Study Notes Exam 1
Chapter 20: Classification of Living Things
Taxonomy: the branch of biology concerned with identifying and naming organisms
- a natural system of classification reflects the evolutionary history of organisms
- naming and identifying organisms began with the Greeks and Romans
- in the middle ages, organisms were described using long Latin descriptions
- much later, John Ray, a British naturalist argued that each organism should have a set name
- the number of known organisms expanded greatly in mid-eighteenth century due to European travel
- common names vary with different languages, & the same name may refer to different organisms in different regions
- Carolus Linnaeus developed the binomial system to name species
- the binomial system of nomenclature names organisms using a two-part Latin name
o first part is the genus; closely related species are assigned to the same genus
o second part is the specific epithet; it usually provides something descriptive about an organism
o a scientific name consists of both genus and specific epithet (e.g., Panthera tigris and Panthera leo)
o both names are italicized or underlined; the first letter of only the genus name is capitalized
o the genus can be abbreviated when used with a specific epithet if the full name was given before (H. sapiens)
- the classification of organisms is an ongoing process
o there are estimated to be between 3 and 30 million species living on earth
o we have currently named one million species of animals and a half million plant and microorganismic species
o some groups, such as birds, are nearly all known; some insect groups are mostly unknown
- Linnaeus considered each species to have a unique structure that made it distinct
o distinguishing species on structure can be a problem because variations occur among members of the same species
o males and females may have a different form, as well as juveniles and adults
- the biological definition of a species: a group of organisms that interbreed and share the same gene pool
o distinguishing species on the basis of reproductive isolation can be a problem
o some species do not reproduce sexually
o some species hybridize where their ranges overlap
- when a species has a wide geographic range,they may tend to interbreed where they overlap; these populations may be named as subspecies
o the rat snakes Elaphe obsoleta obsoleta and Elaphe obsoleta bairdi are subspecies of Elaphe obsoleta
o including the subspecies makes this a trinomial, or three-part, name
- in this chapter, a classification approach is taken to the definition of species
o the term "species" is used for a taxonomic category below the rank of genus
o species share a more recent common ancestor with species in same genus than with those in other taxa
o a taxon is a group of organisms in a classification category; Rosa or Felis are taxa at the genus level
o a common ancestor is an ancestor held in common by at least two lines of descent
- Aristotle classified life into 14 groups (e.g., mammals, birds, etc.), and subdivided them by size
- Ray grouped animals and plants according to how he thought they were related
- Linnaeus grouped plants by flower parts; his categories were published in Systema Naturae in 1735
- today, we use a minimum of 7 categories of classification:
o kingdom, phylum (or division for plants), class, order, family, genus & species
o a higher category, the domain, has been proposed to be added to these 7 categories
o the higher the category, the more inclusive it is
o members of a kingdom share general characters; members of a species share quite specific characters
o characters are any structural, chromosomal, or molecular feature that distinguishes groups
o additional levels of classification can be added by adding super-, sub-, or infra- (e.g., suborder)
- Systematics is the study of the diversity of organisms using information from cellular to population levels
o classification reflects phylogeny; one goal of systematics is to create phylogenetic trees
o phylogeny is the evolutionary history of a group of organisms
o a phylogenetic tree indicates common ancestors and lines of descent or lineages
o a primitive character is a trait that is present in a common ancestor and all members of a group
o a derived character is present only in a specific line of descent
o different lineages diverging from a common ancestor may have different derived characters
- Fossil Record
o because fossils can be dated, fossils can establish the age of a species
o it can be difficult to associate fossils with currently living groups; a new view of turtle fossils could place them closer to crocodiles
o the fossil record is often incomplete because soft-bodied organisms do not fossilize well
o most organisms decay and the chances of becoming a fossil are low
- Homology
o homology is a character similarity that is due to having a common ancestor
o homologous structures are related to each other through common descent but may differ in structure and function (e.g., the forelimbs of a horse and the wings of a bat)
o analogous structures have the same function but are not derived from the same organ in a common ancestor (e.g., the wings of an insect and the wings of a bat)
o homology helps indicate when species belong to a related group
o convergent evolution may make it difficult to distinguish homologous from analogous structures
o convergent evolution is acquisition of similar traits in distantly related lines of descent as a result of adaptation to similar environmental conditions
• both spurges and cacti are adapted to a hot, dry environment and are both similar, but details of flower structure indicate these two groups are not closely related
o parallel evolution produces similar characters in related lineages without occurring in a common ancestor
- Molecular Data
o speciation occurs when mutations bring about changes in base pair sequences of DNA
o each distinct lineage accumulates changes in DNA base pair sequences and amino acid sequences in proteins over time
o Protein Comparisons
• earlier studies used immunological reactions to antibodies, made by injecting a rabbit with cells of one species, to determine the relatedness of two species
• we now use amino acid sequences to determine the differences in proteins between two species
• cytochrome c is a protein found in all aerobic organisms; the amino acid differences in cytochrome c between chickens and humans is 13 but between chickens and ducks is only 3
• since the number of universal proteins is limited, most new studies use RNA and DNA.
- RNA and DNA Comparisons
o all cells have ribosomes for protein synthesis; comparing rRNA sequences provides a reliable indicator of similarity
o DNA-DNA hybridization separates the DNA strands of two species and combines the strands; the more closely related the two species, the more the DNA strands stick together
o Chimpanzees and Humans
• DNA hybridization shows chimpanzees closer to humans than to other apes
• yet humans are kept in a separate family and chimpanzees are with the ape family because humans are markedly different in adaptation to the environment
o Mitochondria DNA (mtDNA) changes ten times faster than nuclear DNA
• mtDNA is often used for closely related species; North American songbirds were found to have diverged well before retreating glaciation 250,000-100,000 years ago
- Molecular Clocks
o nucleic acid changes are not tied to adaptation; the fairly constant changes provide a "molecular clock."
