Unit 3.1 Bacteria & Archaea

Unicellular, wide, abundant, first, 0.5-5

Prokaryotes
➔ ________ organisms that make up domains Bacteria and Archaea
◆ Some species remain attached to each other after cell division
➔ Can thrive in a ____ range of environments
◆ Also adapted to more “normal” habitats
➔ Most _______ organisms on Earth
➔ ____ organisms to inhabit Earth (3.5 billion years ago)
➔ Diameters of ____ μm (smaller than eukaryotic cells 10 to 100 μm)
◆ Exception: Thiomargarita namibiensis which is 750 μm in diameter

Bacteria & Archaea

1. Structural & Functional Adaptations
2. Genetic Diversity
3. Nutritional & Metabolic Adaptations
4. Diverse Lineages
5. Roles In The Biosphere
6. Human Impact

Prokaryote Shapes

1. Cocci (spherical)
2. Bacilli (rod-shaped)
3. Spiral

Cocci

- singular: coccus
- spherical prokaryotes
- can occur
1. singly
2. in chains of two or more cells
3. clusters resembling grapes

Bacilli

- singular: bacillus
- rod-shaped prokaryotes
- usually solitary, but in some forms the rods are arranged in chains

Spiral

- usually includes spirochetes
- corkscrew-shaped, commas, or loose coils

Structural & Functional Adaptations

1. Cell-Surface Structures
2. Motility
3. Internal Organization & DNA
4. Reproduction

Cell-Surface Structures

1. Cell Wall
2. Capsule/Slime Layer
3. Endospore
4. Fimbriae

shape, protects, hypotonic, hypertonic

Cell Wall
● Maintains cell _____, ______ the cell, and prevents it from bursting in a ______ environment
● Lose water and shrink away from cell wall in a _______ environment
○ Salt causes food-spoiling prokaryotes to lose water and prevents reproduction

Bacterial Cell Wall

➔ Contains peptidoglycan

Peptidoglycan

◆ Polymer composed of modified sugars cross-linked by short polypeptides
◆ Encloses the entire bacterium
and anchors other molecules on its surface

lacks

Archaeal Cell Wall
➔ Contains a variety of polysaccharides
and proteins but ____ peptidoglycan

Hans Christian Gram, composition

Gram stain
➔ Developed by 19th-century Danish physician ____ ________ ____
➔ Categorizes many bacterial species according to differences in cell wall __________

violet, iodine, alcohol, safranin

Gram stain process
1. Samples are rinsed with crystal _____ dye and
_____
2. Then rinsed in ______
3. Stained with red dye _____ which enters
the cell and binds to its DNA

Gram-positive

➔ relatively simple walls composed of a
thick layer of peptidoglycan
➔ stain a darker color (peptidoglycan traps crystal violet)

Gram-negative

➔ have less peptidoglycan and are structurally more complex (outer membrane that contains lipopolysaccharides)
➔ peptidoglycan in periplasmic space between membrane bilayer
➔ stain a lighter color because crystal violet is easily rinsed away revealing the safranin

toxic, negative, resistant, positive

Medical Applications of Gram Staining
➔ A valuable tool in medicine for quickly determining patient’s infection source

◆ Lipid portions of lipopolysaccharides are ____ causing fever or shock
◆ Outer membrane of gram-______ protects bacterium from body’s defenses
◆ Gram negative tends to be more _______ to antibiotics because outer membrane impedes entry of some drugs
◆ Some gram ______ have virulent strains that are resistant to antibiotics

Staphylococcus aureus (MRSA)

- Gram-positive spherically shaped bacterium
- one of the most important bacteria that causes disease in humans

peptidoglycan cross-linking

➔ Effectiveness of certain antibiotics (penicillin) derives from inhibition of of ____________ _________
◆ Destroy bacteria without adversely affecting humans cells which do not have peptidoglycan

polysaccharide, protein, slime, adhere, dehydration, immune

Capsule
● Sticky layer of _____________ or ______ that surrounds the cell wall
○ If it is not dense and well-defined, it is called a _____ layer
● Enable prokaryotes to ______ to their substrate or to other individuals in a colony
● Protect against _________, shield pathogenic prokaryotes from host’s ______ system

resistant, boiling, dormant, viable

Endospore
● _________ cells that are developed when bacteria lack water or essential nutrients

