Lecture 2 Powerpoint Flashcards
Bacteria are ________, whereas fungi, protozoa, parasites are _________.
prokaryotes; eukaryotes
What structures and organelles do bacteria have?
-Bacteria do not have internal membrane-bound organelles
-Bacteria have no sophisticated internal structures: no nuclear membrane, no mitochondria, no Golgi, no endoplasmic reticulum
List and describe the 6 common shapes of bacteria
Cocci: round
Coccobacilli: two cocci attached to each other
Curved: horseshoe shaped
Diplococci: two cocci next to each other
Bacilli: rod-shaped
Spiral: wavy-shaped
Define morphology
The form and structure of an organism or group of identical organisms
What do you need to know about a bacteria cell to identify its morphology?
What stage of growth a bacteria is in
Patterns of groups of identical bacteria are reflective of what?
cell division/ binary fission
Define pleomorphic
Each cell of a species has a slightly different shape when it divides
Describe aggregation properties
-Determined by the orientation of the cell division plane to the axis of the cell and the tendency of progeny cells to adhere to one another
-Can be characteristic of a species
What functions do structures from the cytoplasmic (inner) membrane and outward perform?
1) Protection from the external environment (includes host defense)
2) Permeability barrier for selective transport of nutrients and information
3) Control over physical location (ex: through flagella)
What does an environment primarily see first about a bacteria? Why?
Structures, because they are both external and unique (or foreign)
What do bacterial structures allow for?
Structures are often important antigens, so they can be used as vaccine targets and in diagnostics and epidemiology
Bacterial structures and their composition often reflect what?
Adaptations to the environment
Cell surface _______ can be targets for antibiotics
Cell surface _______ can be a barrier to antibiotics
structures; properties
What do bacterial cells use external structures for?
1) Cell surface structures often used to attach to and invade host cells and “sense” their environment to appropriately express virulence factors
2) Certain structures are not necessarily essential for viability, but are often important in pathogenesis as virulence factors
True or false: Structures are not expressed at all times and may be lost during continuous culture in laboratory media
True
Define peptidoglycan (murein)
One of the key components of bacteria that makes up cell wall and is the basis for a Gram stain reaction
The cell membrane of a bacteria is called the _______ membrane
cytosolic
List the 4 characteristics of peptidoglycan
1) Key contributor in overall shape of bacteria
2) Crucial for osmotic stability
3) Unique structure found only in bacteria
4) Makes a good target for antimicrobial agents (since it’s unique to bacteria and crucial to their survival)
Define lipopolysaccharide
An endotoxic structure found in the outer membrane (of the cytosolic membrane) of gram-negative bacteria.
How can you tell lipoteichoic acid and teichoic acid apart?
Lipoteichoic acid has a connection down to the cell membrane, whereas teichoic acid is only on the surface of the cell wall.
Lipoteichoic acids and teichoic acids are only found in gram-_______ bacteria
positive
Describe the characteristics of a gram-negative cell envelope
1) Inner membrane: symmetrical bilayer of phospholipids
2) Periplasm: sandwiched between IM and OM / gel-like matrix
3) Outer membrane: asymmetrical bilayer of lipids
4) Phospholipids in the inner leaflet and LPS in outer leaflet
5) Outer membrane serves serves as a selective permeability barrier that is virtually impermeable to hydrophilic solutes
How does the difference between gram-positive and gram-negative bacteria affect treatment plans for patients?
Since gram-negative bacteria’s outer membranes are virtually impenetrable to hydrophilic solutes, it affects which antibiotics are used in treatment
Define porins
Channel-forming proteins for the purpose of allowing
influx of nutrients and extrusion of waste products
True or false: The fluid mosaic model applies to the lipid bilayer of bacteria
True
Define a phospholipid
Has a head group and long hydrophobic fatty acid chains
Describe the importance of phospholipids to bacteria
-There’s a lot of diversity in just phospholipids; there are numerous fatty acids that can make up the fatty acid chains.
-Can vary in saturation (triple bonds, double bonds, single bonds, etc), length, cis/trans bond confirmations, isomerase, branched fatty acids, anteiso, and modification with OH groups
-Aids in membrane homeostasis (particularly with environmental changes like pH, salinity, oxygen, pressure, temperature, etc)
If a bacteria needed to change an element of itself to avoid lyseing due to environmental changes, what element would that be?
