biology 112 exam 2

taxonomy

science of classifying organisms

all organisms share 5 characteristics

• Composed of one or more cells

• Carry out metabolism

• Transfer energy with ATP

• Reproduce

• Encode hereditary information in DNA

bacteria

cells do not contain a nucleus

archaea

cells do not contain a nucleus, they have a different cell wall from bacteria

eukarya

cells do contain a nucleus;include the plants, animals, fungi, and protists

biologists group organisms based on shared characteristics

• Fossil records

• Morphology

• Physiology

• Behavior

• Embryological development

• DNA/RNA sequences

systematics

the field that scientists use to oganize and classify organisms based on evolutionary relationships

bionomial nomenclature of species formula:

species name = genus + species 'epithet'

phylogeny

evolutionary history and relationship of an organism or volutionargroup of organisms

taxonomy uses what system type

Linnaean system

Linnaean System

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

why do phylogenies matter

• Understanding of evolutionary processes

• Research on related species may help to better understand human health, medical issues

• Track evolution of parasites and viruses

• Use biotechnology to produce more productive crops, domesticated animals

• Produce more effective drugs (e.g. human insulin)

• Improve conservation efforts for threatened and endangered species

2 types of phylogenetic trees

rooted, unrooted

rooted phylogenetic trees

single lineage at the base represents a common ancestor

unrooted phylogenetic tree

show relationships but not a common ancestor

root

indicates that an ancestral lineage gave rise to all organisms on the tree

branch point (node)

splitting represents single lineage evolving into two clades

nodes

most recent common ancestor of subsequent clades

taxon

group(s) of organisms

2 types of taxon

basal, sister

clade

any branch or lineage = monophyletic taxonomy

polytomy

a branch with more than two lineages

monophyletic group

consists of an ancestral species and all of its descendants

paraphyletic group

consists of an ancestral species and some, but not all, of its descendants

polyphyletic group

includes distantly related species but does not include their most recent common ancestor

cladistics

A phylogenetic classification system that uses shared derived characters and ancestry as the sole criterion for grouping taxa.

shared characteristics

used to determine relatedness when constructing a cladogram

plesiomorphy

shared ancestral character, identify membership to the larger group

synamorphy

shared derived character, identify branch points within the larger clade

rule of parsimony

choose the simplest cladogram with the fewest steps or events

convergent evolution

structure evolving from same evolutionary pressures but not from a common ancestral trait

evolutionary reversal

ancestral traits are sometimes lost in descendants in one group

homologous structures

similar structures that related species have inherited from a common ancestor

analogous structures

structures that do not have a common evolutionary origin but are similar in function

limitations to the classic model of inheritance

Mendelian inheritance and its modifications assume that genes are transferred from parent to offspring (vertical gene transfer), and mutations are the primary sources new genetic information This is not the complete story in prokaryotes, and even some eukaryotes

horizontal gene transfer

tranfer of genetic material between unrelated species

where is horizontal gene transfer more prevalent

prokaryotes

three primary modes of hgt in prokaryotes

transformation, transduction, conjugation

transformation

naked DNA uptake by bacteria

transduction

genes transferred by virus

conjugation

genes transferred between two bacteria via pilus

endosymbiont

cell which lives inside another cell with mutual benefit

mitochondria and chloroplasts originated by the ungulfment of a prokaryotic cell by a _________

protoeukaryotic cell

genome fusion

some espects of gene transfer between endosymbionts

gram-negative bacteria

may have resulted from fusion of an archean and a gram-postive bacteria

hgt has been proposed to be:

important in the evolution of prokaryotes

web of life model

phylogenetic model that attempts to incorporate the effects of horizontal gene transfer on evolution

ring of life model

phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes

What is virus?

• "acellular"

• no metabolism

• depend on host cells to make copies of themselves

• made of DNA or RNA

• can infect nearly all life forms

• not only species specific but tissue specific

viruses were first discovered after the development of a _______

porcelain Chamberland-Pasteur filter

who demonstrated that a disease of tobacco plants could be transferred from a diseased plant to a healthy one via plant extracts?

adolph meyer

dmitri ivanowski

disease can be transmitted from plant to plant after the Chamberland-Pasteur filter had removed all viable bacteria from the extract… eventually discovered as virus - not bacteria

electron microscopy

developed in 1930s, first view of viruses

tobacco mosaic virus (TMV)

first to be seen and described

3 main hypotheses about the evolution of viruses

• regressive or devolution

• progressive or escapist

• virus first

regressive or devolution

viruses evolved from free-living cells or from intracellular prokaryotic parasites

progressive or escapist

viruses originated from pieces of RNA and DNA that escaped from a host cell and gained the ability to move between cells

virus first

viruses existed before all life as self-replicating entities that over time became more organized and more complex

a single virus particle may be only ____ nm across

20

the invention of the electron microscopes led to

the discovery of many types of viruses in many types of organisms

a single virus particle may also be known as

a virion

each virion has:

