Fall 2008

Bio 51 Lab 1 Classification & Evolution + the PV92 Experiment

PV92 locus

Classification & Evolution

Taxonomy the field devoted to the classification of organisms Carolus Linnaeus invented the modern taxonomic system Kingdom Phylum Class Order Family Genus - Species Natural Selection Charles Darwin stated that all organism are

descended from a common ancestor, survival of the fittest Phylogenetic tree- show the evolutionary relationship between organisms

Vertical axis represents time & horizontal axis represents the amount

of divergence that occurred between different groups (the greater the distance, the more different the appearance) Fossil record can help construct a phylogenetic tree but they are incomplete Convergent Evolution some species resemble each other because

they independently evolved similar structures in response to similar environments or ways of life.

PV92 Experiment
Test for presence of ALU sequence in an intron in

locus PV92 on human chromosome 16

Lacks ALU insert 641 base pairs Contains ALU insert 941 base pairs

ALU sequence is a DNA sequence of about 300 base

pairs long

ALU sequence is dimorphic element is present in some

individuals and not others

Used polymerase chain reaction (PCR) and

electrophoresis

PV92 gene locus is amplified and visualized

PV92

Bio 51 Lab 2 Population Genetics & the Hardy-Weinberg Theorem

Population Genetics
H-W Theorem states that the frequency of alleles in the

population will remain the same regardless of the starting frequencies General Equation: p2+2pq+q2=1
p2 = expected frequency of homozygous dominant 2pq = expected frequency of heterozygous q2= expected frequency of homozygous recessive

The equation is met under 5 conditions Large population No gene flow No mutations No natural selection Random mating

Chi Squared Test

2 test a statistical procedure that can be used to compare observed data with expected values
2=(o-e)2/e 2 < critical value Ho accepted 2 > critical value Ho rejected
critical value larger, conclude that the observed

numbers are significantly different from our expected numbers and the difference between them are due to something other than random variation

Genetic Drift
Genetic Drift the change in allelic frequencies in small

population as a result of chance alone Genetic Fixation the loss of all but one possible allele at a gene locus in a population is a common result of genetic drift in small natural population Bottleneck Effect occurs when a population undergoes a drastic reduction in size as a result of chance events. The results come out in unpredictable proportions of genes passing to the next generation on the other side of the bottleneck Founder Effect when a small group of individuals becomes separated from the larger parent population, the allelic frequencies in this small gene pool may be quite different from those of the original population as a result of chance alone.

Bio 51 Lab 3 Microscopes & Mitosis/Meiosis

Microscope Anatomy

Arm Stage Base Oculars (eyepieces) Objective Condenser Diaphragm Diaphragm lever coarse adjustment Fine adjustment

Microscopes contd
Resolving Power measures of the microscopes ability to

distinguish between adjacent points on a slide Parfocal when an image is in focus under low power, it will be nearly in focus when a higher power objective is rotated into position Inter-ocular distance distance between the two eyepieces Inter-pupillary distance distance between the pupils Field- the area of observation or the area that is seen under the microscope Working distance distance between the slide and the objective lens Depth of field amount of object that is in focus at one time

The Cell Cycle

The Cell Cycle = G1, S, G2, M, C (G0: alternate form of G1) Interphase (G1, S, & G2) G1: cell grows & prepares to replicate its chromosomes S: when the chromosomes replicate G2: more biochemical activity takes place as the cell prepares for M phase (mitosis or meiosis) and usually cytokinesis G0: cells are busy carrying out all the important biochemical processes that allow the cell to function properly and carry out its job within the organism M: mitosis or meiosis phase where the chromosomes separate C: Cytokinesis or where the cytoplasm splits and becomes two cells

Mitosis
Mitosis nucleus breaks down, duplicated chromosomes are separated from each other, and the chromosome are repackaged into 2 separate nuclei Cytokinesis division of the cytoplasm to form 2 separate cells Prophase nuclear membrane breaks down, the chromosomes condense, and the spindles attach to the chromosomes Metaphase chromosomes are aligned at the equator of the cell (metaphase plate) Anaphase the chromosomes are separated and moved towards the poles of the cell Telophase & Cytokinesis the chromosomes de-condense, the spindle breaks down, and two nuclei are reformed around the chromosomes. The cytoplasm divides into 2 separate cells Forms 2 daughter cells exactly like the parental cell Somatic cells body cells that undergo mitosis Germ cells sex cells that undergo meiosis