o comparison of mtDNA sequences equated a 5.1% nucleic acid difference among songbird species to 2.5 million years
o the fossil record can then be used to calibrate the clock and confirm the hypothesis drawn from molecular data
Systematics Today
- Cladistic Systematics
o cladistic systematics is based on work of Willi Hennig
o cladistics analyzes primitive and derived characters and constructs cladograms on the basis of shared derived characters
o cladogram: a diagram showing relationships among species based on shared, derived characters
o a clade is an evolutionary branch that includes a common ancestor and all its descendent species
o Parsimony
• cladists are guided by principle of parsimony‹the minimum number of assumptions is most logical
• this approach is vulnerable if convergent evolution produces what appears to be common ancestry
• reliability of cladograms is dependent on knowledge and skill of a particular investigator gathering data
- Phenetic Systematics
o phenetic systematists cluster species on the basis of the number of shared similarities, regardless of whether they might be convergent, parallel, or depend on one another
o systematists of this school do not believe that a classification that actually reflects phylogeny can be constructed; it is better to rely strictly on a method that does away with personal prejudices
o results of their analysis are depicted in a phenogram
o phenograms vary for the same group of organisms, depending on how the data are collected and handled
- Traditional Systematics
o traditional systematics stresses common ancestry and the degree of structural difference among divergent groups in order to construct phylogenetic trees
• the traditional school accepts the tenet that mammals and birds evolved from reptilian ancestors, even though the reptile group is monophyletic‹it does not include all groups from all ancestors
• to cladists, the traditional method of determining phylogeny is arbitrary
• birds are more closely related to dinosaurs and crocodiles than they are different
o cladists would not use "reptiles" because it does not include all organisms derived from reptiles
Classification Systems
- Naming the Kingdoms
o early biologists recognized two kingdoms: animals (kingdom Animalia) and plants (kingdom Plantae)
o the microscope revealed unicellular organisms; in the 1880s, Ernst Haeckel proposed the kingdom Protista
o Haeckel originally placed bacteria and cyanobacteria in Monera since they lacked a nucleus
o in 1969, R. H. Whittaker suggested a five kingdom system based on cell type, organization, and nutrition:
• Monera: prokaryotic bacteria that obtain organic molecules by absorption or photosynthesis
• Protista: mainly unicellular eukaryotes that obtain organic molecules by absorption, ingestion, or photosynthesis; the classification of protists is debated
• Plantae: multicellular eukaryotes, autotrophic by photosynthesis
• Animalia: multicellular eukaryotes, heterotrophic by ingestion, are generally motile
• Fungi: multicellular eukaryotes, heterotrophic saprotrophs that form spores, lack flagella and have cell walls containing chitin
o generally, protists are considered to have evolved from monerans, and the fungi, plants, and animals evolved from protists via three separate lineages
- Three-Domain System
o sequencing of rRNA suggests all organisms evolved along three distinct lineages: domains Bacteria, Archaea, and Eukarya
o bacteria diverged first; archaea and eukarya are more closely related than either is to bacteria
o the archaea live in extreme environments: methanogens in anaerobic swamps, halophiles in salt lakes, and thermoacidophiles in hot acidic environments
o the archaea cell wall is diverse but not the same as the bacterial cell wall
o eukarya contains unicellular to multicellular organisms, always with a membrane-bound nucleus
Chapter 21: Viruses, Bacteria & Archaea
- viruses are not organisms: they are noncellular; cannot metabolize; cannot respond to stimuli; multiply only within living cells by parasitizing the synthetic machinery of the infected cell; and evolve as a result of mutation and natural selection
- all viruses are infectious
- in 1884, Pasteur suspected something smaller than bacteria caused rabies; he chose the Latin term for "poison."
- in 1892, Russian biologist Dimitri Ivanowsky, working with tobacco mosaic virus, confirmed Pasteur's hypothesis that an infectious agent smaller than a bacterium existed
- with the invention of the electron microscope, these infectious agents could be seen for the first time
- Viral Structure
o viruses are similar in size to a large protein, generally smaller than 200 nm in diameter
o many viruses can be purified and crystallized, and the crystals stored for long periods of time... viral crystals become infectious when the viral particles they contain invade host cells
o all viruses have at least two parts:
• an outer capsid is composed of protein subunits
• an inner core contains either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid), but not both
⋅ the viral genome at most has several hundred genes; a human cell contains thousands of genes
⋅ the viral envelope is usually partly host plasma membrane (phospholipids) with viral glycoprotein spikes
⋅ viral particles have proteins, especially enzymes (e.g., polymerases), to produce viral DNA or RNA
- the classification of viruses is based on: their type of nucleic acid (including whether it is single-stranded or double-stranded); their size and shape; and the presence or absence of an outer envelope
- Parasitic Nature
o viruses are obligate intracellular parasites that cannot multiply outside a living cell
o animal viruses in laboratories are raised in live chick embryos or in cell tissue culture
o viruses infect all sorts of cells, from bacteria to human cells, but are very specific (tobacco mosaic virus only infects certain plants; the rabies virus infects only mammals; the AIDS virus, HIV, infects only certain human blood cells; hepatitis virus invades only liver tissues; polio virus only reproduces in spinal nerve cells)
- Virus Evolution
o viruses are likely to have originated from the very cells that they infect
• if so, viral nucleic acids originated from the host cell genome, & viruses evolved after cells came into existence; so new viruses are probably evolving now
o viruses often mutate; therefore, it is correct to say that they evolve
o viral mutation can be troublesome: a vaccine effective today may not be effective tomorrow
o influenza (flu) viruses mutate regularly
- Viral Reproduction
o viruses gain entry into and are specific to a particular host cell because portions of the capsid (or spikes of the envelope) adhere to specific receptor sites on host cell surface
o viral nucleic acid then enters a cell, where the viral genome codes for production of protein units in the capsid
o a virus may have genes for a few special enzymes needed for the virus to reproduce and exit from a host cell
o the virus relies on host cell enzymes, ribosomes, transfer RNA (tRNA), and ATP for its own replication
o the virus takes over the metabolic machinery of the host cell when it reproduces
- Replication of Bacteriophages
o bacteriophages (phages) are viruses that parasitize a bacterial cell
o lytic cycle: a bacteriophage "life" cycle of five stages where a virus takes over operation of the bacterium immediately upon entering it and then destroys the bacterium
• attachment: portions of the capsid bind with receptors on the bacterial cell wall
• penetration: a viral enzyme digests part of cell wall; the viral DNA is injected into a bacterial cell
• biosynthesis: synthesis of viral components - begins after the virus brings about inactivation of host genes not necessary to viral replication
• maturation: viral DNA and capsids are assembled to produce several hundred viral particles and lysozyme, coded by the virus, is produced
• release: when lysozyme disrupts the cell wall (breaks down peptidoglycan), the viral particles are released and the bacterial cell dies (lysis)
o lysogenic cycle: a cycle where the virus incorporates its DNA into the bacterium but only later does it produce phage
• following attachment and penetration, viral DNA becomes integrated into bacterial DNA with no destruction of host DNA
• at this point the phage is latent and the viral DNA is called a prophage
• a prophage is replicated along with host DNA; all subsequent cells (lysogenic cells) carry a copy
• certain environmental factors (e.g., ultraviolet radiation) induce a prophage to enter the biosynthesis stage of the lytic cycle, followed by maturation and release
- Reproduction of Animal Viruses
o animal viruses replicate similarly to bacteriophages but there are modifications
o if the virus has an envelope, glycoprotein spikes allow it to adhere to plasma membrane receptors
o the virus genome covered by the capsid penetrates the host cell
o once inside, the virus is uncoated as the envelope and capsid are removed
o free of its covering, the viral genome (DNA or RNA) proceeds with biosynthesis
o newly assembled viral particles are released by budding
o components of viral envelopes (i.e., lipids, proteins, and carbohydrates) are obtained from the plasma or nuclear membrane of the host cell as viruses leave
o retrovirus: an RNA animal virus with a DNA stage
• retroviruses contain reverse transcriptase that carries out reverse transcription producing cDNA from RNA
• viral cDNA is integrated into host DNA and is replicated as host DNA replicates
• viral DNA is transcribed; new viruses are produced by biosynthesis, maturation and release by budding.
