L1: Phylogeny and Morphology of Bacteria Flashcards
What is the traditional definition of a prokaryotes in terms of: Chromosome number: Chromsome ploidy: Chromosome shape: Nuclear membrane presence: Mitosis occurrence: Ribosome size: Mitochondria, ER presence: Phagocytosis occurring: Sterols in membrane:
Chromosome number: 1 Chromsome ploidy: Haploid Chromosome shape: Circular Nuclear membrane presence: No Mitosis occurrence: No Ribosome size: 70S Mitochondria, ER presence: No Phagocytosis occurring: No Sterols in membrane: No
What is the traditional definition of eukaryotes in terms of: Chromosome number: Chromsome ploidy: Chromosome shape: Nuclear membrane presence: Mitosis occurrence: Ribosome size: Mitochondria, ER presence: Phagocytosis occurring: Sterols in membrane:
Chromosome number: >1 Chromsome ploidy: Dipoid or higher Chromosome shape: Linear Nuclear membrane presence: Yes Mitosis occurrence: Yes Ribosome size: 80S Mitochondria, ER presence: Yes Phagocytosis occurring: Yes Sterols in membrane: Yes
What problems have arisen with the traditional definition of prokaryotes? (4)
- Many bacteria have >1 chromosome
- Ploidy is variable based on growth rate
- Many bacteria have linear chromosomes
- Shouldn’t use negatives to define a category
What is the only remaining defining feature of bacteria?
Ribosome size
What is the ribosome made of?
What does this mean for defining bacteria?
What does this mean for evolution?
RNA
Differences between pro and euk are differences in RNA composition.
Can use nucleotide sequencing to determine the evolutionary relationships of all organisms
Using recent analysis, what has the traditional all-encompassing kingdom of prokaryotes been split into?
(Eu)Bacteria
Archaea
All known human bacterial pathogens are from what domain of prokaryotes?
Eubacteria
All of the kingdoms of eukaryotes have been united into what?
Eukarya domain
Which has more subdivisions, eukarya or the two prokaryotic domains?
What does this mean?
Two prokaryotic domains
Bacteria are more diverse than eukaryotes
The genomes of chloroplast and mitochondria are related to many bacterial species, suggesting what?
That the endosymbiotic theory of eukaryotic cellular evolution is correct.
Do the vast majority of bacteria have any impact on humans?
No
Bacteria are critical for what two things? (2)
- Recycling of environmental materials
2. Maintaining a healthy environment
Can bacteria be domesticated?
Yes such as in fermentation of alcohol
Of the few bacteria that interact with humans, are most harmful, harmless, and/or beneficial?
Harmless or beneficial
These bacteria that are harmless or beneficial to humans are called what?
Natural flora
In the human body, how do the cell numbers of human cells and bacterial cells compare?
10X more bacterial cells than human cells in human body.
In the human body, how do gene numbers of human genes and bacterial genes compare?
100X more bacterial genes than human genes in body.
What is the rigidity of the bacterial cell wall due to?
Peptidoglycan
Which is the first big stain to use when determining bacteria?
Gram stain
The gram stain separates cells based on what?
Being either Gram positive or Gram negative which is based on their cell wall architecture
Relatively speaking, how many bacteria have peptidoglycan in their walls?
Nearly all
What does a peptidoglycan consist of?
- Peptide: Amino acids
2. Glycan: sugars
The glycan portion of peptidoglycan consists of what? (2)
- N-acetylglucosamine (NAG)
2. N-acetyl-muramic acid (NAM)
What are the two exceptions to bacteria with peptidoglycan in their cell walls?
- Mycoplasma
2. L-Forms
Describe the organization of the sugars in peptidoglycan?
Alternating NAG and NAM
Describe the organization of peptide in peptidoglycan.
A chain of mixed D- and L- amino acids attached to NAM with a di-amino acid in the third to last position and ending with D-ala-D-ala.
what is a di-amino acid? (2)
- lysine
2. diaminopimilic acid
Is the composition of the D- and L- amino acids always the same for bacterial peptidoglycan?
