exam 1 (bacteria and archaea) Flashcards
The Prokaryotes (bacteria and archaea)
• The oldest organisms on earth
• The only inhabitants of earth for >1.5 billion yrs.
• Represent 2 of the 3 Domains of life
• The smallest organisms (0.5-5 um) not counting
viruses
• First discovered in late 1600s
• Probably the most diverse and abundant organisms
on earth, and may make up the highest biomass
• “Microbial dark matter.” Perhaps the least is known
about these organisms (estimated that 99% have
yet to be discovered). Recently discovered 30 new
phyla.
• Highly adaptable—Found in virtually all
environments on earth, rapidly evolve
• Found in extreme environments where no other
organisms can live (extreme salinity, heat, pH
Ecological and Human Impacts
- Decomposers and recyclers of nutrients
- Only organisms that fix, “release”
nitrogen - Release oxygen to atmosphere
- Symbiotic relationships—mutualists,
parasites
– Human microbiome—30-50 trillion bacteria! - Pathogens—cause disease, damage
crops - Important model research organisms
- Can be genetically engineered to
manufacture useful products - Breakdown pollutants, produce food,
Prokaryote Structure and Function
• Most are unicellular, some aggregate in colonies 1. Cellular shapes 2. Internal structure 3. Cell surface structure
The 3 common cellular shapes
(a) Spherical (b) Rod-shaped (c) Spiral
Internal Structure
• Simple, when compared to eukaryotic cells
• Lack well-formed organelles, but carry out
the functions of eukaryotic organelles
• Some have internal membranes
The Prokaryote Genome
• Less DNA, fewer genes than eukaryotes • Usually a single circular chromosome in a nucleoid region • Many also can have small rings of DNA called plasmids (sometimes used in vectors in gene transfer, genetic engineering)
Cell Wall
• Main functions—protective, maintains shape
• Composition of bacteria and archaea cell walls is each
unique and different from the cell walls of plants and
fungi (animal cells lack cell walls)
• Bacteria
– 2 main types, composed mainly of peptidoglycan
(amino acids and sugar polymers complexed
together)
– Staining distinguishes “gram-positive” and “gramnegative” types (important in clinical settings)
• Archaea
– Lack peptidoglycan, have proteins and
polysaccharides
Gram staining—basic method
- Stained with crystal violet and iodine
- Rinsed in alcohol
- Stained with safranin a red dye
Color change has to do with thickness of the
cell wall
Gram – vs. Gram +
• Gram –
– Most pathogenic bacteria (not all gram –
bacteria are pathogenic)
– Outer membrane can be toxic, protective
– Higher resistance to antibiotics, drugs
• Gram +
– Some can be pathogenic, resistant
• Penicillin is an antibiotic that disrupts
bacterial cell walls by attacking
peptidoglycan (most effective on gram +
bacteria)
• Some bacteria have an outer capsule of
protein or polysaccharide or a “slime
layer” that has a sticky quality
– Protective
– Allows bacteria to stick to a substrate
Other structures of attachment
• Fimbriae (shown below)—protein shafts
– Help bind to substrate, other bacteria, or host
cells
• Pilus (pili), sex pili—longer, fewer
– Attach between 2 bacteria during DNA transfer
Motility
• Some bacteria and archaea are capable of
directional movement toward or away
from some stimulus (taxis) by using
flagella
– Chemotaxis
• Bacterial, archaeal, and eukaryotic flagella
are different structurally from each other
Reproduction
• A key feature of prokaryote biology • Prokaryotes reproduce asexually by binary fission • Under certain conditions, may develop endospores • Prokaryotes are noted for having very short generation times • Population sizes can be enormous (trillions)
Endospores
• In response to changing environment – Tough protein coat develops – Metabolism shuts down – Dehydrates • Adaptive? • Can survive extreme heat, freezing, drying for very long periods
Although prokaryotes are asexual, they are
extremely adaptable
• What do we mean when we say an organism is
adaptable?
• But without sex, how can they adapt?
• Prokaryotic traits that contribute to adaptability:
– High genetic diversity—How?
