Bio 94 Midterm #2: Emerson/Gaut

Monophyletic group

A group that includes an ancestor of the group and all of its descendants but no others.

Paraphyletic group

A group that contains some but not all of the descendants from a common ancestor.

Eukaryotes

One of the three taxonomic domains of life, monophyletic, consisting of unicellular organisms (most protists, yeast) and multicellular organisms (fungi, plants, animals) distinguished by a membrane-bound cell nucleus, numerous organelles, and an extensive cytoskeleton.

Prokaryotes

Unicellular organisms that consist of a single cell without a nucleus or organelles. Contain two domains of life, Bacteria and Archaea (not monophyletic; paraphyletic)

Bacteria

One of three taxonomic domains of life, monophyletic, consisting of unicellular prokaryotes distinguished by cell walls composed largely of peptidoglycan, plasma membranes similar to those of eukaryotic cells, and ribosomes and RNA Polymerase that differ from those in Archaea or eukaryotes.

Archaea

One of three taxonomic domains of life, monophyletic, consisting of unicellular prokaryotes distinguished by cell walls made of certain polysaccharides not found in bacterial or eukaryotic cell walls, plasma membranes composed of unique isopropene-containing phospholipids, and ribosomes and RNA Polymerase similar to those of eukaryotes.

Peptidoglycan

Polymer of sugars and amino acids that form the cell wall for most bacteria; Example of a synapomorphy for all bacteria

RNA Polymerase of bacteria

Just one type (has 5 subunits)

RNA Polymerase of archaea

Just one type (consists of 13 subunits, similar to RNA Polymerase II in Eukaryotes

First amino acid incorporated during translation for bacteria

formylmethionine

First amino acid incorporated during translation for archaea

methionine

Are histones associated with bacteria DNA?

No

Are histones associated with archaea DNA?

Yes

Cyanobacteria

A lineage of photosynthetic bacteria formerly known as blue-green algae. Likely the first life-forms to carry out oxygenic photosynthesis

Carl Woese

Sequenced rDNA and made phylogenies; discovered archaea was a separate domain of life

Prokaryotes are diverse and interesting:

1. They represent two of the three domains of life

2. The vast majority are single-celled organisms

3. They are the most abundant organisms on earth

4. They are essential of the functioning of life as we know it

5. They contribute to human illness, but also human health

Streptococcus pneumoniae

Pneumonia

Streptococcus pyogenes

Strep throat, scarlet fever

Only __________ species can be grown in lab

10,000-20,000

Metagenomics

The inventory of all the genes in a community or ecosystem created by sequencing, analyzing, and comparing the genomes of the component organisms. Often refers to the study of microbial communities.

What are the most abundant photosynthetic organisms on earth?

Prochlorococcus and Synechococcus; they are marine bacteria that do photosynthesis (both cyanobacteria)

coccus =

Spherical

bacillus =

Rod-shaped

What shape is Treponema pallidum?

Helical (Gram-negative syphyllis)

Neiserria gonorrhea

Gram-negative species, causes gonorrhea (STI)

Gram Stain

A staining technique used for the preliminary identification of prokaryotes based on cell wall composition (can only use with cultured cells)

Gram-positive

Bacteria that appears purple with a Gram stain. They have cell walls composed of a thick layer of peptidoglycan and no outer phospholipid layer.

Gram-negative

Bacteria that appears pink with a Gram stain. They have cell walls composed of a thin layer of peptidoglycan and an outer phospholipid layer.

Penicillin

Inhibits formation of peptidoglycan, killing the cell.

