Lab Practical Study Guide

I. Bacteriology A. Introduction

1. Taxonomy went from a 5 kingdom scheme to a 3; Eukarya, Archea, & Bacteria. (Monera became obsolete)

2. Bacteria: prokaryotic (oldest organisms; extremophiles), single-celled, cell wall of peptidoglycan, no membrane bound organelles or nuclear envelope, lack chromosomes(ring DNA called plasmids),binary fission: cell duplicates and divides into two.

B. Exercise 1: Characteristics of Bacteria 1. bacterial colony: millions of cells grown from a single bacterium. 2. Terminology used in describing bacterial colonies:

a. Common colony shapes: punctiform, round, filamentous, irregular. b. Common colony margins: smooth, curled, wavy, lobate, filamentous. c. Common colony surface characteristics: smooth, concentric, wrinkled

contoured. C. Bacteria can be classified according to 3 basic shapes

1. Bacilli (rods) <- 2. Cocci (spheres) ->

a. Found  in  tooth  plaque 3. Spirilla (spirals)  <-­‐  

D. GRAM STAIN PROCEDURE 1. Gram Positive, Gram Negative, or Gram Variable. 2. Positive & Negative are most common. 3. The response of the cells to the stain is due to the cell wall. 4. Three stains are used:

a. Violet (purple) b. Gram iodine c. Safranin (pink/red)

5. SUMMARY TABLE

Gram-Negative Bacteria Gram-Positive Bacteria

Complex cell wall Simple cell wall

Thin peptidoglycan cell wall layer

Thick peptidoglycan cell wall layer *The reason it absorbs more violet.

Outer lipopolysacccharide wall layer No outer lipop. Wall layer

Retain safranin Retain crystal violet/iodine

APPEARS PINK/RED APPEARS BLUE/PURPLE

E. Gram Staining: 1. Crystal violet/iodine stains all cells blue/purple. 2. Alchohol/acetone wash destains gram-negative cells. 3. Safranin stains gram-negative cells pink/red. 4. How to make a Gram Stain:

a. Cover the slide with 3-4 drops of crystal violet (wait 1 minute) b. Rinse the stain. c. Cover the smear with Gram iodine for 1 minute (setting the stain) d. Destain: drop the 95% alcohol/acetone mixture down the slide one at a

time. This removes the violet stain from the gram-negative bacteria. Rinse. e. Cover the smear with safranin for about a minute. Stains the destained

gram-negative bacteria pink/red. F. Observations:

1. E. Coli: Gram + (purple) 2. Staphylococcus Aureus: Gram – (pink)

G. Summary: 1. Prokaryotes v. eukaryotes: plasmids free (eukaryote) & circular DNA (pro)

H. Exercise 2: Ecological Succession of Bacteria in Milk 1. Pasteurizing milk doesn’t starilize; it destroys pathogenic bacteria. 2. Community Succession: as one community grows, it modifies it’s

environment, and creates a different community as a result. a. Lactobacillus & Streptococcus (gram-positive coccus) survive

pasteurization; they ferment lactose to lactate and acetic acid. b. Acidic environment causes casein to curd. (Yeasts & Molds grow well) c. Pseudomonas & Achromobacter (gram-negative rods), give milk a bad

smell. II. WATER COLIFORM LAB

A. Introduction: Intestinal bacteria are of prime concern when testing water. It is cheaper to test for E.Coli and coliforms (bacteria that resemble it). Coliforms: small, nonsporulating, anaerobic, gram-negative RODS, which ferment lactose to acid and gas.

B. 3 part test used to evaluate the quality of drinking water: 1. Presumptive: gas present within 24 hours is positive presumptive.

2. Confirmed 3. Completed

C. First Period Procedures 1. 5 tubes of double-strength lactose broth 2. 10 tubes of lactose broth 3. Start with a 60 mL sample; dilute with tapwater. 4. Incubate @ 35 degrees C; examine @ 24 hours.

D. Second Period Procedures 1. If gas is present within 24 hours it is a positive Presumptive test. (a lot of

tubes should have positive confirmed and completed tests.) 2. If gas was not present after 24 hours, but is present after 48 hours, the test as a

doubtful positive test, Confirmed test are likely to be negative. 3. No gas after 48 hours is a negative test. 4. Selected a positive tube that received the least amount of water. 5. Streak for isolation on a plate of EMB agar; confirmed test.

E. Third Period Procedures 1. Positive Confirmed test: presence of dark-red colonies or metallic green. 2. Take some “positive” colony growth and put it into a tube of lactose broth

and a nutrient agar slant. Incubate Completed test. F. Fourth Period Procedures

1. Lactose broth should have acid and gas within 24 hours. 2. Nutrient agar slant should be non-sporulating, gram-negative, small rods.

G. Analysis: 1. Calculated the approximate number of coliforms per 100 mL of water from

the MPN chart. # of Positive test tubes multiplied by 100. 2. A high number of positive tubes meant that the samples contained a relatively

high number of coliforms. III. MITOSIS & MEIOSIS EX. 1-5

A. Introduction: Interphase consists of G1, S, & G2; it’s where DNA replication, cell’s growth, and biochemical activity take place. M Phase: nucleus divides in mitosis, cytoplasm divides in cytokenisis.

B. Ex. 1 Modeling the Cell Cycle & Mitosis in an Animal Cell 1. Homologus chromosomes are the same length, same centromere position, and

contain genes for the same characters. 2. Interphase

a. A cell performs it’s specific functions. b. G1, S, G2 begin as cell division ends. c. The nuclear envelope contains uncoiled/decondensed chromosomes

chromatin is DNA in this state.

d. Centrosome: located outside of the nucleus; contains a pair of centrioles in animal cells; the organizing center for microtubules.

e. G1 phase: cytoplasmic mass increases and continues to do so throughout interphase. Proteins are synthesized, new organelles are formed, and some organelles grow and divide into two. Throughout interphase, one or more nucleoli are visible in the nucleus. Centriole duplication begins in late G1 or early S.

f. S Phase: DNA replication; create two homologous chromosomes connected by a (magnet) centromere. Synthesis of chromosomal proteins occurs during s phase. DNA synthesis continues until chromosomes have been duplicated. Each strand of a duplicated chromosome is called a sister chromatid. Sister chromatids are identical.

g. G2 Phase: continue cell activities; cells prepare for mitosis. Enzymes and necessary proteins for cell division are synthesized during this phase.

