L1 Prokaryotic Structure and Function Flashcards
Prokaryotic vs. Eukaryotic
Prokaryotic lack of nuclei in cell nucleus - not enclosed DNA - double stranded chromosomal, plasmid morphology - simple examples - bacteria and archaea division - binary fission
Eukaryotic contain nuclei in cell nucleus - enclosed DNA - chromosomal morphology - complex examples - larger than prokaryotes, fungi, algae, protozoa, plants, animals division - mitosis
Prokaryotic cell organisation Three architectural regions
- Cytoplasmic region – everything in the core area / inside
- Cell envelope – plasma membrane and cell wall
- Cell surface attachments – what’s on the outside
what is cytoplasmic region and what does it contain
Viscous substance found between the cell membrane and the nucleus
- it is highly structured
- nucleoid (DNA)
- ribosomes (where proteins are produced)
- inclusion bodies
- cytoplasmic matrix
is highly organised
Three cytoskeletal elements: how its supported
- Actin filament- made from actin
- Microtubules- made from tubulin
- Intermediate filaments- a mixture of different classes of proteins
- actin filament (made from actin; 6nm, found beneath the cell membrane)
- microtubules (made from tubulin, 25nm, provide basic organisation of the cytoplasm incl. positioning of organelles)
- intermediate filaments (a mixture of different classes of proteins, 10nm, work in tandem with microtubules to provide support & functions vary for different cell types)
Inclusion bodies
- Granules of organic or inorganic material that are stockpiled by the cell for future use
- Some are enclosed by a single-layered membrane
membranes vary in composition
some made of proteins; others contain lipids
important for cell function, cell metabolism & long-term survival (storage of granules of organic or inorganic material stockpiled for future use)
- some enclosed by a single-layered membrane made of proteins and/or lipids
- found in PROKARYOTES
Organic inclusion bodies
- Glycogen
- Poly-β-hydroxybutyrate (PHB)
- Gas vacuoles
- Cyanophycin granules
- Carboxysomes
- glycogen (carbon source)
- poly-β-hydroxybutyrate (PHB) (carbon source surrounded by protein shell, seen as ‘bubble’ within cytoplasm in imaging)
- gas vacuoles allow organisms to float to a certain level in water to get the required wavelength of light)
- cyanophycin granules
- carboxysomes (involved in carbon fixation)
Inorganic inclusion bodies
- Polyphosphate granules
- Sulphur granules
- Magnetosomes
- polyphosphate granules (chain of phosphate compounds; required by all living organisms e.g. DNA)
- sulfur granules (required by some which use sulfur as their energy source)
- magnetosomes (some aquatic microorganisms use these to line up with the earth’s magnetic field; mode of transport, are bound to both the plasma membrane and the cytoskeletal filament and can flex them to move within the water column)
Ribosomes
- complex structures consisting of protein and RNA
- sites of protein synthesis
- Prokaryotic smaller than eukaryotic ribosomes
Prokaryotic ribosomes ⇒ 70S (50S+30S)
eukaryotic ribosomes ⇒ 80S (60S+40S)
S = Svedburg unit
The nucleoid
In actively growing cells, the nucleoid has projections; these probably contain DNA being actively transcribed
- a non-membrane-bounded region in a prokaryotic cell where the DNA is concentrated
- usually a single closed circle consisting of double stranded chromosome
- in actively growing cells, the nucleoid has projections which look like a many legged spider; it is supercoiled with proteins to maintain the multi-projection shape
Plasmids
- Usually small, closed circular DNA molecules
- Exist and replicate independently of chromosome – own way of replicating
- Not required for growth and reproduction
- May carry genes that confer selective advantage (e.g., drug resistance)
The Cell Envelope in prokaryotes contains
- Cytoplasmic or plasma membrane
- Cell Wall
- Capsules and slime layer
The plasma membrane
- Dynamic structure / changes
- Selectively permeable
- Facilitates movements in and out of cell
- Encompasses the cytoplasm
- Contains lipids and proteins
- Highly organised, asymmetric, flexible and dynamic
The asymmetry of most membrane lipids
- Usually form a bilayer