- Viral Infections
o viruses cause infectious diseases in plants and animals, including humans
o some animal viruses are specific to human cells: papillomavirus, herpes virus, hepatitis virus, and adenoviruses, which can cause specific cancers
o retroviruses include the AIDS viruses (e.g., HIV) and also cause certain forms of cancer
o some viruses are cancer-producing because they bring with them oncogenes, normal genes transformed so they can cause the cell to undergo repeated cell divisions
o in humans, viral diseases are controlled by preventing transmission, administering vaccines, and only recently by the administration of antiviral drugs
o antibiotics do not cure viral infections because viruses use host cell enzymes, not their own enzymes; interfering with the enzyme kills the host cell
o over 1,000 plant viruses cause diseases; virus infections are difficult to distinguish from nutrient deficiencies and plants are propagated to stay free of virus infection
o viroids are naked strands of RNA, a dozen of which cause crop diseases
o prions are newly discovered disease agents that vary from viruses and bacteria
• prions are proteins with a wrongly shaped tertiary structure that cause other proteins to distort
• Creutzfeldt-Jakob disease in humans and scrapie and mad cow disease (BSE) in cattle are due to prions
The Prokaryotes - the bacteria and archaea
- Antonie van Leeuwenhoek (Dutch naturalist, 17th century) discovered bacteria while examining scrapings from his teeth
- the organisms Leeuwenhoek observed were thought to arise spontaneously from inanimate matter
- ~ 1850, Pasteur devised an experiment showing that the bacteria present in air contaminated the media
- a single spoonful of soil contains 1010 prokaryotes; these are the most numerous life forms
- Structure of Prokaryotes
o prokaryote means "before a nucleus" and their cells lack a eukaryotic nucleus
o prokaryotic fossils date back to 3.5 billion years ago... fossils indicate prokaryotes were alone on earth for 2 billion years - they adapted & evolved very diverse metabolic capabilities
o prokaryotes range in size from 1-10 µm in length and from 0.7-1.5 µm in width
o most prokaryotes have a rigid cell wall (made from peptidoglycan in bacteria) outside the plasma membrane that keeps the cell from bursting or collapsing due to osmotic changes
o glycocalyx surrounding the cell wall can be an organized capsule &/or a loose gelatinous sheath called a slime layer; in parasitic forms, these outer coverings protect the cell from host defenses
o flagella: structure outside cell used for locomotion by some prokaryotes
• the flagellum is a filament composed of three strands of the protein flagellin wound in a helix and inserted into a hook that is anchored by a basal body; it's capable of 360° rotation which causes the cell to spin and move forward
o fimbriae: short hairlike filaments extending from the surface that allow many prokaryotes adhere to surfaces
• the fimbriae of Neisseria gonorrhoeae allow it to attach to host cells and cause gonorrhea
o prokaryotic cells lack the membranous organelles of eukaryotic cells
o metabolic pathways are located on the plasma membrane
o nucleoid: a dense area in prokaryotes where the chromosome is located; it is a single circular strand of DNA
o plasmids: accessory rings of DNA found in some prokaryotes; they can be extracted and used as vectors to carry foreign DNA into bacteria during genetic engineering procedures
o protein synthesis in prokaryotic cells is carried out by thousands of ribosomes, which are smaller than eukaryotic ribosomes
- Reproduction in Prokaryotes
o binary fission is a splitting of a parent cell into two daughter cells; it is asexual reproduction in prokaryotes
• the single circular chromosome replicates; the two copies separate as the cell enlarges... newly formed plasma membrane and cell wall separate the cell into two cells
• mitosis, which involves formation of a spindle apparatus, does not occur in prokaryotes
o because prokaryotes have a short generation time, mutations are generated and distributed through a population more rapidly
o in bacteria, genetic recombination can occur in three ways:
• conjugation: a bacterium passes DNA to a second bacterium through a tube (sex pilus) that temporarily joins two cells; this occurs only between bacteria in the same or closely related species
• transformation: bacteria take up free pieces of DNA secreted by live bacteria or released by dead bacteria
• transduction: a bacteriophage transfers portions of bacterial DNA from one cell to another
o plasmids can carry genes for resistance to antibiotics and transfer them between bacteria by any of these processes
- Endospore Formation
o some bacteria form resistant endospores in response to unfavorable environmental conditions
o the chromosome & some cytoplasm dehydrate and are encased by three heavy, protective spore coats... the rest of the bacterial cell deteriorates and the endospore is released
o endospores survive in the harshest of environments: desert heat and dehydration, boiling temperatures, polar ice, and extreme ultraviolet radiation
o endospores also survive very long periods of time; anthrax spores 1,300 years old can cause disease
o when environmental conditions are again suitable, the endospore absorbs water and grows out of spore coat... in a few hours, newly emerged cells become typical bacteria capable of reproducing by binary fission
o endospore formation is not reproduction but it is a means of survival and dispersal to new locations.