C. M PHASE 1. Five subphases

a. Prophase: begins when chromosomes begin to coil and condense; chromosomes become visible in a microscope; centrioles continue to move to opposite poles; spindle is formed between the centrioles.

b. Prometaphase: centrioles are @ the poles of the cell; chromosomes condense; nuclear envelope breaks down; spindles continue to form; kinetochore: spindle fibers associated with chromosomes @ protein structures. Each sister chromatid has one at the centromere; spindle microtubules now extend from the chromosomes to the Centrosome @ the poles. When centromeres lie on the equator, prometaphase ends.

c. Metaphase: all chromosomes are lined up @ the equator d. Anaphase: sister chromatids are pulled apart; and move toward opposite

poles. e. Telophase: spindle breaks down; chromosomes uncoil, nucleoli reappear,

nuclear envelope forms around each cluster. f. Cytokenisis: in animal cells a cleavage furrow forms; in plant cells a cell

plate forms. D. Ex. 2 Observing Mitosis & Cytokinesis in Plant Cells

1. Introduction: Plant cells don’t have centrioles, yet they have bundles of micro fibrils that connect to the poles at the ends of spindle; cell walls dictate cytokinesis.

2. Longitudinal Section through an onion root tip. a. Zone of cell division: root tip pushed into soil.

E. Ex 3: Animal Cells 1. Introduction: Look @ Whitefish blastula.

Zone  of  cell  division  

2. Mitosis in Whitefish Blastula a. Good source of cells is in the early embryo. b. Whitefish Blastula Cross Section Slide:

c. Identify: 1. Nucleus, nuclear envelope, & nucleolus. 2. Chromosomes 3. Mitotic spindle 4. Asters: array of microtubules surrounding each centriole pair @ the

poles of the spindle. 5. Centrioles: small dots seen @ the poles around which the microtubules

of the spindle and asters appear. 6. Cleavage furrow.

3. Differences between mitosis in animal & plant cells. a. Plant cells lack centrioles; cell plate b. Animal cells have centrioles; cleavage furrow.

F. Human Chromosomes in Dividing Leukocytes (white blood cells) 1. Condensed chromosomes but are not aligned on a spindle equator. 2. More or less than the normal number of chromosomes & abnormalities in

banding patterns can also be an indication of mental retardation. G. Ex. 4 Modeling Meiosis

1. Introduction: interphase between meiosis I and meiosis II doesn’t involve growth or synthesis of DNA.

2. Interphase is the same as in mitosis. 3. Two nuclear divisions: meiosis I and meiosis II.

4. Early in prophase I each chromosome finds its homologue and pairs. Synapsis. Tetrad: the chromosomes are duplicated; each paired duplicated chromosome complex is made of 4 strands. Ex) How many tetrad complexes do you have in your cell, which is 2n= 4? 2 tetrads.

5. Crossing over: represented by detaching and exchanging identical segments of any 2 non-sister chromatids in a tetrad. The crossover site forms a chiasma; crossing over produces new allelic combos among genes along a chromatid.

6. Metaphase: the 2 tetrads are lined up @ the equator; centromeres do not split as they do in mitosis.

7. Anaphase I: move one homologue toward each pole. 8. Metaphase II: the centromeres finally split. 9. Anaphase II: single chromosomes move to the poles.

H. Ex. 5 Meiosis in Sordaria fimicola: A Study of Crossing Over 1. Introduction: Sordaria fimicola is a fungus that spends most of its life as an n

mycelium: a mass of cells arranged in filaments. When these n fungi meet and fuse a 2n Zygote forms inside an ascus which is protected by a perithecium. Zygotes does meiosis and the resulting cells, ascopores, remain aligned. Ascopores do mitosis. 8 ascopores per ascus.

I. REVIEW: Lab Manual pg. 25 1. Define: mitosis, meiosis, cytokinesis, chromosome, chromatin, centromere,

centriole, Centrosome, kinetochore, spindle, aster, homologous, chromosome, synaptonemal complex, synapsis, tetrad, chiasma, sister chromatid, nucleolus, cell plate, cleavage furrow, diploid, haploid, crossing over, mycelium, perithecium, ascus.

2. Describe the activity of chromosomes in each stage of mitosis. 3. Describe the activity of chromosomes in each stage of meiosis I and II. 4. Why would the method of cytokinesis in animal cells not work in plant cells?

In order for the plant cell to make a new cell wall it can’t pull apart like the animal cell does; plant cells are packed tightly like bricks.

IV. Quantitative Variation in Sunflower Seeds (seed stripes) Lab. A. Language of comparing characteristics of populations.

1. Measures of central tendency: mean, median, & mode. a. Mean: (Σ x)/n x is a value & n is the number of values; it is the

“Average”; adding all values with a character and dividing it by total. b. Median: middle value. c. Mode: number that occurs the most frequently.

2. Distribution of values a. Standard deviation: √[Σ (x- frequency mean)²/(n-1)] where x is the value

and n is the number of values; this is a measure of the spread of distribution; this tells you where most of the values are found;

3. Histogram: represent the distribution of populations; character being discussed is on one axis & number of individuals in the population with that character are on the other.

B. Procedures of the lab 1. Separate the sunflower seeds in groups according to # of stripes. 2. Calculated the mean, median, & mode of the data.