- Polar ends
interact with water
hydrophilic - Nonpolar ends – fatty acid tails
insoluble in water
hydrophobic - encompasses the cytoplasm
- highly organised, asymmetric, flexible and dynamic
- consists of a phospholipid bilayer consisting of polar head (phosphate and glycerol) and non-polar fatty acid tails
The prokaryotic cell wall
- Rigid structure that lies just outside the plasma membrane
- Just outside cell membrane
- Basic units of peptidoglycan are NAM (N-acetylmuramic acid) and NAG (N-acetylglucoseamine)
- Two alternating sugars (NAM and NAG) – connected by β-1,4 glycosidic bond
Peptidoglycan synthesis
- Occurs inside and outside cell membrane
- Autolysins, cleaves β-1,4 glycosidic bond linking NAM & NAG in small areas of pre-existing PG
- Newly synthesised PG inserted until crosswall forms and cell divides
- 2 carriers involved:
uridine diphosphate (UDP)
bactoprenol
Teichoic acid
Teichoic acids
- Polymers of glycerol and ribitol joined by phosphate groups
- Only present in Gram positive bacteria
- Extend beyond the surface of peptidoglycan
Importance of the LPS
- Protection from host defenses (O antigen)
- Contributes to negative charge on cell surface (core polysaccharide)
- Helps stabilize outer membrane structure (lipid A)
- Can act as an endotoxin (lipid A)
Other characteristics of the outer membrane
- Serves as a protective barrier
- More permeable than plasma membrane
Effect of β-lactam antibiotics
- Enzymes that catalyse transpeptidation of peptidoglycan also called penicillin binding proteins
- Lysozyme cleaves β-1,4 glycosidic bond
The cell wall and osmotic protection
- Osmosis
movement of water across selectively permeable membrane from dilute solutions to more concentrated solutions - Cells are often in hypotonic solutions
[solute]outside cell < [solute]inside cell
Osmotic protection
- Osmotic lysis
can occur when cells are in hypotonic solutions
movement of water into cell causes swelling and lysis due to osmotic pressure - Cell wall protects against osmotic lysis
Cell walls do not protect against plasmolysis
- Plasmolysis
occurs when cells are in hypertonic solutions
— [solute]outside cell > [solute]inside cell
— concentration inside is quite low compared to outside
water moves out of cell causing cytoplasm to shrivel and pull away from cell wall
Practical importance of plasmolysis and osmotic lysis
- Plasmolysis useful in food preservation e.g., dried foods and jellies - Osmotic lysis basis of lysozyme and penicillin action
Gram positive vs. gram negative
gram positive gram stain colour - purple thickness of peptidoglycan - thick techoic acids - present outermembrane - absent lipopolysaccharide - absent sensitivity to penicillin - more
gram negative gram stain colour - pink thickness of peptidoglycan - thin techoic acids - absent outer membrane - present lipopolysaccharide - present sensitivity to penicillin - less
Capsules and slime layers
- Layers of material lying outside the cell wall
- Capsules
usually composed of polysaccharides
well organized and not easily removed from cell - slime layers
similar to capsules except diffuse, unorganized and easily removed
Capsules and slime layers
Glycocalyx
- network of polysaccharides extending from the surface of the cell
- a capsule or slime layer composed of polysaccharides can also be referred to as a glycocalyx
Functions of capsules and slime layers
- Attachment to surfaces
- Motility of gliding bacteria
- Protection from:
harsh environmental conditions (e.g., desiccation)
viral infection or predation by bacteria
chemicals in environment (e.g., detergents)
osmotic stress
host defenses (e.g., phagocytosis)
slime > lubrication > allows movement > less friction
Capsules and avoiding host defences
- Survive unrecognised in host and avoid detection
Prevent complement activation by masking activating molecules
Avoid phagocytosis by preventing effective contact (e.g. Streptococcus pneumoniae)
Capsules that are not antigenic as resemble host tissue (e.g. S. pyogenes)
Cell surface attachments
- Pili
- Fimbriae
- Flagella
what structure in both prokaryotes and eukaryotes maintains the cell’s shape, internal structure, and helps cells carry out division/movement?
