biology 2 exam 2

What characteristics enable prokaryotes to reach huge population sizes and thrive in diverse environments?

• single celled organisms that make up domains Bacteria and Archea

• adapted to diverse and extreme environments, they are the most abundant organisms on Earth

• first organisms to inhabit Earth, most are unicellular but some for colonies

• most of them are .5- 5 micrometers, smaller than 10-100 micrometer most eukaryotic cells are

• come in variety shapes like spheres (cocci), rod (bacilli) and spirals

cell wall

maintains shape, protects the cell, and prevents it from bursting in a hypotonic environment

• eukaryote cell walls are made of cellulose or chitin

• most in bacteria contain peptidoglycan

• archaea contain a variety of polysaccharides and proteins in theirs but lack peptidoglycan

prokaryotes in hypertonic environments

• they lose water and experience plasmolysis

• salt is used as a preservative because water loss slows reproduction of food spoiling prokaryotes

peptidoglycan

a network of sugar polymers cross-linked by polypeptides

Scientists use the gram-stain to classify bacteria cell wall composition

• gram-positive bacteria have simpler walls with a large amount of peptidoglycan

• the walls of gram-negative bacteria have less peptidoglycan and are more complex with an outer membrane that contains lipopolysaccharides

gram-negative bacteria

• tend to be more resistant to antibiotics

• many antibiotics target peptidoglycan and damage the cell walls

Humans cells lack——and are unaffected to antibiotics

peptidoglycan

the capsule

• many prokaryotes have a sticky layer of polysaccharide or protein surrounding the cell wall if it is dense and well defined

slime layer

• many prokaryotes have a sticky layer of polysaccharide or protein surrounding the cell wall if it is not well organized

slime layer and capsule

enable adherence to the substrate or other individuals, and protect the cell from the host’s immune system

endospore

• some bacteria form metabolically inactive—— when water or nutrients are lacking, and can withstand extreme conditions and remain viable for centries

-the cell copies its chromosome and surrounds it with multilayered structure

Fimbriae

some prokaryotes have hairlike appendages that allow them to stick to their substrate or other individuals in a colony

Pili (sexpili)

longer than fimbriae and function to pull cells together enabling the exchange DNA

Taxis

about half of prokaryotes exhibit the ability to move toward or away from a stimulus

Chemotaxis

the movement toward or away from chemical stimulus

Flagella

• most common structures used by prokaryotes for movement

• they may be scattered over the entire surface or concentrated at the ends of the cell

• differ between prokaryotes and eukaryotes in structure, mechanism of propulsion, and molecular composition

bacterial flagella are composed of—- different kinds of proteins that form a motor, hook, and filament

42

only HALF of the flagella’s proteins are essential and about HALF of those are modified versions of proteins with different functions

true

Exaptation

where structures adapted for one function take on new functions through descent with modification (ex.flagella)

prokaryotic cells lack

complex internal compartmentalization

some—-have specialized membranes that perform metabolic functions, which are usually infoldings of the cell membranes

prokaryotes

Plasmids

smaller rings of independently replicating DNA

Nucleoids

where the chromosomes for prokaryotes are, a region with no membrane

promote genetic diversity in prokaryote populations

• rapid reproduction- enables rapid adaptation by natural selection

• mutation

• genetic recombination

Mutation in prokaryotes

• mutation rates are typically low but accumulate rapidly with short generation times and large populations

genetic recombination

the combining of DNA from two sources, contributes to prokaryote diversity

DNA from different individuals can be combined by

transformation, transduction or conjugation

horizontal gene transfer

the movement of genes between individual prokaryotes of different species

transformation

prokaryotic cells incorporate foreign DNA taken up from their surroundings

• a nonpathogenic cell could take up a piece of DNA carrying an allele for pathogenicity and replace its own allele with the foreign allele

