Bio2 Slides Exam 1

What is a character?

defined attribute of a single species

Highlight the main differences between homologous & analogous structures

Homologous

• Common evolutionary history + shared CA

Analgous

• independently acquired structures because of environmental pressures

• No shared CA

• convergent evolution

What is a polytomy in an phylogenetic tree?

2 or more descendant groups with unclear evolutionary relationships

What is the difference between a shared ancestral trait and a shared derived character?

Shared ancestral trait is not unique to clade, it originated in the ancestor. Derived is unique to a clade.

What is a monophyletic group in a phylogenetic tree?

A CA and all of its descendants (the ideal clade)

What is a paraphyletic group in a phylogenetic tree?

The common ancestor and some of its descendants

What is a polyphyletic group in a phylogenetic tree?

Distantly related species not including most recent CA

What is evolution?

changes in allele frequency in populations over time

Are viruses part of the domains of life?

No, they are considered non-living

Are viruses cellular? Also, can they reproduce?

Viruses are non-cellular and cannot reproduce, only replicate

All viruses are obligate intracellular parasites. What does this mean?

They invade susceptible host cells & use the host cells’s resources as well as processes

Do viruses have DNA or RNA?

They can have either DNA or RNA.

Explain the role of a capsid in viruses.

The capsid is the protein coat that surrounds the genetic material, determining the:

• Shape of virus

• plays role in attatchment

What is the capsid made of in viruses?

capsomere (protein subunit)

What is the envelope structure in viruses and do all of them have it?

It is the bilayer membrane outside the capsid obtained from the host cell during budding

not all viruses have it

How does host range or specificy differ between different viruses?

Some have narrow host ranges (even with specific tissues), while other have broad ranges

Explain the mechanism behind the specifity of viruses (why they are particular with what they infect)

They have viral surface proteins that connect to specific host receptor molecules

What does a virulent phage do and what cycle does it use?

• Kills the host at the end of the cycle and utilizes the lytic cycle

SEQ LYTIC CYCLE

1. Attachment & Injection: the virus attatches self to the host cell and injects into it

2. The phage DNA remains separate from the host

3. Replication - The phage replicates its DNA

4. The phage makes its respective proteins by hijacking the host’s mechanism + self-assembly

5. The cell lyses, & phages exit

What cycles do temperate phages use?

Lysogenic & Lytic cycle

SEQ LYSOGENIC CYCLE

1. Attatchment + injection

2. phage dna intergrates self into host genome, it is a prophage now

3. host cell divides and DNA is passed onto host daughter cells

What 2 domains of life to prokaryotes belong to?

Archaea & Bacteria (which is what we are focusing on)

Which of these do prokaryotes have: nucleus, organelles, ribosomes?

Ribosomes

In prokaryotes, where is the cell wall located and what is its function?

It surrounds the plasma membrane and maintains cell shape

What are the 3 common prokaryotic cell shapes (and what maintains these shapes?)

1. cocci = spherical

2. bacilli = rod shaped

3. spirilli/spirochetes = spiral
   
   The cell wall maintains the shapes

In prokaryotes (only bacterial prokaryotes) what is the cell wall made of?

Peptidoglycan, which is a polymer made of polypetides and sugars

When it comes to prokaryotic cell structure, what is the function of all these components:

1. Cell Wall

2. Capsule

3. Pili

4. Plasma membrane

5. Cytoplasm

6. Ribosome

7. flagellum

8. plasmids

9. nucleiod

10. Chrosome

1. Cell Wall: Maintains cell shape

2. Capsule: surrounds cell wall + protects against dehydration & phagocytosis

3. Pili: attatchment

4. Plasma membrane: letting things in/out of cell

5. Cytoplasm: cytosol + contents

6. Ribosome: protein synthesis

7. flagellum: locomotion

8. plasmids: small dna circles that have non-essential genes

9. nucleiod: unenclosed area where DNA is stored

10. Chromosome: DNA, always haploid (n)

What are the two stains used in a gram stain?

Crystal violet (purple) & safranin (pink)

If a bacterial cell wall is gram positive, what does that mean?

It means the cell wall has thick peptidoglycan, which traps crystal violet, and stains purple

If a bacterial cell wall is gram negative, what does that mean?

The wall has thin peptidoglycan and can’t trap crystal violet, therefore letting safranin show and staining pink.

CC positive/negative taxis

positive: movement towards the stimulus
negative: movement away from the stimulus

What are the 3 main parts of the bacterial flagellum?