V. SCIENTIFIC WRITING A. Introduction: Purpose of scientific papers is to be clear and concise so that your

work can be repeated. 6 key parts to a scientific paper. 1. Abstract: brief summary of experiment; critical background info; general

procedures and conclusions, key results. 2. Introduction: explains the context of the research; current understanding of the

topic; present other findings; objectives and hypotheses should be stated. 3. Materials &Methods: written in past tense; clearly describe every procedure

so that it could be duplicated; 4. Results: summarized data are presented in tables or figures; analyzed data; do

not discuss what the data means though. 5. Discussion: author’s interpretation of the data; compare original objectives

and hypothesis; unexpected results, errors, or problems should be mentioned. 6. Literature Cited: alpha order; for this course cite like a journal format.

a. For a journal article: Linhart, Y. B. and D. F. Tomback. 1985. Seed dispersal by nutcrackers causes multi-trunk growth form in pines. Oecologia (Berlin) 67:107-110.

b. For a chapter in a book: Hamrick, J. L. and M. J. Godt. 1990. Allozyme diversity in plant species. In Plant Population Genetics, Breeding, and Genetic Resources. A. D. H. Brown, M. T. Clegg, A. L. Kahler, and B. S. Weir, editors. Sinauer Associates Inc., Sunderland, MA. 43-63.

c. For an entire book: Darwin, C. R. 1877. The different forms of flowers on plants of the same species. University of Chicago Press, London, UK.

d. For a class lab or lecture notes: Gibson, J.P. 1997. Biology 308 lecture. April 18. Agnes Scott College, Decatur, GA.

e. For an internet citation: United States Department of Agriculture, National Resources Conservation Service. 2001. The PLANTSDatabase, Version 3.1 (http://plants.usda.gov). National Plant Data Center, Baton Rouge, LA 70874-4490 USA.

f. In text citations should have author and year (Linhart 1985). 7. Tables & Figures: each table and figure should be able to stand on its own;

numbered; captions; clear data; no raw data; referenced in the text. B. Scientific Writing Appendix in Lab Manual

1. Scientific paper includes: Title (statement of question or problem), Abstract (short summary of paper), Introduction (background & significance), Methods, Results, Discussion, References, Conclusion, Acknowledgements.

2. Use metric units; italicize scientific names; clearly label sections; past tense. 3. Start by writing the materials and methods section.

VI. POPULATION GENETICS: THE HARDY WEINBERG THEOREM A. General Terms:

1. Gene pool: all the alleles at all gene loci of all individuals in a population. 2. Microevolution: small scale changes in the genetic structure of populations.

B. Hardy-Weinberg Theorem: states that the frequency of alleles will stay the same from generation to generation. Only valid if the 5 assumptions are met: 1. Large population 2. Random mating 3. No mutations 4. No migration of individuals 5. No selection; all genotypes are equal

C. Mathematical Formulas of Hardy-Weinberg 1. Frequencies of dominant allele (p) & frequency of recessive allele (q); when

added together they equal 1 p + q = 1 2. Genotypic frequencies: p² + 2pq + q² = 1 3. Summarize:

a. p² = frequency of AA b. 2pq = frequency of Aa c. q² = frequency of aa

D. Testing HW Equilibrium using a bead model 1. Sampling with replacement: returned the beads to the bag and shook them

up to reinstate the gene pool and probability. 2. The HW expected results varied from our ACTUAL results. 3. Chi-square test: used to compare observed and expected results.

a. Observed value (o) of AA, Aa, & aa. b. Expected value (e) of AA, Aa, & aa. c. Deviation (o-e)=d d. Chi-square = Σd²/e e. Degrees of freedom: the number of variables -1; (n-1)

E. Ex 2: simulation of evolutionary change using the bead model. 1. Terms:

a. Gene flow: migration of individuals between two populations b. Genetic Drift: effects of small population size. c. Natural Selection

d. Mutation 2. Simulation of Genetic Drift

a. Change in allelic frequencies in small populations by just chance. b. Genetic fixation: the loss of all but one possible allele @ a gene locus in a

population. c. Bottleneck effect d. Founder effect

3. Simulation of Migration (results in gene flow) 4. Simulation of Natural Selection

a. Peppered moth & industrial revolution. F. POPGEN FISHBOWL

1. Initial conditions of the popgen fishbowl were in HW equilibrium 2. Collected data for intervals of 100-1000. 3. Entire phenotypes and genotypes or even alleles have the possibility to

disappear within a population; depending on the strains put on them. VII. PHYLOGENETIC TREE BUILDING LAB

A. Terms: 1. Folk taxonomies: simple ways to organize life into different groups. (dog,

fish, shrubs, fruit trees) 2. Natural Classifications: group organisms into a hierarchical system based

upon their characteristics using specific criteria. 3. Polytomy: multiple branches 4. Monophyletic: one common ancestor & all descendents. 5. Paraphyletic: one common ancestor & SOME descendants. 6. Polyphyletic: more than one ancestor & decendents. 7. Parsimony: “simplicity” 8. Outgroup: species that is a member of a closely related genus; it represents

the characteristics most likely found in a common ancestor. 9. UPGMA: unweighted pair group method and arithmetic mean. 10. Phenogram: the tree generated by UPGMA phenetic analysis. 11. Cladograms: uses the outgroup to “evolutionarily root” the ingroup species;

used to compare primitive and advanced traits. 12. Homoplasy: same/similar derived traits appear in different lineages; the

consistency index(CI) is a measure of this. 13. Dendrogrammacea/Caminalcules: Plants/Animals

VIII. PLANT ANATOMY A. Unlike animal cells and organs which have specific unique cell types; plant

organs have many common tissues and cell types; they’re just organized in different ways. Their structure is directly related to their function.

B. 3 Tissue Systems:

1. Dermal: outer layer; usually one cell thick; flattened and rectangular shape; cuticle (prevents water loss) & epidermis (protection & regulates movement of materials). Specialized dermal cells: guard cells, trichomes (hairs), and unicellular root hairs.

2. Ground: found throughout the plant; beneath epidermis & surrounding vascular tissues.

• 3 cell types: 1. Parenchyma: thin walled & large vacuoles. Functions:

photosynthesis, support, storage, and lateral transport. 2. Collenchyma: found near the surface of the stem, leaf petioles,

and veins. Similar to parenchyma BUT have an uneven thickening of cell walls. Function: flexible support (young). “Cartilage.”

3. Sclerenchyma: thick cell walls (may contain lignin); function: strength & support to mature plant structures; may be dead @ functional maturity. Commonly long thin fiber cells.

•

• Look @ slides on page 281 in your lab manual. 3. Vascular: functions: transport of materials throughout the plant; complex.

• XYLEM: Parenchyma cells function in storage and lateral support; Fibers also provide additional support. Overall Xylem Function: transports water and minerals & support. 1. Tracheids: long, thin cells w/ perforated tapered ends 2. Vessels: large diameter, open-ended, & joined end-to-end; forms

continuous transport systems. • PHLOEM: Parenchyma cells function in storage and lateral transport;

Fibers function as additional support. Overall Phloem Function: transports the products of photosynthesis throughout the plant as part of the vascular tissue system. 1. Sieve-tube members: lack a nucleus; living conduction cells; have

sieve plates for end walls; cells are joined end-to-end throughout the plant

2. Companion cells: associated with each sieve-tube member; function: regulate sieve-tube function

C. Meristematic Tissue: 1. Primary meristems: small, actively dividing cells located in buds of the

shoot & root tips of plants; produce the primary tissues along the plant axis throughout the life of the plant.

