Cell Structure and Function in Bacteria and Archaea

Chapter 3

Prokaryotes: two distinct domains

The prokaryotes are divided into two very distinct groups:– Eubacteria– Archaea

Essential distinctive points are the cell wall composition, the type of lipids synthesized by the cells, and the structure of RNA polymerase.

Major morphologies of bacterial cells

Cocci (singular coccus) round cells

Diplococci (when cocci divide and remains together to form pairs

Long chain cocci when cells adhere to each other after repeated cell division in one plane such as Streptococcus agalactiae

Grapelike structure when they divide in random planes such as Staphylococcus aureus

Major morphologies of bacterial cells Bacilli (singular bacillus) rod shaped cells and

differ in their length to width ratio

Some they are arranged in chains such as Bacillus megaterium

Spirilla (singular spirillum) spiral shaped cells or Spirochetes, flexible

Comma shaped such as Vibrio cholera In addition to the basic shapes there are star

shaped cell, rectangular flat cells and triangular cells

Pleomorphic (do not have certain size or shape)

Bacterial morphology

Cell Size and the Significance of Smallness

Size range for prokaryotes: 0.2 µm to >700 µm in diameter– Most cultured rod-shaped bacteria

are between 0.5 and 4.0 µm wide and <15 µm long

– Some small nanobacteria range from 0.2μm-0.05μm

– Examples of very large prokaryotesSize range for eukaryotic cells: 10 to

>200 µm in diameter

Bacterial sizes

Cell Size and the Significance of Smallness

Surface-to-Volume Ratios, Growth Rates, and Evolution

Advantages to being small– Small cells have more surface area

relative to cell volume than large cells (i.e., higher S/V)

– support greater nutrient exchange per unit cell volume

– tend to grow faster than larger cells

Cell Size and the Significance of Smallness

Elements of Microbial Structure Eukaryotic Cells

DNA enclosed in a membrane-bound nucleusCells are generally larger and more complexContain organelles

Elements of Microbial Structure

• Prokaryotic cellNo membrane-enclosed organelles, no

nucleusGenerally smaller than eukaryotic cells

Bacterial structure

Prokaryotes Vs Eukaryotes

Single cell organisms. Discriminating characteristics are:– No defined nucleus (no nuclear

membrane) NUCLEOID– Circular DNA. Bacterial cells are HAPLOID

(one single copy of the chromosome)– Plasmids (can be found in yeast as well)– No membrane bound organelles – Presence of a CELL WALL– 70S ribosomes– Inclusion bodies (storage of C, P and

other)

The Cytoplasmic Membrane in Bacteria

Cytoplasmic membrane:– Thin structure that surrounds the cell– 6–8 nm thick– Vital barrier that separates cytoplasm from

environment– Highly selective permeable barrier;

enables concentration of specific metabolites and excretion of waste products

– Transport of nutrients and waste products

Bacterial Cell Membranes

The prokaryotic plasma membrane is not only a selective barrier, but also the location of a variety of crucial metabolic processes: respiration, photosynthesis, and synthesis of lipids and cell wall constituents. Consists primarily of phospholipids and proteins

Arranged as phospholipid bilayer with scattered proteins. Phospholipids and proteins move freely within the surface giving rise to a fluid mosaic.

Fluid mosaic model

X

Membrane lipids are phospholipids

No Sterol such as cholesterol, instead bacteria has hapnoids

Phospholipid bilayer membrane

Composition of Membranes

– General structure is phospholipid bilayer Contain both hydrophobic and hydrophilic components

– Can exist in many different chemical forms as a result of variation in the groups attached to the glycerol backbone

– Fatty acids point inward to form hydrophobic environment; hydrophilic portions remain exposed to external environment or the cytoplasm

Cell membranes

Membrane lipids are amphipathic with polar and non-polar ends.

Two types of proteins Peripheral- are loosely associated to the

membrane and can be easily separated. Generally they make up between 20 and 30% of the total membrane proteins

Integral proteins- are amphipathic like the lipids, much more strongly associated to the membrane, and make up about 70 to 80% of total proteins.

Archaeal membrane

Can exist as lipid monolayers, bilayers, or mixture

Bilayer

Monolayer

General structure of lipids

Ether linkages in phospholipids of Archaea (Bacteria and Eukarya that have ester linkages in phospholipids

Diether and tetraether

Major lipids are glycerol diethers and tetraethers

The Cytoplasmic Membrane

Archaeal Membranes– Ether linkages in phospholipids of

Archaea (Bacteria and Eukarya that have ester linkages in phospholipids

– Archaeal lipids lack fatty acids, have isoprenes instead

– Major lipids are glycerol diethers and tetraethers

– Can exist as lipid monolayers, bilayers, or mixture

Membrane infoldings in bacteria

Bacteria lack membrane bound organelle like mitochondria, chloroplasts, etc…but some has plasma membrane infoldings

Plasma membrane infoldings are common and can become extensive and complex in photosynthetic or nitrogen fixing bacteria. They provide a larger surface for greater metabolic activity

STORAGE GRANULES

Bacteria exist in a very competitive environment where nutrients are usually in SHORT SUPPLY, so they tend to store up extra nutrients when possible.

Organic inclusion bodies

Glycogen- storage of glucose polymers Poly-β-hydroxybutyrate (PHB) for lipid storage

Inclusion bodies

Inorganic inclusion bodies Polyphosphate and sulfur granules.