Gram-negative cell walls are:

more resistant to antibiotics due to phospholipid layer (outer and inner phospholipid layers with peptidoglycan in between)

Strepto =

chain of cells

Staphylo =

bunch of cells (like grapes)

Autotrophs

"self feeders"; Synthesize their own compounds from simple starting materials such as CO2 and methane (CH4)

Photoautotrophs

Organisms that use light as a source of energy to synthesize organic compounds; 6CO2 + 12H2O + light --> C6H12O6 + 6O2

Chemoautotrophs

Obtain energy by the oxidation of electron donors in their environment (from compounds like ammonia and hydrogen sulfide); 6H2S + 2O2 --> SO4 + 2H + energy

Five comments about Photosynthesis:

1. The process is complex

2. Photoautotrophs use glucose as the raw material to make other organic compounds needed for life

3. A byproduct is free O2

4. We do not know how photosynthesis evolved

5. Most of life is dependent on photosynthesis

Black smokers produce ___________ at the bottom of the ocean

H2S (Hydrogen sulfide)

Summary of Deep-Sea Communities

1. These communities rely on chemoautotrophic Bacteria and Archaea.

2. Most of the larger organisms live in symbiosis with chemoautotrophic bacteria.

3. Most of the free-living prokaryotes in the deep-sea vents are Archaea, which are often adapted to extreme environments.

Symbiosis

Relationship between organisms of different species

Mutualistic Symbiosis

Benefits both species

Parasitism

Symbiosis that benefits one species, but bad for the other

Commensalism

Symbiosis that is beneficial for one, and neutral for the other.

Thermophiles

Organisms that are adapted to high temperatures (ex: Archaea)

Extremophiles

Organisms that are adapted to extreme conditions (ex: Archaea)

Heterotrophs

"other-feeders"; absorb ready-to-use organic compounds- called building block compounds- produced by other organisms in their environment.

Photoheterotrophs

An organism that uses light to generate ATP but that must obtain carbon in organic form.

Chemoheterotrophs

An organism that must consume organic molecules for both energy and carbon.

Traits of bacteria and archaea (prokaryotes):

Binary fission, Haploid, Circular DNA, Unicellular (mostly)

Traits of eukaryotes:

Nuclear envelope, Mitosis, Meiosis (sex), Mitochondria, Cytoskeleton, Linear chromosomes, Mostly diploid, Unicellular + Multicellular, Organelles enclosed by membranes

Protists

A eukaryotic organism that cannot be classified as an animal, plant, or fungus. Tremendously abundant in marine and freshwater plankton and other aquatic habitats. They provide food for many organisms in the aquatic and fix a lot of carbon.

Foraminifera

Protist; mostly in ocean, have shells, important food source, very abundant fossil record, sensitive to environmental variations, making them good indicators of past climate change.

Euglenids

Protist that digests food; Trichonympha species are symbionts in the termite gut, bacterial symbiont (mutualistic)

Apicomplexans

Parasitic protist that moves by flexion; Plasmodium falciparum causes malaria

Plasmodium life cycle

1. Mosquito bite infects human liver cell, bursts out (n)

2. Infects blood cells, split into male and female (n)

3. Female and male gametes (n), fertilize and become a zygote (2n)

4. Meiosis, then mitosis

Dinoflagellates

Protist; mostly unicellular, appx. 50% are photoautotrophic, important members of the marine and freshwater food chains, about 4000 living species, most are plankton, covered in silica-based shells (red tide)

Algae

Paraphyletic group of 'plant-like' protists (photosynthetic), mostly autotrophic, aquatic, and multicellular. Responsible for fixing half of the world's carbon through photosynthesis. Red, green, and brown (Red and green are more closely related to land plants)

Brown Algae

Multicellular, photosynthetic, kelp, alternation of generations (spend time in both diploid and haploid state)

Green Algae

Photosynthetic algae, multicellular, most likely the ancestors to land plants, alternation of generations

Takeaways of Diversity among Protists:

1) Most are unicellular, but some are complex, multicellular organisms

2) All eukaryotic autotrophic algae contain chlorophyll a. Green algae contain chlorophyll a and b. Brown algae gas chlorophyll c and a, and red algae only has chlorophyll a

3) Green algae is the closest to land plants

4) Most eukaryotes, including the protists, make haploid gametes of separate sexes to make diploid zygote (sex), unlike bacteria and archaea reproduction by binary fission

5) Alternation of generations (multicellular diploid and haploid phase, not all protists do this)

Alternation of Generations

the alternation between the haploid gametophyte and the diploid sporophyte in a plant's life cycle

Endosymbionts

An organism that lives in a symbiotic relationship inside the body of its host.

