lectures 1-12 Flashcards
How many bacteria are there estimated to be?
0.8-1.6 million bacterial species
Where are bacteria found?
- plants, animals, soil, water, air, arctic ice, volcanic vents (everywhere)
How much bacteria does skin, teeth and colon have?
Skin: 5-50 x 10^3/sq inch
Teeth: 5- x 10^6/sq inch
Colon: 3 x 10^11 /g
What are the features of a bacterial cell?
- No mitochondria (functions performed by cytoplasmic membrane)
- Ribosomes (70s-30s and 50s subunits) free in the cytoplasm
- No ER
- Single chromosome (nucleoid) - no nuclear membrane
What is the difference between Gram-negative and Gram-positive
- gram negative has a much thinner cell wall (peptidoglycan), also outer membrane
- Gram positive has a thicker cell wall
Why is the cell wall important?
- necessary for viability
- one of the most important sites for attack by antibiotics
- Provides ligands for adherence and receptor sites for drugs or viruses
- activates host signaling cascades
What is unique about peptidoglycan?
- Unique to bacteria
- provides mechanical strength
- not a ‘hard-shell’, it is flexible
- connected by peptide crosslinks
- biosynthesis is disrupted by many cell wall antibiotics
What is peptidoglycan made of?
B-14, glycosidic linkages (glycan chain, sugar)
- side chain (peptides)
What are peptide chains made of?
5 different amino acids:
- L-alanine
- D-glutamate
- L- diaminopimelic
- D - alanine
- D- alanine
What do peptide chains do in gram-negative bacteria?
there is a direct cross link between the 3rd and 4th group. There is a direct cross-link in most Gram-negative bacteria
What happens to peptide chains in Gram-positive peptidoglycan
-There is a cross-bridge in most Gram-positive bacteria, an anchoring site for some cell-wall proteins
How does penicillin affect peptide side chains in peptidoglycan?
-It prevents linking two side chains together
What is the structure of a Gram-negative cell envelope?
- Outer membrane (phospholipid inner face, LPS outer face)
- Inner membrane (phospholipid on inner and outer face)
What is the function of the outer membrane in bacteria?
- mechanical stability (helps with structure)
- defensive player - protects against antibiotics, bacteriophages, antimicrobial peptides
- permeability barrier
What is LPS (located in the outer membrane)?
It is a barrier against hydrophobic agents, detergents, bile, antibiotics
- it forms a tightly packed layer - strong lateral interactions between LPS molecules
- proinflammatory: interacts with receptors on macrophages and B-cells to cytokine release (can cause endotoxic shock)
What is the structure of LPS?
-O-antigen (3-5 sugars repeated)
-Core oligosaccharide (Glc – D-Galactose, Gal – D-Glucose, Hep – Heptose, KDO – Keto deoxyoctanate
-Lipid A (outer membrane)
+it has a conserved structure
What is a LPS?
It is proinflammatory and binds to the TLR4 and triggers upregulation of pro-inflammatory cytokines. Which can cause shock
What are the 3 forms of LPS?
- Lipid A
- Rough LPS (poor adherence to host cells)
-Smooth LPS (good adherence to host cells)
What happens when the O-antigen is lost?
-It allows the bacteria to “hide” from the host
What happens when bacteria can modify their LPS?
- dampen proinflammatory immune responses or provide resistance to cationic antimicrobial peptides (CAMPs)
What is another thing that gram-positive bacteria have (not a thicker cell wall)
- They have teichoic acids
What are teichoic acids (found in gram-positive bacteria)?
-They are negatively charged polymers there are 2 types
1. Lipoteichoic acid (membrane-anchored)
2. Wall teichoic acid (peptidoglycan-anchored)
What is the role of teichoic acids?
- Binding to receptors + surfaces
- negative surface charge
- growth and division
- host cell recognition
- protection from harmful molecules
6 Cation homeostasis
What can happen to teichoic acids?
They can be modified, but these modifications are not always beneficial: glycosylation may increase susceptibility to bacteriophages, D-alanine can reduce ability to adhere to host cells and establish infection
What are key parts of cell wall anchored proteins?
- key role in attachment/adhesion
- they are translocated across the cytoplasmic membrane and synthesized in the membrane
What are the functions of surface surface proteins?
- bacterial adhesion
- invasion of mammalian cells
- binding to plasma proteins
- Immune evasion
inducing inflammation
-Biofilm formation
What do capsules, EPS and biofilms have in common?