• the resulting recombinant cell would pathogenic

transduction

phages carry prokaryotic genes from one host cell to another

• generally an unintended result of the phage replication cycle

bacteriaphages

viruses that infect bacteria

conjugation

the process through which DNA is transferred between two prokaryotic cells

• in bacteria, the DNA transfer is always one way- one cell donates the DNA and the other receives it

conjugation in E.coli

1. A pilus of the donor cell attaches to the recipient

2. the pilus retracts, pulling the two cells together

3. DNA is transferred through a temporary structure called the “mating bridge”

F factor (f for fertility)

required for the production of pili

• can exist either as a plasmid or segment of DNA within the bacterial chromosome

• cells containing it (F+ cells) function as DNA donors

• F- cells are recipients

• An F+ cell can convert an F- cell to an F+ cell if it transfers F plasmid to the F- cell, if only part of it is transferred the recipient cell will be recombinant

Hfr cells

• named for high frequency for recombination

• cells that have the F factor in their chromosome

• function as donors during conjugation

R plasmids

plasmids that carry resistance genes

• antibiotics cannot kill bacteria if they have this

• have genes that encode the pili used to transfer DNA between cells, enabling the rapid spread of resistance

phototrophs

obtain energy from light

chemotrophs

obtain energy from chemicals

autotrophs

require CO2 or related compounds as a carbon source

Heterotrophs

require an organic nutrient to make other organic compounds

obligate aerobes

require O2 for cellular respiration

obligate anaerobes

poisoned by O2 and live by fermentation or use substances other than O2 for anaerobic respiration

facultative anaerobes

can use O2 if it is present or carry out fermentation or anaerobic respiration if not

Nitrogen fixation

prokaryotes use to convert atmosphere nitrogen (N2) to ammonia (NH3)

• isolated in cells called heterocysts that prevent oxygen penetration

• Nitrogen essential for the production of amino acids and nucleic acids in all organisms

Biofilms

cells of one or more prokaryotes species cooperate to form surface-coating colonies

• channels allow nutrients to reach cells in the interior and wastes to be expelled

Biofilms are common in nature, but can cause many problems for humans

• corrosion of industrial structure and products

• contamination of medical devices

• tooth decay

• chronic, antibiotic-resistant infections

proteobacteria

gram-negative bacteria including photoautotrophs, chemoautotrophs, and heterotrophs

Thiomargarita namibiensis

an autotroph that obtains energy by oxidizing H2S and producing sulfur as a waste product

heterotrophic proteobacteria

neisseria gonorrhea- gonorrhea

vibrio cholerae- cholera

helicobacter pylori- stomach ulcers

chlamydia trachomatis

causes nongonococcal urethritis, the most common std in the US

Spirochetest

helical gram-negative heterptrophs that spiral through the environment by rotating internal filaments

• many are free living, but others are pathogens

• Treponema palidum- syphilis

• Borrelia burgdorferi- lyme disease

cyanobacteria

gram-negative photoautotrophs

• plants chloroplasts likely evolved from them by the process of endosymbiosis

• solitary and filamentous are abundant components of freshwater and marine phytoplankton

Gram positive bacteria

diverse group

• Actinomycetes are colony-forming bacteria including pathogens and soil decomposers.

• Soil-dwelling species of Streptomyces are cultured as a source of antibiotics, including tetracycline.

• Other subgroups include pathogens such as Staphylococcus aureus; Bacillus anthracis causes anthrax; and Clostridium botulinum causes botulism.

Bacteria

Nuclear envelope- absent

Membrane enclosed organelles- absent

Peptidoglycan in cell wall- present

Membrane lipids- unbranched hydrocarbons

RNA polymerase- one kind

Initiator amino acid for protein synthesis- formyl-methionine

Archea

Nuclear envelope- absent

Membrane enclosed organelles- absent

Peptidoglycan in cell wall- absent

Membrane lipids- some branched hydrocarbons

RNA polymerase- several kinds

Initiator amino acid for protein synthesis- methionine

Eukarya

Nuclear envelope- present

Membrane enclosed organelles- present

Peptidoglycan in cell wall- absent

Membrane lipids- unbranched hydrocarbons

RNA polymerase- several kinds

Initiator amino acid for protein synthesis- methionine

Extreme halophiles

either tolerate or require highly saline environments

extremeopiles

archea that live in extreme environments, uninhabitable for most organisms

extreme thermopile

have adaptations that make their DNA and proteins stable at high temperatures, even above 100 degrees C

