General Biology II Exam I Review

Taxomy (Binomial Nonmenclature)

The science of naming, classifying organisms

Phylogeny

Evolutionary history of a species or group of related species → only represents a evolutionary hypothesis

Taxon

General name for group at any level

Domain to Species

This means smaller groups within larger groups

Evolution

Change of alleles overtime that involves a population

Natural Selection

This means differential survival and adaptations based on phenotypes.

Better survival skills

What do better alleles mean for organisms?

Monophyletic

Ancestor and all descendants (true tree)

Paraphyletic

Ancestor and some descendants

Polyphyletic

Missing a common ancestor

Nonliving, No cells, metabolism requires a host, and replication requires a host

What are some characteristics of viruses

DNA & RNA

What are the types of genetic material that you can find in viruses?

20-300 nm

What is the typical size for viruses

2-1000 genes

What is the number of genes in viruses?

Linear, circular, segmented

What is the typical shape of the genetic material in viruses?

Caspid

The protein coat that surrounds DNA/RNA in viruses that determines what host the virus can attach to

capsomeres

What is the caspid made out of?

A parasitic relationship

What type of relationship do viruses need in order to survive?

Envelopes

These are acquired during the process of budding out in the host cell (exiting) which surrounds the caspid, hosts glycoprotein, virses proteins, and is formed from the phospholipid bilayer

Host

Species or tissue that is infected

1) Virus binds and finds to cell through receptors

2) Genomes will enter the host cell

3) Host copies viral genome and make proteins

4) New virus assembles

5) virus is released

What are the typical steps of viruses replicating?

Virulent Phage

This type of phage will kill the host at the end of the cycle ( the lytic cycle)

Temperate Phage

This can either be lytic or lysogenetic cycle

Lysogenic Cycle

Replicates cycle as virus DNA hides in the host for many cycles as a prophage

The host DNA

Where is the viral DNA hidden within

Viral DNA also reproduces

When the host bacteria reproduces, what happens to the viral DNA?

Lytic Cycle

This will kill the host in the end of the cycle

Attachment

First step of Lytic Cycle?

Genome will enter the cell and host cell DNA degrades

Second step of Lytic Cycle?

Viral proteins are produced and replicated as viral DNA

After the host cell DNA degrades, what happens after?

They begin to assemble and virus is released

After replication and protein production, what happens to the viruses?

It is incorporated as a prophage

Although the first 2 steps are similar to a lytic cell in the Lysogenic cycle, what happens to the viral DNA?

Through integrating virus instructions into host DNA

How does bacteria reproduce within the hidden prophage?

Can be done through environmental changes in the cell

How can a phage doing the lysogenic cycle make new phages?

3.5 bya

When did prokaryotes first appear?

Prebiotic soup or iron sulfur

How can you hypothesize life first originating?

Nucleoids

Where is DNA located in prokaryotes that is also a single haploid chromosome?

Ribosomes, Nucleoid, Cytosol, Cell membrane & cell wall, enzymes (respiration and photosynthesis), and plasmids

What parts do prokaryotes have?

Plasmids

Extra DNA in prokaryotes

Cell Wall

This function is to protect the prokaryote, maintain cell shape, and prevent bursting into hypotonic solution (in photosynthetic bacteria)

Peptidoglycan

This is in bacteria in the cell wall.

Horizontal Transmission

Transfer of genetic material between individuals of the same offspring

Vertical Transmission

Transfer of Genetic material from parent to offspring

Gram Straining

This is a 2 step process strain wash to identify bacteria based on their cell wall

Gram positive (purple)

This color contains thick cell walls with lots of peptidoglycan

Gram negative (pink)

This has a thin peptidoglycan layer that has an outer membrane of lipopolysaccharides

This means movement

Taxis

Flagella

Although this is found in all domains, this doesn’t show up in analogous (convergent evolution)

Through ATP synthase and pumping of protons (no cellular membrane)

How can the flagella be powered up for movement?

Binary Fission

How do prokaryotes divide?

Rapid mutations or different gene transfers, genetic recombination, etc.

How can prokaryotes effectively be genetically unique when they only undergo binary fission?