The fatty acids of phospholipids
Define a cell wall and describe where they can and can’t be found
-Defined as a semirigid structure surrounding the cytoplasmic membrane enabling the cell to resist bursting from osmotic pressure
-Found only in true Eubacteria, not found in Mycoplasmas
True or false: the cell membranes of bacteria are porous
True, so nutrients/ metabolites can actively diffuse to the plasma membrane
What is the main component of a bacteria’s cell wall?
Peptidoglycan (murein)
Describe what peptidoglycan (murein) is composed of
-Consist of a polymer of sugars and amino acids that forms a mesh-like layer located outside the cytoplasmic membrane
-Carbohydrate portion consists of alternating residues of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
-A peptide chain (3-5 amino acids) is attached to N-acetylmuramic acid
-Contains cross-linking bridges
How does the peptidoglycan of bacterial cell walls undergo degredation?
Undergoes degradation and remodeling through autolysins that introduce controlled breaks for growth/division
Describe the importance of peptidoglycans for immune response
-Peptidoglycan is conserved microbial structure that is immunogenic; recognized by the Nod proteins (innate immune response)
-Bacteria incorporate D-amino acids (unlike humans’ L-amino acids), so we know to attack it
Peptidases only recognize the ______ of amino acid residues
L-isomers
Are the peptides found in peptidoglycan produced ribosomally or enzymatically?
Enzymatically
There are _______ layers of peptidoglycan in Gram-positive organisms and _______ layers of peptidoglycan in Gram-negatives
20-40; 1-2
What increases the structural integrity of bacterial cell walls?
Peptidoglycan subunits are cross-linked between the peptides
Describe the difference in the cross-linkage of peptidoglycan subunits in Gram-positive and Gram-negative cells
Gram negative: DAP to D-Ala via direct attachment
Gram positive: Glycine linker (D-Ala to L-Lys)
Describe how lysozymes damage bacterial cells, and where lysozymes are found
-An enzyme that damages the cell wall of bacteria by catalyzing hydrolysis of the 1,4-beta-linkages between NAG and NAM residues in peptidoglycan
-Defense of the innate immune response: lysozyme is present in various secretions including tears, saliva, and mucus.
Describe Transpeptidation/ Carboxypeptidase reactions
-Penicillin-binding proteins (PBPs) are the targets for penicillin and other β-lactam antibiotics
-Penicillin and related β-lactam antibiotics resembles the ‘transition state’ conformation of the D-Ala-D-Ala substrate when bound to these enzymes.
-Basically they make bacteria divert their resources so they can’t make peptidoglycan (as fast), so our body can catch up and kill the bacteria
Describe how the rigid cell wall of bacteria grows
-Peptidoglycan is constantly being synthesized and degraded.
-Autolysins (murein hydrolases) are used to aid in cell wall growth
-A group of enzymes that exist in all bacteria contains peptidoglycan and can break down the peptidoglycan chains in small sections to allow for growth and cell divisions
-Like lysozymes, they cleave the β-1,4 linkages in the glycan chain
-The process must be regulated as to not allow osmotic rupture of the cell
Describe teichoic and lipoteichoic acids
-Defined as polymers of chemically modified ribose or glycerol
-Only found in Gram-positive bacteria and are connected by phosphate groups (ester linkage)
-May be covalently modified with sugars, choline, or D-alanine groups that serve as antigenic determinants
Teichoic and lipoteichoic acids are only found in Gram-________ bacteria
positive
Teichoic acids may be covalently attached to the ________ _______, whereas lipoteichoic acid contains a lipid moiety that anchors the polymer in the _________ ________.
peptidoglycan layer; cytoplasmic membrane
LTA (lipoteichoic acids) are recognized by the innate immune system as what?
One of the conserved microbial structures (Pathogen Associated Molecular Pattern, aka PAMPs)
Describe the characteristics of gram-positive bacteria
-Thicker cell wall, no outer membrane, no LPS, no endotoxin, sensitive to lysozymes, more susceptible to penicillin
-Often have teichoic acid, some strains do sporulation, capsule is sometimes present, and some strains prudence exotoxins.
Describe the characteristics of gram-negative bacteria
-Thinner cell wall, has an outer membrane, has LPS, has endotoxins, no teichoic acid, no sporulation, resistant to lysozymes.
-More resistant to penicillin, sometimes has a capsule, and some strains produce endotoxins
Describe the discovery of Hans Christian Joachim Gram (1853-1938)
Discovery of Gram stains was made while attempting to distinguish between two pneumonia causing organisms: Streptococcus pneumoniae (Gram-positive) and Klebsiella pneumoniae (Gram-negative)
-Bacteria are primarily colorless (transparent) and exhibit a variety of shapes.
