Bio 2 Lab Midterm

Dissecting microscope

Shows whole objects in 3D at LOW magnification (good for big things like a whole plant or a surface)

Compound microscope

Shows small, thin specimens on slides at HIGH magnification (under 1000x)

Which objective lens do you start with on a compound microscope?

The lowest-power one (smallest number). It gives the widest view and most working distance, so the specimen is easiest to find and focus

Scanning electron microscope (SEM)

Shows surface details; high-resolution image that looks 3D

Transmission electron microscope (TEM)

Shows the inside of cells (internal ultrastructure) in thin slices; image is flat (2D)

Phylogeny

The evolutionary history and relationships of organisms

Phylogenetic tree (cladogram)

Diagram showing the hypothesized evolutionary relationships among species (cladogram = phylogenetic tree)

Node (branch point) on a phylogenetic tree

A shared common ancestor

Endpoints (tips) on a phylogenetic tree

Specific taxa or species

Clade (monophyletic group)

A common ancestor plus ALL of its descendants (the whole family, nobody left out)

Paraphyletic group

Includes a common ancestor but NOT all of its descendants (some relatives left out)

Polyphyletic group

Includes species that have different ancestors (like grouping unrelated lookalikes together)

Homology (homologous structure)

A trait inherited from a common ancestor and kept. Ex: human forelimb and bat wing; pelican hooked beak with gular pouch

Divergent evolution

Related species (recent common ancestor) adapt to different environments and become MORE dissimilar

Convergent evolution

A similar trait appears in species that do NOT share a recent common ancestor. Ex: dorsal fins of sharks and dolphins; wings of birds and dragonflies

Homoplasy

A similar trait that evolved independently, NOT inherited from the most recent common ancestor (the result of convergent evolution)

Why are wolves and foxes similar, versus sharks and dolphins?

Wolves and foxes: shared ancestry. Sharks and dolphins: convergent evolution

How can molecular data (DNA, RNA, protein) change a phylogeny built only on looks?

It can revise the groupings, because things that look alike may not actually be closely related

Parsimony

Building the tree with the simplest evolutionary path (fewest changes); it assumes divergent evolution and minimizes convergent evolution

Prokaryote

Organism with no nucleus and no membrane-bound organelles (DNA is not enclosed by a nuclear membrane); usually unicellular

The two prokaryote domains

Bacteria and Archaea

Eukaryotic cell

Has a nucleus and membrane-bound organelles; found in protists, fungi, plants, and animals (unicellular or multicellular)

Which prokaryote domain is far more common and found nearly everywhere?

Bacteria

Most Archaea are…

Extremophiles (live in harsh environments like very hot, salty, or acidic places)

Coccus

Spherical / round bacterial cell

Bacillus

Rod-shaped bacterial cell

Spirillum

Rigid spiral with relatively few turns

Spirochete

Thin, flexible corkscrew with many turns

Gram stain

A differential stain that separates bacteria by cell wall type (thick vs thin peptidoglycan)

Gram stain steps in order

Heat fixation > Crystal violet > Gram's iodine > Decolorizer > Safranin

Crystal violet (Gram stain)

Primary stain; turns BOTH Gram-positive and Gram-negative cells purple

Gram's iodine - what it does and what step it is

Mordant: helps the cell hold onto the crystal violet (Step 3)

Decolorizer

Washes the crystal violet out of Gram-negative cells (Gram-positive stay purple)

Safranin

Counterstain: turns the decolorized Gram-negative cells pink/red

Gram-positive cell wall

Thick peptidoglycan layer, no outer membrane

Gram-negative cell wall

Thin peptidoglycan layer PLUS an outer membrane

Gram-positive cells end up this color

Purple (the thick wall traps the crystal violet)

Gram-negative cells end up this color

Pink or red (they lose the purple, then take up safranin)

Staphylococcus epidermidis

Gram-positive cocci

Serratia marcescens

Gram-negative rods

Cyanobacteria

Photosynthetic bacteria that make oxygen and fix carbon dioxide and nitrogen from the air

Why are cyanobacteria no longer called 'blue-green algae'?

The word algae is now reserved for eukaryotes; cyanobacteria are prokaryotes

Cyanobacteria pigments

Chlorophyll a (green), phycocyanin (blue), phycoerythrin (red). The mix gives green, blue-green, reddish, brown, or olive colors

Cyanobacterial bloom

Rapid growth caused by high nutrient levels; can be toxic and lowers water quality (cyanobacteria are water-quality indicators)

Mucilaginous sheath

Jelly-like covering that protects cells (it holds a Merismopedia colony together)

Anabaena

Cyanobacterium that forms chains (filaments) of cells and makes heterocysts and akinetes

Vegetative cell (Anabaena)

The ordinary cells in the filament; they do photosynthesis

Heterocyst

Enlarged, pale specialized cell that fixes nitrogen (turns N2 gas into a usable form); forms when nitrogen is scarce

Akinete

Thick-walled dormant (resting) cell; survives cold, drying out, and winter, then regrows

Oscillatoria

Long, unbranched filaments; named for its oscillating / gliding movement (slides to orient toward light)

Merismopedia

Round cells arranged in grid-like sheets (cells divide in only two directions)

Protists

Eukaryotes that are NOT plants, animals, or fungi

Are protists a monophyletic group?