No, varies by species
How does cross linking occur between peptides of the same peptidoglycan?
The penultimate D-ala of one peptide chain joins with diamino acid of another which causes deletion of the terminal D-ala of the first.
Does the peptide bridge vary much?
Yes, from direct linkage between the two peptides to several amino acids
What allows for the crosslinking between glycan chains?
The peptide chain flexibility
Purpose of crosslinking of peptidoglycans?
Formation of meshwork that provides tensile strength necessary to (1) restrain the cytoplasm and (2) give the cell shape.
What pressure does crosslinking try to combat?
Turgor pressure
Gram positive cell walls have what 3 main features?
- Thick (up to 30 layers) of peptidoglycan externally
- Wall- and lipo-techoic acids
- Integral membrane proteins
Is PTG permeable?
Yes
Which have a higher internal osmotic pressure, gram positive or gram negative bacteria?
Gram positive
In layman’s terms, what are wall- and lipo-techoic acids?
Repeating sugar phosphate chains
Function of wall-and lipo-techoic acids?
Give cell negative charge in order to attract positive charges adding strength to the wall
Do gram-negative cells have wall- and lipo-techoic acid?
No
3 components of gram-negative cell wall?
- Outer membrane
- Thin peptidoglycan layer
- Peri-plasm separating inner and outer membranes and contains the peptidoglycan and proteins for processing solutes
What does the outer membrane act as for gram-negative bacteria?
Permeability barrier
The outer membrane of gram-negative bacteria consists of what four parts?
- Phospholipids like those in inner membrane
- Lipoproteins: Attach PTG layer to Outer
- Porins: Allow some diffusion
- Lipopolysaccharide
What are the 4 parts of lipopolysaccharide?
- O-antigen
- Core polysaccharide
- Disaccharide diphosphate
- Fatty acids
Together, the disaccharide diphosphate and fatty acids of LPS make up what?
Lipid A
Lipid A of LPS is known as what?
Endotoxin
Result of Endotoxin in the blood?
Fever, shock, and death during gram-negative infections
The O-Antigen has what significance in immunology?
It is a major antigenic determinant and is used to characterize bacteria
What are the five steps of a gram stain.
- Fixation
- Crystal violet
- Iodine treatment
- Decolorization
- Counter stain of safranin
What is the key step of a gram stain?
Decolorization step
How does decolorization affect both gram positive and gram negative?
Gram positive: Dehydrates the PTG thus trapping the stain
Gram negative: Strips the outer membrane from the cell allowing the primary stain to escape
Mycoplasma stain what?
Gram negative even though they are closer to Gram-positive since they dispensed with a cell wall
What color is gram positive?
Purple
what color is gram negative?
Pink
Describe the set up of a mycobacterial cell wall
Gram positive cell wall with an outer membrane that is NOT similar to a gram negative OM.
Mycobacterial cell wall consists of what 3 things?
- Thick peptidoglycan layer
- Arabinogalactan (sugar) layer
- Mycolic acids/Wax D
What 3 main bacteria don’t have a cell wall
- Mycoplasma
- L-forms
- Domain archaea
What causes mycoplasma to have such a strong membrane?
Sterols
What do archaea have instead of peptidoglycan?
Pseudopeptidoglycan
Why don’t mycobacteria stain well?
Stains can’t penetrate the mycolic acid wax
How does one stain for mycobacteria?
Acid fast stain
What are the steps of the acid fast stain?
- Carbol Fuchsin primary stain steamed in to penetrate the membrane and stian the cells red.
- Acid alcohol leaches the stain out of all cells that are NOT mycobacteria
- Methylene blue counterstains the leached cells
What shape is coccus?
Spherical
What bacteria are in cocci? (5)
- Strep
- Staph
- Pneumococcus
- Gonococcus
- Meningococcus
What shape is bacilli or rod?
Cylindrical
What bacteria are bacilli/rods? 2
anthrax
bacillary dysentery
What shape is coccobacilli?
What bacteria is this?