Mitosis contd
Most cells are in interphase, since interphase is the longest Second would be prophase, because it goes after interphase Metaphase Anaphase Telophase Cytokinesis

Meiosis
Meiosis I Prophase I - long stage during which the chromosomes become shorter and thicker and

visible, the nucleus breaks down, and the spindle forms

Synapsis the pairing up of homologous chromosomes to form tetrads Crossing over

Metaphase I Both homologous chromosomes line up together and the spindle is attached to

just one sister chromatid from each homologous chromosome Anaphase I each homologous chromosome of a pair will move to opposite poles of the spindle, and each chromosome still consists of two sister chromatids Telophase I, no Cytokinesis Meiosis II Prophase II Metaphase II Anaphase II Telophase II and Cytokinesis 4 haploid cells Alleles alternate version of the same gene Independent assortment cause more genetic diversity and new combinations of alleles (happens in prophase I only)

Bio 51 Lab 4 Bacteriology 1

Gram Staining Procedure

Gram Staining contd

Gram Negative Bacteria
More complex cell wall Thin peptidoglycan cell wall

Gram Postitive Bacteria

Simple cell wall Think peptidoglycan cell wall

layer Outer lipopolysaccharide wall layer Retain safranin Appear pink/red

layer No outer lipopolysaccharide wall layer Retain crystal violet/iodine Appear blue/purple

Bio 51 Lab 6 Protists, Fungi, & Bryophytes

PROTISTA

Kingdom Protista
If an eukaryotic organism cannot be classified as either animal,

fungi, or plant, it is classified as a protist Unicellular, Colonial, Filamentous, or Multicellular forms Move by means of flagella, cilia or pseudopodia Protozoa heterotrophic (animal-like) protists that ingest food materials Algae plant-like photosynthetic autotrophs Mixotrophs protists that can carry out photosynthesis and absorb nutrients like an animal Auxotrophs protists are autotrophic and largely self-sufficient, but have very specific requirements for certain nutrients Protists typically reproduce asexually, reserving sexual reproduction for times of stress

Supergroup Unikonta
Clade Amoebozoa Group Gymnamoeba (the Amoebas)

Aquatic heterotrophs that move using pseudopodia

Group Myxogastrida (the Slime Molds)

Plasmodial slime molds Heterotrophic diploid multinucleate plasmodium Amoeboid movement by streaming

Gymnamoeba The Amoebas

Amoeba proteus Pseudopodia: the finger-like projections of the cell membrane

Used for loco-motion and engulfing prey

Myxogastrida
veins

Physarim Plasmodium
(multinucleate mass)

Supergroup Archaeplastida
Clade Chlorophyta Green algae Photosynthetic with chlorophyll A & B Unicellular , filamentous, or multicellular Many species with flagella

Chorophyta - Chlamydomonas

Group Chlorophyta Volvox

Volvox Colony Vegetative Cells

Supergroup Chromalveolata
Clade Aveolata Group Ciliophora

Ciliates are hetrotrophic Unicellular with cells of a fixed shape Two or more nuclei Many cilia present

Clade Stramenopila Group Bacillariophyta

Diatoms Photosynthetic Unicellular Many with double shell of silica

Group Ciliophora Paramecium caudatum

Ciliates are heterotrophic,

unicellular with a fixed shape, with two or more nuclei, and many cilia present

Bascillariophyta The Diatoms

Single diatom cell Surrounded by a glass-like cell wall (frustule in 2 parts)

Epitheca: larger half Hypotheca: smaller half

Fucoxanthin: pigment that causes the diatom to be non-green

FUNGI

Kingdom Fungi
Include a large variety of heterotrophic organisms that

obtain their food by secreting digestive enzymes onto the food & then absorbing the simple organic molecules released by the enzymatic action Two types of heterotrophs found:
Parasites: obtain food from living organisms Saprobes: obtain food from nonliving organic materials

The fungal body is formed by a network of tiny filaments

called hyphae which may be packed together to form complex solid structures called mycelia (mycellium) The cell walls of fungi are composed of chitin

Supergroup Unikonta
Phylum Chytridiomycota: Chytrids Hyphae lack septa & form flagellated spores called zoospores Phylum Zygomycota: Fusion of hyphae leads directly to the formation of a zygote Hyphae lack septa Phylum Ascomycota: Hyphae fusion leads to formation of a stable dikaryotic mycelium that forms zygotes in sac-like structures called asci which form inside a fruiting body called an ascoma Hyphae are sepate Phylum Basidiomycota: Sexual reproduction similar to Ascomycota, but zygotes formed in club-shaped reproductive structures called basidia which form in a fruitign body called a basidioma Hyphae are septate Imperfect Fungi (Deuteromycetes): Fungi in which sexual reproduction has never been observed