2. Pericycle: layer of Meristematic cells just outside the vascular cylinder in the root; produce lateral branch roots.

3. Vascular cambium: lateral meristems; composed of small, actively dividing cells that are located between the xylem & phloem vascular tissue. Divide to produce secondary growth; increase “girth”

4. Cork cambium: lateral meristems located inside the cork layer of a woody plant; produce secondary “girth” growth.

D. EX. 1 Plant Morphology

1. Herbaceous plant anatomy: non-woddy plant structures in the shoot.

• Nodes: regions of the stem where leaves, buds, and branches arise; contain Meristematic tissue.

• Internodes: regions of the stem between the nodes. • Terminal buds: located @ the tips of stems & branches; enclose the

shoot apical meristem (gives rise to leaves, buds, & all primary tissue of the stem). Only stems produce buds.

• Axillary/lateral buds: located in the leaf axes @ nodes; produce lateral branches.

• Leaf Parts: flattened blades attached @ the node of a stem by a stalk (petiole).

• Primary root: first root produced by a plant embryo & may become a long taproot.

• Secondary root: arise from Meristematic tissue deep within the primary root.

• Root tip anatomy: root apical meristem that gives rise to a root cap (protective layer of cells covering the root tip) AND to all the primary root tissues. Root hairs: specialized epidermal cells; function in water and mineral absorption.

• • CROSS SECTION SLIDES OF A HERBACEOUS PLANT

MAIN  FUNCTIONS  

Stems:  transport  nutrients  

Roots:  absorb  nutrients  

Leaves:  photosynthesis  

E. Ex 2: Plant Primary Growth & Development 1. Primary growth: tissues produced from apical meristem are primary tissues,

this growth is “primary growth.” It occurs along the plant axis @ the shoot & root tip; Certain meristem cells divide in a way that one cell product becomes a new body cell & the other remains in the meristem; beyond the zone of active division, new cells become enlarged & specialiazed (vessels, parenchyma, epidermis).

2. Procedure: • Examine a slide of longitudinal section through a terminal bud of Coleus.

• Youngest cells are @ the apex of the bud; cells of increasing maturity and differentiation can be seen as you move away from the apex.

• Locate undifferentiated vascular tissue: narrow/dark tracks in the leaf primordia.

• The size of the cells increases as you move away from the apex; the vascular tissues elongate & develop spiral cell walls.

• Intermediate growth: meristems of plants continue to grow throughout their lifetime. Contrast with growth patterns in humans: humans grow to a certain size and age, after that the only growth is for maintenance & repair; not increasing in size. DETERMINATE GROWTH.

• most immature cells @ the tip. F. Ex 3: Cell Structure of Primary Tissues

1. The plant body consists of organs (roots, stems, leaves, flowers, fruits) & tissue systems (ground, vascular, dermal).

2. Stems: only organ that makes buds and leaves; support leaves & conduct water & inorganic substances from root to leaves & products of photosynthesis from leaves to roots.

3. Vascular Bundle. 4. Microtome: instrument used for cutting thin sections for microscope study. 5. Paraffin: what we embedded the tissue in for the slide. 6. Trichomes: occasionally on the outer surface of the plants. (hairs) 7. Cortex: between the vascular bundles & the epidermis; made mostly of

parenchyma, but the outer part may have collenchyma too. 8. Pith: center of the stem, inside the ring of vascular bundles; made of

parenchyma; in herbaceous stems these cells provide support through turgor pressure. Pith is also important for storage.

9. Vascular System: continuous system of xylem & phloem; transport & support.

10. Vascular Bundles: phloem tissue toward outside & xylem toward the inside; narrow layer of vascular cambium is between the xylem and phloem.

• VB Phloem Tissue 3 Cell Types: 1. Sclerenchyma: dead, fiberous, thick walled; support for phloem &

appear in a cluster as a “bundle cap”.

2. Sievetube Members: large, living, elongated, lack a nucleus at maturity; they become vertically aligned to become sieve-tubes; their cytoplasm is interconnected through sieve plates.

3. Companion Cells: small, nucleated parenchyma cells; connected to sieve-tube cells by cytoplasmic strands.

• VB Xylem Tissue 2 Cell Types: 1. Tracheids: elongated, thick walled, closed/tapered ends; dead at

maturity; lumens connected through pits in cell walls. 2. Vessel Elements: cylindrical cells, large diameter, dead at

maturity; joined end to end lose their end walls & make long, vertical vessels.

• Vascular Cambium: tissue that is located between the xylem & phloem; actively divides & gives rise to secondary tissues/growth.

11. Xylem cells are larger & more distinct then phloem cells. 12. Collenchyma & Sclerenchyma provide support for the stem; collenchyma is in

the cortex & Sclerenchyma is in the vascular bundles. 13. How does the structure of collenchyma & Sclerenchyma cells relate to their

function of support? Thick & Fiberous bundles; Rigid; above ground (roots don’t need support).

14. What’s the function of xylem & phloem? 15. The pith & cortex are made up of parenchyma cells; Relate their structure &

function: Functions: photosynthesis, storage, transport, support. Structure: packed loosely so CO2 can circulate; thin walls allow for transport, irregular shapes & storage. Roots= cortex Stem=pith.

G. Roots 1. 4 primary functions of roots: anchors, absorption, conduct water and minerals

from soil to base of stem, and starch storage (depends on the plant) 2. Primary root: radical; first root after seed germination; its branches are

lateral roots. 3. Taproot: primary root is the largest & most important part of the root system.

(Carrots, dandelions, and pine trees). Advantage: better in times of drought. 4. Fibrous: many main roots have formed. (grasses) Advantage: absorbs water

better. Monocots are usually fibrous. 5. Cross Section through a buttercup root: lacks a central pith; vascular tissue

is located in the center of the root & is called the vascular cylinder.

6. In the slide above, the cortex is mostly made of large parenchyma cells w/ numerous purple stained organelles. Which of the 4 functions do you think is related to these cells and their organelles? Storage.