1. The motor: the rings in the cell wall and plasma membrane

2. Hook

3. Filament

SEQ Bacterial flagellum function

H+ pumped out across PM by ETC → Form gradient → Diffuse into cell through motor → Produces force → Hook turns → Filament rotates —→ Now we moving!

SEQ binary fission (the process in which prokaryotes reproduce)

1. The single circular chrosome in the prokaryote cell is replicated

2. The FtsZ proteins then go to middle forming a Ftsz ring, then a septum

3. Cell fully splits, now we have 2 identical cells

What are the two main mechanisms of genetic diversity in prokaryotes?

A. Mutation + Rapid Reproduction

B. Genetic Recombination

SEQ/CC the 3 types of genetic recombination in prokaryotes

1. Transformation: external DNA taken up and integrated into genome

2. Transduction: During phage replication, an error occurs where a fragment of host DNA is packaged into the new phage. The new phage transfers that DNA to another cell, incorporating it into its genome.

3. Conjugation: Genetic info transferred between two living prok cells via a F factor in the form of a plasmid. F+ cell uses pilus to attatch to F- cell, making a mating bridge to transfer plasmid DNA.

What are the SDC (shared derived characteristics) of eukaryotes?

1. Nucleus 

2. Endomembrane system (organelles)

3. Cytoskeleton: network of fibers

4. Mitochondria

What is the main process for evolution in eukaryotes and what are the two steps?

• Main process: Serial Endosymbiosis

  • 1st step: Primary Endosymbiosis (a prokaryote was engulfed)

  • 2nd Step: Secondary Endosymbiosis (a eukaryote was engulfed)

SEQ Primary Endosymbiosis

An ancestral prokaryote enfolds its plasma membrane → gains endomembrane system, becomes ancestral eukaryote → then does endosymbiosis by engulfing aerobic proteobacterium → becomes modern heterotrophic eukaryote w/ mitochondria + is anaerobic → might do endosymbiosis again by engulfing photosynthetic cyanobacterium →becomes modern photosynthetic eukaryote w/ chloroplasts + mitochondria

SEQ Secondary Endosymbiosis (remember this occured in two lineages of protists)

A heterotrophic eukaryote engulfs a photosynthetic eukaryote → gains a secondary plastid

What are protists?

The “very first” eukaryotes that emerged before plants, animals, and fungi (still very complex)

Are protists unicellular or multicelluar?

Most are unicellular, but some are multicellular

Explain the 3 nutritional strategies of protists

1. Photoautotrophs: chloroplasts

2. Heterotrophs: organic molecules

3. Mixotrophs: photosynthesis & heterotrophic

Draw the tree of what the 3 biology domains look like

In the domain Eukarya, what is the main SDC?

Mitochondria

What are the 5 supergroups in Domain Eukarya? (use the mnemonic Archie..)

A - Archaeplastida

S - SAR

A - Amoebozoa

O - Opisthokonta

D - Discoba

Draw a tree of just the names of the 5 eukarya supergroups (nothing that’s in them). Which ones are sister taxa?

• Archaeaplastids + SAR

• Amoezoba + Opisthokonta

What is the SDC of Archeaplastids?

• their chloroplast from primary endosymbiosis of a cyanobacterium —> whick makes them all photosynthetic

What is the SDC for SAR?

a secondary endosymbiosis plastid from red algae

What are the SDC for Amoebozoa?

1. GENETIC SIMILARITIES,

2. BLOB SHAPE,

3. PSEUDOPODIA: a temporary, cytoplasm-filled projection of a eukaryotic cell membrane used for movement and capturing food

What are the SDC for Opisthokonta?

1. Genetic similarities

2. Single, posterior flagellum

What is the SDC for Discoba?

a crystalline rod in the flagellum

What are the 4 types of Archeaplastids?

1. red algae

2. chlorophytes

3. charophytes

4. land plants

What makes red algae red? Also what eukaryotic supergroup do they fall under?

• Phycoetherin is the red photosynthetic pigment responsible for the red color, and it absorbs blue and green light

• Red algae falls under the Archaeplastida super group

What two types of Archaeplastidas classify as green algae?

Chlorophytes & Charophytes, who’s cholorplasts are very similar to land plants

What are the 3 types of SAR?

1. Stramenopiles

2. Alevolates

3. Rhizaria

What are the two main examples of stramenopiles? And what eukaryotic supergroup do they belong to?