- Prokaryotic Nutrition:
o bacteria differ in the need for, and tolerance of, oxygen (O2)
• obligate anaerobes are unable to grow in the presence of O2 (anaerobic bacteria that cause botulism, gas gangrene, and tetanus)
• facultative anaerobes are able to grow in either the presence or absence of gaseous O2
• aerobic organisms (including animals and most prokaryotes) require a constant supply of O2 to carry out cellular respiration
o autotrophic prokaryotes
• photoautotrophs are photosynthetic and use light energy to assemble the organic molecules they require
⋅ primitive photosynthesizing bacteria (e.g., green sulfur bacteria and purple sulfur bacteria) use only photosystem I that contains bacteriochlorophyll; they do not give off O2 because hydrogen sulfide (H2S) is used as an electron and H + donor instead of H2O
⋅ advanced photosynthesizing bacteria (e.g., cyanobacteria) use both photosystem I and II that contain the same types of chlorophylls found in plants; they do give off O2 because H2O is used as an electron and H + donor
• chemoautotrophs make organic molecules by using energy derived from the oxidation of inorganic compounds in the environment
⋅ deep ocean hydrothermal vents provide H2S to form of chemosynthetic bacteria
⋅ methanogens are chemosynthetic bacteria that produce methane (CH4) from hydrogen gas and CO2; ATP synthesis and CO2 reduction are linked to this reaction and methanogens can decompose animal wastes to produce electricity as an ecological friendly energy source
⋅ nitrifying bacteria oxidize ammonia (NH3) to nitrites (NO2) and nitrites to nitrates (NO3)
o heterotrophic prokaryotes
• most free-living bacteria are chemoheterotrophs that take in pre-formed organic nutrients
• as aerobic saprotrophs, there is probably no natural organic molecule that cannot be broken down by some prokaryotic species
• decomposers are critical in recycling materials in the ecosystem; they decomposing dead organic matter and make it available to photosynthesizers
o commercial uses
• prokaryotes produce chemicals including ethyl alcohol, acetic acid, butyl alcohol, and acetones
• prokaryotic action produces butter, cheese, sauerkraut, rubber, cotton, silk, coffee and cocoa
• antibiotics are produced by some bacteria
o some chemoheterotrophs are symbiotic, forming intimate, long-term relationships with members of other species; includes mutualistic, commensalistic, and parasitic relationships
• mutualistic nitrogen-fixing Rhizobium bacteria live in nodules on roots of soybean, clover, and alfalfa where they reduce N2 to ammonia for their host; bacteria use some of a plant's photosynthetically produced organic molecules
• mutualistic bacteria that live in the intestines of humans benefit from undigested material and release vitamins K and B12, which we use to produce blood components
• in the stomachs of cows and goats, mutualistic prokaryotes digest cellulose (produce cellulase)
• commensalistic bacteria live in or on organisms of other species and cause them no harm
• parasitic bacteria are responsible for a wide variety of infectious plant, animal and human diseases
The Bacteria
- Gram Stain and Shape
o the Gram stain procedure (developed in the late 1880s by Hans Christian Gram) differentiates bacteria
• Gram-positive bacteria have a thick peptidoglycan cell wall & stain purple
• Gram-negative bacteria have a thin cell wall & stain pink
o bacteria and archaea have three basic shapes: spirillum (spiral-shaped), bacillus (elongated or rod-shaped bacteria) and coccus (spherical bacteria)
o cocci and bacilli tend to form clusters and chains of a length typical of the particular species
- Types of Bacteria
o earlier classification of bacteria was based on metabolism, nutrition, etc.
o work by Carl Woese since 1980 has revised bacterial taxonomy based on similarity of 16S rRNA
o 12 groups are now recognized based on bacterial 16S ribosomal RNA sequences
- Cyanobacteria
o cyanobacteria are Gram-negative bacteria with a number of unusual traits
o they photosynthesize in same manner as plants; are responsible for introducing O2 into the primitive atmosphere
o they were formerly mistaken for eukaryotes and classified with algae
o they have pigments that mask chlorophyll (blue-green, red, yellow, brown, black)
o they are relatively large (1-50 µm in width)
o they can be unicellular, colonial, or filamentous
o some move by gliding or oscillating
o some possess heterocysts, thick-walled cells without a nucleoid, where nitrogen fixation occurs
o cyanobacteria are common in fresh water, soil, on moist surfaces, and in harsh habitats (e.g., hot springs)
o some are symbiotic with other organisms (e.g., liverworts, ferns, and corals)
o lichens are a symbiotic relationship where the cyanobacteria provide organic nutrients to the fungus and the fungus protects and supplies inorganic nutrients
o cyanobacteria were probably the first colonizers of land during evolution
o cyanobacteria "bloom " when nitrates and phosphates are released as wastes into water; when they die off, decomposing bacteria use up the oxygen and cause fish kills
- Relationship to Domain Bacteria and Domain Eukarya
o Archaea are prokaryotes with molecular characteristics that distinguish them from bacteria and eukaryotes; their rRNA sequence is different from rRNA in bacteria
o because archaea and some bacteria are both found in extreme environments (hot springs, thermal vents, salt basins), they may have diverged from a common ancestor
o later, the eukarya split from the archaea; archaea and eukarya share some ribosomal proteins not found in bacteria; initiate transcription in the same manner, and have similar types of tRNAs
- Structure and Function
o Archaea have unusual lipids in their plasma membranes that allow them to function at high temperatures: glycerol linked to hydrocarbons rather than fatty acids
o cell walls of archaea do not contain the peptidoglycan found in bacterial cell walls
o only some methanogens have the ability to form methane
o most are chemoautotrophs; none are photosynthetic; this suggests chemoautotrophy evolved first
o some are mutualistic or commensalistic but none are parasitic‹none are known to cause disease
- Types of Archaea
o methanogens live under anaerobic environments (e.g., marshes) where they produce methane
• methane is produced from hydrogen gas and carbon dioxide and is coupled to formation of ATP
• methane released to the atmosphere contributes to the greenhouse effect; about 65% of methane found in our atmosphere is produced by methanogenic archaea
o halophiles require high salt concentrations (e.g., Great Salt Lake)
• their proteins have unique chloride pumps that use halorhodopsin to synthesize ATP in presence of light
• usually they require 12-15% salt concentrations; ocean is only 3.5% salt
o thermoacidophiles live under hot, acidic environments (e.g., geysers). a. They survive best at temperatures above 80šC; some survive above boiling
• metabolism of sulfides forms acidic sulfates; these bacteria grow best at pH of 1 to 2
Chapter 22: The Protists
- Protists are classified in the domain Eukarya and the kingdom Protista
- the endosymbiotic hypothesis explains how the eukaryotic cells arose
o it proposes that aerobic bacteria became mitochondria & cyanobacteria became chloroplasts after being taken up by eukaryotic cells; spirochetes became flagella