cytoskeleton
Membrane Proteins
- Proteins are embedded in or associated with lipids
- Peripheral proteins
loosely associated with the membrane and easily removed - Integral proteins
embedded within the membrane and not easily removed
Functions of the plasma membrane
- Separation of cell from its environment
- Selectively permeable barrier
- Location of crucial metabolic processes
- Sensory
what is the permeability barrier of the plasma membrane responsible for?
prevents leakage and functions as a gateway for transport of nutrients into and out of the cell
what is the protein anchor of the plasma membrane responsible for?
site of many proteins involved in transport, bioenergetics and chemotaxis
what is the prokaryotic cell wall
rigid structure that lies just outside the plasma membrane
What is the peptidoglycan structure?
NAM & NAG attached through a β-1,4 linkage, then a peptide chain is attached to NAM (4-5 amino acids, some of which are only found in peptidoglycan)
Where is peptidoglycan synthesised?
Both within the cytoplasm and outside of the cytoplasm (outside cell membrane)
How does the antibiotic lysozyme work on the peptidoglycan structure?
works by cutting the β-1,4 linkage
How do the peptidoglycan units combine to form the cell wall?
The NAM and NAG sugar units link together via a β-1,4 linkage, creating a long chain, or backbone. The peptide chains linked to the NAM subunit links to the peptide chain of another NAM subunit, and thus links chains together, forming a 3D structure
How does penicillin work on the peptidoglycan layer?
prevents the peptide interbridge and/or bond forming between the peptide chains
What is the linkage of NAM and NAG units called in the peptidoglycan 3D structure?
polysaccharide backbone
What are the two carriers involved in peptidoglycan synthesis?
- uridine diphosphate (UDP)
- bactoprenol
Which sugar unit of peptidoglycan does the peptide side chain link to?
NAM
How are the peptide chains of the peptidoglycan subunits linked?
Via either a single bond or a peptide interbridge (otherwise known as a pentaglycine interbridge)
What do NAM and NAG stand for?
N-Acetylmuramic acid & N-Acetylglucosamine
How is peptidoglycan synthesised?
- autolysins cleave the β-1,4 glycosidic linkage between NAM and NAG in small areas of existing peptidoglycan
IN THE CYTOPLASM
- glucose is made into NAG
- NAG is attached to the NAM via the UDP carrier
- the pentapeptides (amino acid chain) are added to the NAM tail
- UDP transports the newly synthesised NAM and NAG from the cytoplasm to the plasma membrane surface (because the peptidoglycan unit must be on the outside of the cell; i.e. it is made inside the cytoplasm then transported across the plasma membrane)
- bactoprenol transports the peptidoglycan repeat unit across the plasma membrane to the growing point of the cell wall
WHERE THERE IS A CUT IN THE β-1,4 LINKAGE BETWEEN NAG AND NAM UNITS IN THE CELL WALL
- at this point, it’s inserted into the break in the peptidoglycan layer and it extends it by one more unit
- bactoprenol returns to the cytoplasm to pick up another peptidoglycan unit
After the peptidoglycan subunit is inserted into the peptidoglycan layer, how is the peptide interbridge formed?
One terminal D-alanine is cleaved and a peptide bond forms between the sub-terminal D-alanine (of the peptide chain which has been cleaved) and the DAP amino acid of the other peptidoglycan subunit
How are the cell wall (consisting of the peptidoglycan layer) and the plasma membrane held together in Gram positive cell walls?
The peptidoglycan layer is held together by its structure, but also via teichoic acid.
Lipoteichoic acid is held both in the peptidoglycan layer and the plasma membrane, which anchors the cell wall to the plasma membrane
Is teichoic acid found in Gram positive or Gram negative bacteria?
Gram positive (needed due to the thicker peptidoglycan layer)
How thick are the peptidoglycan layers of Gram positive and negative bacteria?