7. Identify: epidermis, parenchyma of cortex, vascular cylinder, xylem, phloem, endodermis, & Pericycle.

8. Endodermis & Pericycle are unique to roots. 9. Endodermal cells: have a casparian strip- made of suberin; this strip forms a

barrier to the passage of anything moving between adjacent Endodermal cells. 10. Pericycle: layer of dividing cells immediately inside the endodermis; gives

rise to lateral roots. 11. ROOT VS STEM: roots don’t have a pith; roots have cortex parenchyma,

vascular cylinder (stem has vascular bundles), roots don’t have a cuticle because a cuticle would prevent the root from taking in water.

12. Parenchyma in the cortex is used for storage in the roots; Casparian strip: waxy material, barrier & filter for all ground water & nutrients to go through.

13. Endodermis: protection against water loss; land plants need it because they don’t live in water.

H. Leaves 1. Leaf is basically a layer of parenchyma cells (the mesophyll) between two

layers of epidermis. Loose arrangement of parenchyma cells within the leaf allows for an extensive surface area for rapid gas exchange; guard cells allow the exchange of gases & evaporation of water; guard cells are photosynthetic (unlike other epidermal cells) & change in shape in response to their environment. Opening of stomata is the result of the active uptake of K+ & changes in turgor pressure in the guard cells.

2. Cuticle: waxy layer secreted by the epidermis. 3. Veins: the vascular bundles of the leaf; xylem is on top in the leaf.

4. Where are the stomata more abundant? Lower epidermis. Because they’re not as exposed to the sun and heat, which makes them lose less water.

5. Epidermal peel: stimulated stomatal closure by changes in turgor pressure due to saline rather than K+ transport.

I. Ex 4: Cell Structure of Tissues Produced by Secondary Growth 1. Secondary growth arises from the meristematic tissue “cambium.” There are

two types of cambium: • Vascular Cambium: single layer of meristematic cells located

between the secondary phloem & secondary xylem. One cell is made toward the xylem (inside) and one toward the phloem (outside); increases girth. The secondary phloem cells become Sclerenchyma fiber cells, sieve-tube members, and companion cells. Secondary xylem cells become tracheids & vessels.

• Cork Cambium: produces cork tissue to the outside of the stem and other cells to the inside. The cork cambium & secondary tissues derived from it are called periderm. The periderm layer replaces the epidermis and cortex in stems and roots with secondary growth.

2. Outer cork cells of the periderm: have thick walls with suberin; these cells are dead at maturity

3. Cork cambium: thin layer of nucleated cells. 4. Periderm: layers of cork and associated cork cambium. 5. “bark”: the periderm & phloem on the outside of woody plants. 6. Sclerenchyma fibers: thick, dark-stained walls & are in the bands of the

phloem. 7. Secondary Phloem Cells: thin cell walls alternate with the rows of fibers.

8. Lateral Rays: parenchyma cells in lines that radiate from the pith through the xylem and expand to a wedge shape in the phloem; making a phloem ray.

9. Annual Rings: xylem; they make up the wood of the stem surrounding the pith; early wood: thin-walled, large-diameter cells, grew in the spring. Late wood: outside of the early wood; thick-walled, smaller-diameter cells that grew in the summer, when water is less available.

10. Indicate on the slide where the primary tissues may be found. 11. Xylem provides structural support for trees. Parenchyma cells transport

materials. Latewood= summerwood, produced slowing down cambium activity; less rain in the summer= less wood.

J. Ex 5: Grocery Store Botany: Modifications of Plant Organs. 1. Roots have been selected so often as food because roots store nutrients. 2. The endodermis is essential in the root for water retention. 3. Plants have indeterminate growth; unlike humans. 4. ADAPTIONS OF LAND PLANTS:

• Vascular Tissues: xylem & phloem • Stomata on leaves for gas exchange. • Leaves for photosynthesis • Roots for anchorage and to take up materials. • Seeds and Pollen for reproduction without water. • Avoid desiccation by retaining water in the roots and regulation of

open/closed stomata. 5. C3 & C4 Plants:

• They use different photosynthetic pathways. • C3 plants do uptake & fixation in the same place. • C4 plants do uptake & fixation in different places.

6. Monocot v. Eudicot: • Monocot’s flowers are in multiples of 3; eudicots are 4 or 5. • Monocot’s pollen grain has one hole; dicot’s has 3. • Monocots veins are parallel

K. Plant Nutrient Deficiency 1. Macronutrients: required in a large amount; N, P, K, Ca, Mg, & S. 2. Micronutrients: required in a small amount; Cl, Cu, Fe, Mn, Zn. 3. “C. HOPKiNS CAFÉ MIGHTY GOOD” mnemonic device. 4. Observed nutrient deficiencies:

• Complete- dark green, thin projections out of leaves, more leaves, longish, thick stem.

• N- pale, thin leaves, less leaves, shorter, thin stem, red stalk. • P- medium stem, similar to complete. • K- like “P”; but shorter leaves.

• Fe- less, lighter leaves, thin stem. • Ca- really thin leaves, brown & green leaves.

IX. Transpiration Lab A. Introduction:

1. The cohesiveness of water allows it to be pulled through the plant body. Other water molecules evaporate from cells in the mesophyll and exit the leaf via stomata & into the air.

2. Stomata regulate water loss, CO2 & Oxygen exchanges. 3. Transpiration also provides turgor pressure & the hydrologic cycle.

B. Visualizing stomata & guard cells: 1. Leaves from two different species; painted clear finger-nail polish on them &

used tape to peel it off; look @ it under a microscope & identify the guard cells of the stomata.

2. How do the guard cells compare among different species? Monocots have dumbbell shaped guard cells; dicots have kindney-shaped guard cells.

C. Measuring Transpiration: 1. Potometer: measuring device; a plant placed in a piece of rubber tubing,

attached to a calibrated pipette. 2. DID NOT GET THE LEAVES WET; that would have messed with the results

and could’ve prompted the stomata to react to things not being tested. 3. Transpiration rates can be affected by the amount of leaf surface area; along

with environmental conditions. 4. Results: control group’s transpiration rate was fairly constant and water loss

gradually increased; “no leaves” did not transpire at all; fan low had the highest transpiration rate; fan high didn’t have a transpiration rate.