Chytridiomycota Chytrids
Largely aquatic Saprobic and parasitic Only flagellated fungi Synchytridium endobioticum Causes Potato Wart Disease Each chytrid body is a single cell

residing within a single potato cell Lives within the potato cell and feeds on it, eventually killing it The parasite enlarges, undergo mitosis but not cytokinesis, and produce zoospores bearing flagellae in a multi-parted organ (Sorus)

Zygomycota The Molds

Hypha Basic unit that makes up the

fungal body Mycelium: mass of hyphae Lacks Septate (cross walls) Coenocyte: One large multinucleate cell Rhizopus stolonifer (black bread mold) Stolons: horizontal, surface hyphae Rhizoids: anchoring structures Sporangiophores: upright stalks Sporangia: terminal sacs Columella: the balloon-like cross wall that separates the sporangium from the rest of the hyphae

Rhizopus stolonifer

Zygomycota Rhizopus contd

Sporangium Sporangium wall

Spores
Columella Sporangiophore Hyphae

Zyogomycota Rhizopus contd

Single live sporangium Sporangium Sporangium wall Spores Columella

Zygomycota Rhizopus contd

Zygosporangia: resulting from the

fusion of two hyphaei Zygospore: multicleate, inside the zygosporangia Suspensor: enlarged structure which leads back to an ordinary hypha Progametangia: youngest stage where two cigar shapes are touching 2nd Stage: shows the gametangia (small cells isolated at the end of each suspensor by a septum) 3rd stage: gametangia fusing Final stage: mature zygosporangium

Mature zygosporangium

Ascomycota The Sac Fungi

Hypha fusion leads to formation

of a stable dikaryotic mycellium that forms zygotes in sac-like structures called asci which form inside a fruiting body called an ascoma Hyphae are septate

Preserved Morel

Peziza

Ascomycota Contd
Peziza Ascoma: inner surface of the cup The spore baring sacs (asci) form a

regular layer on the inner surface of the cup, the hymenium layer Each ascus contains 8 ascospores 1st part of fertilization: plasmogamy (fusion of the cytoplasm) 2nd part of fertilization: karyogamy (fusion of the nuclei) 3rd: followed by meiosis and mitosis (8 acospores) Ascocarp (ascoma) mycelium Hymenium contains paraphyses (slender sterile hairs), which stick out like fingers among the asci

Deuteromycetes Imperfect Fungi

Thought to be mainly

ascomycetes Few of them are known to reproduce sexually so their placement in the correct phylum is problematic The genera Penicillium and Aspergillus belong to a group commonly known as the bluegreen molds and are of great importance to human life

Basiodiomycota Club Fungi

All members have a basidium

Veil

(club shaped cell) Basidium produces 4 external basidiospores Sterigmata: the tiny stalks that basidiospores are located on Basidioma: the large fruiting body that holds all the basidia Agaricus bisporus Gills- fertile layer (hymenium is on the surface of the gills)
Lined with basidia Sterigmata are the two pointed

Annulus
Pileus (cap) Stipe

projections that extend from the basidium and bare the basidospores

Stipe (stalk) Cap (pileus) Annulus: ring of tissue

Gills

Basidiomycota contd
Hyphae
(comprising of the gills)

Gill
(comprising of hyphae)

Basidiospores Basidia Sterigmata

PLANTAE

Supergroup Archaeoplastida
Bryophytes (non-vascular plants) Phylum Hepatophyta (Liverworts & Marchantia) Phylum Anthocerophyta (Hornworts) Phylum Bryophyta (Mosses, Polytrichum, Mnium) Vascular Plants Seedless Vascular Plants

Phylum Lycophyta (Club Mosses, Spike Mosses, Quillworts) Phylum Pterophyta (Whisk ferns, Horsetails, Ferns)

Seed Plants Gymnosperms Phylum Ginkgophyta (Ginkgo or Maidenhair Tree) Phylum Cycadophyta (Cycads) Phylum Gnetophyta (Mormon Tea, Welwitschia) Phylu Coniferophyta (Conifers) Angiosperms Phylum Anthophyta (Flowering Plants)