• Forms of genetic recombination
– Short generation times, rapid reproduction
– Very large populations
– High, and perhaps variable, mutation rates—
approximately 1,000x more mutations/gene/unit
time/individual than eukaryotes
• Thus, they have a high capacity to adapt (evolve)
rapidly in response to environmental change (e.g.
become resistant to antibiotics)
Can prokaryotes evolve rapidly in
response to environmental change?
• Experimental study by Cooper and Lenski (just one
example of many studies)
• Founded 12 populations of E. coli
• Been running for 30 years
• Serial transfer each day
• Grew in suboptimal media (a “selective”
environment)
• Periodically grew in competition with ancestral
population in the suboptimal environment
• Assessed relative fitness by measuring rate at which
each population grew
• Conclusion?
Example of a long term study
• Cooper’s lab has continued these experiments since 1988, for over 50,000 generations (started with 1 cell) • Rapid evolutionary change (an adaptive change) early, slows down but does not cease with time • Mutations allowed continued adaptation over this long period of time
Factors that Promote Adaptability
and Genetic Diversity
1. Rapid reproduction, short generation times 2. Mutation rate 3. Genetic recombination – What is genetic recombination and how does it relate to genetic diversity? – The combining of DNA from 2 sources – When recombination occurs between species (genomes) it is a type of horizontal (lateral) gene transfer (HGT)
Sources of Genetic Recombination
(within and between species in
Prokaryotes):
1. Transformation – can take up DNA from their surroundings 2. Transduction – viruses act as a vector to transfer genes from one individual to another 3. Conjugation – a one-way transfer of genes from one individual to another (sex pilus)
Nutritional and Metabolic Adaptations:
All types of nutrition are found in
prokaryotes
Terminology relating to an organism’s energy and carbon source: 1. Phototrophs (energy from light) 2. Chemotrophs (energy from chemicals) 3. Autotrophs (carbon from inorganics) 4. Heterotrophs (carbon from organics) Combining energy and carbon sources gives 4 modes of nutrition
The need for oxygen is variable and
dependent on metabolic requirements
1. Aerobes—require oxygen for cellular respiration • Obligate 2. Anaerobes—do not require oxygen • Obligate • Facultative
Nitrogen and Metabolism
Nitrogen and Metabolism
• Why is nitrogen important to all
organisms?
• Because it is required to synthesize amino
acids for proteins, coenzymes, and nucleic
acids
• Availability of N for eukaryotes is limited
even though our atmosphere is 79% N2
• Natural sources are few; it is commonly
the limiting nutrient for plants
• Life depends on prokaryotes to make N
available by nitrogen fixation and
Nitrogen Fixation
• The process of reducing atmospheric N2 to NH3 (ammonia) • NH3 ionizes to NH4 \+ (ammonium) • Only prokaryotes (some bacteria and archaea) can carry out this process
Nitrification
• Many organisms (including plants and animals) cannot utilize ammonia or ammonium • Hence, other prokaryotes that carry out nitrification (nitrifying bacteria) are essential • Convert ammonium (NH4 \+) into nitrate (NO3-) or nitrite (NO2-)
Biofilms—Another form of metabolic
cooperation
• A community of prokaryotes and, sometimes,
yeasts and protists
• Natural (e.g. aquatic envs.), hospital, inside
organisms (e.g. mouth, heart, respiratory,
middle ear) and industrial examples are
common
• These communities undergo “ecological
succession”
• Complex interactions between species
Sociality, “multicellularity” in bacteria:
Quorum sensing
• A communication system, decision making
process among bacteria that is a function of
density
• Chemical signals are received (from same or
different species) that alter gene expression
• Can affect: biofilm formation, antibiotic
resistance, virulence, cell division, motility,
aggregation
Human Intestinal Bacteria: A developing
story
• Live in large intestine—just one part of the human microbiome
• Over 500 species (also fungi, archaea present)
• Species composition varies with individual, age, health, diet,
geography
• Help digest food, absorb nutrients, contribute key nutrients
• Help protect from pathogenic bacteria
• Affect immune system development
• Play a role in inhibiting autoimmune diseases, allergic reactions,
inflammatory reactions
• Alleviate, protect from inflammatory bowel diseases, colon
cancer
• Species composition related to heart disease, atherosclerosis,
obesity
• Translocations, probiotics
Archaea
• Distinguished in 1977
• Live in extreme (extremophiles) and
moderate environments
• Chemoautotrophs and chemoheterotrophs