X. PLANT DIVERSITY: SEED PLANTS/ ANGIOSPERM REPRODUCTION A. Adaption to the land environment traits:

GYMNOSPERMS • Seeds • Xylem & phloem • Pollen grain • More time as a sporophyte

ANGIOSPERMS • Seeds • Xylem & phloem (more specialized) • Short life cycle. • Pollen grain • More sporophyte • Embryo sac= female gametophyte

B. Gymnosperms: 1. Vascular Seed Plants; “Naked Seeds” 2. Dominated during the Mesozoic era; earth became warmer & drier. Vertebrate

animals became fully terrestrial during this period too. The development of the amniote along with internal fertilization is somewhat analogus to gymnosperms development of the pollen grain and seeds.

3. Features responsible for success: • Reduced gametophytes • Pollen grain (male gametophyte) which is desiccation resistant &

adapted for wind pollination. • Ovule: seed is protected and had nutrients easily accessible. • Xylem (tracheids) & Phloem

4. Trees or shrubs; large investments in woody tissue; long life cycles. C. Angiosperms:

1. Arose during the Cretaceous period; mammals & birds dominated; now occupy over 90% of the vegetated surface of Earth.

2. Flower evolution: resulted in big advances; efficient pollination. 3. Embryo sac = “eight-nucleated” 4. Endosperm: triploid; provides nutrients for the developing embryo. 5. Fruits: unique adaptation; the ovary. 6. Can be woody; mostly herbaceous; short life cycles; superior conducting

tissues; xylem has tracheids AND vessels; phloem cells are sieve tube members.

D. Phyla of Gymnosperms

Coniferophyta Pines • Cones • Largest • Shrubs/trees

Ginkgophyta Ginkgos (Fan shaped leaves)

• Were thought to be extinct.

• Found in Asia

Cycadophyta Cycads • Palm-like • tropics

Gnetophyta Ephedera • Desert plant • Sometimes tropics.

1. Key characteristics shared by all gymnosperms: • Seeds • Wind pollinated • Trees or shrubs • Dominant sporophyte stage • Heterosporous: making two kinds of spores; microspores (develop into

pollen) & megaspores (develop into female gametophyte, not free living like in ferns but retained within the megasporangium.

2. Conifers: shelter & lumber. 3. Pine Life Cycle:

• Becomes haploid when the microsporocyes produce 4 microspores. • Becomes diploid after fertilization. • During the second year, the ovule develops into a multicellular female

gametophyte with two archegonia; fertilization does not occur until the second year; only one of the archegonia and its zygote develop into a seed. The outer tissues of the ovule will harden to form the seed coat.

• The function of the wings on the pollen grain are travel & protection • Microspores/ megaspores are produced by mitosis.

E. Angiosperms phylym Anthophyta

1. 3 unique characteristics of angiosperms: • Flowers, Fruits, & double Fertilization. • Increase in the rapidity of reproduction process, additional reduction of

gametophyte, & the carpel. 2. Perianth: petals; leaf-like structures. 3. Flower Morphology:

Longitudinal  section  of  a  pollen  cone:  

• Alstromeria: two spotted petals, one huge sterile anther; predicted pollinator = bee or a butterfly.

• Snapdragons: tubular, predicted pollinator= moth. 4. Pollinators:

• Flowers with inconspicuous sepals & petals are usually wind pollinated.

• Dichotomous key was used to determine the pollinator of flowers. • Moth- white, distinct strong/heavy/sweet odor. • Bat- white, strong fruitlike odor; strong flower parts. • Fly- white, feces odor. • Bee- blue/yellow/or orange speals/petals, not tubular, sweet odor. • Beetle- regular flower shape; spicy/sweet/fruity odor. • Butterfly- tubular flowers, strong/sweet odor. • Hummingbird- red flowers; tubular; little or no odor. • *regular flower shape- radial symmetry. *irregular= bilateral

symmetry. 5. Angiosperm Life cycle:

• Slide of lilium anther: four anther sacs (microsporangia); microspores forming with a single nucleus.

• slide of lilium ovary: ovules are composed of the megasporangium and megaspores. Only one megaspore survives; it divides 3 times by mitosis to make 8 nuclei in the embryo sac. Don’t produce an archegonium.

• The female gametophyte in angiosperms is larger than in gymnosperms.

• The seed develops from the ovule; the fruit develops from the ovary. 6. Fruit types & Dispersal Mechanisms:

• Berry: tomato; squash. • Drupe: “pits” peaches, plums, coconut • Legume: green beans, peanut. • Aggregate: blackberry, strawberry • Hesperidium: orange (citrus) • Pome: “core”; apple. • Nut: can be separated from the seed; acorn. • Capsule: ovary with several cavities & too many seeds. • Follicle: mature ovary opens along one side. • Multiple fruit: formed from ovaries of many flowers; pineapple. • Pepo: squash berry family.

• Achenes: in grass family, they’re “grains”; ovary wall & seed coat are fused.

7. Review Section: • Pollen grain: move sperm to egg. • Microsporangium: create sperm. • Flower: attract pollinators. • Carpel: reproductive enclosed structure.

• Angiosperms have pollen grain & fruit. Gymnos do not.

XI. PROTISTS & FUNGI A. Introduction:

1. Protista include all organisms not placed in other eukaryotic kingdoms; it’s a “catchall” kingdom with unicellular & multicellular eukaryotes. It’s a “general term”, not a taxonomic category. Familiar protists are algae & protozoans. Their phylogeny is difficult to determine; clade: group of species, all of which have one common ancestor. Pay attention to nutrition, locomotion, & cellular complexity of each example.

B. Ex. 1 The Protists. 1. Groups of Protists in this Exercise:

• Euglenozoans, Alveolates, Stramenopiles, Foraminiferans/Radio, Amoebozoans, Rhodophyta (red algae), Chlorophyta (green algae).

2. Characteristics: • Autotrophic (ALGAE) /heterotrophic (PROTOZOANS) • Primary production: amount of energy stored by autotrophs. • Phagocytosis: protozoans; uptake of large particles or whole

organisms by pinching inward of the plasma membrane.