- Giardia has two nuclei but no mitochondria; the nucleus therefore came before the mitochondria
- although unicellular to multicellular, protists are highly complex & can have complex life cycles
- euglenoids have both flagella and chloroplasts
- plasmodial slime molds are usually amoeboid; during drought, they produce a sporangium
- protists use asexual reproduction and, when conditions become stressful, sexual reproduction
o formation of spores allows free-living and parasitic protists to survive hostile environments
o a cyst is a dormant cell with a resistant outer covering
- amoeboids and ciliates are more complex, with organelles not seen among other eukaryotes
o food is digested in food vacuoles & excess water is expelled by contractile vacuoles
- ecological importance of protists:
o some are of great medical importance in causing disease; others are ecologically important
o plankton float near the surface and serve as food for heterotrophic protists and animals
o plankton that photosynthesize produce much of the oxygen in the atmosphere
o many protists enter symbiotic relationships; coral reefs rely on symbiotic photosynthetic protists
- evolution of protists:
o multicellular algae are not plants; they do not protect their gametes and zygote from drying out
o none are fungi; those that resemble fungi lack flagella and do not have chitin in their cell wall
o none are animals; the heterotrophic protists do not undergo embryonic development
o due to complexity, protists may deserve more than a dozen kingdoms
Diversity of the Protists
Algae: refers to many phyla that carry out photosynthesis; at one time, algae were grouped with plants because they have chlorophyll a and photosynthesize
- The Green Algae: Phylum Chlorophyta
o they live in the ocean but are more likely found in fresh water and can even be found on moist land
o green algae are not always green; some have pigments that give them an orange, red, or rust color
o body organizations include single cells, colonies, filaments and multicellular forms
o plants are considered to be most closely related to the green algae
o Chlamydomonas, a uicellular green algae
• Chlamydomonas is less than 25 m long; it has a cell wall and a single, large, cup-shaped chloroplast with a pyrenoid for starch synthesis
• the chloroplast contains a light-sensitive eyespot (stigma) that directs the cell to light for photosynthesis
• 2 long whiplike flagella project from the anterior end to propel the cell toward light
• Chlamydomonas reproduces asexually with zoospores when growth conditions are favorable, & reproduces sexually when growth conditions are unfavorable
• gametes from two different mating types join to form a zygote with a heavy wall; the resistant zygospore survives until conditions are favorable
• some are heterogametes similar to sperm and egg that stores food, a condition called oogamy
• in most, gametes are identical, a condition called isogamy
o Spirogyra, a filamentous green algae
• cell division in one plane produces end-to-end chains of cells or filaments
• Spirogyra is a filamentous algae found on surfaces of ponds and streams
• it has ribbonlike spiral chloroplasts
• 2 strands may unite in conjugation and exchange genetic material, forming a diploid zygote
• the zygotes withstand winter; in spring they undergo meiosis to produce haploid filaments
o Multicellular Green Algae
• plants are probably related to green algae because both have a cell wall with cellulose, have chlorophyll a and b, and store food as starch
• the multicellular Ulva is called sea lettuce because of its leafy appearance
⋅ the thallus (body) is two cells thick but can be a meter long
⋅ Ulva has an alternation of generations life cycle, as do plants, but the generations look alike
⋅ the gametes look alike (isogametes) and the spores are flagellated
• Stoneworts are green algae that live in freshwater lakes and ponds
⋅ the stonewort Chara forms a cell plate during cell division and has multicellular sex organs making plants most closely related to this group
⋅ Chara also has a stemlike body with nodes and internodes; the cells of the body originate from apical meristem, features that are homologous with plants
o Volvox, a colonial green algae
• Volvox is a hollow sphere with thousands of cells arranged in a single layer
• Volvox cells resembles Chlamydomonas cells; a colony arises as if daughter cells fail to separate
• Volvox cells cooperate when flagella beat in a coordinated fashion
• some cells are specialized forming a new daughter colony within the parental colony
• daughter colonies are inside a parent colony until an enzyme dissolves part of a wall so it can escape
- The Red Algae: Phylum Rhodophyta
- red algae are chiefly marine multicellular algae that live in warmer seawater
- they are generally much smaller and more delicate than brown algae
- some are filamentous, but most are branched, having a feathery, flat, or ribbonlike appearance
- coralline algae are red algae with cell walls with calcium carbonate; they contribute to coral reefs
- red algae are economically important
o mucilaginous material in cell walls of Gelidium and Gracilaria is the source of agar used in drug capsules, dental impressions, cosmetics
o in the laboratory, agar is a major microbiological media, and when purified, is a gel for electrophoresis
o agar is used in food preparation to keep baked goods from drying and to set jellies and desserts
o carrageen is an emulsifying agent extracted from Chondrus crispus ans used in production of chocolate and cosmetics
- The Brown Algae: Phylum Phaeophyta
o they range from small forms with simple filaments to large multicellular (50-100 m long) seaweeds
o brown algae have chlorophylls a and c and a fucoxanthin giving them their color
o their reserve food is a carbohydrate called laminarin
o seaweed refers to any large, complex alga
o their cell walls contain a mucilaginous water-retaining material that inhibits desiccation (drying out)
o Laminaria is an intertidal kelp that is unique among protists; this genus shows tissue differentiation
o Nereocystis and Macrocystis are giant kelps found in deeper water anchored to the bottom by their holdfasts
o individuals of the genus Sargassum sometimes break off from their holdfasts and form floating masses
o brown algae provide food and habitat for marine organisms, and they are also important to humans
• brown algae are harvested for human food and for fertilizer in several parts of the world
• Macrocystis is a source of algin, a pectinlike substance added to give foods a stable, smooth consistency
• most have an alternation of generations life cycle
o Fucus is an intertidal rockweed; meiotic cell division produces gametes and adult is always diploid
- The Diatoms: Phylum Bacillariophyta (diatoms and golden brown alga)
o diatoms are the most numerous unicellular algae in the oceans and an important source of food and O2 in aquatic systems
o diatom cell walls consist of two silica (glass)-containing halves or valves with a variety of markings formed by pores
o asexual reproduction: each new diatom receives one old valve & one smaller new one (each generation decreases in size)
o sexual reproduction: when new diatoms reach ~ 30% original size, a zygote grows and divides mitotically to form diatoms of normal size
o diatom remains accumulate on the ocean floor and are mined as diatomaceous earth for use as filters, abrasives, etc.