● Most are so durable that they can survive in _______ water
○ To kill them requires heating lab equipment to 121°C under high pressure

● In less hostile environment endospores remain _______ and _____ for centuries
○ Can rehydrate and resume metabolism once environment improves

chromosome, multilayered, water, metabolism, lyses

Endospore Process
1. Original cell produces a copy of its _________ and surrounds that copy with a __________ structure which forms it
2. ____ is removed from endospore and its _________ halts
3. Original cell ____ and releases the endospore

fimbria, hairlike, shorter, numerous, pili, sex

Fimbriae
● Singular: _______
● _______ appendages that help prokaryotes stick to substrate
○ Neisseria gonorrhoeae uses fimbriae to fasten itself to the mucous membranes of its host
● Usually _______ and more _______ than ___
○ Singular: pilus
○ Pili are appendages that pull two cells together prior to DNA transfer from one cell to another
○ Sometimes referred to as ___ pili

Motility

1. Taxis
2. Flagella

stimulus, half

Taxis
● From Greek taxis, to arrange
● Directed movement toward or away from a
________
● About ___ of all prokaryotes are capable of
this
● Some species can move at velocities
exceeding 50 μm/sec (up to 50x their body length/sec)

Chemotaxis

➔ Change of movement pattern in
response to chemicals

Positive chemotaxis

move toward nutrients or oxygen

Negative chemotaxis

move away from a toxic substances

flagellum, common, scattered, concentrated, plasma, composition, propulsion, proteins, analogous

Flagella
● Singular: ________
● Most ________ motility structure
● May be ________ over the entire surface of the cell or ________ at one or both ends
● Differ from eukaryotic flagella
○ Are 1/10 the width of eukaryotic flagella
○ Not covered by an extension of the ________ membrane
○ Differ in molecular ________ and mechanical ________
■ Bacterial and archaeal flagella are similar in size and rotational mechanism but have different and unrelated ________

● Are ________ structures because they perform similar functions but not related by common descent

motor, hook, filament, stepwise, secretory

Evolutionary Origins of Bacterial Flagella
● Have 3 main parts: ________, ________, ________ and are composed of 42 different kinds of proteins
● Originated from simpler structures that were modified in a ________ fashion over time

● Bacterial genome analysis indicates only half of the flagellum’s protein appears to be necessary for its function
○ 19/21 proteins are modified versions of proteins that perform other tasks in bacteria
○ 10 proteins in the motor is homologous to 10 similar proteins in secretory system
○ Proteins that comprise rod, hook, and filament are all related to each other and descend from an ancestral protein that formed a pilus-like tube

● Suggest that bacterial flagellum evolved as other proteins were added to an ancestral ________ system

Examptation

➔ Process in which structures originally adapted for one function take on new functions through descent with modification

Internal Organization & DNA

Prokaryotic cells are simpler than those of eukaryotes in internal structure and physical arrangement of DNA

1. Membranes
2. Genome

compartmentalization, metabolic, infoldings, proteins

Membranes
● Lack complex ________________ associated with membrane-enclosed organelles
● Have specialized membranes that perform ___________ functions
○ Usually ___________ of the plasma membrane
1. Respiratory membrane
2. Thylakoid membrane

● Some prokaryotes can store metabolic by-products in simple compartments made of ________
○ Non-membranous

Respiratory membrane

- aerobic prokaryote
- reminiscent of the cristae of mitochondria

Thylakoid membrane

- photosynthetic prokaryote (cyanobacteria)
- function like chloroplasts

DNA, circular, nucleoid, plasmids

Genome
● Structurally different from eukaryotic genome and has considerably less ____
● Only have 1 ________ chromosome vs several linear chromosomes in eukaryotes and has fewer proteins
● Lacks a nucleus; their chromosome is located in the _______
● Have much smaller rings of independently-replicating DNA called _______ (mostly carrying only a few weeks)