FOOD Beans Angiosperm

BEVERAGE Orange juice Angiosperms

MEDICINE Taxol, pacific yews Gymnosperms

FIBERS Cotton plants Angiosperms

MATERIALS Oak trees Angiosperms

DYES Blackberries Angiosperms

DRUGS Cannibus Angiosperms

Uses of plants Example Angiosperm/gymnosperm

• Mixotrophic: capable of photosynthesis and ingestion. • Plankton: community of organisms floating in the ocean.

3. Lab Study A: trypanosome levesi clase Euglenozoa • Grouped together based on their ultrastructure (can be seen only with

an electron microscope) of their flagella & their mitochondria. Mixotrophic; contains auto & hetero organisms. Autos have chloroplasts.

• Trypanosoma levisi locomotion: flagella supported by microtubules. • Nutrition: parasitic; rat blood, transmitted by fleas.

• 4. Lab Study B: Paramecia & Dinoflagellates

• Alveolates are single-celled; some hetero/ some auto; alveoli: unique characteristic, membrane-bound sac-like structures just under the cell membrane.

• • Food Vacuole: forms @ end of the gullet; appear as dark vesicles

throughout the cell. • Macronucleus: large, grayish body in center of the cell. Many

genome copies & controls cellular activities (asexual reproduction) • Micronucleus: hard to see; small round body close to macronucleus;

sexual reproduction; more than one micronucleus.

Flagellum  -­‐>  <-­‐  nucleus  

Undulating  membrane  -­‐>   <-­‐kinetosome  

• Contractile Vacuole: water balance; two of these/one @ each end. • Observe feeding in a paramecium: add a drop of yeast stained congo

red to edge of coverslip & watch it diffuse around the paramecium; see the food particles go through the oral groove; observe trichocysts: structures that lie under the outer surface of the paramecium; paramecium discharge these when irritated by a chemical or predator; they’re long, thin threads used as defense/anchor/prey capture.

5. Dinoflagellates: • Photosynthetic single-celled organisms. • Cellulose wall often an armor of plates with 2 perpendiculate grooves;

each with a flagellum; autotrophic & key role in primary production. 6. Lab study C: Stramenopiles—Diatoms & Brown Algae

• Water molds, diatoms, golden algae, & brown algae. Grouped based on their flagella structure (when present); many hair-like projections flagellum.

• Diatoms (Bacillariophyta): important in plankton; unicellular OR can be chains of star-like groups; diatomaceous earth: cell wall deposites that are mined and have economic importance (pool filters & toothpast abrasive); carbs and oxygen production ecological use. Shapes: pinnate or centric. Locomotion: uncertain; contractile fibers make waves of motion.

• Brown Algae (Phaeophyta): kelps; fucoxanthin: give brown appearance; commercial value- smooth icecream & extracts of algin (polysaccharide in cell wall) used as thickening agents in paint ect.. body plan: blades, stipe (stem-like), & holdfast (anchor).

7. Lab Study D: Formainiferans & Radiolarians: • Ameboid, heterotrophic & thread-like pseudopodia. Pseudopodia are

cellular extentions used in feeding & some locomotion. • Formainiferans: “forams” move & feed using pseudopodia. Secrete a

calcium-carbonate shell-like “test”

•

Pinnate  shaped.  

• Radiolarians: common in plankton; secrete skeletons of silicon dioxide. Axopodia: tread-like, extend out through pores int eh skeleton in all directions.

8. Lab Study E: Amoeboxoans: Amoeba, SlimeMolds • Have lobe-shaped pseudopodia; • Amoeba: moves using lobe-shaped pseudopodia; no fixe dbody shape;

no shell; by extending pseudopodia, cellular membrane follows and that’s how they move.

• Slime-Molds: heterotrophic; phagocytic; decended from unicell-amoeba-like organisms; two types: plasmodial slime molds and cellular slime molds: vegetative stage is called a plasmodium ; multinucleated mass of protoplasm no cell walls; converted into fruiting bodies and produce spores.

9. Lab Study F: Red Algae (Rhodophyta) • Do not have flagella • Autotrophic; chlorophyll a; phycocyanin & phycoerythrin mask the

chlorophyll & make the algae look red. • Agar: extracted from the cell wall of red algae. • Carrageenan: gives texture of thickness to foods. • 3 body forms are: single-celled, filamentous, colonial & leaf-like.

10. Lab Study G: Green Algae (Chlorophyta) - the protist-plant connection. • Share many characteristics with land plants. A hypothesis is that plants

are derived from green algae. • Filamentous algae Spirogyra; a long chloroplast; freshwater. • Ulva: sea lettuce; fond on rocks or docks in marine water. • Chara algae: muddy or sandy bottoms of clear lakes or ponds;

complex body from & often mistaken for a plant; cylindrical branches & has nodes.

XII. THE KINGDOM FUNGI A. Introduction: Fungi are unicellular or multicellular, heterotrophic (absorption),

digest their food outside their bodies. They have complex life cycles with alternating sexual & asexual (vegetative) reproduction. May make spores either asexually my mitosis or sexually by meiosis. Fungi are made up of hyphae which are organized into the body of the fungus called the mycelium. They have cell walls made of chitin & cellulose.

• Economic Benefits of Fungi: antibiotics, wine, beer, leavened bread, mushrooms

• Ecological benefits of Fungi: decomposition; mycorrhizae. • Destructive roles of Fungi: parasites; sudden oak death, wheat rust.

B. Zygomycota (Zygote fungi):

1. Cells of Hyphae are haploid & they grow over a substrate. 2. Rhizopus reproduce sexually when compatible mating types (+) or (-) grow

side by side. 3. Karyogamy: haploid nuclei that fuse. 4. Pilobus crystallinus: shotgun fungus; grows on dung. Positively

phototrophic; and the entire sporangium is released not just spores. C. Sac-Fungi Ascomycota

1. “ascopore producing fungi” 2. Peziza specimen: cup fungi.

3. 4. The spores in the ascus are haploid; the ascocarp is diploid. 5. Morels: cup fungi that resemble mushrooms. But the cap is convoluted. Asci

are in the ridges. 6. Ergot fungus: large black structures seen among the grains (wheat/rye grass). 7. All sac-fungi produce asci in ascospores.

D. CLUB FUNGI- Basidiomycota 1. “club fungi” or “basidiospore-producing fungi” 2. A mushroom is a reproductive structure called a basidiocarp that makes spores

by meiosis.