No. They don't all share one direct common ancestor (some are closer to plants, animals, or fungi than to each other)

Primary endosymbiosis

One free-living cell engulfs a bacterium and keeps it (it becomes an organelle)

Secondary endosymbiosis

The product of primary endosymbiosis is itself engulfed and kept by another eukaryote (this is why you get extra membranes)

The four protist supergroups to know

Excavata, SAR clade, Archaeplastida, Unikonta

Excavata: where does the name come from?

A feeding groove that looks 'excavated' (dug out) of the cell surface

Euglena, Trypanosoma, and Giardia belong to which supergroup?

Excavata

Euglena pellicle

Flexible cell surface (plasma membrane + protein strips) that lets Euglena change shape as it swims

Stigma (eyespot)

Light-sensitive reddish spot near the base of the flagellum (Euglena, Chlamydomonas)

Euglena nutrition

Depends on conditions: photosynthesis, absorbing nutrients, or phagocytosis

Why can some Euglena photosynthesize?

They got plastids through secondary endosymbiosis (from green algae)

Trypanosoma

Parasitic excavate found in blood; eel-like with an undulating membrane

Undulating membrane

Flagellum + body wall structure used to swim through thick liquid like blood

Trypanosoma brucei

Causes sleeping sickness; spread by the tsetse fly

Giardia

Parasitic excavate from feces-contaminated water; causes giardiasis (diarrhea, cramps)

Giardia appearance

Bilaterally symmetrical cell with two nuclei (twin nuclei)

The SAR clade contains

Stramenopila, Alveolata, and Rhizaria

Stramenopila: where does the name come from?

Straw-like hairs on the flagella (they help swimming)

Stramenopila includes

Diatoms, brown algae (Fucus, Sargassum), and giant seaweeds

Diatom cell wall

Silicon dioxide (silica), built in two overlapping halves

Diatom importance

Fix about 25% of Earth's organic carbon, make oxygen, and are food for many organisms

Alveolata: where does the name come from?

Alveoli = sac-like vesicles just under the plasma membrane

Alveolata includes

Dinoflagellates, Paramecium, and Stentor

Dinoflagellate flagella

Two perpendicular flagella (gives a whirling swim)

Dinoflagellate armor

Cellulose plates

Red tide

Toxic bloom caused by certain dinoflagellates (Florida red tide)

Paramecium

Slipper-shaped ciliate covered in cilia; cilia are used for movement and feeding

Stentor

Large trumpet-shaped ciliate with a ciliated corona (SAR - Alveolates)

Taxis

Directional movement in response to a stimulus

Rhizaria

Planktonic marine protists (radiolarians, foraminiferans) with axopodia

Axopodia

Very narrow pseudopodia

Unikonta is also called

Amorphea

Unikonta includes

Amoebozoans and opisthokonts (fungi, animals, choanoflagellates)

Choanoflagellates

Close protist relatives of animals

How does an amoeba move?

Pseudopodia (false feet) pushed out by cytoplasmic streaming

How does an amoeba eat?

Phagocytosis: it engulfs a solid particle into an internal compartment

Contractile vacuole

Collects and expels excess water to keep water balance

Slime molds

Once thought to be fungi, but they ingest food and digest it internally and lack hyphae and chitin walls (Amoebozoa supergroup)

Archaeplastida

Protists with plastids (photosynthetic organelles) that came from engulfed cyanobacteria; includes red and green algae

Green algae (Chlorophyta) and land plants

Green algae are the closest algal relatives of land plants (charophyceans are the closest)

Green algae share these pigments with land plants

Chlorophyll a and b

Green algae share this with land plants for storage and walls

Starch for energy storage and cellulose cell walls

Red algae (Rhodophyta) get their color from

Phycoerythrin

Chlamydomonas

Unicellular green alga with two flagella

Spirogyra

Filamentous green alga (long unbranched chain of cells)

Volvox

Colonial green alga (hollow sphere, makes daughter colonies)

Caulerpa and Ulva

Multicellular green algae - looks like lettuce

What did land plants evolve from?

Green algae (charophyceans)

Rhizoids and roots

Anchor the plant and absorb water and minerals