- The Flagellates: Phylum Pyrrophyta (unicellular dinoflagellates)
o these algae are bounded by protective cellulose plates, & most have two flagella
o some species of dinoflagellates are heterotrophic; they are parasitic on their host
o they are extremely numerous (30,000 per cubic millimeter) and an important source of ecosystem food
o under certain conditions, Gymnodinium and Gonyaulax increase in number enormously and cause a "red tide": they produce a powerful neurotoxin killing fish and causing paralytic shellfish poisoning
- The Euglenoids: Phylum Euglenophyta
o euglenoids are small (10-500 µm) freshwater unicellular organisms
o one-third of all genera have chloroplasts; those that lack chloroplasts ingest or absorb their food
o their chloroplasts resemble those of green algae (have three rather than two membranes) & are probably derived from a green algae through endosymbiosis
• the pyrenoid outside the chloroplast produces an unusual type of carbohydrate polymer (paramylon) not seen in green algae
o they possess two flagella, one of which typically is much longer than the other and projects out of a vase-shaped invagination; it is called a tinsel flagellum because it has hairs on it
o near the base of the longer flagellum is a red eyespot that shades a photoreceptor for detecting light
o they lack cell walls, but instead are bounded by a flexible pellicle composed of protein strips side-by-side
o a contractile vacuole, similar to certain protozoa, eliminates excess water
o euglenoids reproduce by longitudinal cell division; sexual reproduction is not known to occur
- The Zooflagellates: Phylum Zoomastigophora
o these protozoa are covered by a pellicle often reinforced by underlying microtubules
o Trypanosoma brucei, a trypanosome transmitted by the bite of a tsetse fly, is the cause of African sleeping sickness
o Giardia lamblia cysts are transmitted through contaminated water; it causes severe diarrhea
o Trichomonas vaginalis is a sexually transmitted organism that infects vagina and urethra of women and prostate, seminal vesicles and urethra of men
- Protists with Pseudopods
o protists that move with pseudopods usually live in aquatic environments and are part of the zooplankton, microscopic floating organisms
o they engulf prey with pseudopods, cytoplasmic extensions formed as cytoplasm streams in one direction
o amoeboids (Amoeba proteus, phylum Rhizopoda) phagocytize their food; pseudopods surround and engulf prey; food is digested inside food vacuoles
o freshwater amoeboids have contractile vacuoles to eliminate excess water
o Entamoeba histolytica is an amoebic parasite that invades the human intestinal lining
o Foraminiferans (phylum Foraminifera) have a multi-chambered CaCO3 shell; thin pseudopods extend through holes
o Radiolarians (phylum Actinopoda) have a test (skeleton) composed of silica or strontium sulfate; most have a radial arrangement of spines
o pseudopods (actinopods) project from an external layer of cytoplasm and are supported by rows of microtubules
o since the Precambrian, tests of dead foraminiferans and radiolarians have formed deep layers of ocean floor sediment; each layer has distinctive foraminiferans which helps date rocks
o over hundreds of millions of years, the CaCO3 shells have contributed to the formation of chalk deposits (i.e., White Cliffs of Dover, limestone of the great Egyptian pyramids)
- The Ciliates: Phylum Ciliophora
o ciliates are diverse with over 8,000 different species
o ciliates move by coordinated strokes of hundreds of cilia projecting through holes in a semirigid pellicle
o they discharge long, barbed trichocysts for defense and for capturing prey; toxicysts release a poison
o most are holozoic and ingest food through a gullet and eliminate wastes through an anal pore
o asexual reproduction: ciliates divide by transverse binary fission
o ciliates possess two types of nuclei‹a large macronucleus and one or more small micronuclei
o the macronucleus controls the normal metabolism of the cell
o the micronucleus is involved in sexual reproduction. 1) The macronucleus disintegrates and the micronucleus undergoes meiosis. 2) Two ciliates then exchange a haploid micronucleus. 3) The micronuclei give rise to a new macronucleus containing only housekeeping genes
o members of the genus Paramecium contain barrel-shaped didiniums expand to consume paramecia much larger than themselves
• suctoria rest on a stalk and paralyze victims, sucking them dry
o Stentor resembles a giant blue vase with stripes
- The Sporozoans: Phylum Apicomplexa (nonmotile parasites)
o the phylum name describes the unique apical complex of organelles
o their common name recognizes they form spores at some point in their life cycle
o Pneumocystis carinii causes the pneumonia seen primarily in AIDS patients
• during sexual reproduction, thick-walled cysts form in the lining of pulmonary air sacs; cysts contain spores that successively divide until the cyst bursts and the spores are released; each spore becomes a new organism, reproduces asexually and can enter an encysted sexual stage
o Plasmodium vivax causes one type of malaria; it is the most widespread human parasite
• after bite of infected female Anopheles mosquito, the parasite eventually invades red blood cells
• chills and fever appear as red blood cells burst and release toxin into the blood
• malaria remains a major world disease due to insecticide-resistant strains of mosquitoes and drugresistant strains of Plasmodium
o Toxoplasma gondii causes toxoplasmosis, particularly in cats but also in humans
• in pregnant women, the parasite can infect the fetus and cause birth defects
• in AIDS patients, it can infect the brain and cause neurological symptoms
- The Slime Molds and Water Molds
o these organisms resemble fungi but all have flagellated cells that fungi never have
o water molds possess a cell wall but it is made of cellulose, not chitin as in fungi
o water molds produce diploid (2n) zoospores and meiosis produces the gametes
o The Plasmodial Slime Molds (phylum Myxomycota)
• exist as a plasmodium: a diploid multinucleated cytoplasmic mass that creeps along, phagocytizing decaying plant material
• fan-shaped plasmodium contains tubules of concentrated cytoplasm in which liquefied cytoplasm streams
• under unfavorable environmental conditions (e.g., drought), the plasmodium develops many sporangia, called a fruiting body, that produce spores by meiosis
• when mature, spores are released and survive until more favorable environmental conditions return; then each releases a haploid flagellated cell or an amoeboid cell
• two flagellated or amoeboid cells fuse to form a diploid zygote that produces a multinucleated plasmodium again
o The Cellular Slime Molds (phylum Acrasiomycota)
• exist as individual amoeboid cells, live in soil and feed on bacteria and yeast
• as food runs out, amoeboid cells release a chemical that causes them to aggregate into a pseudoplasmodium
• the pseudoplasmodium stage is temporary; it gives rise to sporangia that produce spores
• spores germinate when more favorable environmental conditions return to release haploid amoeboid cells, which again begins the asexual cycle
