertebrate Skeletal Muscle
 Contract/relax:
pairs w/skeleton antagonistic

 Muscles: bundle of….  Muscle fibers: single cell w/ many nuclei
consisting of….

 Myofibrils: longitudinal bundles
composed of….

 Myofilaments:

•Thin~ 2

strands of actin protein and a regulatory protein •Thick~ myosin protein

 Sarcomere: repeating unit of muscle
tissue, composed of….

 Z lines~sarcomere border  I band~only actin protein  A band~actin & myosin protein overlap  H zone~central sarcomere; only myosin

Sliding-filament model
Theory of muscle contraction Sarcomere length reduced Z line length becomes shorter Actin and myosin slide past each other (overlap
increases)

Actin-myosin interaction
 1- Myosin head hydrolyzes ATP to ADP and inorganic phosphate

(Pi); termed the “high energy configuration”  2- Myosin head binds to actin; termed a “cross bridge”  3- Releasing ADP and (Pi), myosin relaxes sliding actin; “low energy configuration”  4- Binding of new ATP releases myosin head  Creatine phosphate~ supplier of phosphate to ADP

Muscle contraction regulation, I
Relaxation:
tropomyosin blocks myosin binding sites on actin

Contraction:
calcium binds to toponin complex; tropomyosin changes shape, exposing myosin binding sites

Muscle contraction regulation, II
Calcium (Ca+)~ concentration
regulated by the….

Sarcoplasmic reticulum~

a specialized endoplasmic reticulum

Stimulated by action potential in

a motor neuron T (transverse) tubules~ travel
channels in plasma membrane for action potential

Ca+ then binds to troponin

I am the Lorax. I speak for the trees. I speak for the trees, for the trees have no tongues.

Index

Ecology
Components:

•abiotic~nonliving chemical &
physical factors

•biotic~living factors Population~group of
individualsof the same species in a particular geographical area

Community~assemblage of
populations of different species

Ecosystem~all abiotic factors
and the community of species in an area

Rachel Carson, 1962,

Silent Spring

Abiotic factors
Biosphere~the sum of all
the planet’s ecosystems

Biome~

areas of predominant flora and fauna

Temperature Water Sunlight Wind Rocks & Soil Periodic
Ecotone: biome grading areas

disturbances

Global climate
• Precipitation & Winds

Lake stratification & turnover
Thermal stratification~ vertical temperature layering Biannual mixing~ spring and summer Turnover~ changing water temperature profiles; brings
oxygenated water from the surface to the bottom and nutrient rich water form the bottom to the surface

Aquatic biomes
Vertical

stratification:

•photic zone~ photosynthetic light •aphotic zone~ little light •thermocline~ narrow stratum of rapid temperature chang •benthic zone~ bottom substrate

Benthos~
organisms

community of

Detritus~ dead organic
matter; food for benthic organisms

Freshwater biomes
Littoral zone~
shallow, well-lit waters close to shore well-lit, open water farther from shore deep, aphotic waters

Limnetic zone~

Profundal zone~

Lake classification:
•oligotrophic~ deep, nutrient poor •eutrophic~ shallow, high nutrient content •mesotrophic~
moderate water productivity

Wetland~ area covered with Estuary~ area where freshwater
merges with ocean

Marine biomes
Intertidal zone~ area
where land meets water

Neritic zone~ shallow
regions over continental shelves

Oceanic zone~ very deep
water past the continental shelves

Pelagic zone~ open water
of any depth

Benthic zone~ seafloor
bottom

Abyssal zone~ benthic
region in deep oceans

 Tropical forests~ equator; most complex; constant temperature and rainfall;       

Terrestrial biomes

canopy Savanna~ tropical grassland with scattered trees; occasional fire and drought; large herbivores Desert~ sparse rainfall (<30cm/yr) Chaparral~ spiny evergreens at midlatitudes along coasts Temperate grassland~ all grasses; seasonal drought, occasional fires; large mammals Temperate deciduous forest~ midlatitude regions; broad-leaf deciduous trees Coniferous forest~ cone-bearing trees Tundra~ permafrost; very little precipitation