Origin of the nucleus:

Infoldings of plasma membrane surrounds chromosomes (diploid), forming a nuclear envelope and ER

Giardia lamblia

A parasitic zooflagellate with many primitive features, including two haploid nuclei.

The origin of mitochondria:

1. Host cell surrounds and engulfs bacterium

2. Bacterium lives within host cell

3. Endosymbiosis: Host cell supplies bacterium with protection and carbon compounds. Bacterium supplies host cell with ATP. (Process happens once)

The origin of chloroplasts:

First symbiosis leads to photoautotrophic eukaryote with a nucleus and chloroplast; sunlight + CO2 --> glucose. Secondary symbiosis starts with photosynthetic protist being engulfed. The nucleus from photosynthetic protist is lost, and the chloroplast is left with four membranes.

Evidence that supports the endosymbiosis of mitochondria and chloroplasts:

1. Chloroplast and mitochondria are the right size

2. The membranes of chloroplasts and mitochondria have enzyme and transport systems similar to prokaryotes

3. Organelles divide by a splitting process similar to binary fission

4. Both have circular DNA, like prokaryotes

5. Both contain machinery for DNA replication + translation, suggesting they were once free living. Translation machine (ex: ribosomes), are small and prokaryote-like.

6. Phylogenies show that mitochondrial and chloroplast genes are more similar to prokaryotic genes than eukaryotic genes

Binary Fission

A form of asexual reproduction in which one cell divides to form two identical cells.

Algae Alternation of Generations

1. Diploid sporophyte (2n) undergoes meiosis, producing haploid spores (n)

2. Spores undergo mitosis, forming haploid male and female gametophytes (n)

3. Sperm and egg are made from gametophytes; sperm needs water to swim

4. Come together, fertilize, produce diploid zygote (2n).

5. Undergoes mitosis, forms sporophyte (2n), and process repeats

Sporophyte

Diploid (2n) multicellular form that produces spores by mitosis

Spores

Haploid (n) cells that multiply by mitosis to generate a multicellular haploid form

Gametophyte

Haploid (n) multicellular form that produces gametes

Egg and Sperm

Haploid (n) gametes

Zygote

The results of fertilization (syngamy) between egg and sperm.

Embryo

The zygote develops into an embryo and the diploid (2n) embryo develops into the sporophyte.

First evidence of land plants:

475 mya, cuticle, spores, sporangia

How to plants invade land?

1) Sexual reproduction on land

2) The ability to survive on land and in contact with air

Embryophyte

"embryo-bearing plant", when sperm and egg come together, they stay on plant

Cuticle

A protective coating secreted by the outermost layer of cells of an animal or a plant; often functions to reduce evaporative water loss.

Stomata

Opening surrounded by specialized guard cells; the pore opens or closes as the guard cells change shape. When guard cells lose water, they become flaccid or limp and the stomata close. Pores close at night to limit water loss from the plant when CO2 uptake is not needed. When guard cells absorb water, they become turgid, or "taut," opening the pore. Open stomata allow CO2 to diffuse into the interior of leaves and stems where cells are actively photosynthesizing.

Four Major Groups of Land Plants

1. Non-vascular plants: embryophyte, cuticle, stomata

2. Seedless vascular plants: vascular tissue

3. Gymnosperms: naked seeds

4. Angiosperms: flowers and fruits

What group of plants is the most successful?

Angiosperms, 250,000 species, most recent as well

Which group of plants marked the ability to live on land?

Nonvascular plants; cuticle, stoma, and embryophyte

Which trait did seedless vascular plants introduce?