• a sexual cycle occurs under less dry conditions
- The Water Molds: Phylum Oomycota
o aquatic water molds parasitize fishes, forming furry growths on their gills, and decompose the fish remains
o terrestrial water molds parasitize insects and plants; a water mold caused the 1840s Irish potato famine
o most water molds are saprotrophic, living off dead organic matter
o water molds have a filamentous body; cell walls are composed largely of cellulose
o during asexual reproduction, they produce diploid motile spores (2n zoospores) with flagella
o unlike fungi, the adult is diploid; gametes are produced by meiosis
o eggs are produced in enlarged tips called oogonia
Chapter 23: The Fungi
Characteristics of Fungi
- Fungi are mostly multicellular eukaryotes that are heterotrophic and consume preformed organic matter
- fungi are heterotrophic by absorption (animals are heterotrophic by ingestion)
- fungal cells secrete digestive enzymes; following breakdown of molecules, the nutrients are absorbed
- most fungi are saprotrophic decomposers, breaking down wastes or remains of plants and animals
- some are parasitic, living off tissues of living plants and animals
o fungi enter leaves through stomates; plants are especially subject to fungal diseases
o fungal diseases account for millions of dollars in crop losses each year; fungal diseases also have decimated some tree species
o fungi also cause human diseases including ringworm, athlete's foot, and yeast infections
- several types of fungi are adapted to mutualistic relationships with other organisms
o fungi associated with plant roots acquire inorganic nutrients for plants and receive organic nutrients
o fungi form an association with a green alga or cyanobacterium to form a lichen
- Structure of Fungi
o most fungi are multicellular (yeasts are unicellular)
o the thallus (body) of most fungi is a mycelium
o a mycelium is a network of hyphae comprising the vegetative body of a fungus
• hyphae are filaments that provide a large surface area and aid absorption of nutrients
• when a fungus reproduces, a portion of the mycelium becomes reproductive structures
o fungal cells lack chloroplasts and have a cell wall made of chitin, not cellulose
• chitin, like cellulose, is a polymer of glucose molecules organized into microfibrils
• in chitin, unlike cellulose, each glucose has an attached nitrogen containing amino group
o the energy reserve of fungi is glycogen as in animals, and not starch
o fungi are nonmotile; their cells lack basal bodies and do not have flagella at any stage in their life
o fungi move to a food source by growing toward it; hyphae can grow up to a kilometer a day!
o nonseptate hyphae lack septa or cross walls; hyphae are multinucleated
o septate fungi have cross walls in their hyphae; pores allow cytoplasm and organelles to pass freely
o the septa that separate reproductive cells, however, are complete in all fungal groups
- Reproduction of Fungi
o fungal sexual reproduction: haploid hyphae->dikaryotic stage->diploid zygote->meiosis->spores->haploid hyphae...
• during sexual reproduction, haploid hyphae from two different mating types fuse; if nuclei do not fuse immediately, the resulting hypha is dikaryotic (contains paired haploid nuclei, n + n)
• when the nuclei fuse, the resulting zygote undergoes meiotic cell division leading to spore formation
• fungal spores germinate directly into haploid hyphae without embryological development
o fungal spore formation: spores are an adaptation to life on land and ensure that the species will be dispersed to new locations
• a spore is a reproductive cell that can grow directly into a new organism
• fungi produce spores both during sexual and asexual reproduction; the spores are readily dispersed by wind
o asexual reproduction can occur by three mechanisms:
• production of spores by a single mycelium is the most common mechanism
• fragmentation is when a portion of a mycelium becomes separated and begins a life of its own
• budding is typical of yeasts; a small cell forms and gets pinched off as it grows to full size.
- evolutionary origin of fungi is not known; they had evolved by about 570 million years ago; they may have evolved separately from protist ancestors
- some biologists propose that fungi evolved from red algae; both lack flagella in all stages of the life cycle (fungi share similarities and have differences with other groups of protists)
- since fungi are generally multicellular & heterotrophic (saprophytic decomposers), R. H. Whittaker argued for their own kingdom
- not knowing phylogeny, fungal groups are classified according to differences in life cycles and types of sporangia
Zygospore Fungi: Phylum Zygomycota (about 665 species)
- most are saprotrophs living off plant and animal remains in the soil or bakery goods in a pantry
- some are parasites of small soil protists, worms, or insects
- the black bread mold, Rhizopus stolonifer, is a common example
- with little cellular differentiation, fungal hyphae specialize for various functions
o stolons are horizontal hyphae that exist on the surface of the bread
o rhizoids are hyphae that grow into the bread, anchor the mycelium, and carry out digestion
o sporangiophores are stalks that bear sporangia; a sporangium is a capsule that produces spores called sporangiospores
- the division name refers to the zygospore seen during sexual reproduction
o hyphae of different mating types (+ and -) are chemically attracted and grow toward each other
o ends of hyphae swell as nuclei enter; cross walls develop behind each end, forming gametangia
o gametangia merge into a large multinucleate cell in which nuclei of two mating types pair and fuse
o a thick wall develops around the cell, forming a zygospore
o the zygospore undergoes a period of dormancy before meiosis and germination takes place
o asexual reproduction: germination involves the development of one or more sporangiophores, with sporangia at their tips
o the spores are dispersed by air currents and give rise to new haploid mycelia
- most are saprotrophs with an essential role digesting cellulose, lignin, collagen and other resistant materials
- red bread molds, cup fungi, morels, and truffles are also sac fungi
- many ascomycetes are plant parasites and include the powdery mildews that grow on leaves, leaf curl fungi, chestnut blight, and Dutch elm disease
- ergot is a parasitic fungus on rye; it produces a toxin that can cause hysteria and death
- most ascomycetes are composed of septate hyphae
- sexual reproduction involves production of eight ascospores within an ascus contained within saclike ascocarp
o ascus-producing hyphae remain dikaryotic except in a walled-off portion that becomes the ascus
o each ascus contains eight haploid nuclei and produces eight ascospores
o in most ascomycetes, the asci become swollen and burst, expelling the ascospores; if released into the air, the spores are windblown
- asexual reproduction, which is the norm, involves the production ofa
o conidiospores (conidia) develop directly on tips of conidiophores, modified aerial hyphae, and are windblown when released.