Index

Behavior
Ethology~ study of animal behavior Causation: •proximate~
physiological & genetic mechanisms of behavior •ultimate~ evolutionary significance of behavior

Sign stimulus~ external sensory
stimulus

Fixed action pattern (FAP)~
sequence of acts; unchangeable; carried to completion

Ex: 3-spined stickleback
(Tinbergen ‘73 Nobel)

Supernormal stimulus

Learning?
 Maturation~ behavior due to developing physiological changes  Habituation~ loss of responsiveness to stimuli that convey  no information; simple learning  Imprinting~ limited learning within a specific time period

•critical period (Lorenz, ‘73 Nobel)
 Associative learning:

•classical conditioning~ Pavlov’s dogs •operant conditioning (trial and error)~ “Skinner’s box”

Social behavior
Sociobiology~
evolutionary theory applied to social behavior (Hamilton) determining access to resources

Agonistic behavior~ contest behavior Dominance hierarchy~
“pecking order” defends excluding others linear

QuickTime™ and a Cinepak decompressor are needed to see this picture.

Territoriality~ an area an individual Mating systems:

•promiscuous~ no strong pair bonds •monogamous~ one male/one female •polygamous~ one with many •polygyny~ one male/many females •polyandry~ one
female/many males

Altruistic behavior
Inclusive fitness~ total effect
an individual has on proliferating its genes by its own offspring and aid to close relatives

Coefficient of relatedness~
proportion of genes that are identical because of common ancestors

Kin selection~ aiding related
individuals altruistically

Reciprocal altruism~
exchange of aid; humans?

Index

Population characteristics
Density~ # of individuals per unit of area

•counts •sample size estimate •indirect indicators •markrecapture Dispersion~ pattern of spacing •random~ unpredictable, patternless
spacing (a)

•clumped~ patchy aggregation (b) •uniform~ even spacing (c)

Demography: factors that affect growth & decline of
populations
 Birthrate (natality, fecundity)~ # of offspring produced  Death rate (mortality)  Age structure~ relative number of individuals of each age  Survivorship curve~ plot of numbers still alive at each age

Population Growth Models
Exponential model (red)
• idealized population in an unlimited environment (Jcurve); r-selected species (r=per
capita growth rate)

Logistic model (blue)
•carrying capacity (K):
maximum population size that a particular environment can support (Scurve); K-selected species

Population life history “strategies”
r-selected
(opportunistic)

K-selected
(equilibrial)

Short maturation &

Long maturation &

lifespan Many (small) offspring; usually 1 (early) reproduction; no parental care High death rate

lifespan Few (large) offspring; usually several (late) reproductions; extensive parental care Low death rate

Population limiting factors
Density-dependent

factors

•competition •predation •stress/crowding •waste accumulation

Density-independent

factors •weather/climate
•periodic disturbances

Index

Community structure
Community~ an assemblage of
populations living close enough together for potential interaction

Richness

(number of species)

& abundance……. Species diversity Hypotheses: •Individualistic~ chance
assemblage with similar abiotic requirements

•Interactive~ assemblage
locked into association by mandatory biotic interactions

Interactions
Interspecific
(interactions between populations of different species within a community):

•Predation
including parasitism; may involve a keystone species/predator

•Competition •Commensalism •Mutualism

Predation defense
Cryptic
(camouflage)

coloration Aposematic (warning) coloration Mimicry~ superficial resemblance
to another species

√ Batesian~ palatable/
harmless species mimics an unpalatable/ harmful model aposematically colored species resemble each other

Mullerian~ 2 or more unpalatable,

Competition: a closer look
Interference~ actual fighting
over resources

Exploitative~ consumption or
use of similar resources

Competitive Exclusion

Principle

(Lotka / Volterra)~ 2 species with similar needs for the same limiting resources cannot coexist in the same place