Vascular tissue

What trait did gymnosperms introduce?

Seeds

What trait did angiosperms introduce?

Flowers, fruits

Nonvascular plants are a ______________ group

Paraphyletic

Nonvascular plants

A paraphyletic group of land plants that lack vascular tissue and reproduce using spores. Include three lineages: liverworts, mosses, and hornworts. AKA Bryophytes

Non-vascular plants Alternation of Generations (mosses):

1) Mature female haploid gametophyte (n) produces a mature diploid sporophyte (2n)

2) Produces spores through meiosis, haploid spores (n) dispersed by wind

3) Spores undergo mitosis, producing a mature male and female gametophyte (n)

4) Eggs develop in archegonia, and sperm develop in antheridia. Sperm swim (water needed) to the egg.

5) Zygote (2n) fertilized in the archegonium, making plan an embryophyte.

6) Developing sporophyte (2n) undergoes mitosis to become mature diploid sporophyte (2n), which grows from the mature female gametophyte (n)

Non-vascular plants Alternation of Generations (mosses) Key Takeaways:

- Gametophyte (n) is dominant, in mosses, sporophyte is physically attached to the gametophyte

- Male and female gametophyte (n) are independent of the sporophyte (2n)

- Sperm develop in the antheridium

- Egg and the zygote develop in the archegonium

- In nonvascular plants, fertilization still requires water, because the sperm swim to the archegonium

Types of mosses:

Polytrichum, Sphagnum squarrosum

Types of liverworts:

Allisonia, Marchantia polymorpha

Types of hornwarts:

Folioceros fuciformis

Seedless Vascular plants

Paraphyletic group that has vascular tissue, which transports water, nutrients, and sugars. Made of complex tissues (xylem and phloem). Includes club mosses, whisk ferns, ferns, and horsetails.

Functions of vascular tissue:

1) Moves water, nutrients, and food (organic compounds) up and down the plant

2) Supports the plant

Xylem

Nonliving vascular tissue that carries water and minerals (like nitrogen) up the plant. Has a 1) primary wall (cellulose), 2) secondary wall (lignin), 3) tracheids (long, thin, water conducting cell with pits that increases structural support) and 4) vessel elements (bigger water conducting cell, mainly in angiosperms, perforation and pits, more effective than tracheids)

Vessel elements evolved:

more than once; club mosses and ferns (seedless vascular), gnetophytes (gymnosperms), and angiosperms.

Transpiration

Evaporation of water from leaves into the air through the stomata. Process requires no energy, and can transport an enormous amount of water. >90% of the water that is transported up the xylem sap is lost to evaporation.

Phloem

Living vascular tissue that conducts sugars and hormones down the plant; contain sieve-tube elements (few organelles) and companion cells (many organelles)

says moves down in notes, but textbook says both directions

The plant vascular system Key Takeaways:

To sum, the water that is taken up by roots and transferred by transpiration to leaves has three uses:

1) Most of it is lost to evaporation. Not a total loss, however, column of water provides support for the plants in addition to the lignin in the xylem

2) Some of it is used for photosynthesis and other cellular processes

3) Some of it enters the sieve elements and contributes to the phloem sap. This water will go to any "sink" (fruit or roots) and may be returned to leaves via xylem.

Seedless vascular plants Alternation of Generations:

1) Mature sporophyte (2n) undergoes meiosis, producing haploid spores (n) in sporangia.

2) Haploid spores are dispersed by wind, undergoing mitosis, and forming an independent gametophyte (n).

3) Gametophyte undergoes mitosis forming a mature gametophyte. On the gametophyte, the sperm develops in antheridia and the eggs develop in the archegonia.

4) Sperm swims to egg (water needed), fertilization occurs, and a zygote (2n) is produced in archegonium.

5) Through mitosis, sporophyte (2n) grows off of the gametophyte (n), and the cycle restarts from the mature sporophyte.