Driessen lecture 2 and 3 Flashcards
Build of the prokaryotic cell
How do the cytoplasmic membranes of bacteria and eukarya differ from those of archaea?
While the hydrophobic fatty acid tails are bound to glycerol by ester linkages in bacteria and eukarya, the lipids of archaea have hydrophobic isoprenoid tales, bound to glycerol by ether bonds.
What are the three main functions of the cytoplasmic membrane?
- Permeability barrier of the cell
- It anchors proteins that catalyze a suite of key cell functions
- It plays a major role in energy consumption and conservation.
What are the three basic mechanisms of active transport?
- Simple transport: only a transmembrane transport protein.
- Group translocation: several proteins involved, while chemical modification of the transferred substance takes place.
- ABC transport: binding protein, a transmembrane transporter and an ATP-hydrolizing protein.
What is a classic example of a simple transporter?
Uptake of lactose in E.coli by the lac permease, a symporter in E.coli.
What are two important differences between group translocation and simple transport?
- In group translocation, the substance is chemically modified (glucose in E.coli is transferred using group translocation, the phosphotransferase system)
- In group translocation, an energy-rich compound drives the transport, while in simple transport, the proton motive force drives it.
What are the differences in membrane structure between gram-positive and gram-negative cells?
- Gram positive cells have a cytoplasmic membrane and a thick peptidoglycan cell wall.
- Gram negative bacteria have a cytoplasmic membrane, thin peptidoglycan cell wall, an outer membrane, and a periplasm (= space between the cytoplasmic and outer membrane, containing the peptidoglycan wall)
What is the sugar backbone of peptidoglycan composed of? Through which bonds are they linked?
The sugar backbone of peptidoglycan is composed of two alternating repeats of N-acetylglucosamine and N-acetylmuramic acid, joined by a B(beta) -1,4 linkage.
Attatched to the N-acetylmuramic acid is a short peptide side chain.
What is this peptide side chain composed of in E.coli?
In E.coli this peptide contains the amino acids L-alanine, D-alanine, D-glutamic acid and diaminopimelic acid (DAP)
Which type of bonds confer to strength of peptidoglycan around the circumference of the cell and which bonds around the axis of the cell?
Glycosidic bonds (B-1,4 linkages)
confer strength on peptidoglycan around the circumference of the cell whereas
peptide bonds (between side chains) confer strength along the axis of the cell.
What is the function of teichoic acids?
- they help maintain the rigidity of the cell wall
- They help regulate ion homeostasis
- They aid in adhesion and biofilm formation
What are teichoic acids composed of and which type of bacteria (gram positive or gram negative) have these?
Gram positive bacteria have teichoic acids.
Teichoic acids are composed of glycerol phosphate or ribotol phosphate with attatched molecules of glucose or D-alanine.
Which component in human secretions (tears, saliva etc.) functions as a major defence against bacterial infection?
Lysozyme in human extretions forms a line of defence against bacterial infection by cleaving the glycosidic bond between N-acetylglucosamine and N-acetylmuramic acid. This weakens the peptidoglycan and causes cell lysis.
Penicillin is an important antibiotic.
What is the difference in how penicillin kills bacteria and in how lysozyme does this?
Penicilin blocks the formation of peptide cross-links, while lysozyme destroys preexisting peptidoglycan, both causing cell lysis.
What is the cell wall of methanogens composed of?
Pseudomurein, composed of N-acetylglucosamine and N-acetyltalosaminuronic acid, linked by B-1,3 linkages.
Pseudomurein is immune from destruction by both lysozyme and penicillin.
What bacteria (gram positive or negative) have LPS and what are its main functions?
Gram-negative bacteria have an outer membrane surrounding the peptidoglycan wall, often called lipopolysaccharide (LPS).
Its main functions are:
- Facilitate surface recognition
- Important virulence factors for some bacterial pathogens
- Contribute to the mechanical strength of the cell
Which part of LPS is linked with toxicity of pathogens?
Lipid A.
What do Braun lipoproteins do?
They anchor the outer membrane to the peptidoglycan layer. They span the gap between the outer LPS layer and the peptidoglycan layer.
What is the periplasm?
The periplasm is the space between the outer surface of the cytoplasmic layer and the inner surface of the outer membrane. (So it contains the peptidoglycan layer).
The periplasm can contain several different classes of proteins. What are some of these different proteins:
- hydrolytic enzymes, for the initial degradation of polymeric substances
- binding proteins that begin the process of transporting substrates
- chemoreceptors that govern the chemotaxis response
- proteins that construct extracellular structures
What are the main functions of S-layers?
- In many archaea, S-layers take on the role of the cell wall, providing strength, protecting from cell lysis and conferring cell shape.
- The S-layer can create a periplasmic space in archaea
- S-layers can facilitate cell-surface interactions (such as attatchment)
- In bacterial pathogens, S-layers can increase their ability to cause disease
What is the difference between a capsule and a slime layer?