Positive = 80nm Negative = 10nm
Describe the layers of the cell wall of Gram negative bacteria.
Starting from the inner parts of the cell wall, the Gram negative bacteria has the plasma membrane, the periplasmic space and the peptidoglycan layer in common with Gram positive bacteria (though the peptidoglycan layer is thinner and lacks the teichoic acid and lipteichoic acid required in Gram positive bacteria to anchor the peptidoglycan and plasma membrane layers together). However, the outer membrane differs. There is an additional lipoprotein layer and lipopolysaccharide.
Describe the structure of the outer membrane of Gram negative bacteria.
The outer membrane sits on top of the lipoprotein layer, and it is made up of lipopolysaccharide.
Describe Lipopolysaccharide (LPS)
The innermost layer of the lipopolysaccharide (Lipid A) forms a bilayer with a layer of phospholipid. Then there is the core, which is made up of polysaccharide. The outermost layer of the LPS is the O-antigen/O side chain which floats around in the environment. The O-antigen is the part which can become toxic (virulence factor)
What happens to Lipid A in the LPS layer of Gram negative cells when the cell is lysed?
It is released and forms an endotoxin
What is the importance of the lipopolysaccharide?
- the O-antigen protects from host defences (since they can change their O-antigen very quickly, when the host is able to detect the bacteria, it changes its antigen)
- the core polysaccharide contributes to the negative charge on the cell surface
- the lipid A component helps stabilise the outer membrane structure (helps create a bilayer of the LPS)
- lipid A acts as an endotoxin when the cell is lysed
Both the outer membrane and the plasma membrane serve as protective layers for the cell, but which is more permeable?
The plasma membrane is selectively permeable, while the outer membrane is much more permeable, thus allowing much more to get in. This is due to the presence of porin proteins
What are porin proteins, and where are they found?
Found in the outer membrane. The three parts of the porin form a trimer, and the central part forms a channel which compounds can pass through (marked in blue)
What is the effect of β-lactam antibiotics?
β-lactam antibiotics are enzymes which stop the pentapeptide bridge (glycine linkage between peptidoglycan peptide chains)
What does it mean to say cells are often in hypotonic solution?
The solution has a lower concentration of solutes than the cell does
Can the cell wall protect against osmotic lysis?
Yes - thus the cell does not swell and lyse
What does it mean when a cell is in a hypertonic solution?
The concentration of solutes in the solution is higher than the concentration of solutes inside the cell
Can the cell wall protect against plasmolysis?
No - thus the cytoplasm can shrivel and pull away from the cell wall if placed in a hypertonic solution
What are the practical uses of plasmolysis and osmotic lysis?
- plasmolysis (shrivelling) is useful for food preservation e.g. dried foods and jellies
- osmotic lysis (swelling) is the basis of lysozyme and penicillin action (i.e. breaks down the cell wall and water can flow into the cell)
What are the implications of the difference cell wall structures for Gram Negative and Gram positive bacteria?
- Gram staining
- Gram negative bacteria, with their outer membrane are very important in pathogenesis
What is the role of the cell wall in osmotic protection?
It enable the cell to survive in a hypotonic solution; prevents water from flowing into the cell
What are components external to the cell wall?
capsules and slime layers
What is a spheroplast?
cell with some cell wall remaining
What are capsules?
- made up of polysaccharides
- well organised and not easily removed from cell
- very important for pathogenesis because the capsule cannot be detected by the host’s immune system
What are slime layers?
- made up of polysaccharides
- similar to capsules except diffuse, unorganised and easily removed
What is the glycocalyx?
Network of polysaccharides extending from the surface of the cell
What else can be referred to as the glycocalyx?
The capsule/ slime layer
What are the functions of capsules and slime layers?
- attachment to surfaces
- motility of gliding bacteria
- protection from harsh environmental conditions (e.g. dessication), viral infection or predation by bacteria, chemicals in environment (e.g. detergents), osmostic stress, host defences (e.g. phagocytosis)
How do capsules help bacteria avoid host defences?