Small rods
E. coli
What shape is vibrios?
What bacteria is this?
Comma-shaped
Vibrio cholerae
What shape is spirillae?
Spiral-shaped
Which bacteria are spirillae?
Treponemes
Borrelia
What are the four most common organizations of pathogenic bacteria?
And example of each
- Tetrads of cocci: Micrococcus
- Diplococcus (two cocci): Strep pneumoniae
- Streptococcus (cocci in chains): Group A strep
- Staphylococcus (cocci in clusters): S. aureus
Bacterial colonies are most often developed on what?
Agar plate
What is a bacterial colony?
Mass of cells that arise from a single cell
What makes up a flagellum?
Protein
Flagella are responsible for what?
Motility
What direction do flagella move?
Rotary/Propellar-like
Flagellum is actually a polymer of a single protein called?
Flagellin
Can flagellum help bacterial pathogenesis?
Yes!
What is it called if the bacteria only has one flagellum?
Monotrichous
What is it called if the bacteria has many flagellum?
Peritrichous
which is longer, pili or flagellum?
Pili
Which is thicker, pili or flagellum
Flagella
How are pili composed?
Protein subunits of pilin protein
3 functions of pili?
- Attachment to host or other bacterial cells
- Movement (twitching motility)
- Conjugation DNA transfer
What is the other word for pili?
Fimbria
What are the two types of pili and what is each involved in?
- Common pili = attachment
2. sex pili = hollow for conjugation transfer
Define a capsule
Polysaccharide or poly-glutamic acid layer outside of the OM in Gram- bacteria and outside PTG in Gram+ bacteria
What is the general function of a capsule?
Protection from host defenses
What is a slime layer or glycocalyx?
Outer polysaccharide layer that adheres lsess firmly to cells
DIfference between glycocalyx and capsule?
Capsule: Distinct gelatinous layer
Slime: Irregular diffuse layer
Does the chemical structure of glycalyx and capsules differ across different bacteria?
Yes: allows for antigenic characteristics used in determining bacterial strains
Define endospore
Non-replicating resting cell that is highly resistant to environmental stresses
What can an endospore withstand? (4)
- Boiling
- Radiation
- Chemicals
- Drying
Endospores are the result of what?
Program that replaces a vegetative cell with a spore?
Are endospores reproductive spores?
No
How many spores can a mother cell create?
Just one
What will cause a cell to come out of being an endospore?
What is this process called?
If conditions improve (less stress)
Germination
What is the primary reason for sterilization and autoclaving?
Killing spores
Can spores last a long time?
Decades, centuries
Why was canning introduced?
Elimination of spores
All bacteria require what six elements for growth?
CHNOPS
Which element is most useful in distinguishing bacteria?
Carbon
Bacteria capable of direct use of CO2 are called?
Autotrophs
Bacteria that must obtain carbon from organic carbon are called?
Heterotrophs
Bacteria that use light as a source of energy are called?
Phototrophs
Bacteria that use chemicals as a source of energy are called?
Chemoautotroph
Bacteria that use inorganic chemicals are called?
Lithotrophs
Bacteria that use organic chemicals are called?
Organotrophs
All known disease-causing bacteria are what category?
Chemo- and organo-heterotrophs
Two ways bacteria are separated by oxygen?
- Whether O2 is used in metabolism (respiration, fermentation)
- Whether the bacterium can detoxify oxygen
End products of fermentation include? (6)
- lactic acid
- ethanol
- butyric acid
- propionic acid
- 2,3-Butanediol
- Mixed acids
Fermentation products are produced in a series of reactions whose goal is what?
Production of terminal electron acceptors
What is bacterial respiration?
Same as normal biochem except that some bacteria can use other chemicals other than nitrate as the final electron acceptor.
How does fermentation differ from respiration? (3)
- Organic compound as final electron acceptor
- Can only do substrate level phosphorylation which is inefficient
- Pyruvate is central intermediate but end products can vary
Reduction of oxygen during during respiration leads to formation of what? (2)
- Superoxide anion
2. Hydrogen peroxide
What detoxifies the toxic superoxide anion and hydrogen peroxide in bacteria? (2)
- Superoxide: Superoside dismutase
2. H2O2: Catalase
What will the catalase test distinguish?