1. Diatoms

2. brown algae (multicellular large protists, seaweed)

- Stramenopiles belong to the SAR super group

What are the two main examples of aleveolates? And what eukaryotic supergroup do they belong to?

1. Dinoflagelletes that have 2 flagella to spin

2. Apicomplexans (parasite)

What is the main examples of rhizaria? And what eukaryotic supergroup do they belong to?

Foraminiferans (forams), which have porous shells of CAC03

What are the two types of discoba?

1. Trypanosomes - Can cause African sleeping sickness

2. Euglenids

   1. Have an additional SDC: 2 secondary endosymbiosis plastids from green algae

What are the two types of Amoebozoa?

What are the 3 types of Opisthokonta?

1. Animals & fungi are in this group

2. Nucleariids are also in this group ((protists, sister taxon fungi)

3. Choanoflagellelates (protists, sister taxon animals)

Now draw a complete pholygenetic tree of the Domain Eukarya with all supergroups, all examples, and all SDC of the 5 supergroups

Explain the origin of fungi. What were their ancestors like? When did their ancestors diverge from animals, and who do they share a sister taxon with?

1. They have a unicellular flagellated ancestor

2. ancestors of animals and fungi diverged 1-1.5 bya

3. sister taxa with nucleariids (hetetrophic protists)

When did fungi colonize land, and what was life on land like when they colonized it?

1. Fungi colonized land -635 mya 

2. Life on land was “green slime”

   1. Cyanobacteria 

   2. Protists 

   3. Fungi 

What are two general SDCs for Fungi?

1. Chitlin (in cell wall)

2. Being absorptive heterotrophs (Rely on organic nutrients for their needs, Do not ingest food or digest inside body)

What domain and maybe supergroup do Fungi belong to?

THE DOMAIN EUKARYA WITHIN THE SUPERGROUP OPISTHOKONTA

What type of cell structure do Fungi have?

A eukaryotic cell structure & a cell wall

What are the basic building blocks of multicellular fungi, and what is their function?

• Hyphae which are basically tubular cell wall segments, and they secrete hydrolases

What is mycelium(lia)?

1. A tangled mass of hyphae (the basic building blocks of fungi) that serves as a feeding network in multicellular fungi

SEQ the nutrition mechanism of Fungi

1. Secrete hydrolases 

2. They break down polymers into monomers

3. Then absorb predigested molecules

CC The 3 Ecological Roles of Fungi

1. Decomposers: absorb nutrients from non-living organic material & break down matter

2. Mutualists: absorb nutrients from living host, but also provide benefit to host

3. Parasites: absorb nutrients from living host, but provide no benefit to host

What are the two main/overall SDC of fungi?

1. Cell wall made of chitin

2. Being absorptive heterotrophs

What are spores?

Spores are the haploid (n) reproductive units of fungi that can be reproduced se*ually or ase*ually

What are the two ways that spores can be produced?

1. Aerial hyphae → easy dispersal 

2. Fruiting bodies (mushroom)

Question: How do fungal spores move on their own, and do they have flagella?

Answer: They are non-motile and do not have flagella, instead, they are dispersed by wind, H20, or animals.

Question: What type of environment do fungal spores require to thrive, and what happens if they land in such an environment?

Answer: A moist environment with plenty of nutrients.

• If they land in an ideal environment like that, they → germinate → new mycelium

What are the two main types of fungi mentioned that participate in asexual reproduction, and how do they do it?

Filamentous fungi: Produce asexual spores by mitosis, like mold on bread

yeasts: Cell division or budding

SEQ Sexual Reproduction Of Fungi

1. If mycelia are two different mating types, when their hyphae produce pheromones, they will grow towards each other

2. Hyphae meet & fuse but nuclei do not fuse = plasmogamy —→ heterokaryon (n + n)

3. Then the (n+n)/heterokaryon mycelium grows, and the nuclei divide without fusing

4. Karyogamy: the nuclei finally fuse and produce a zygote (2n)

5. zygote then undergoes meiosis and produces haploid se*ual spores

What are the 5 fungal phyla and their corresponding SDCs? (use mmnemic)

1. Phylum chytridiomyctora (Chytrids)

   1. SDC = Zoospores (flagellated spores)

2. Phylum Zygomycota

   1. SDC =Zygospores (diploid, favorable env → undergo meiosis →  spores (n)

3. Phylum Glomeromyctota

   1. SDC = Arbuscular mycorrhizae (nutrients to 80% plants)

4. Phylum Ascomycota 

   1. SDC= Apscopores (produced in ascus)

5. Phylum Basidiomycota

   1. SDC = Basidiospores (Produced on a basidium)

Explain the cell structure of animals.

