BIOL 1108

Review Materials for Lab Practical #1

Lab 1:

Dichotomous Keys and Microbes are Everywhere

Taxonomic keys are used to help identify unknown organisms.

They are designed to arrange facts and features into mutually exclusivecouplets (organism has a tail; organism does not have a tail).

Keys designed with two (and only two) choices are said to be "dichotomous".

These dichotomous couplets require you to choose one path or the other.

For the virus key, you are required to decide whether each virus does ordoes not have: an envelope, DNA or RNA, single-stranded or double-strandednucleic acid, whether the host is a vertebrate or invertebrate, and whether thevirus has a tailpiece or not.

Dichotomous keys

Rules for writing good dichotomous keys:

1. Questions are written as dichotomous couplets that are mutually exclusive.

2. The first words of each couplet are identical (Tail piece is ., Tail piece is not .)

3. The key should have an indented format, so that each successive question is indented from the previous question.

4. Couplets should be specific (<15 cm or >15 cm; not "large" or "small").

5. Couplets should be based on features that are observable or measurable.

6. Couplets should be lettered (A or AA, B or BB) or numbered (1 or 1', 2 or 2')

7. In species names, the genus is always capitalized and the species is alwaystrivialized (Homo sapiens, Escherichia coli).

8. Species names are italicized or underlined (Homo sapiens or Homo sapiens)

Viruses

(= capsid)

(= envelope)

Nucleic acidRNA or DNA

Parts of a virus: each virus is unique, but all have a nucleic acid (RNA or DNA) surrounded by a protein coat (capsid or capsomere).

Some (flu virus) also have an envelope.

Viruses (from the Latin word for poison) cause a variety of diseases in Humans

Microbes

Prokaryotes:

– no true nucleus; no organelles.- divided into the Bacteria and Archaea

Bacteria:

- can be divided into 2 groups: gram-positive & gram-negative- based on whether the peptidoglycan in cell wall is exposed (gram positive) or covered by capsule (gram negative)

- capsule protects bacterium from hosts' enzymes, so gram negative bacteria are usually more pathogenic (disease- causing) and virulent.

Bacteria: gram staining

Staphylococcus aureusGram positive bacteriumCoccus = round shape

Escherichia coligram negative bacterium

bacilli = rod shaped

Size of bacteriabacteria are much smaller (~1 m) than Eukaryotic cells (~100 m)

Eukaryoticcell

Shapes of bacterial cells3 basic shapes: coccus, bacillus, spirillus

1. COCCUS: A spherical or oval-shaped bacterium; plural=cocci.

Streptococcus pyogenes

2. BACILLUS:A cylindrical-shaped bacterium; plural=bacilli.

gram negative bacilli gram positive bacilli

3. SPIRAL or SPIRILLUS: A corkscrew-shaped bacterium;pl. spirilli.

Spirilli bacteria occur in 3 forms:vibrio

spirillumspirochete bacteria

RBC = red blood cell; WBC = white blood cell

Cyanobacteria (= blue-green bacteria) used to be incorrectly called blue-green "algae"

"Pond scum" on a Georgia pond – blue-green bacteria are probably

the earliest organisms to photosynthesize; some also fix nitrogen

Nostoc

Oscillatoria

Special features of some bacteria:

1.Flagellum

2.Capsule

3.Endospore

1. FLAGELLUM: In bacteria, a rotating appendage arising from the bacterial surface and used for locomotion. Plural = flagella.

Arrangement of Flagella:

1. Monotrichous – single flagellum on one end

2. Amphitrichous – one flagellum at each end

3. Lophotrichous – more than one flagellum at each end

4. Petritrichous – flagella occur over the whole bacterium

1. Monotrichous 2. Amphitrichous

3. Lophotrichous 4. Petritrichous

2. BACTERIAL CAPSULES

Bacterial cell walls are normally composed of protein and lipid (fat) substances, but some bacteria also have a slime capsule, composed of a complex carbohydrate.

