Module 4: Microbiology Flashcards
Microbes make up ____ the biomass on Earth
half
Where is the chromosome of a prokaryotic cell found
Nucleoid
What is the order of layers of a prokaryotic cell (inside to out)
Plasma membrane, cell wall, glycocalyx
What shapes can bacteria be
Cocci, rods, spirals
What is the function of a prokaryotic cell membrane
Cell regulation
What is the function of a prokaryotic cell wall
Cell integrity, shape, strength, prevent desiccation, osmotic lysis
What is the purpose of the glycocalyx
Extracellular: cell protection
Do archaea have peptidoglycan cell walls
No
Describe the bacterial genome and its location
One circular chromosome restricted to an area known as the nucleoid, and plasmids in the cytosol
What are plasmids
Small circular self replicating DNA molecules found in the cytosol
What are prokaryotes that lack cell walls called
Mycoplasmas (group of pathogenic bacteria)
Describe the structure of peptidoglycan
NAM-NAG sugar chains cross linked laterally by amino acid chains and vertically by amino acid side chains
What is the enzyme that cross links NAM-NAG sugar chains and amino acid chains
Transpeptidase
What are the most common gram stain reference bacteria
Staphylococcus aureus (gram positive) and escherichia coli (gram negative)
What colour are gram positive bacteria stained
Purple
What colour are gram negative bacteria stained
Red/pink
What are the four steps of the gram stain procedure
Application of crystal violet (purple dye), application of iodine (mordant), alcohol wash (decolourisation), application of safranin (counterstain)
Describe the structure of a gram positive bacterial cell wall
Thick peptidoglycan layer makes up the cell wall, plasma membrane underneath
Why do gram positive bacterial cells retain the crystal violet
Peptidoglycan traps violet, masks red
How thick is the peptidoglycan layer of gram positive bacteria
THICK: 20-80 nm
Describe the structure of a gram negative bacterial cell wall
Thin peptidoglycan layer and outer membrane make up the cell wall, plasma membrane underneath
Why do gram negative bacterial cells not retain the crystal violet
It is easily rinsed away, revealing red safranin dye
How thick is the peptidoglycan layer of gram negative bacteria
THIN: 5-10 nm (between two plasma membranes)
What does the gram negative bacterial outer membrane have that gram positive doesn’t
Carbohydrate portion: lipopolysaccharide
What are flagella made of
Flagellin protein
What is the diameter of flagella
10-20 nm
How many flagella per cell
5-10
How do flagella work
Act like propeller, cell rotates them to move through liquid medium
Chemotaxis
Bacteria move along a concentration gradient towards a chemical attractant (positive) or away from a chemical repellent (negative)
Function of fimbriae (can also be called adherence pili or adhesins)
Structures with adhesive properties that cause bacteria to stick/adhere to surfaces
What is the diameter of pili
2-8 nm
How long are pili
1µm
How many pili per cell
100-1000
Difference between fimbriae and pili
Fimbriae are for adhesion to surfaces, pili are for attachment to other bacteria
Purpose of a sex pilus
Horizontal gene transfer (conjugation)
What are the two forms of glycocalyx
Capsule (organised), slime layer (disorganised without cell shape, attached loosely to cell wall)
What is the glycocalyx
A gelatinous polysaccharide and/or polypeptide outer covering of a bacteria
Function of capsules
Virulence factors: evade immune system, protection from phagocytosis and engulfment by immune cells. Prevent cell from drying out (desiccation)
What is a bacterial endospore
Highly differentiated cells resistant to heat, harsh chemicals, antibiotics, disinfectants and radiation. Enable bacteria to stay dormant for a very long time
What cells have endospores
Some types of gram positive bacteria
Why do bacterial endospores form
Formed during unfavourable growth conditions to protect cells from stress, germinate under favourable conditions
Why are prokaryotes so dominant
Because they evolve so fast due to fast growth rate (exponential), have existed for so long so colonised most habitats resulting in extreme ecological and metabolic diversity
What does colonially pure mean
All cells identical
What is binary fission
The process of one cell becoming two (asexual)
Outline the process of binary fission
DNA replication (one origin of replication), two origins move to cell poles, two cells differentiate