Plants
Green algae-like organisms characterized by being autotrophic, having cellulose walls, and a sporic life cycle (alternations of generations) Bryophytes Includes many species that entirely lack vascular tissues and move material by simple cell diffusion Some bryophytes process simple vascular tissues, but these tissues differ from vascular plants Generally smaller, short, and possess a simpler body Vascular plants Most plants are vascular plants, which possess an internal system of specialized cylindrical cells extending from the tips of their leaves for the movement of water, minerals & dissolved foods

Xylem: carries water and dissolved minerals upward from the roots Phloem: conducts carbohydrates in solution away from the points where photosynthesis occurs

Vascular plants are larger, taller and more conspicuous of the terrestrial plants

Bryophyta The Mosses

Small plants that live in

moist areas stems called stems leaves called leaves Rhizoids: root-like structures that only have an anchorage function

Polytrichum

Bryophya Mosses Contd

Male plants have a series of leaves

Antheridia

at the tip which forms a cup Antheridia: male gameteproducing structures sperm Antheridia are elongate & oval in shape and consist of a sterile layer of cells (sterile jacket cells) Sterile jacket cells surrounds the spermatogenous tissue Spermatogenous tissue produces sperm Sperm is released into the cup & can be splashed out by water

Bryophyta Mosses contd

Archegonium: female specialized

Archegonium

gamete-producing structures egg Archegonium are flask-shaped and consist of a swollen basal portion (venter), which contains the egg Also, has an elongate neck with a row of cells in the center called the neck canal cells When the archegonium is mature and the egg ready to be fertilized, the neck canal cells disintegrate leaving a neck canal through which the sperm can reach the egg

Neck Neck canal cells

Egg

Venter

Stalk

Bryophyta Mosses contd

Sporangium (capsule): site of meiosis

and spore production Seta: slender & supports the capsule Seta surmounts a tiny foot that is embedded into the gametophyte tissue
Gametophyte nourishes the

sporophyte by passing nutrients through the foot

Epiphragm Capsule Wall

Grows on top of the archegonium Torn piece of archegonium (sporophyte

tears off) called the calptra and forms a cap on top the capsule Operculum: tiny lid covering the very tip of the capsule Peristome teeth cover the opening in the capsule peristome: the form that the peristome teeth make
Assists with spore dispersal

Capsule

Columella: center pillar Sporogenous tissue: appear as two

longitudial strands

Hepatophyta The Liverworts

Two forms of liverworts:
Leafy: resemble mosses from a

distance but differ by having a flattened appearance Thalloid: ribbon-like body, with rhizoids on the underside that anchor the body to the soil

Marchantia Female gametophyte with

receptacles Archegonium Archegoniophore Sporophyte

Marchantia

Heptatophyta The Liverworts contd

Sporophyte of thalloid liverwort Marchantia Shallow, wide foot Short, thick seta Oblong capsule full of spores Elaters found with the spores Elaters sensitive to moisture & will twist and bend with humidity changes and push out the spores

Bio 51 Lab 7 Vascular Plant Reproduction and Diversity

Vascular Plants
Vascular plants have an internal system of specialized

cylindrical cells extending from the tips of their roots into their leaves for the movement of water, minerals, and dissolved foods
Xylem: carries water and dissolved minerals upward from the

roots (roots to leaves) Phloem: conducts carbohydrates in solution away from the points where photosynthesis occurs (leaves to roots)

Two types of vascular plants: Seedless vascular plants : lycophytes and ferns, which produce only sperm Seed plants: gymnosperms and angiosperms, that produce seed addition to spores

Lycophyta lycophytes
Earliest vascular plants Club mosses, spike mosses, quillworts Lycopodium (club moss) Resembles a large moss plant Underground rhizome: small leaves that possess only a single, unbranched vein Terminal strobilus on the tip of the stem

A cone-like structure that produces the spores

Lycophyta Club Mosses contd

Longitudinal section of Lycopodium strobilus Central axis bearing sporophylls Sporophyll is a type of leaf that is reproductive, will produce a sporangium (spore container)
All spores are the same size Plant producing single-sized

spores usual produce bisexual gametophytes

Sporangium is connected to the

sporophyll by a thick stalk Sporangium jacket (wall)

Lycophyta Spike Mosses contd

Selainella (spike moss) Have a more feathery, wispy appearance Strobili are hard to locate because the sporophylls closely resemble normal leaves A major difference between club mosses and spike mosses is that spike mosses produces two different types of spores, large and small, within its strobili Plants that produce two sizes of spores usually produce unisexual gametophytes (male and female plants each bearing sperm and eggs, respectively)