Capsules often make the bacterium more pathogenic and difficult for your body to attack.

Slime capsules on the surface of Pneumonia bacteria

capsules

3. Endospores - a dormant, tough structure that forms when a bacterium produces a thick internal wall that encloses its DNA and part of its cytoplasm. The function of an endospores is to ensure the survival of a bacterium through periods of environmental stress.

Bacillus subtilis showing endospores as green and the vegetative cell as red

Clostridium botulinum, the bacteriathat causes botulism, showing

endospores in green.

Antibiotic Sensitivity: a term used to describe the susceptibility of bacteria to antibiotics. Tests are conducted to see which antibiotic will be most successfulin treating a bacterial infection. Testing is done using the Kirby-Bauer method (K-B). Small disks containing different antibiotics are placed onto a plate upon which bacteria are growing (=bacterial lawn). If the bacteria are sensitive to the antibiotic, a clear ring, is seen around the wafer indicating poor growth.

Bacteriallawn

Disk with anitbiotic

Petridish

Compare these twodisks. The bottom oneis more effective, it killsmore bacteria, thanthe top one. Noticethat the clear ring islarger on the bottomone.

Protista:

Their form and methods of locomotion

1. Protozoans: unicellular heterotrophs

2. Algae: unicellular, colonial, and multicellular autotrophs

3. Slime molds: fungus-like protistans

1. Protozoans: unicellular heterotrophs

Pelomyxa (Chaos) carolinensis Pelomyxa (Chaos) carolinensis

The giant amoeba is common in freshwater habitats. It moves by pushinga pseudopodium ("false foot") forward, then streaming the cytoplasm in that direction.

Amoebas feed by surrounding, engulfing, and digesting food.

Plasmodium vivax

Plasmodium vivax is a protozoan parasite that causes malaria in humans.They attack and infect red blood cells causing them to burst. The host

often dies from anemia (lack of oxygen delivery to the cells).

sporozooites – free-living form

mature bacteria in red blood cells

Trypanosoma gambiensisstained purple below among red blood cells

Trypansoma gambiensis is a flagellated protozoan parasite that causesAfrican (Gambian) sleeping sickness in humans.

Paramecium caudatuma ciliate

conjugation in Paramecium

Paramecium are covered with cilia (look hard) and have many organellesincluding an oral groove, anal pore, macronucleus and micronucleus.

2. Algae – are Protists that can be unicellular, multicellular, or colonial (forming colonies). All photosynthesize.

Ceratium species

Ceratium is a genus of single-celled aquatic algae common in fresh water and salt waterfrom the Arctic to the tropics.

They are armored dinoflagellates with two unlike flagella.

They have characteristics that are both "plant-like" and "animal-like".

Aerial photo of a "red tide" caused by dinoflagellates

Diatoms

•Diatoms are the most numerous unicellular algae in the oceans and as such are an important source of food and oxygen.

•They are also important in freshwater environments.•The cell walls of diatoms contain silica (a component of glass) formed in 2 halves

like a pillbox.•They are a major component of phytoplankton in freshwater and marine environments.

Diatom showing the glass-like silica wallsand two halves

Green Algae – Phylum Chlorophyta

There are about 8,000 species of green algae. Most are aquatic, but a few species live on land. They all photosynthesize. The green algaeare thought to have given rise to the plants.

Many species of green algae are multicellular (one individual made up of many cells)

But, Spyrogyra, Volvox and other Chlorophytes are colonial (one-celled individuals make up a colony).

SpyrogyraVolvox

Chlamydomonis

Golenkinia

Other Chlorophytes are unicellular

Brown algae – Phylum Phaeophyta

The Phaeophyta are almost entirely marine, frequently dominating rocky shores in cold and temperate waters throughout the world. The giant kelp, Macrocystis pyrifera , forms expansive kelp forests off the west coast of North America and provides habitat and shelter for many other organisms.

Red Algae – Phylum Rhodophyta

The Rhodophyta are a distinct clade characterized by the accessory reddishphotosynthetic pigments and the absence of flagella and centrioles.

