BIOL 112 Exam 2 - TAMU

3

Bacteria, Archaea, and Eukarya

Composed of cells, carry out metabolism, transfer energy with ATP, reproduce, and encode hereditary information in DNA

Woese, Kandler, and Wheelis

Bacteria and Archaea

Eukarya

Cells do not contain a nucleus

Cells do not contain a nucleus and have a different cell wall from bacteria

Cells do contain a nucleus. Include the plants, animals, fungi, and protists

Plants, animals, fungi, and protists

Yes, without peptidoglycan

Yes, with peptidoglycan

Varies. Plants and fungi do, while animals do not

No

No

Yes

Shared characteristics

Fossil records, morphology, physiology, behavior, embryological development, and DNA/RNA sequences

Systematics

Genus + species

The science of classifying organisms into taxa

A hypothesis about the relationships among taxonomic groups depicted as a phylogenetic tree or cladogram

Dear King Phillip Came Over From Great Spain

Traditional Linnaean system

It enriches our understanding of how genes, genomes, species (and molecular sequences more generally) evolve

Rooted and unrooted

Single lineage (at base) represents common ancestor

Shows relationships but not a common ancestory (they still share common ancestors, but only show the relationship)

That an ancestral lineage gave rise to all organisms on the tree

The splitting represents a single lineage evolving into two clades

A lineage that evolved early and remains unbranched (separate from all other taxons/species)

Two lineages that branch off from the same node

Any branch or lineage all stemming from the same node (must all be included) also known as monopholytic taxon

A polytomy

Clade - consists of an ancestral species (node) and all of its descendants

Consists of an ancestral species (node) and some, but not all, of its descendants

Includes distantly related species but does not include their most recent common ancestor (MRCA is not the same node for all)

The process to arrange taxa by homologous characters into clades to create a monophyletic cladogram

Shared ancestral character found in a common ancestor of taxa that all members of the clade have

Shared derived character that arose within a large clade that is used to identify nodes within the clade and distinguishes those that share it

Choose the simplest cladogram with the fewest steps or events

Analogous traits - when strucutures evolvefrom the same evolutionary pressures but not from a common ancestral trait (they are not related)

When ancestral traits are sometimes lost in descendants of one group

Horizontal gene transfer

The transfer of genetic material between unrelated species - more prevalent in prokaryotes

Mutations and HGT

Transformation, transduction, and conjugation

Naked DNA uptake by bacteria

Genes transferred by virus

Genes transferred between two bacteria via pilus

The theory of eukaryote evolution in which an endosymbiote formed within a cell and developed mitochondria and chloroplasts, thus evolving into a eukaryote

Proposed by Lake that all three domains evolved from a pool of prokaryotes swapping genes via HGT

A virus

An acellular organism of types that cannot grow, cannot replicate themselves without host cells, and can be extremely specific as to what they will infect

Via nucleic acid and PCR (polymerase chain reaction)

They cannot grow and replicate outside of the cell

Chamberland-Pasteur when creating a porcelein filter

Tobacco mosiac disease

Adolph Meyer in 1886

A special type of microscope that allowed first view of viruses (1930s)

Around 20 - 50 nm

Fossils

Nothing, we only have theories

Viruses evolved from free living cells or from intracellular prokaryotic parasites (regressive or devolution)

Viruses originated frin pieces of RNA and DNA that escaped from a host cell and gained the ability to move between cells (progressive or escapist)

Viruses existed before all life as self-replicating entities that over time became more organized and complex (virus first)

A nucleic acid core and protein capsid

Could be made up of DNA or RNA and could be either single or double stranded

Capsomeres

Long and cylindrical

Roughly spherical shaped

Have membranes surrounding the capsid

Infect bacteria and have a head that is similar to icosahedrak viruses and a tail that is shaped like helical viruses

Nucleic acid type, genome structure, capsid structure, or Baltimore classification system (current)

They are often double stranded, but can be single stranded, replication takes place in the nucleus (in most), and a few have DNA polymerases and can complete replication in the host cell's cytoplasm

They are usually single stranded, but can be double stranded, replication takes place in the cytoplasm (in most), and mutation happens at a very high rate because RNA polymerase does not have proof reading abilities