- outermost layer of protection
- commo structure, biogenesis and export pathways
- Assist in adhesion to solid surfaces
- protect against antibiotics, antimicrobial pesticides and host immune responses
- make infections hard to treat
What is a capsule (bacteria)
They are a type of glycocalyx (sticky sugar coat)
- distinct, gelatinous
- high water content
- resists phagocytosis
What is the function of a capsule?
- barrier to toxic hydrophobic molecules (e.g. detergents)
- protect against desiccation (high water content)
- resistance to bacteriophage
evade host defenses
What are often encapsulated?
Invasive bacterial pathogens
What is the function Extracellular polysaccharides (EPS) and biofilms?
- They are important for structure and function of biofilms
What are the types of EPS?
- Soft, loose polymer
- Tight scaffold
- Fabric-like matrix
what are bacteria in biofilm like?
- Impervious to phagocytosis by
neutrophils and macrophages - Resistant to antimicrobial peptides and
complement - Semi-dormant - difficult to inhibit with
antibiotics
What is an S-layer (bacteria)
- extracellular layer coating the entire bacterial cell surface
- gram-negative, gram-positive and archea
What is the S-layer made of (bacteria)
- 2 D Crystalline surface layers
- Composed of protein or glycoprotein
- Usually a single protein (MW 40-200 kDa)
What is the function of an S-layer?
- molecular sieve: cut off determined by size and morphology of pores
- protection: resistance to bacteriophage, complement, phagocytosis, extreme environments
- Adhesion to host cells: scaffold for adhesion proteins
What are Fimbriae?
- bristle-like small fibers present in large numbers (100’s-1000’s)
- help attach cells to a solid surface or tissues
- help bacteria cling together
- Gr- and Gr+
- adhesion present at the tip, recognizes host molecules
What is pili?
-Longer fewer and thicker tubes (1-2 per cell)
-Made of pilin protein
- Attach to other bacteria
- Motility
- Mostly gram-negative
What is manufacturing in bacteria?
building the cell and its components
What is transport (bacteria)?
import raw materials and export products
What is energy production in bacteria?
respiration and fermentation
What is the currency in a bacteria?
adenosine triphosphate (ATP)
What does Lag mean in bacterial economy?
Acclimatize to a new environment
What does exponential mean in bacterial economy?
Rapid increase in central metabolism including protein translation machinery
What does the stationary phase mean in bacterial economy?
The cell begins to run out of nutrients/toxins accumulate
How many ATP does anaerobic fermentation make?
2 ATP molecules
How much ATP does aerobic respiration generate?
28-36 ATP molecules (better at generating energy)
What are the 4 steps for ATP synthesis?
- glycolysis
- Tricarboxylic acid cycle (TCA cycle)
- Electron transport chain
- Oxidative phosphorylation
What does oxidative phosphorylation do?
ATP synthase energy from proton motor force to catalyze formation of ATP
What is simple diffusion? (passive)
- small, uncharged molecules and gasses, e.g. O2, CO2
- Molecules/gasses move along a concentration gradient
- No energy required
- Low specificity
- Bidirectional
What is facilitated diffusion?(passive)
- suitable for larger or charged molecules (e.g. glucose, glycerol or water)
- Involves carrier/transport proteins (permeases)
- No energy required
- Bidirectional
What is an example of facilitated diffusion (passive)?
- Aquaporins - membrane channels for facilitated diffusion of water
- Escheria coli: the glycerol uptake facilitator transports water across membrane
What is active transport?
- movement of molecules across membrane against a concentration gradient
- requires energy
- nutrients enter through a carrier protein/permease
- High specificity
What does active transport require?
- requires chemical energy (i.e. ATP)
- transports substrates in or out of the cell
What are three components of active transport?
- Membrane spanning carrier protein (pore)
- ATP binding region
- substrate-binding protein
What is Symport?
two substances (including H+) e.g. lactose permease encoded by the lac operon (bring energy into cell)
What is an Antiport?
two substances in opposite directions (exchange) e.g. sodium (Na+) and potassium (K+) antiporters (kick out of cell)
What is flagellar motility?
powered by the movement of flagella
What is gliding motility?
sliding or gliding movement on surfaces using slime. Flagella independent.
What is Twitching motility?
propelled by the extension, tethering and retraction of type IV pili (like a fishing rod). Flagella independent.
Why is motility important?
- Allow movement to favorable environments
- Adherence and colonization
- Nutrient acquisition
- Evading harmful substances
- Evading predators or parasites
What are the different flagella positions?
- Monotrichous
- Lophotrichous
- Amphitrichous
- Peritrichous
What are the 3 components of motor structure?