They survive unrecognised in host and avoid detection by:
- preventing complement activation by masking activating molecules
- avoid phagocytosis by preventing effective contact (e.g. Streptococcus pnemoniae)
- capsules that are not antigenic as they resemble host tissue (S. pyogenes)
Describe the structure of the plasma membrane in prokaryotes.
Plasma membrane is a dynamic and flexible structure. It is classified as a selectively permeable barrier, so it allow some things through and prevent others. It has transport proteins embedded, to facilitate the movement of proteins made by ribosomes. Many metabolic processes occur here e.g. generation of energy, respiration, photosynthesis. It contains receptors. It contains proteins that are embedded in lipids, in which there are peripheral proteins and integral proteins.The membrane is asymmetric, usually forms a bilayer, has polar ends (interact with water & are hydrophilic) and non-polar ends (insoluble in water & hydrophobic)
Detail the structure of the outer membrane and describe the importance of the lipopolysaccharides.
The outer membrane sits on top of the lipoprotein layer, and it is made up of lipopolysaccharide.
importance:
1. the O-antigen protects from host defences (since they can change their O-antigen very quickly, when the host is able to detect the bacteria, it changes its antigen)
2. the core polysaccharide contributes to the negative charge on the cell surface
3. the lipid A component helps stabilise the outer membrane structure (helps create a bilayer of the LPS)
4. lipid A acts as an endotoxin when the cell is lysed
Describe the attachment of the flagella hook to the cell surface in a gram-negative microorganism.
Flagella hook links filament to basal body - a series of rings that drive flagellar motor
Why is the peptidoglycan structure so rigid
Strong, rigid structure prevents cell from lysing/bursting
List several functions for the outer membrane in gram negative bacteria
- Serve as protective barrier
- More permeable than plasma membrane
In the Gram-negative Bacteria (which do not retain the crystal violet), the cell wall is composed of a single layer of peptidoglycan surrounded by a membranous structure called the outer membrane. … In the Gram-positive Bacteria, the cell wall is thick (15-80 nanometers), consisting of several layers of peptidoglycan
What is the purpose of the nucleoid in Bacterial cells?
- Has projections in actively growing cells
- Contain DNA being actively transcribed
- It includes enzymes & proteins that transcribe RNA & DNA.
- Some enzymes & proteins included in it act as biological catalysts
- Nucleoids also assist in cell development & growth.
Describe the arrangement of genetic information in bacteria.
Tightly coiled double-stranded circular DNA w/out membrane
Describe the structure and functions of capsule and slime layers.
Capsules: organised polysaccharides = hard to remove
Slime: unorganised = easy to remove
- Attach to surfaces
- Motility
- Protect from changes or chemicals in enviro, viral infection or predation, host defenses
A gelatinous material which coats the surface of some bacteria : Glycocalyx
Two types;
Capsules
- highly organised
- firmly attached
- protect against phagocytosis
- some bacteria are typed by capsule composition (HiB)
slime
- not highly organised
- not firmly attached
- helps bacteria to slide on surface
- protect from drying
- easily washed of
made up of polypeptides (chain AA) and/or polysaccharides (sugar molecules/ carbohydrates)
virulence- bacteria with glycocalyces often more pathogenic
- adherence- helps them stick and makes them harder to get off
- protection from phagocytosis
- ? some protection from antibiotics
How is the movement of the flagella powered?
By rotation powered by proton motive forcethe flagellum rotates like a propeller. The counter clockwise rotation causes forward motion and clockwise rotation disrupts run causing tumbling.
How is a motile bacteria able to sense an attractant and move toward it.
Chemoresptors on surface cells - detect [attractant]
What is the function of the plasma membrane in bacterial cells?
- Separates cell from enviro.
- Selective permeable memb.
- Metabolic processes (e.g. endocytosis)
- Sensory
Define plasmids.
Circular single stranded DNA carrying many genes
smaller than nucleoid
what makes up the cell envelope
plasma membrane, cell wall and slime or capsule layer
membrane-associated lipids are amphipathic, what mean
structurally asymmetric with polar and nonpolar ends