• nucleic acid core

• protein capsid

• some also have an "envelope" similar to a cell membrane

nucleic acid core

might be DNA or RNA, double stranded or single stranded

helical

long and cylindrical

icosahedral

roughly spherical shape

enveloped

have membranes surrounding the capsids

complex/head and tail

infect bacteria and have a head that is similar to icosahedral viruses and a tail shaped like helical viruses

several ways to classify viruses

-according to nucleic acid type and function -according to capsid structure -enveloped/non-enveloped -genome structure

genome structure may be:

• single or double stranded

• circular or linear

• may be in one piece of in multiple segments

Baltimore classification system

-developed by Nobel laureate David Baltimore

• based around mRNA production methods

• separates viruses into seven classes

DNA viruses

• often double stranded, can be single-stranded

• replication takes place in nucleus

• few have DNA polymerases and can complete replication in the host cell's cytoplasm EX: smallpox virus

RNA viruses

• usually is single-stranded, can be double stranded

• replication takes place in the cytoplasm

• mutation happens at a very high rate because RNA polymerase does not have proofreading capabilities EX: influenza viruses

genome

total genetic content of the virus

viral genomes are very small…

contain only those genes that code proteins that the virus cannot get from the host cell

the viral DNA directs the host cell to…

-make new virus copies by using the host cellular machinery (like DNA polymerase and ribosomes

RNA viruses do what:

• encode their own enzymes for replication and transcription, stealing host ribosomes

• use enzymes that make more errors

• mutate for frequently than DNA viruses

• retroviruses

• + stranded

• - stranded

steps of virus infections

attachment, entry, replication and assemble, egress (release)

attachment

• receptors on the surface of the host cell bind to virus capsid proteins or virus envelope glycoproteins

• viruses can attach only to cells that have the right receptor molecules

• viruses can be specfic about what species or cell type they can infect

entry

• naked viruses (non-enveloped)

• enveloped viruses

• bacteriophages

prokaryotes

• 1st organisms on earth

• millions of species

• live on and in every other living organism

• many essential to all life

• took long time to be discovered because they are so small

• using single lensed microscopes of his own design and make

  • leeuwenhoek a=was the first to observeve and to experiment with microbes

Robert Kock

credited with discovering the techniques for pure culture, including staining and using growth media

culture medium

contains all the nutrients needed by the target organisms for growth and reproduction. It can be liquid or solid, providing a controlled environment for microbiological studies.

pure culture

a laboratory culture containing a single species of microorganism

4 postulates to prove a casual relationship between a microorganism and an individual

• microorganism must be found in abundance in all organisms suffering from disease, shouldn’t be found in healthy organisms

• must be isolated from a diseased organism and grown in pure culture

• cultured microorganism should cause disease when introduced into a healthy organism

  • must be reisolated from the inoculated, diseased experimentntal host and identified as being identical to the original specific causative agent

are prokaryotic cells are eukaryotic cells bigger

prokaryotic cells are significantly smaller. 0.1-5.0 nanometers

3 shapes of prokaryotic cells

cocci (spherical), bacilli (rod-shaped), spirilli (spiral-shaped)

what characteristic aggregates are there for prokaryotic cells

pairs, chains, tetrads, clusters, etc.

what four common structures do all cells have

plasma membrane, cytoplasm, doubel stranded DNA genome, ribosome

plasma membrane

barrier for the cell and separates the cell from its environment

cytoplasm

complex solution of organic molecules and salts inside the cell

double stranded DNA genome

informational archive of the cell

ribosomes

sites of protein synthesis

prokaryotes

non membrane bound organelles, no nucleus, dna in nucleid, ribosomes free, no microtubules

almost all cells have ____ that lies outside the _____ ______, that protects and prevents cell _______

cell wall, plasma membrane, lysis

bacteria is protected by:

peptidoglycan

archaea is protected by

polysaccharides

gram-strain

reflects cell wall types

gram + (pos)

bacteria w/ thick PG layer… stains purple in Gram stain

gram - (neg.)

bacteria with thinner PG layer plus outer lipid bilayer membrane

pink in gram stain

outer lipopolysaccharide layer.. often toxic, resists drugs and immune system