Methanogens

obligate anaerobes that produce methane as a by product of their metabolism

- Found in diverse environments

• under kilometers of ice in Greenland

• in swamps and marshes

• in the guts of cattle, termites, and other herbivores

Euryarcheaota

the clade that includes many of the extreme halopiles, most methanogens, and some extreme thermopiles

• most of the extreme thermopiles belong to another clade

TACK

• a supergroup composed of the remaining, closely-related clades of archaea that is named for its component clades:

–Thaumarchaeota.

–Aigarchaeota.

–Crenarchaeota – includes most extreme thermophiles.

–Korarchaeota.

Lokiarchaeotes

a recently discovered group, closely related to the T A C K archaea, that may represent the sister group of the eukaryotes:

–Characteristics of this group could shed light on how eukaryotes arose from their prokaryotic ancestors.

Prokaryotes play crucial roles in the biosphere.

•If prokaryotes were to disappear, prospects for any other life surviving on Earth would be dim:

–Prokaryotes play a major role in recycling of chemical elements between living and nonliving components of the environment.

–Some chemoheterotrophic prokaryotes are decomposers that break down dead organisms and wastes and release carbon and other elements.

Autotrophic prokaryotes

use CO2 to produce sugars and O2 that are consumed by other organisms.

Nitrogen-fixing bacteria

transform atmospheric nitrogen into forms available to other organisms.

Some prokaryotes can increase the availability of soil nutrients that plants require for growth.

True

Symbiosis

an ecological relationship in which two species live in close contact: a larger host with a smaller symbiont.

mutualism

both symbiotic organisms benefit.

commensalism

one organism benefits while neither harming or helping the other

parasitism

an organism called a parasite harms but does not usually kill its host.

pathogens

parasites that are diseases

Bacteroides thetaiotaomicron

has genes involved in synthesizing carbohydrates, vitamins, and other important nutrients.

–It also produces signals that activate human genes involved in absorption and antimicrobial production.

Exotoxins

are proteins secreted by bacteria that can cause disease even if the bacteria are no longer present:

–Cholera is a diarrheal disease caused by an exotoxin secreted by Vibrio cholerae.

Endotoxins

are lipopolysaccharide components of the outer membrane of gram-negative bacteria:

–They are released only when bacteria die and their cell walls break down.

– released by species in the genus Salmonella cause food poisoning.

Humans reap many benefits from bacteria including the production of many foods

–Cheese and yogurt from milk.

–Beer and wine.

–Pepperoni.

–Fermented cabbage (sauerkraut).

–Soy sauce.

Experiments using prokaryotes have led to important advances in DNA technology

–E. coli is used in gene cloning.

–DNA polymerase from Pyrococcus furiosus is used in the P C R technique.

•The CRISPR-Cas9 system, which helps prokaryotes defend against viral attack, has been developed as a gene altering tool:

–This system has been used to study HIV, the virus that causes AIDS.

Bacteria can be used to produce natural plastics

–Some bacteria synthesize PHA, a polymer used to store chemical energy.

–P H A can be extracted, formed into pellets, and used to make durable, biodegradable plastics.

Engineering bacteria

to produce ethanol from agricultural waste, switchgrass, and corn can help reduce dependence on petroleum.

Prokaryotes can also be used in bioremediation

the use of organisms to remove pollutants from soil, air, or water

–Bacteria that metabolize oil can be used to increase the breakdown of oil following a spill.

Protist

is an informal term referring to all eukaryotes that are not plants, animals, or fungi

–This group is no longer considered a kingdom because some protists are more closely related to plants, fungi, or animals than other protists.

–Cells of protists and other eukaryotes have a nucleus and other membrane-enclosed organelles that isolate functions within eukaryotic cells, making them more complex than prokaryotic cells.