-Some bacteria have a thick “cell wall” (peptidoglycan), which stains _____ and is gram-positive.
-Some bacteria have only small amounts of peptidoglycan, which stains _____ and is gram-negative.
purple; red
Describe the 6 steps of a Gram stain
1) Spread bacteria out on a microscope slide using a drop of water or saline if needed, then bacteria are fixed onto the slide (and dead) using heat.
2) Then the slide is flooded with crystal violet, rinsed with water (by now all bacteria are purple).
3) Then the slide is flooded with iodine and rinsed with water.
4) Iodide exchanges with chloride ions in dye; iodide is bigger and causes dye to precipitate.
5) Then the slide is decolorize with alcohol for 2-5 seconds (this is a very easy step to mess up), then rinsed with water.
6) Alcohol permeabilizes the envelope of gram-negatives, so the precipitated purple dye comes out. The thick cell wall prevents dye from coming out in gram-positives.
Give 2 examples of bacterium that are exceptions to the Gram stain
1) Intracellular bacteria (i.e. bacteria that grow inside a eukaryotic cell)
2) Mycobacterium tuberculosis
Why doesn’t the Gram stain work on some bacteria?
The organisms produce a waxy coat [long-chain hydrocarbons, sugars, additional components], and waxy coats are resistant to acids
Describe an Acid-Fast stain
-Dye is introduced into tubercule bacteria using heat
-Washing in acid will not remove the dye [i.e., “acid-fast”]
What are the 3 ways to classify bacterial colony morphology?
Form, elevation, and margin
Describe the use of agar in the lab
-Agar has a semi-solid matrix and porous nature which allows for infusion of nutrients
-Bacteria-containing samples are either streaked or spread on plates to isolate individual bacterial cells
-Each colony grows from a single viable bacterium (a ‘colony-forming unit’ or CFU)
Define simple, comlex, enriched, selective, and differential mediums
1) Simple medium: defined, minimal nutrients
2) Complex medium: nutrients not precisely defined
3) Enriched medium: specific components added for “difficult to grow” bacteria
4) Selective medium: contains chemicals, antibiotics that inhibit some bacteria and allow growth of other bacteria
5) Differential medium: contains substates for biochemical reactions and indicators to illustrate the byproducts of reactions
What 3 characteristics of bacteria are important to know when studying colonies?
1) Some bacteria produce natural colors
2) Some bacteria secrete enzymes such as hemolysins (lyse RBCs)
3) Some bacteria ferment specific sugars
List 8 external bacterial structures
Flagella
Pili
Fimbriae
Sex Pilus
Type III Secretion Apparatus
Capsule
Glycocalyx (slime layer)
Polysaccharides
Describe flagella and their importance
-Highly specialized, complex organelles for locomotion/ motility
->50 genes involved in assembly and function
-Very long proteinaceous filaments that have an a-helical arrangement [corkscrew-like]
-Apparatus spans the entire envelope of bacteria
-Within the host, flagella are critical for reaching mucosal surfaces (especially areas with fast flow)
Define monotrichous, lophotrichous, amphitrichous, and peritrichous flagellum
1) Monotrichous flagella: one flagella
2) Lophotrichous: multiple flagella (6-8) from one pole
3) Amphitrichous: one flagella on each of the two poles
4) Peritrichous: has flagella all over its body
List the 3 components of flagella
1) Basal body: anchored into the membrane
2) Hook region: extends just beyond the outer membrane
3) Helical filament: extends to the external environment
How are flagella assembled?
In a step-by-step manner using a specialized protein secretion pathway called type 3 secretion
How fast can flagella go?
Up to 100mph
Describe the use of flagella in H. Pylori
H. Pylori will create a “sheath” of flagella using synthesized sugar; the most vulnerable point of a flagella is its very tip, so they have extra proteins that create a “terminal bulb” at the ends of the flagella.
Coordinated counterclockwise motion of flagella leads to swimming, and is a(n) __________
Clockwise motion of flagella leads to tumbling, and is a(n) _________.
Counterclockwise swimming is an attractant; clockwise tumbling is a repellent
Define chemotaxis
Swimming motility; movement toward or away
Describe the structure of flagella
1) There’s a protein structure across the envelope, called the basal body or rotor.
2) Just above the basal body there’s a hook, called a universal joint
3) The filament acts as a propeller
What are flagella driven by?