Nucleoid

○ A region of cytoplasm that is not enclosed by a membrane

Plasmid

○ a genetic structure in a cell that can replicate independently of the chromosomes

smaller, erythromycin, tetracycline

Genome
● DNA replication, transcription, and translation are fundamentally the same but slightly differ

○ Prokaryotic ribosomes are slightly _______ and differ in protein and RNA content
○ Allows for certain antibiotics (_______ and _______) to bind to ribosomes to block protein synthesis in prokaryotes but not eukaryotes

1-3, small, binary, generation

Reproduction
● Under optimal conditions: divide every ___ hours (some in 20 minutes)
● Eventually exhaust their nutrient supply, poison themselves with metabolic waste, face competition, or consumed
● The potential of many prokaryotes for rapid population growth highlights:
1. Are _______
2. Reproduce by _______ fission
3. Often have short _______ times

Binary Fission

➔ Single prokaryote divides into 2 cells, then divides into 4, 8, 16, and so on

Genetic Diversity

1. Rapid Reproduction and Mutation
2. Genetic Recombination

Rapid Reproduction and Mutation

1. Sexually reproducing species
2. Asexually reproducing species

meiosis, fertilization

Sexually reproducing species
● Genetic variation results from recombination of alleles during _______ and _______

rapid, mutation

Asexually reproducing species
● Genetic variation results from combination of ______ reproduction and _______

1. Prokaryote (binary fission)
2. E. coli gene

identical, errors

Prokaryote reproducing by binary fission
○ After repeated rounds of division, most offspring cells are genetically _______
○ If _____ (insertions, deletions, base-pair substitutions) occur during DNA replication, some offspring cells may differ genetically

spontaneous, 10 million

E. coli gene
○ Probability of _________ mutation from errors in DNA replication found in 1 in ___ _______ (1x10−7) per cell division
○ Among 2x1010 new E. coli cells that arise each day in an intestine, there will be (2x1010) x (1x10−7) = 2,000 bacteria with a mutation in that gene
○ If E. coli has 4,300 genes, the total number of mutations is 4,300 x 2,000 = 8.6M per day per intestine

increase, generation, populations, highly

Asexually reproducing species
● Even if new mutations are rare, genetic diversity can quickly ________ in species with short _________ times and large __________
○ Can lead to rapid evolution – better-equipped individuals tend survive and reproduce more prolifically
○ Prokaryotes are not “primitive” or “inferior” because they are simple in structure. They are _____ evolved (with 3.5 billion years of evolution behind them)

2, horizontal gene transfer

Genetic Recombination
● Combination of DNA from __ sources
● Cause for additional diversity aside from
mutations
● ___________________ - movement of
gene from one organism to another (different
species)
● There is evidence that these mechanisms can
transfer DNA within and between domain Bacteria and domain Archaea

Eukaryotes

Genetic Recombination
1. Meiosis
2. Fertilization

Prokaryotes

Genetic Recombination
1. Transformation
2. Transduction
3. Conjugation

foreign DNA

Transformation
- genotype and possibly phenotype of prokaryotic cell are altered by uptake of ________ ____ from its surroundings

recognize, recombinant

Transformation
● Bacteria have cell-surface proteins that ________ DNA from closely related species and transport it into the cell
● Ex. Harmless Streptococcus pneumoniae can be transformed into pneumonia-causing cells if the cells are placed in a medium containing DNA from a pathogenic strain
○ Nonpathogenic cell takes up a piece of DNA carrying the allele for pathogenicity and replaces its own allele with the foreign allele (exchange of homologous DNA segments)
○ Cell is now a __________ – its chromosome contains DNA derived from two different cells

bacteriophages

Transduction
- phages aka ____________ (viruses that infect bacteria) carry prokaryotic genes from one host cell to another

accidents, phage replicative cycle, recombinant

Transduction
● Results from ________ that occur during the ____________________
● Virus may not be able to replicate (because of lacking genetic material)

○ Virus can attach to another prokaryotic cell (recipient) and inject prokaryotic DNA acquired from the first cell (donor)
○ If this injected DNA is incorporated into the recipient cell’s chromosome, a ________ cell is formed

prokaryotic, one

Conjugation
- DNA is transferred between two _________ cells (usually of the same species) that are temporarily joined
● In bacteria – DNA transfer is always ____-way (donate and receive)
○ Ex. In E. coli , a pilus of the donor cell attaches to the recipient. The two cells are pulled together. A bridge is formed through which the donor transfers DNA.
■ *This is still being studied.
■ Another possibility: DNA
passes through the hollow pilus