What is a closed batch culture system
Defined (limited) supply of nutrients provided, once used cells cannot proliferate
What are the 4 stages of microbial growth in a closed batch system
Lag, exponential, stationary, death
Describe the lag phase
Time taken to get biosynthetic reactions running
Describe the log phase
Cells are actively dividing and nothing is limiting for growth. Population is doubling in a constant time interval under ideal conditions
Describe the stationary phase
Cells stop growing and cryptic growth is observed, equilibrium between growing and dying cells
What is cryptic growth
When organisms survive by consuming lysed cell constituents of other dead cells within the culture
Describe the death phase
Equilibrium between growing and dying cells is skewed toward death
What do batch culture assays measure
The average behaviour of cells
What do prokaryotes need to multiply
Carbon source, energy source (electrons to power anabolic and catabolic reactions), reducing power (carriers of electrons (NAD+, NADP+))
Catabolism
Breakdown: energy generation
Anabolism
Build up: energy consumption
Photoautotroph (plants, algae, cyanobacteria, green and purple sulfur bacteria)
Light energy source, inorganic carbon source
Photoheterotroph (green and purple non sulfur bacteria)
Light energy source, organic carbon source
Chemoautotroph (hydrogen, sulfur and nitrifying bacteria)
Chemical energy source, inorganic carbon source
Chemoheterotroph (animals, fungi, protozoa)
Chemical energy source, organic carbon source
What is a wild type strain
Bacteria with all essential genes, can grow by itself and be isolated in pure culture
What is an auxotroph (98% of microorganisms sequenced lack essential pathways for synthesis of amino acids)
Bacteria lacking or defective in one or more essential genes, cannot grow unless missing factor supplied
What is cross feeding (also known as syntrophy)
When one species gains metabolic products of another species. Can benefit one or both species
Microbiome definition
The complete collection of microorganisms and their genes within a particular environment
Microbiota definition
Individual microbial species in a biome- bacteria, fungi, archaea and viruses
Opposite of being dependent on others
Autonomy
Culture dependent methods pros
Access to phenotype, can study one organism at a time, can manipulate conditions to see response of organism
Culture dependent methods cons
Not all organisms can be cultured, too many species to grow them all, culturing requires precise conditions to match microbes needs, doesn’t match real world conditions
Culture independent methods pros
Allows access to genotype, can study many organisms at a time, shows communities as they are in nature, can target non-culturable organisms, provides access to unknown information/species
Culture independent methods cons
No pure culture so no ability to manipulate, expensive and complex
What is a culture dependent method
Culturing of microbes in lab, uses pure cultures or simple (reduced diversity) enrichments
What is a culture independent method
Relies on nucleic acid based methods, uses sequencing or metabolic profiling to study all microbes in a sample
What is microbial ecology
The field of study focused on the relationship between microbes and their environment (interrelationships among organisms and their environment)
What is a microbial population
Individual microbial cells of a species proliferated
What is a microbial community
Interaction of populations of microbes
Anabolism and catabolism must be
Coupled (harvesting of building blocks = harvesting of energy)
For every oxidation reaction in the body there must be
An equal and opposite reduction
What are the electron carriers in the body
NAD+ and NADP+ (NADH and NADPH when they have electrons)
Facilitate redox reactions without being consumed
Photoautotroph
Light energy source, inorganic carbon source
e.g plants
Chemoautotroph
Chemical energy source, inorganic carbon source
e.g hydrogen, sulfur and nitrifying bacteria
Photoheterotroph
Light energy source, organic carbon source
e.g green and purple non sulfur bacteria
Chemoheterotroph
Chemical energy source, organic carbon source
e.g animals, fungi, protozoa
Decomposers are
Heterotrophs (reliant on primary producers)
Primary producers are
Autotrophs (fix CO2)
Chemical energy source examples
Glucose: organic, H2S: inorganic