Ionic potential/ proton motive force
The motor that turns the flagella rotates on average _____ rpm.
E. coli = ______rpm
Vibrio = ______rpm
500; E. coli is 5,000rpm; Vibrio is 100,000rpm
How does flagella motion activate for chemotaxis?
Chemoreceptors in envelope relay information to flagellar apparati, so the flagella turn on when the bacteria senses food
Why is adherence so important to bacteria?
Provides an advantage, prevents removal by fluids
True or false: Virtually all pathogenic bacteria having ways of attaching themselves firmly to host cells
True
Define pili (fimbriae) and what they do
Defined as filamentous appendages composed of “pilin” protein that are anchored to the outer membrane of Gram negative bacteria
-Mediate attachment to eukaryotic host cells
Pili are primarily found in Gram-________ bacteria
negative
Pili are peritrichou; define peritrichou
Hairy all over
Give an example of a specialized pili
Sex or F pilus for bacterial conjugation
What can be described as “rod-shaped protein structures extend from the bacterial surface and bind to host cell surface molecules (typically carbohydrates.)”?
Pili
True or false: Pili can be evenly distributed or located preferentially to one part of the bacterial cell.
True
Define afimbrial adhesins. What kind of bacteria are they found in?
Defined as bacterial surface proteins that are not organized in a rodlike structure and mediate tight binding between bacteria and host cell.
-All bacteria have these
Bacteria may produce both pili and afimbrial adhesins. Why?
To lock into the surface if it’s in an area of fast flow
Define capsules
Capsules are an enormous layer of polysaccharides
(With the exception of Bacillus anthracis poly-D glutamic acid, a polypeptide capsule)
What does the capsule of bacteria do?
It’s anti-phagocytic; it’s also called the K-antigen and has thousands of serotypes
What is the K antigen?
Capsules
Define glycocalyx and what it does
-Also known as the slime layer, it’s a “loose” layer of polysaccharides
-It functions in attachment/adherence/motility and is a key feature of biofilm formation
What is a key feature of biofilm formation?
Glycocalyx
Define the S-layer and what it does
-A layer composed of a single protein species [sometimes glycosylated] that forms a crystalline array
-This layer is small; you’d need electron microscopy to observe it
-Aids in protection against environmental stress (osmotic, pH, enzymatic) and in phagocytosis
Lipopolysaccharide (LPS) is found on the surface of Gram-________ bacteria; it is not present on the other type of Gram bacteria
negative
Name and describe the 3 components of lipopolysaccharides (LPS)
1) Lipid A domain: phosphorylated lipid with sugar backbone
2) Core region: oligosaccharide chain
3) O-antigen: polysaccharide chain
Describe the role of the lipid A domain (region I) of lipopolysaccharides (LPS)
-Hydrophobic anchor, holds LPS in the outer membrane.
-The portion of LPS responsible for endotoxicity
-Activates Toll-receptor (innate immune response)
–Changing the lengths of the acyl chains, changing the number of acyl chains, adding ethanolamine/phosphate/etc to the phosphate groups to alter its surface charge, or adding amino acids to Lipid A can prevent Lipid A from activating the Toll-receptor
-Important: Some bacteria synthesize a non-inflammatory lipid A to evade immune recognition
What is the portion of LPS responsible for endotoxicity?
The lipid A domain (region I)
What activates the Toll-receptor?
Lipid A domain
Describe the role of the core oligosaccharide region (region II) of lipopolysaccharides (LPS)
-Consists of short chain of sugars attached directly to lipid A
-Not required for growth in laboratory
-Clinical Relevance: During infection thought to be required for maintaining permeability properties of the outer membrane
Describe the role of the O-antigen/ O-polysaccharide region (region III) of lipopolysaccharides (LPS)
-Repeating unit of oligosaccharide subunits made up of 3-5 sugars attached directly to the outer core region (up to 40 units long)
-Major antigenic determinant with great variation between species and even strains
-Used as basis for determining serogroup of a bacterial strain
-Clinical Relevance: Loss of O-antigen results in loss of virulence; O-antigen provides protection from host defenses
The loss of what part of a lipopolysaccharide leads to loss of virulence?
The O-antigen; it provides protection from host defenses
Give 5 examples of internal structures found in bacteria
Gas vacuole, ribosomes, inclusions, nucleoid, endospore
What is the purpose of a gas vacuole?
Buoyancy for floating in aquatic environments
What is the purpose of ribosomes?
Protein synthesis
What is the purpose of inclusions?