√Gause experiment

Competition evidence
Resource Character

partitioning~ sympatric
species consume slightly different foods or use other resources in slightly different ways

displacement~
sympatric species tend to diverge in those characteristics that overlap

Ex: Anolis lizard sp. perching sites in the Dominican Republic

Ex: Darwin’s finch beak size on the Galapagos Islands

The Niche
Ecological niche~ the sum total of an
organism’s use of biotic and abiotic resources in its environment; its “ecological role”

√ fundamental~ the set of resources
a population is theoretically capable of using under ideal conditions √ realized~ the resources a population actually uses

Thus, 2 species cannot coexist in a

community if their niches are identical

Ex: Barnacle sp. on the coast of Scotland

Succession
Ecological

succession~ transition in
species composition over ecological time

Primary~ begun in lifeless
area; no soil, perhaps volcanic activity or retreating glacier

Secondary~ an existing
community has been cleared by some disturbance that leaves the soil intact

Index

Relationships, I
Trophic structure / levels~ feeding
relationships in an ecosystem

Primary producers~ the trophic level
that supports all others; autotrophs

Primary consumers~ herbivores Secondary and tertiary

consumers~ carnivores Detrivores/detritus~ special
consumers that derive nutrition from nonliving organic matter

Food chain~ trophic level food pathway

Relationships, II
Food webs~
interconnected feeding relationship in an ecosystem

Energy Flow, I
 Primary productivity (amount of light energy converted to chemical

•Gross (GPP): total energy •Net (NPP): represents the storage of energy available to consumers •Rs: respiration  NPP = GPP - Rs  Biomass: primary productivity reflected as dry weight of organic material  Secondary productivity: the rate at which an ecosystem's consumers convert chemical energy of the food they eat into their own new biomass

energy by autotrophs)

Energy Flow, II Ecological efficiency
: % of E transferred from one trophic level to the next (5-20%) multiplicative loss of energy in trophic levels

Pyramid of productivity: Biomass pyramid:

trophic representation of biomass in ecosystems trophic representation of the number of organisms in an ecosystem

Pyramid of numbers:

Chemical Cycling
   

 Biogeochemical cycles: the various nutrient circuits, which involve

both abiotic and biotic components of an ecosystem Water Carbon Nitrogen Phosphorus

Human Impact
Biological magnification: trophic
process in which retained substances become more concentrated at higher levels

Greenhouse effect: warming of
planet due to atmospheric accumulation of carbon dioxide

Ozone depletion:

effect of chlorofluorocarbons (CFC’s) released into the atmosphere

Rainforest destruction Cause: Overpopulation?

Index

Biodiversity crisis
 Extinction ~ natural phenomenon, however, rate is of concern…..  50% loss of species when 90% of

habitat is lost  Major Threats:
 Habitat destruction ~ single greatest threat; cause of 73% of species designation as extinct, endangered, vulnerable, rare; 93% of coral reefs  Competition by exotic (nonnative) species ~ cause of 68% of species designation as extinct, endangered, vulnerable, rare; travel  Overexploitation ~ commercial harvest or sport fishing; illegal trade

Biodiversity: Human welfare
25% of all medical

prescriptions Genetic variability Aesthetic and ethical reasons Species survival

Conservation biology focus
Preservationism: setting side
select areas as natural and underdeveloped

Resource conservation:
public lands to meet the needs of agriculture and extractive industries, i.e., ”multiple use”

Evolutionary / ecological

view:

natural systems result from millions of years of evolution and ecosystem processes are necessary to maintain the biosphere

Geographic distribution of biodiversity
Energy availability
solar radiation ~ environmental patchiness ~

Habitat heterogeneity Niche specialization
narrow resource range specialization ~

Population

interactions

~ complex population interactions

Population & species level conservation
Biodiversity hot spot:
small area with an exceptional concentration of species

Endemic species:
found nowhere else

species

Endangered species:
organism “in danger of extinction”

Threatened species:
to become endangered in the foreseeable future

likely

Bioremediation:

use of living organisms to detoxify polluted systems

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