- Filament
- Hook
- Basal body
What does the flagellar motor structure do? (filament)
- It has a rigid structure, constant width
- Protein flagellin arranged in helical chains to form hollow core
- filament can vary in diameter and form of helical curvature between species
- During synthesis, flagellin proteins move through hollow core to growing filament tip
What are characteristics of the hook? (motor structure)
- Flexible
- Slightly wider then filament
- Connects filament and the basal body
- Composed of a different protein (not flagellin)
What is the basal body in the flagellar motor structure?
-Rotary molecular motor powered by proton motive force
- Located entirely within cell envelope
- Consists of a central rod and system of rings
How do bacteria control direction?
- Bacteria can move along a concentration gradient either positive or negative direction
- Flagellar rotation controls direction of movement
- Movement strategy differs depending on flagella location on cells
What makes bacteria special?
- They are prokaryotic
- Unicellular
What are the costs to multicellualrity?
- requires energy to make adhesion and communication molecules
- physical limitations
- competition between individuals
What are the benefits of multicellularity?
- resistance to physical and chemical stresses
- resource acquisition
- protection against predators
- improved colonization ability
What is bioluminescence?
Some bacteria generate light
What is biofilm formation?
the transition from a planktonic (free-swimming) to a community-based lifestyle within a matrix constructed from biomolecules is often guided by quorum sensing.
What is virulence?
the expression of virulent phenotype by pathogenic bacteria may occur under the influence of quorum sensing molecules. This may occur when a large number of bacteria is needed to establish a successful infection.
What does it mean to be a Quorum sensing bacteria (QS)?
ability to detect and respond to population density
What does Quorum sensing in bacteria require?
- Enzyme that makes the autoinducer (signal)
- The autoinducer itself - Gram-negative: (AHLs) & Gram-positive: peptides
- receptor that binds to autoinducer (often has R in the name)
What is the Lux operon?
- set of five genes that are involved in bacterial bioluminescence.
What do a lot of gram-negative bacteria use?
-Lots use AHL’s for quorum sensing
What are other types of autoinducers?
- AHL’s (most common type and most species specific)
- Atypical (B-H): species specific
- Autoinducer 2 (AI-2)(E): example LuxS
How do different bacteria communicate with each other?
They communicate with each other via AHL’s this is intraspecies and (AI-2) is interspecies. Helps regulate QS systems.
What are microbial public goods behaviors?
- Biofilm formation, quorum sensing, nutrient acquisition and dispersal
What is juxtracrine signaling?
- Contact-dependent signaling
1. gaps junctions between animal cells
2. plasmodesmata between plant cells
3. cell-cell regulation
What is autocrine signaling?
-T-cell stimulation by antigen presentation of an epitope
What is paracrine signaling?
- cytokines released by immune cells act on multiple populations
- Morphogens released to drive patterning during development
- Neurotransmitters released locally act on multiple targets
What are morphogens?
WNT proteins act as morphogens by secretion and formation of gradients within tissues, cell respond in a concentration dependent manner.
What are WNT proteins?
- Act as morphogens by secretion and formation of gradients within tissues. Cells respond in a concentration-dependent manner through establishing positional specificity.
What is insulin?
a hormone released by the pancreases to promote uptake of glucose from blood (into liver, muscle) to store more energy containing molecules.
How do neurons communicate?
- Structure: cell, axon, synapse
- Neurotransmission is the conversion of an electrical signal into a chemical signal at the synaptic cleft
What are the types of Neurotransmitters?
- Biogenic amines - dopamine, noradrenaline, serotonin
- Amino acid neurotransmitters - glutamate, GABA
- Other types - acetylcholine, NO, d-serine, neuropeptides
What are glutamate and GABA (neurotransmitters)?
Major excitatory, inhibitory neurotransmitters
- interneurons w/short axons - local signaling
What are the 4 criteria for designation as a neurotransmitter?
- Synthesis in neuron
- Verifiable release from neuron
- Effect on post-synaptic neuron
- Appropriate termination of mechanisms
What are 4 major thigs that influence how an ion will move with respect to the neuronal membrane?
- Chemical gradient
- electrical gradient
- permeability of membrane
- Na/k ATPase
What is resting membrane potential? (neurotransmitter)?
-resting membrane potential is -65 to -70 mV.
What is an electrical trigger for deplarisation?
Na+ is the trigger, changes the voltage (depolarizes the neuron)
What are the 6 core proteins for CA2+ induced exocytosis?