-The well-developed cytoskeleton of eukaryotic cells allow them to have asymmetric shape and to change shape over time.

Unicellular protists

the most complex of all cells because each cell must carry out all functions of life.

–Some unicellular protists have organelles not found in most other eukaryotic cells – some dinoflagellates have an eye-like organelle called an ocelloid.

mixotrophs

that combine both photoautotrophs containing chloroplasts and heterotrophs that absorb organic molecules or ingest larger food particles

secondary endosymbiosis

Red and green algae themselves have been ingested by heterotrophic eukaryotes

Excavata

This supergroup includes three clades: parabasalids, diplomonads, and euglenozoans:

–Giardia intestinalis is a diplomonad parasite that causes intestinal infections in mammals.

SAR

•This supergroup includes three large clades: Stramenopila, Alveolata, and Rhizaria:

–Diatoms are important photosynthetic stramenopiles

–Many rhizarians are amoebas with threadlike pseudopodia, such as Globigerina.

Archaeplastida

•This supergroup includes unicellular, colonial, and multicellular red and green algae; and plant:

–Volvox is a multicellular green algae.

Unikonta

•This supergroup includes amoebas with lobe- or tube-shaped pseudopodia, animals, fungi, and non-amoeba protists closely related to animals or fungi:

–Amoeba proteus is a tubulinid amoeba.

protists with modified mitochondria and protists with unique flagella.

•Excavata is characterized by its cytoskeleton:

–Some members have an “excavated” feeding groove on one side of the body

Diplomonads and parabasalids

lack plastids, have reduced mitochondria, and most live in anaerobic environments.

•Diplomonads

• have reduced mitochondria, called mitosomes, that lack electron transport chains:

–Energy is derived from anaerobic pathways.

–They have two equal-sized nuclei and multiple flagella.

–Many are parasites, such as Giardia intestinalis.

Parabasalids

• have reduced mitochondria, called hydrogenosomes, that generate some energy anaerobically:

-Trichomonas vaginalis, a sexually transmitted parasite that infects about 140 million people per year worldwide

Euglenozoans

includes predatory heterotrophs, photosynthetic autotrophs, mixotrophs, and parasites that have a spiral or crystalline rod inside each flagella.

•This clade includes the Kinetoplastids and Euglenids

Euglenids

have one or two flagella that emerge from a pocket at one end of the cell.

•Some are mixotrophs that switch between autotrophic and heterotrophic modes, depending on environmental conditions.

Kinetoplastids

have a single mitochondrion containing an organized mass of DNA called a kinetoplast.

–Free-living species consume prokaryotes in freshwater, marine, and moist terrestrial ecosystems but some species are parasitic

– Trypanosoma infect humans causing sleeping sickness and Chagas’ disease.

Stramenopiles

include some of the most important photosynthetic organisms on Earth:

–Most have a “hairy” flagellum paired with a “smooth” flagellum.

•Diatoms, oomycetes, and brown algae are three important groups

Diatoms

are unicellular algae with a unique two-part, glass-like wall of silicon dioxide:

–The wall withstands pressure up to 1.4 million kg/m2, protecting from the crushing jaws of predators.

•compose much of the phytoplankton in the ocean and lakes and includes about 100,000 species:

–abundant and widespread that their photosynthetic activity affects global CO2 levels.

•After it blooms, many dead individuals fall to the ocean floor, where decomposition is slow:

–The breakdown and release of carbon stored as it blooms on the ocean floor can take centuries.

•Promoting their blooms by fertilizing the ocean with essential nutrients is a proposed approach to reduce atmospheric CO2 levels.

among the multicellular algae, some have——in which both haploid and diploid stages are multicellular.

alternation of generations

The diploid generation of multicelluar algae is called—- because it produces spores.

Fertilization of gametes results in a diploid zygote, which develops into a new ——

sporophyte

Haploid spores develop into multicellular haploid —- that produce haploid gametes.

gametophytes