In capsules, the polysaccharide layer is organized in a tight matrix that excludes small particles and is tightly associated to the cell.
In contrast, in slime layers the surface is easily deformed and loosely attatched.
What are pili and what are fimbriae?
Pili are thin, filamentous protein structures that extend from the cell. Pili that mediate attatchment are called fimbriae.
What do conjucative pili do? What do type IV pili do?
Conjucative pili facilitate genetic exchange by causing cell-to-cell attatchment. Type IV pili are for twitching motility.
Which group of archaea form hami and what is the function of these hami?
The SM1 group of archea form a hamus, which is a unique attatchment structure that forms tiny grappling hooks. The hami help to affix the cells to the surface and prevent the cells from being washed away.
What is one of the most common inclusion bodies called and what does it store?
One of the most common inclusion bodies is the poly-B-hydroxybutyric acid (PHB/PHA). It is a class of carbon- and energy-storage polymers.
Where in the cell are sulfur globules present?
In the periplasm
Of which two proteins are gas vesicles composed? What is their function?
Gas vesicles are composed of GvpA and GvpC. They confer buoyancy and allow the cell to position itself optimally in the water column. (Photosynthetic bateria: algal bloom)
By what bateria (gram-positive or gram-negative) and what order of bacteria are endospores formed?
Endospores are only formed by the gram-positive bacteria of the orders bacillales and clostridiales.
What are the different layers of an endospore?
- the core: contains ribosomes and DNA, develops from the cytoplasm of the vegetative cell.
- Inner membrane: surrounds the core, develops from the cytoplasmic membrane
- Outer membrane: special membrane formed during sporulation
- Endospore coat: composed of layers of core-specific proteins
- Exosporium: outer proteinaceous layer (some, not all endospores)
What is the function of dipicolinic acid?
Dipicolinic acid facilitates dehydration of the core. The large amounts of calcium in an endospore complex with dipicolinic acid to help dehydrate the developing endospore. Additionally, the calcium-dipicolinic acid complex inserts between bases of DNA, stabilizing and protecting it against heat denaturation.
What is the function of small acid-soluble proteins (SASPS)?
- They bind to DNA in the core and protect it from uv radiation, dessication and dry heat
- They are a carbon and energy source for the outgrowth of a new vegetative cell from the endospore.
Name the different kinds of flagellation with regards to where the flagella are located.
- polar flagellation: the flagella are attatched to one or both ends of the cell
- lopotrichous flagellation: a tuft of flagella on one end of the cell
- amphitrichous flagellation: a tuft of flagella on both ends of the cell
- peritrichous flagellation: flagella around the whole surface of the cell
How does movement in peritrichously flagellated cells go?
Peritrichously flagellated cells move by run and tumble. The cell runs when all flagella form into a bundle and rotate counterclockwise. Clockwise rotation causes the bundle to break apart and the cell to tumble.
How does movement in polarly flagellated cells go?
Polarly flagellated cells can either be unidirectional or reversible.
- reversible: counterclockwise rotation: cell runs, clockwise rotation: cell reverses
- unidirectional: clockwise rotation: cell runs, rotation stops, cell reorients itself at random, clockwise rotation, cell takes off in new direction
Where are the different rings of the base of a flagellum located?
- L ring: in the outer membrane
- P ring: in the peptidoglycan layer
- MS rings: cytoplasmic membrane
- C rings: cytoplasm
what is the stator of a flagellum composed of?
The stator of a flagellum is composed of Mot proteins, which function as the flagellar motor.
What are the differences between archaella and flagella?
- Archaella proteins are unrelated to those of flagella, and are more closely related to type IV pili
- Archaella are smaller
- Archaella are not hollow like flagella and are assembled from their bases (instead of the tips like flagella
- Archaellar rotation is driven by ATP hydrolysis, instead of the pmf in flagella
- The archaellar motor is structurally simpler
archaea typically move slower than bacteria. What is one exception of this?
The methanocaldococcus
Where does the energy for twitching motility come from?
From ATP hydrolysis
How is gliding motility thought to work and what is the energy that drives it?
Gliding motility requires a helical intracellular protein track that interacts with gliding motors and extracellular adhesion proteins. The pmf drives rotation of gliding motors that translate this force to the helical track, causing adhesion proteins to move in a helical pattern, resulting in forward motions and counterclockwise rotation of the cell.
What is the difference between phototaxis and scotophobotaxis?
Phototaxis is movement in response to a gradient of light intensity, while scotophobotaxis is movemente in response to the absence of light.
How does the gram stain work?
Staining with a basic dye makes the cells purple. After treatment with ethanol, gram-negative cells are decolored, but gram-positive cells are not. Counterstaining with a differently colored stain makes the gram negative cells turn pink
So:
gram-positive: purple
gram-negative: pink