Horizontal Gene Transfer

Transferring genetic material from one cell to another

Vertical Gene Transfer

Transferring genetic material from parent to offspring

Transformation

When DNA from surroundings incorporate foreign DNA as plasmids or into the bacterial genome within the same species

Transduction

Phages transfer bacterial DNA where the bacteria is now using the virus to transmit bacterial DNA- Generally same species of bacteria

Conjugation

DNA shared between two individual species (different)

• F (fertility) Factor F+ = allele to grow pilus

• F+ bacterium grows a pilus

• Transfers DNA plasmid (including F+ allele) to another bacteria

Carbon and Energy

What are the main energy sources used in prokaryotes?

Phototrophs

Light centered energy source

Chemotrophs

Chemical reactions

Autotrophs

This has a carbon source of CO₂

Heterotrophs

Uses the carbon source as food

Chemoheterotrophs

This eats others as food and does chemical reactions (us)

Obligate Aerobe

Needs Oxygen to survive

Obligate Anaerobe

If oxygen is used, WILL KILL! Can only go through fermentation

Facultative Anaerobe

This can live with or without oxygen

2 (bacteria and archaea)

How many domains of prokaryotes do we have?

4

How many groups of archaea do we have?

5

How many groups of bacteria do we have?

Horizontal Gene Transfer

In order to obtain this prokaryotic diversity, what type of gene transfer do we do?

Proteobacteria

These are gram negative and are considered the ancestor of mitochondria (includes mitochondria and other mutualistic prokaryotes)

Cyanobacteria

Photoautotrophs that are gram negative that have phytoplankton and are typically ancestors of chloroplasts

Extremophiles

Prokaryotes that have cell walls (no peptidoglycan) and no nucleus

Halophiles

Archaea that prefers to live in high salty environments

Thermophiles

Archaea that preferably wants to live in very hot environments

Methanogens

These are unique to archaea that releases methane by product metabolism AND CANNOT BE POISONED BY O₂

Plasmids

Extra DNA/foreign DNA taken up into the bacterial genome

Horizontal Gene Transfer

What type of gene transfer was found in prokaryotes when they are divided into 2 domains?

This is unknown

What is the root of the Eukarya?

Polytomy

Is the Eukaryotic tree a polytomy, monophyletic or paraphyletic?

Evolutionary time

When a phylogenetic tree proceeds from left to right, what does that mean?

Derived Traits

New traits that have just emerged after the most recent branch point. This is what H is to stramenopiles

Ancestral Traits

Old traits that emerged before the most recent branch point.

Eukaryotes

This has a size of 10-100 micrometers, has a cytoskeleton, a nucleus, membrane bound organelle and endosymbiosis of a mitochondria

An endosymbiotic relationship where they will all live together in symbiosis

What relationship do all eukaryotes have?

Cytoskeleton

This part helps with structure, support and motility

Nucleus, Membrane bound organelles, and endosymbiosis of a mitochondria

What are 3 derived traits of an eukaryotic cell?

Primary Endosymbiosis

When an eukaryote engulfs a prokaryote to result in a heterotrophic eukaryote with mitochondria.

Alpha proteobacteria

This was consumed by archaea to create mitochondria (endosymbiotic event in 1st primary endosymbiosis)

Cyanobacteria

What did heterotrophic eukaryotes engulf to help chloroplasts arise? (Secondary endosymbiotic event)

Secondary Endosymbiosis (2^o)

This is the process when small eukaryotes are engulfed by large eukaryotes

Serial Endosymbiosis

Multiple endosymbiosis events at once (both mitochondria and chloroplast were once free living before being engulfed)

2^o plastid

Any organelle resulting from 2^o endosymbiotic event

Monophyletic

Is eukaryotic evolution monophyletic, paraphyletic, or polyphyletic?

Protists

These are paraphyletic where they are known as the first eukaryote that arose through endosymbiosis, mostly unicellular (some can be multicellular), complex cell organization, and some examples are heterotrophs, phototrophs, and autotrophs

Primary endosymbiotic event of mitochondria forming

A (Eukarya)

Archaeaplastida

2 (Eukarya)

Eukarya

1 (what is this phylogenetic tree grouping)

SAR

3 (Eukarya)

Amoebozoa

4 (Eukarya)

Opisthokonta

5 (Eukarya)