Catalase positive: Gram positive cocci Staph
Catalase negative: strep
What do obligate aerobes require?
Do they do fermentation?
Do they have catalase or SD?
Examples? (2)
Oxygen No Yes Pseudomonas Bacillus
What do microaerophilic bacteria require?
What is toxic to them?
Examples (2)
Low oxygen
Too much oxygen
Campylobacter
Helicobacter
What do facultative anaerobes do for metabolism?
Examples 2
Respire aerobically until oxygen is gone then ferment
Enterobacteriaceae and Staph
What do facultative aerobes do for metabolism?
Do they have catalase or SD?
Examples? (2)
Ferment
Lack both
Streptococci and enterococci
How do aerotolerant anaerobes interact with oxygen?
Example?
Do they have catalase or SD?
They are anaerobic but can tolerate oxygen for brief periods.
Actinomyces
Often SD
How do obligate anaerobes do metabolism?
Do they have catalase or SD?
Examples? (2)
What is a defining feature?
Ferment
Lack both
Bacteroides and Clostridia
Stink
What does a capnophile require?
How does one facilitate that in a lab? 2
Increased CO2
Candle jar or CO2 incubator
A microaerophile requires what compared to a capnophile?
How does one facilitate that in lab?
Higher CO2
Gastight jar: Chemical packet generates hydrogen and CO2
What other things can bacteria be categorized on? 3
- optimum growth temperature
- pH
- osmotic pressure
4 phases of bacterial growth?
- lag phase
- logarithmic phase
- stationary phase
- death phase
What is the lag phase?
Period of adjustment of new medium requiring enzyme synthesis and gearing up for growth
Logarithmic phase involves what?
Exponentially increasing cell numbers leading to rapid accumulation of cells
What is the generation time?
Time it takes for one cell division cycle
What is the range of generation times?
20 minutes to several hours
Is each generation time the same for a species?
Yes
What is the inverse of generation time?
Growth rate
Why does the stationary phase occur?
Nutrients become limiting and toxic byproducts build up
What happens during stationary phase?
Cells change genetic program to become dormant and may make endospores.
Why is stationary phase important clinically?
Many bacteria become more resistant to anti-biotics
What is the death phase?
Death of cells due to toxic byproducts
What makes the body tough for exponential growth of bacteria? (2)
- Very few areas where nutrients are plentiful
2. Very few areas where toxic byproducts will be washed away
Where is one place where nutrients are good and byproduct washing occurs?
Colon
Do in vitro and in vivo concentration differ for antibiotics?
Yes
What is the form that cells grow in a test tube?
Planktonic
What is the form that cells grow in the body?
Surface biofilms
What makes bilfilms so different from a culture tube?
They are complex structures of regions with metabolitcally differently acting cells
What are the steps of biofilm formation?
- Planktonic cells proliferate
- Monolayer forms
- Type IV pili and twitching motility allows for formation of microcolony
- Biofilm forms
Two things that can happen to mature biofilm?
- Physical detachment shears a piece off
2. Mobilize to form planktonic cells again
Where can biofilms be found in terms of inanimate objects? (3)
- indwelling catheters
- artificial joints
- anything foreignly inserted into body
What is resistance?
Stable genetic change that is passed down to cell progeny
What is persistence?
Metabolic state that allows transient tolerance to antibiotics and other stress but is not passed down to cell progeny
What things do you have to think about in terms of disinfectant and sterilization?
- How it works
- does it sterilize
- what does it work best again
- what does it work poorly against
Where is S. pyrogenes found?
URT
Where is S. agalactiae found?
OB/neonate
Where is S. pneumoniae found? 2
Upper respiratory (ear) Lower respiratory
Where is E. facalis and E. faecium found?
Skin and bone
Where is S. mutans found?
Upper respiratory tract