- Yeasts are unicellular and reproduce asexually by budding
o Saccharomyces cerevisiae is brewer's yeast; a small cell forms and is pinched off as it grows
o sexual reproduction in yeasts occurs when food runs out, and produces asci and ascospores
• ascospores from two different mating types fuse, resulting in a diploid cell
• the diploid cell reproduces asexually, then undergoes meiotic cell division forming ascospores
• the haploid ascospores function directly as new yeast cells
o yeasts produce ATP through fermentation‹ethanol and CO2 are waste products
o yeasts are added to prepared grains to make beer
o because of its ability to produce alcohol, yeast fermentation is important in the production of wine; special strains are added to essentially sterile grape juice and the CO2 is kept for sparkling wines
o because it produces CO2, yeast fermentation is important in the production of bread
o yeasts are also used in genetic engineering experiments requiring a eukaryote
Club Fungi: Phylum Basidiomycota (about 16,000 species)
- they have septate hyphae and include mushrooms, bracket fungi, puffballs, bird's nest fungi, and stinkhorns
- sexual reproduction involves production of basidiospores within clublike basidia contained within a basidiocarp; asexual reproduction is rare and involves the production of conidiospores
o sexual reproduction begins when monokaryotic hyphae of two different mating types meet and fuse to form a dikaryotic (n + n) mycelium
o the dikaryotic mycelium continues its existence for years (perhaps even hundreds of years) and occasionally produces one or more basidiocarps
o basidiocarps are fruiting bodies (e.g., mushrooms and puffballs) composed of tightly packed dikaryotic hyphae whose walled-off ends become the club-shaped basidia
o a basidium contains four projections; cytoplasm and a haploid nucleus enters to form four basidiospores
o released basidiospores are windblown; when they germinate, a new haploid mycelium forms
- in a puffball, spores inside parchmentlike membranes are released through a pore or when the parchment breaks down
- in bird's nest fungi, raindrops splatter basidiospore-containing "eggs" through the air
- stinkhorns have a slimy cap and attract flies by their bad odor to pick up and distribute spores
- rusts & smuts are club fungi that parasitize cereal crops (e.g., corn, wheat, oats, and rye) and cause great economic crop losses every year
o spores of rusts and smuts are small and numerous, resembling soot
o some smuts enter seeds and exist inside the plant, becoming visible only at maturity
o corn smut mycelia grow between the corn kernels and secrete substances to cause tumors on ears
o they have a complex life cycle that may involve more than one host; thus, control measures may center on eradicating the alternate hosts
Imperfect Fungi: Phylum Deuteromycota (about 25,000 species)
- they reproduce asexually by forming conidiospores; these are produced at the tips of aerial hyphae, not in sporangia
- they are "imperfect" because no sexual stage is known and may not exist; thus it cannot be easily classified
- cell morphology and biochemistry indicate some are sac fungi that lost ability to reproduce sexually
- several species of imperfect fungi are of great economic importance
o some species of Penicillium mold provide antibiotic penicillin; others give a characteristic aroma and flavor to certain cheeses (e.g., Roquefort and Camembert)
o cyclosporine suppresses the immune system and is from an imperfect fungus found in soil
o Aspergillus is used in the production of soy sauce, citric acid, and gallic acids
- some imperfect fungi cause human diseases
- Aspergillosis is a respiratory infection caused by inhaling spores
- an Aspergillus that grows on moist seeds secretes aflatoxin, a potent natural carcinogen
- athlete's foot and ringworm are skin infections caused by direct contact
- Candida albicans is a yeastlike fungus causing infections of the vagina, diaper rash, and thrush
Symbiotic Relationships of Fungi
- Lichens are a symbiotic association between fungus and cyanobacterium or green alga
- the body of a lichen is composed of three layers: a thin, tough upper layer, a loosely packed lower layer & protected photosynthetic cells in the middle layer
- special fungal hyphae penetrate or envelope the photosynthetic cells and transfer nutrients directly to the rest of the fungus
- lichens can reproduce asexually by releasing fragments that contain hyphae and an algal cell
o this association was considered mutualistic, but experimentation suggests a controlled parasitism by fungus of the alga
• the algae grow faster when they are alone rather than when they are part of a lichen
• on the other hand, it is difficult to cultivate the fungus, which does not grow naturally alone
• different lichen species are identified based on the fungal partner
o three types of lichens are recognized
• crustose lichens are compact & often seen on bare rocks or tree bark
• foliose lichens are leaflike
• fruticose lichens are shrublike
o lichens are efficient at acquiring nutrients; they survive with low moisture, temperature, or poor soil
o lichens may live in extreme environments and on bare rocks; they help form soil
o lichens also take up pollutants and cannot survive where the air is polluted
- Mycorrhizae are mutualistic relationships between soil fungi and roots of most plants
o fungus enters the cortex of roots but does not enter the cytoplasm of plant cells
o ectomycorrhizae form a mantle that is exterior to the root, growing between cell walls
o it helps the roots absorb more minerals; in turn, the plant passes on carbohydrates to the fungus
o the truffle lives in association with oak and beech tree roots; it can be inoculated with the fungus
o the fossil record indicates that the earliest plants had mycorrhizae associated with them; mycorrhizae helped plants adapt to and flourish on land.