Smallpox

Influenza and coronaviruses

Total genetic content of a virus

They steal directly from the host cell to make new copies

They encode for their own enzymes (RNA-dependent polymerase) for replication and transcription, but they steal host's ribosomes

Groups viruses together according to hwo the mRNA is produced during the replicative cycle of the virus

Double stranded DNA, mRNA is transcribed directly from the DNA template (herpes)

Single stranded DNA, DNA is converted into double-stranded form before RNA is transcribed (canine parovirus)

Double stranded RNA, mRNA is transcribed from the RNA genome (Childhood gastroenteritis)

Single stranded RNA +, genome functions as mRNA (common cold)

Single stranded RNA -, mRNA is transcribed from the genome (rabies)

Single stranded viruses with reverse transcriptase, DNA from the RNA genome, which is then incorporated in the host genome, mRNA is transcribed from the incorportated DNA (RNA-->DNA) (HIV)

Double stranded viruses with reverse transcriptase, the viral genome is double stranded DNA, but viral DNA is replicated through an RA intermediate, so the RNA may serve directly as mRNA or as a template to make mRNA (Hepatitis B)

Attachment, entry, replication and assembley, and egress (release)

Receptors (proteins) on the surface of the host cell bind to virus capsid proteins or virus envelope glycoproteins

Cells that have the right receptor molecules (host protein is the lock and protein from the virus is the key)

Direct penetration or endocytosis

Fusion or endocytosis

The bacteriophages enter the host cell naked and leave the capsid outside

The cell membrane of the host surrounds and engulfs the entire virus inside the host

May involve lysis and death of the host cell

May involve budding, which does not directly kill the host cell, leaves by straling part of the hosts membrane to develop its own envelope then leaves using that

Any group of viruses that infect bacteria, tend to have a central shaft and leglike appendages

Lytic or lysogenic

Lyse the host cell after replication of the virion and the phage progeny are then released to find new hosts

Do not immediately lyse the host, but rather insert their own DNA into the host and allow it to replicate the DNA for them

Prophage

Abnormal cell proliferation

Decreased growth and vigor

Theydo not have to penetrate a cell wall to gain access to the host cell and are associated with a variety of human diseases

Have the ability to cause cancer

Vaccination

Meant to boost immunity and prevent infection and can be prepared by using live viruses, killed viruses, or molecular subunits or viruses

Very small, smaller than viruses, that contain no nucleic acids and can cause fatal neurodegenerative diseases like BSE, scrapie, etc

Only known to infect plants and can reproduce only within a host cell, but do not manufacture any proteins and can cause crop failure

All the nutrients needed by the target microorganism

Robert Koch

0.1 - 5.0 micometers

Archaea and Bacteria

Cocci (circular), bacilli (more tubular), and spirilli (spiral-shaped)

In characteristic aggregates (pairs, chains, tetrads, clusters)

The plasma membrane, cytoplasm, double stranded DNA, and ribosomes

They have no membrane bound organelles, no nucleus, and no microtubules

Nucleoid ribsosomes

Outside of the plasma membrane

Bacteria with a thick cell wall

Purple

Bacteria with a thick cell wall and an additional outer lipid bilayer membrane

Pink

Sticky carbs and proteins decreted outside of the cell wall that helps resist attck from the immune system, hold in moisture, and glues cells together or to surface

Hair-like proteins (short pili) that help cells stick to surfaces and each other and with DNA transfer (conjugation)

Flagellum

They pull two bacteria cells together for DNA transfer (conjugation) and form a mating bridge

The movement directed towards or away from a stimulant

Direct movement of the cell in response to a chemical stimulus (ex. electrochemical gradient)

The movement to or away from light

In response to gravity (in response to megnetism)

Extra tiy DNA rings with few genes that replicate independentyl and are not essential for life but add diversity

Plasma membranes, cell walls, DNA replication, and16 rRNA sequences

Bacteria have unbranched lipids that use ester bonds, while archaea are branched and form with ether linkages

Bacteria and archaea that are adapted to grow under extreme conditions

pH 3 or below

pH 9 or above

60 - 80 C

80 - 122 C

Salt concentrations of at least 0.2 M

High sugar concentrations