Storage of carbon, phosphate, and other substances
What is the purpose of the nucleiod?
Localization of genetic material (DNA)
What is the purpose of an endospore, and in what type of bacteria are they found?
-Survival under harsh environmental conditions; only observed in bacteria
-Specifically only some gram-positive bacteria
What are the 3 main components of the bacterial cytoskeleton, and what do they do?
1) FtsZ: A division protein widely observed in bacteria; forms a disc shape in the center of the cell
2) MreB: maintains cell (rod) shape, localizes proteins
3) Crescentin: introduces crescent-shaped morphology
Name and briefly describe the density of 3 storage inclusions found in bacteria
1) Glycogen (sugar)
2) Polyhydroxyalkanoate granules: Very light
3) Polyphosphate granules: Very dense; store phosphate
What is the purpose of vacuoles?
To store gas for buoyancy in an aquatic environment
What do magnetosomes do?
Aid in orientation to seek nutrients; based on earth’s magnetic poles
What is the purpose of carboxysomes?
A specialized site for CO2 fixation (a protein coat with an enzyme inside)
There are as many as ________ ribosomes growing in a bacterial cell, whereas eukaryotes have up to ________
70K; 10 million
Why is the difference in size and composition between a prokaryote and eukaryote important?
It’s important for antibiotics; they can pick out bacterial ribosomes and keep them from synthesizing proteins
Describe bacterial nucleiods
-Most are circular
-No membrane
-Have proteins and histone-like proteins that interact and organize things
Name 3 types of bacterial plasmids and briefly describe what they do
1) Conjugative plasmids: the F factor; transfers copies of themselves into another bacteria
2) R (resistance) plasmids: can be conjugative (transfered through bacterial “sex”); delivers antibiotic resistance genes
3) Virulence plasmids: encode genes for pathogenicity
Some Gram-_________ bacteria are spore-formers
positive
What is the purpose of sporulation, and what do spores contain?
1) Spores represent a dormant state for long-term survival; formation (sporulation) is induced by harsh environmental conditions
2) Spores contain the entire chromosome enveloped by a membrane, peptidoglycan and an outer protein coat (keratin-like)
Certain conditions will cause spores to become activated; this is called _____________
germination
What aspect of sporulation is useful in diagnosis?
The location of endospores
Name 4 locations of endospores
1) Central
2) Swollen sporangium (makes cell somewhat sperm-shaped)
3) Terminal (at the end of a rod-cell)
4) Subterminal (almost at the end of a rod-cell)
Why do we typically set autoclaves to 121 degrees celcius?
That’s the temperature that can kill endospores
Briefly describe the morphology of protozoa, amoeba, and algae
Protozoa: motile due to cilia that cover their surface, heterotrophs
Amoeba: has a pseudopod and a contractile vacuole to control movement; prevents excess water inside the cell
Algae: have stored starch grains so they have carbon on-demand, use sunlight’s energy or can use organic compounds, extreme diversity, extremely abundant
Describe the differences between passive and facilitated diffusion
1) Passive diffusion: Non-polar lipid-soluble substances diffuse passively from high to low concentration
2) Facilitated diffusion: can control specific (sugars, ions, charged polar molecules, ATP, etc) or nonspecific transport (water, glycerol, urea, etc), allows nutrients in and out.
What are the two types of facilitated diffusion?
Specific and nonspecific transport
Describe the rates of diffusion in passive and facilitated diffusion
The rate of transport is rather linear in passive diffusion, whereas the rate of transport in facilitated diffusion is very quick, but plateaus due to the saturation effect.
Define active transport
Transport of a substance against a concentration gradient
Define primary and secondary transport
Primary active transporters: use ATP for energy
Secondary transporters: use gradient for potential energy
What does primary active transport utilize to move substances?
Uniport transport: The one-way transport of a single molecule
Uniport transport is an example of __________ _______ transport, whereas antiport and symport transport are examples of _________ ________ transport.
Primary active transport; secondary active transport
List and describe the two types of secondary transports
1) Antiport: 2 molecules are transported in different directions
2) Symport: 2 molecules are transported in the same direction
(Can be very complicated and involve multiple subunits or phosphate transfer)
What do phosphotransfer systems (group translocations) require?
Has to have a series of phosphate handoffs, which generates energy and the ability to phosphorylate the sugar.
Define siderophore and what it allows bacteria to do
-A molecule that binds to various forms of iron and makes it available to the cell
-This allows bacteria living in an animal to steal that creature’s iron