F factor

- piece of DNA that enables cell to form pili and donate DNA during conjugation
● Around 25 genes
● Can exist as a plasmid or as a segment of
DNA within the bacterial chromosome

F factor as Plasmid

a. Cells containing the F plasmid (F+ cells) function as DNA donors during conjugation

b. Cells without the F plasmid (F- cells) function as DNA recipients during conjugation

c. F+ condition is transferable
- F+ converts an F - cell to F+ if a copy of the entire F + plasmid is transferred

F factor in the Chromosome

a. Chromosomal genes can be transferred during conjugation when donor cell’s F factor is integrated into the chromosome

b. Hfr cell (high frequency of recombination) – cell with F factor built into its chromosome
i. Functions as donor during conjugation with an F- cell
ii. When chromosomal DNA (from Hfr cell) enters F- cell, homologous regions of the two chromosomes align, allowing segments of their DNA to be exchanged
iii. Recombinant cell is formed (genes derive from two
different cells)

R Plasmids and Antibiotic Resistance

a. 1950s: antibiotic resistance (bacterial dysentery) found in Japan

b. Mutation in a chromosomal gene of a pathogen can confer resistance
i. Mutation in a gene may make it less likely that the pathogen will transport a specific antibiotic into its cell
ii. Mutation may alter the intracellular target protein for an antibiotic, reducing inhibitory effect

c. Bacteria can have “resistance genes” – code for enzymes that specifically destroy or hinder antibiotics
i. Carried by R plasmids (R for resistance)

d. Natural selection would cause bacteria with resistance genes to increase

e. Medical consequences: treatment of bacterial infections becomes more difficult
i. R plasmids also have genes that encode pili and enable DNA transfer by conjugation (like F plasmids)
ii. R plasmids carry as many as 10 genes for antibiotic resistance

Nutritional & Metabolic Adaptations

1. Oxygen Metabolism
2. Nitrogen Metabolism
3. Metabolic Cooperation

obtain, energy

Nutritional & Metabolic Adaptations
● Genetic variation in prokaryotes has resulted in diversity in nutritional adaptation
● Prokaryotes can be categorized by how they _______ _____

Phototrophs

Obtain energy from light

Chemotrophs

Obtain energy from chemicals

Autotrophs

Need only CO2/related compounds as a carbon source
1. Photoautotrophs
2. Chemoautotrophs

Photoautotrophs

Energy source: Light
Carbon source: CO2, HCO3- or related compound
Organisms: Cyanobacteria, plants, certain protists (algae)

Chemoautotrophs

Energy source: Inorganic chemicals (H2S, NH3, Fe2+)
Carbon source: CO2, HCO3- or related compound
Organisms: Unique to certain prokaryotes (Sulfolobus)

Heterotrophs

require at least one organic nutrient such as glucose to make other organic compounds
1. Photoheterotroph
2. Chemoheterotroph

Photoheterotroph

Energy source: Light
Carbon source: Organic compounds
Organisms: Aquatic and salt-loving prokaryotes (Rhodobacter chloroflexus)

Chemoheterotroph

Energy source: Organic compounds
Carbon source: Organic compounds
Organisms: Many prokaryotes, protists, fungi, animals, some plants

Oxygen Metabolism

- Prokaryotic metabolism varies with respect to Oxygen (O2)
1. Obligate aerobes
2. Obligate anaerobes
3. Facultative anaerobes

Obligate aerobes

a. Use O2 for cellular respiration; die without oxygen

Obligate anaerobes

a. Poisoned by O2
b. Some live exclusively by fermentation
c. Some extract chemical energy by anaerobic respiration, where nitrate ions (NO −) or sulfate ions (SO42-) 3 replace O2 in electron transport chain

Facultative anaerobes

a. Use O2 if present but can use fermentation and anaerobic respiration

amino, nucleic

Nitrogen Metabolism
● Nitrogen is essential for the production of _____ acids and ______ acids.
● Prokaryotes can metabolize nitrogen in many forms