1. Eukaryotic 

2. No cell wall

3. SDC = Extracellular matrix (ECM)

Explain the 4 key points of organization for animals (cells..tissues..)

1. All animals are multicellular 

2. All have specialized cells

3. Most animals have specialized tissues

4. Higher forms have specialized organs (ex. kidneys)

After animals sexually reproduce and a zygote (2n) is formed via meiosis, how does this zygote develop into a embryo? OR, SEQ EMBRYONIC DEVELOPMENT in animals.

1. Cleavage: Zygote undergoes mitotic divisions without cell growth

2. Blastulation: Zygote cleaves more and becomes a blastula (hollow ball of cells)

3. Gastrulation: Blastula folds inward on itself & expands into the blastocoel —> is now Gastrula (layers of embryonic tissue)

What is a body plan?

Set of morphological & developmental characters that represent key steps in animal evolution

What is the SDC that every species in Kingdom Animalia/Metazoa have?

ECM (Extracellular Matrix)

KNOW METOZIA (KINGDOM ANIMAL) DIAGRAM IN LG BY HEART, SDCS, CLADES, BASAL TAXONS - LABEL THIS DIAGRAM AND THEN CHECK YOUR LG FOR ANSWERS.

this info applies to tree:

What is the only species in Metazoa (Kingdom Animalia) that does not have specific tissues? And what group do the rest of the species that do have tissues fall under?

1. Porifera (sponges) do not have specific tissues, ONLY HAVE ECM (ancestral SDC), they are the basal taxon

2. Everything else does and is called Eumetazoa (“True animals”)

In Metazoa/Kingdom Animalia, what species has radial symmetry and diploblasty (define later), while the rest of the tree going down has bilatery symmetry and triploblasty?

Cnidaria

In embryonic tissue development for animals, what are these parts of the gastrula

- Two general germ layers:

-Name of the eventual gut:
-Name of opening to outside:

- Two general germ layers: Endoderm and ectoderm

-Name of the eventual gut: Archenteron
-Name of opening to outside: blastopore

What are the two types of gastrula, and what is a key unique feature that only one of them has?

1. Diploblastic - only endo & ecto layers

2. Triploblastic - endo, ecto, and mesoderm

   1. UNIQUE: Has coelom, a fluid-filled space between the body wall & digestive tube

What are the 3 types of coelom?

SEQ ANIMAL DEVELOPMENT/NAME THE 3 MAIN PROCESSES. ALSO, WHAT DO DIFFERENCES IN THESE PROCESSES DETERMINE?

1. 3 processes

   1. Cleavage

   2. Coelom formation 

   3. Fate of the blastopore 

2. Differences in these processes separate the Nephrozoa (LAST MAJOR GROUP/CATEGORY IN METAZOA) into the protostomes & deuterostomes

CC Protosomes and deutorsonomes based on these categories: Cleavage, Coelom formation, Fate of the blastopore 

What is the sister taxon of animals? (Keep in mind that animals belong to eukarya supergroup Opisthokonta)

Choanoflagelletes, which are protists

Explain the morphology of poriferia. also, what domain, subgroup, and category are they iN?

• Morphology:

  • sac like with tiny holes

  • osculum where water passes through

  • has a spongocoel (space/cavity) that acts as a passage for h20 & filters feeders

  • made up of choanocytes (sponge cells) that are flagellated & ingest food

What is the SDC of phylum cnidaria (the basal eumatozeans!)

Cindocytes - specialized cells in the tentacles, which serve as defense & prey capture

ex. jellies, coral, sea anemonome

What is the Spiralia Clade in the Metazoa Tree under? And what are their shared & derived characters?

They are under Prostomia!

What are the 4 phylums in clade Spiralia?

1. platyhelminthes

2. rotiferia

3. mollusca

4. annelida

What are the two key features of Phylum Platyhelminthes under clade Spiralia? And what type of habitats do they live in?

1. Aceolomate - no coelom

2. They are flatworms (“helm”)

3. They are free-living or parasitic and live in hosts

What are the 3 key features of Phylum Rotiferia under clade Spiralia? And what type of habitats do they live in?

1. They are pseudocoelmates

2. they have a corona/crown

3. very smalll

4. they live in freshwater/marine, damp soil