There are ~6000 species.They are found along the coasts in tropical, temperate and cold-water regions.Red algae are ecologically significant as primary producers, providers of habitat for other marine organisms, and their important role in the establishment of coral reefs.

Golden algae – Phylum Chrysophyta

Chrysophyta are Protists. About 10,000 species exist. Most are single-celled freshwater and marine algae. The chrysophytes are characterized by their yellowish xanthophyll pigments, which mask the green of the chlorophyll that is also present. Most have cell walls containing silica or calcium.

Slime molds

slime mold on petri dish

Acellular slime molds are diploid, multinucleate masses that creep along the ground and feed on dead organic material. The mass is one large cell referred to as a plasmodium. (Note- Don't confuse this with the genus Plasmodium shown earlier).

Slime molds play an ecological role similar to that of fungi. They are decomposers, feeding on dead organic material. They differ in that slime molds ingest their food.

The plasmodium has produced dark "fruiting bodies" that contain spores.

Note the traces of the former plasmodium in the background

Could you write a dichotomous key to separate these Protists?

Amoeba Plasmodium Trypanosoma

Paramecium VolvoxPhysarum

Fungal Diversity

Zygomycota

Rhizopus stolonifer – black bread mold

Rhizopus conjugation

Hyphae: can you see septa?

Sporangiospores

Zygosporangium

Pilobus – "hat-thrower" fungusa close relative of black bread mold

Ascomycota – sac fungi

Yeasts, truffles, morels, Chestnut blight

Sordaria

perithecia

Aspergillus

conidiophores

Ergot – a fungus that infects grains

Chestnut blight fungus

Peziza

Close-up of apathocecium with asci and ascospores

ascus with 8 ascospores

Baker's yeast

Saccharomyces cervesisiae

Basidiomycota – club fungi

Coprinus basidiocarp x-section

gills

basidiocarp"mushroom"

Apple rust

Black stem rust of wheat

Basidiomycota fungi cause several important crop diseases

Deuteromycetes

Penicillium chrysogenum magnified

Penicillium chrysogenum on petri dish

Types of lichenslichens are composed of an algae and fungus hyphae

1. Crustose - encrusting2. Foliose – leaf-like, no branching

3. Fruticose – bush-likewith branching

Non-vascular Plants no true stems, leaves or roots

1. Bryophyta – mosses

2. Hepatophytes – liver worts

3. Anthocerophytes – horn worts

Bryophyta – mosses

Moss gametophytes and sporophytes

Hepatophytes – liver worts

Anthocerophytes – horn worts

Vascular Seedless Plants

1. Lycophytes – club mosses

2. Ferns

Club mosses

Whisk "fern"

Ferns

Sori on fern

stained sori

Fern prothallus = gametophyte

Christmas fern

Cinnamon fern

Interrupted fern

Rattlesnake Fern

Maidenhair Fern

The gymnosperms today include 4 plant phyla:

1. Cycadophyta

2. Gingkophyta

3. Gnetophyta

4. Coniferophyta

1. Phylum Cycadophyta

(cycads)

2. Phylum Ginkgophyta:

3. Phylum Gnetophyta

Phylum Gnetophyta

Genus: Ephedra

Phylum Gnetophyta

Genus: Welwitschia

4. Phylum Coniferophyta

Anatomy of an Angiosperm Flower

Fig. 30.7

Petal

Sepal

Anther

Stigma

Ovule

Ovary

Receptacle

Style

Filament

(♀)

(♂)

Carpel

Stamen

Types of Simple Fruits

Aggregated fruit(one flower with multiple pistils)

Multiple fruitscome from multiple flowers

Plant leaf x-section

Gymnosperm cones – x-section

Monocots:multiples of 3

Dicots:multiples of 4 or 5

Dicot root: xylem and phloem clustered in middle

Monocot root: pith in middle surrounded by xylem and phloem

Monocot stem Dicot root

Dicot stem Monocot root