3. E. IMPERFECT FUNGI- Deuteromycota

1. Unknown sexual stage; so asexual or imperfect fungi.

F. Comparing the 4 Phylum of Fungi:

PHYLUM EXAMPLES SEXUAL ASEXUAL STRUCTURE SLIDE

Zygomycota (Zygote Fungi)

-bread mold -fuzzy -shotgun fungus (dung)

Gametangia, plasmyogamy, zygote, karyo, spores.

Sporangia, spores, mycelium

-hyphae filaments -mycelium -chitin wall

Asomycota (sac-fungi)

-yeast -morells -truffles

4 or 8 haploid ascopores after meiosis in an ascus. Asci form in ascocarp.

Conidia: not enclosed, on the surface of reproductive hyphae. Yeast-budding.

-Ascus -Mycelium -Hyphae

Basidiomycota (Club Fungi)

-mushrooms -toadstools - fairy ring - corn smut -wheat rust

Basidiospore reproductive structure makes spores by meiosis.

Conidia by mitosis; mature wind dispersal.

Basidiocarp: stipe, pileus, gills.

Deuteromycota (Imperfect Fungi)

-athletes foot -ring worm -penicillin -LICHENS

G. LICHENS. 1. Symbiotic associations between fungi & algae or cyanobacteria. Fungal

component is usually a sac or club fungus. The algae provides nutrients for the fungus & the fungas provides a moist environment for the algae.

2. Thallus: lichen body. 3. Can withstand extreme environments; usually first to colonize a new one. 4. Different lichen types:

• Folise: leafy thallus • Crustose: crust-like thallus   • Fruiticose: branching thallus  

XIII. PLANT DIVERSITY: NONVASCULAR PLANTS (BRYOPHYTES) & SEEDLESS VASCULAR PLANTS A. Introduction:

1. General adaptations of land plants: cuticle, stomata, vascular tissue, roots, heterospory, seeds, pollen grain.

2. Non-Vascular Plants (Bryophytes): Bryophyta (mosses), Hepatophyta (liverworts), & Anthocerophyta (Hornworts).

3. Vascular Seedless Plants: Lycophyta (club mosses) & Pterophyta (ferns, horsetails, whisk ferns)

4. Seed Plants: Gymnosperms & Angiosperms. B. Plant Life Cycles:

1. Alternation of Generations: alternate between haploid gametophyte & diploid sporophyte.

• Diploid sporophyte does meiosis to make haploid spores inside a sporangium.

• The spores divide by mitosis and make a haploid gametophyte. • The gametophyte makes gametes inside the gametangia. • Eggs are made by mitosis in archegonia & sperm are made in

antheridia. • Fertilization in the archegonium makes a diploid zygote. • Gametes & spores are both haploid in this cycle.

2. Nonvascular plants (Bryophytes) • Phyla: Bryophyta, Hepatophyta, & Anthocerophyta. • Lack vascular tissue. • Dominant GAMETOPHYTE. • Lack stomata on the gametophyte thallus. • No roots, stems, or leaves.

C. BRYOPHYTA MOSSES 1. Gametophyte & sporophyte are usually growing together. 2. Leafy gametophytes & dependent sporophytes. 3. DRAW MOSS LIFE CYCLE

• Turn haploid when sporophytes make spores via meiosis. • Turns diploid when the sperm and egg fertilize in the archegonium.

4. Spores develop by meiosis in the sporangium at the end of the sporophyte; and belong to the gametophyte generation.

5. The gametes are haploid & are produced by mitosis. 6. Mosses protect ground from erosion…

D. LIVERWORTS HEPATOPHYTA 1. Flat thallus, rhizoids (root-like extensions on lower surface), pores (gas

exchange but are always open because they lack guard cells), gemmae cups: curcular cups on upper thallus surface & contain flat green tissue that are washed out of the cups & make new genetically identical liverworts.

2. Ancestral features: motile sperm. Derived features: cuticle, stomata. E. SEEDLESS VASCULAR PLANTS

1. Analogous to amphibians in dependence on water for external fertilization. 2. Have vascular tissues; conduct water, nutrients, & photosynthetic products. 3. Well developed leaves & roots, stomata & structural support tissues. 4. Still have motile sperm, so rely on water. 5. Economic benefits: ferns. 6. Phyla Lycophyta: Club Mosses

• Advanced feature Heterospory: mega & microspores. • Dichotomously branched? • Sporangia: @ clusters at the tips of leafy stems, forming strobili or

cones, or dispersed along the leafy stems. • The leafy plant parts are part of the sporophyte stage because of mega

& micro sporangium • What features determine a seedless vascular plant? Independent

gametophyte & well developed leaves, roots, & support. • Micro and mega spores are made by meiosis. • Megaspores divide to make the gametophyte.

7. Phyla Pterophyta: Ferns, Horsetails, & Whisk Ferns. • Whisk ferns (psilophytes) are diminutive, dichotomously branched

(ancestral), photosynthetic stems, reproduce sexually by aerial spores. • Horsetails (sphenophytes) have green jointed stems with occasional

leaves or branch clusters. • Ferns: most successful.

8. Fern terms: • Rhizome: functions like a root to anchor the plant. Roots arise from

the rhizome. • Sori: dark spots, which are clusters of sporangia on the underside of

some leaves, called sporophylls. 9. FERN LIFE CYCLE:

• • Haploid spores fall to the ground and become gametophyte plants are

heart-shaped. Depends on water for fertilization.

• Each archegonium encloses an egg. • The spores are made by meiosis. • The archegonia & antheridia are diploid.

10. FOSSILS OF SEEDLESS VASCULAR PLANTS. • Seedless plants were @ their peak during the Carboniferous period. • Ancestral features of seedless vascular plants: need for water for

reproduction. • Derived features: land for the plants, water for reproduction; vascular

tissue.

Structure Function Which stage?

Antheridium Contains sperm Gametophyte

Archegonium Contains an egg Gametophyte

Spore Make Gametophytes Gametophyte

Gamete Make sporophytes Sporophyte

Rhizome Anchor Sporophyte

Gemma Asexual Reproduction Sporophyte

Sporangium Meiosis & makes spores

Sporophyte

Strobilus Make spores/gametes Sporophyte

• Sorus: cluster of spores. 11. Rhizoids are the vascular tissues in ferns.