Nitrogen fixation

- conversion of atmospheric nitrogen (N2) to ammonia (NH3)

cyanobacteria, methanogens, amino acids, plants

Nitrogen fixation
○ Carried out by some ________ and some _________ (group of archaea)
○ NH3 is incorporated into ______ _____ and other organic molecules
○ Has a large impact on other organisms, such as increasing nitrogen available for ______

Metabolic Cooperation

● Some prokaryotic cells cooperate to utilize environmental resources they could not previously use as individual cells.
1. Cooperation between same species
2. Cooperation between different species

Anabaena, photosynthesis, nitrogen fixation, filamentous chains, heterocysts

Cooperation between same species
● Ex. cyanobacterium: __________
○ Has genes for both ___________ and _______ ______
○ Single cell cannot carry out both processes simultaneously, as O2 from photosynthesis inactivates enzymes in nitrogen fixation
○ Anabaena forms _________ ______, which have numerous photosynthetic cells, and select cells that specialize in nitrogen fixation called ________
○ Heterocysts are surrounded by thickened cell walls which restrict entry of O2
○ Intracellular connections allow transport of nitrogen from heterocysts and carbohydrates from photosynthetic cells

biofilms, signaling, capsule, channels

Cooperation between different species
● Occurs in surface-coating colonies called _______
○ Cells in biofilms secrete ________ molecules that recruit nearby cells
○ Cells also produce polysaccharides and proteins (which form the cell _______ or slime layer) that stick the cells to the substrate and one another
○ _______ allow nutrients to reach the interior and wastes to be expelled
○ Can cause problems by contaminating industrial products and medical equipment; also contribute to tooth decay and more serious health problems

aggregates, sulfate, methane

Cooperation between different species
● Can also occur in ball-shaped _________ on ocean floor
○ Formed by _____-consuming bacteria coexisting with _______-consuming archaea
○ Bacteria use archaea’s waste products, such as organic compounds and hydrogen
○ Archaea use sulfur compounds that bacteria produce as oxidizing agents when they consume methane
○ Archaea consume 300 billion kg of methane, a greenhouse gas, in a year

Diverse Lineages

1. Prokaryotic Diversity
2. Archaea Diversity
3. Bacteria Diversity

Carl Woese

- concluded using small-subunit ribosomal RNA that Archaea, which were previously classified as bacteria, were actually more related to eukaryotes and had a domain of its own

Cyanobacteria

- monophyletic (descended from a common evolutionary ancestor or ancestral group, especially one not shared with any other group)

Gram-negative Bacteria

spread throughout several lineages

Genetic Prospecting

- use of PCR to analyze prokaryotic genes from the environment (e.g. soil and water samples)
○ Prokaryotic genomes can be obtained from the environment through metagenomics

metagenomics

is the study of genetic material recovered directly from environmental samples

Horizontal Gene Transfer

- prokaryotes acquire genes from even distantly related species; can make it difficult to determine the root of the tree of

Three Domains of Life

1. Bacteria
2. Archaea
3. Eukarya

Absent

Bacteria
nuclear envelope

Absent

Archaea
nuclear envelope

Present

Eukarya
nuclear envelope

Absent

Bacteria
Membrane-enclosed organelles

Absent

Archaea
Membrane-enclosed organelles

Present

Eukarya
Membrane-enclosed organelles

Present

Bacteria
Peptidoglycan in cell wall

Absent

Archaea
Peptidoglycan in cell wall
(made up of polysaccharides and proteins)

Absent

Eukarya
Peptidoglycan in cell wall
(cell wall present in plants and fungi)

Unbranched hydrocarbons

Bacteria
Membrane lipids
(glycerol-ester lipids)
- bond: sn-glycerol-3-phosphate
- straight chains fatty acids
- lipid bilayer

Some branched hydrocarbons

Archaea
Membrane lipids
(glycerol-ether lipids)
- bond: sn-glycerol-1-phosphate
- isoprenoid chains with multiple side branches/rings
- lipid monolayer (responsible for providing rigidity and added protection in extreme conditions)