Lycophyta Selaginella contd

Selaginella strobius Central axis Microspore Microsporangium Microsporophyll Ligule

Lycophyta Selaginella contd

Selaginella strobius Central axis Megaspore Megasporangium Megasporophyll

Pterophyta The Pteridophytes

Psilotum nudum (whisk fern) Dichotomous branching pattern: branches regularly fork into two equal branches Tiny round spore-containing structures located along the stems Each of these structures is a group of 3 sporangia fused into one unit called a synangium Lack of leaves & roots Only a simple horizontial stem (rhizome) which the aerial stems rise

Pterophyta Horsetails contd

Equistum Generally grow near water and posses either a highly-branched or unbranched body and tiny, scalelike leaves No sporophylls The sporangia are borne on the underside of T-shaped structures called sporangiophores, which are arranged spirally on the central axis Sporangia located on the underside of the sporangiophore, facing the strobilus axis Spores are the same size Along with the spores there are curly filaments called elaters (4 elaters with each spore)

Pterophyta Ferns contd

Pinna Sori: Groups of sporangia

Pterophyta Ferns contd

Fern prothallus

gametophytes

Archegonia (darker & tiny) Antheridia (very round & lighter) Spermatogenous cells (dots in the antheridia cells) Rhizoids

Seed Plants
Megaspores: larger female spores where female gametophytes are developed, dependent on the sporophyte for all their nutritional needs Megaspore produced inside of a megasporangium, which is wrapped in an integument After the female gametophyte is complete, the integument wrapped unit is called an ovule Male gametophytes are pollen Microspores: smaller, male spores Seed results when the egg is fertilized and the resulting zygote grows into a tiny embryo The seed is an embryo (young sporophyte) which is wrapped in several tisse layers, with the outer integuments forming the protective seed coat Gymnosperms: the ovule, which becomes the seed, rests exposed upon an ovuliferous scale when it is fertilized Angiosperms: the ovule is enclosed in other sporophyte tissues at the time of fertilization and is therefore not directly exposed to the environment

Cycadophyta Cycads
A little branched trunk is

crowned by a whorl of frond-like leaves Megastrobili: female cones, bear ovules & seeds Microstobili: male cones, bare pollen Each scale of the female cone will produce two large seeds after pollination and fertilization Slow growing and rare

Ginkgophyta Ginkgo biloba

Ginkgo biloba
The plant is heavily

branched tree bearing distinctive fan-shaped leaves Male trees bear small, loose cones that produce pollen Female trees produce many stalked pairs of ovules rather than female cones
Ginkgo biloba

Coniferophyta Conifer
Most conifers bear needle-like leaves and

woody/papery cones Pinus (pine tree) Produces two kinds of cones (strobili) on the same tree Each cone is composed of a central axis that bears spirally-arranged spore-bearing scales Smaller male pollen cones produce pollen Larger female or seed cones produces eggs and develops seeds

Conferophyta Pinus contd

Pinus male strobilus Sac-like microsporangia arranged on the lower surfaces of the scales Mircosporophylls: the scales that are attached spirally to the cone axis Microsporangia microspores pollen grains Cone axis Pollen grain(s)

Pollen Grain

Coniferophyta Pinus contd

Pinus female strobilus Megaspore Nucellus Ovule Integument Cone Scale

Coniferophyta Pinus contd

Pinus Seed Embryo Cotyledons (seed leaves) Stem apex Root apex

Anthophyta Flowering Plants

Flowers, fruits and endosperm

are unique to angiosperms Parts of the Plant Stigma Periantch: corolla & calyx Style Pistil: stigma, style, ovary, ovule anther Gynoecium: innermost whirl consisting of one or more pistils

petals Corolla: all the petals

stamen

Filament

Group of stamen is called an androeceium

sepal

Calyx: All the sepals

Ovaries

Anthophyta contd
Monocots
One cotyledon (seed leaf) per

Eudicots
Two cotyledons (seed leaves)

embryo Flowering parts in threes or multiples thereof Leaves with parallel venation Pollen grains usually with one aperture Multiple rings of vascular bundles in stem

per embryo Flower parts in sets of four or five or multiples thereof Leaves with net-like venation Pollen grains usually with three or more apertures One ring of vascular bundles or cylinder of vascular tissue in stem