- 3 SNARES
- Munc18
- Complexin
- Synaptotagmin
Why are SNARES important?
- assembling the trimeric SNARE complex primes them for neurotransmitter release
What do dendrites do?
- Collect electrical signals
What does the cell body do (neurotransmitter)?
Integrates incoming signals and generates outgoing signal to axon
What does an axon do neurotransmission?
-Passes electrical signals to dendrites of another cell or to an effector cell
What are the 2 types of neurotransmitter receptors?
- Ionotropic: direct gating by neurotransmitter binding (ligand-gated ion channels)
- Indirect gating of ion flux via altered intracellular metabolic/signaling changes
What are the seven steps to extracellular signaling?
- Synthesis
- Release of signaling molecule by signaling cell
- Transport of signal to target cell
- Detection of signal by specific receptor protein
- Transduction of signal
- Response: change in cellular metabolism, function or development triggered by receptor
- Termination of signal
What are examples of cell surface receptors?
- G protein coupled receptors (GPCR)
- Ion-channel receptors
- Tyrosine kinase-linked receptors
- Receptors with intrinsic enzymatic activity
What are G protein coupled receptors?
Ligand binding first activates a GTP-binding protein. This G-protein then either activates or inhibits an enzyme that generates a specific 2nd messenger or modulates an ion channel causing a change in membrane potential e.g. epinephrine.
What is an Ion-channel receptor?
Ligand binding changes the receptor conformation such that a specific ion channel is opened e.g. acetylcholine
What is Tyrosine kinase-linked receptors?
Ligand binding stimulates formation of a dimeric receptor which interacts and activates cytosolic protein tyrosine kinases e.g. erythropoietin.
What is a second messenger?
- Often free to diffuse to other compartments of cell e.g. nucleus, thus influencing gene expression
- Signal may be amplified significantly in generation of second messengers
- Use of common second messengers in multiple signaling pathways creates both opportunities (cross talk) and potential problems
How are proteins phosphorylated?
- specific enzymes, known as protein kinases phosphorylate target proteins. ATP is the most common donor of phosphate groups.
What is important to note about dephosphorylation and phosphorylation?
- They are not the reverse of each other and are irreversible under physiological conditions
What does phosphorylation do?
- It is a valuable regulatory strategy, they can form three or more hydrogen bonds
What is amplification in phosphorylation?
When enzymes activate enzymes, the number of affected molecules increases geometrically in an enzyme cascade
What are G-protein receptors responsible for?
- They relay info from nay diverse signals e.g. photons, hormones, neurotransmitters
- There are seven helices that span the membrane bilayer
What are biological functions mediated by GPCR or 7TM receptors?
- Smell
-Taste - Neurotransmission
- Hormone action
- Hormone secretion
- Control of blood pressure
- embryogenesis
- Development
- Vision
- Viral infection
Why are GPCRs so important?
they have involvement in many diseases e.g. allergies, depression, and blindness
- Also a target for more than half of all modern pharmaceutical drugs
What is the difference between GDP and GTP in heterotrimeric g-proteins?
GDP - bound (inactive)
GTP - bound (active)
- Activated G proteins transmit signals by binding to other proteins often enzymes
What are important classes of molecules involved in signal transduction pathways?
- Signaling molecules or ligands e.g. hormones
- Receptors e.g. GPCRs
- G proteins (GDP-inactive, GTP-active)
- Effector enzymes e.g. adenylate cyclase
- Second messengers e.g. cAMP
- Protein kinases e.g. PKA
- Phosphatases (dephosphorylation)
How is a signaling pathway terminated?
- G-proteins spontaneously hydrolyze GTP to GDP thus resetting themselves. they have intrinsic GTPase activity.
what is epinephrine important for?
When epinephrine binds to hepatic and adipose cells it liberates glucose and FAs
- It also binds to B-adrenergic receptors on the heart increasing contraction rate
What can help lead to an increase or decrease of intracellular signaling molecules?
The binding of ligands to many cell surface receptors
Look up an image for the phosphatide cascade
How are IP3 and DAG initiated signals turned off?
- IP3 is rapidly metabolized to inositol which can open Ca2+ channel
- DAG may be (1) phosphorylated to phosphatide or (2) hydrolyzed to glycerol and fatty acids
What is a widely used second messenger?
Calcium is a widely used second messenger, it binds tightly to proteins and induces conformational changes
What acts as a calcium sensor in nearly all eukaryotic cells?
Calmodulin acts as a calcium sensor, when Ca2+ levels raise over 500 nM it activates