Inorganic inclusion bodies

Magnetosomes include magnetic matter (greigite, magnetite, pyrite)

Aquaspirillum magnetotacticum

Gas Vesicles

– Confer buoyancy in planktonic cells Spindle-shaped, gas-filled structures made of protein

– Gas vesicle impermeable to water– Function by decreasing cell density– Gas vacuole is another type of inclusion

body, are present in photosynthetic bacteria and aquatic procaryotes

– Carboxysomes in photosynthetic bacteria contain the enzyme Rubisco which is used in CO2 fixation

Gas vesicles

Prokaryotic cytoskeleton

Homologous of all eukaryotic cytoskeletal elements (microfilaments, intermediate filaments, and microtubules) have been identified in bacteria. One homologous identified in archaea.

Structurally similar carry out similar functions: cell division, protein localization, cell shape.

Ribosomes

Prokaryotic ribosomes are very abundant in the cell. Structurally and functionally similar to eukaryotic ribosomes. They are the site of protein synthesis and are composed of protein and rRNA.

Smaller than eukaryotic ribosomes. 70S rather than 80S.

Bacterial ribosomes consists of small (30S) and large (50S) subunit

Ribosomes

Arrangement of DNA in Microbial Cells

Genome – A cell’s full complement of genes

Prokaryotic cells generally have a single, circular DNA molecule called a chromosome– DNA aggregates to form the nucleoid region

Ruptured cell where the chromosomes are located in the nucleoid

Nucleoid

Prokaryotic cells do not have a membrane delimited nucleus and the prokaryotic chromosome is located in an irregularly shaped region called the nucleoid.

Prokaryotes contain a single circle of double stranded DNA but some have linear DNA, and some (Vibrio cholerae and Borrellia burgdorferi) have more than one chromosome.

DNA is packaged efficiently to fit inside the cell.

Bacteria do not use histones to package their DNA

Plasmids

Plasmids

Small double strand DNA molecules that exist independently of the chromosome. They can be linear, but the majority are circular.

They have relatively few genes, but they confer a selective advantage to the bacteria in certain environments.

Plasmids replicate autonomously and can be integrated in the chromosome (episomes).

Plasmids

Conjugative plasmids: genes for the construction of hair-like structures called sex pili that help transfer of plasmids from cell to cell during conjugation (F factor).

Resistance factors: confer antibiotic resistance. A single or as many as eight resistance genes.

Bacteriocin-encoding plasmids: coding for bacteriocins that destroy other bacteria.

Col plasmids: specifically kill Escherichia coli (produce colicins)

Plasmids

Virulence plasmids: encode factors that make the bacteria more pathogenic and more able to cause serious disease.

Metabolic plasmids: carry genes for enzymes that degrade specific substances such as aromatic compounds (toluene), pesticides, and sugars (lactose).

Cell wall- Bacteria

– Responsible for the shape of the cell– Involved in virulence.– Prevention of rupture due to osmotic

pressure changes– Point of anchorage for structures.– Antibiotics site of action.

– It consists of peptidoglycan

CELL WALL - Bacteria

Bacterial cell wall consists of peptidoglycanBacteria are divided into two main

groups on the basis of their cell wall structure:

Gram positive- stained blue Gram negative- stained red

Cell walls of bacteria

Peptidoglycan

Repeating disaccharide attached to polypeptides to form a lattice.

The disaccharide portion is made of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked to adjacent rows by polypeptide chains.

Some of the amino acids are D-isomers rather than L. The presence of D-amino acids protects against degradation by most peptidases.

Structure of the repeating unit of peptidoglycan

Structure of the repeating unit of peptidoglycan

Note how glycosidic bonds confer strength on peptidoglycan in the Y direction whereas peptide bonds confer strength on the peptidoglycan in the X direction

These bridges make the peptidoglycan porous and elastic

Peptidoglycan in Escherichia coli and Staphylococcus aureus.

Gram positive cell wall Can contain up to 90% peptidoglycan The Gram positive cell wall consists of a thick

layer of peptidoglycan that contains teichoic acid.

Teichoic acid is composed of polymers of glycerol or ribitol joined by phosphate groups.

The phosphate esters contain sugars or D-alanine

Teichoic acid is either covalently bound to the peptidoglycan itself or to the cell membrane lipids (in this case it is called lipoteichoic acid).

Teichoic acid gives the outer wall negative charge

Gram positive cell wall

Gram positive cell wall

The gram-negative cell wall

•Periplasm: space located between cytoplasmic and outer membranes

Gram negative cell wall

Total cell wall contains ~10% peptidoglycan Most of cell wall composed of outer membrane

(lipopolysaccharide [LPS] layer)– LPS consists of core polysaccharide and

O-polysaccharide– LPS replaces most of phospholipids in outer

Periplasmic space ranges between 1nm to 71 nm. & constitute up to 40% of the total cell volume.

The peptidoglycan layer is generally very thin and in some species, like Escherichia coli, it can be only two sheet thick.

The periplasm of Gram negative bacteria contains enzymes important in nutrient acquisition, transport or in energy conservation.

Gram negative outer membraneThe outer membrane of Gram negative

bacteria contains LIPOPOLYSACCHARIDE

LPS is a large molecule consists of lipids and polysaccharides attached to each other by covalent bond

(LPS), LPS consists of lipid A, core, and O antigen or O polysaccharides

LPS is not a component of gram positive bacteria

Gram negative outer membrane

(LPS), LPS consists of lipid A, core, and O antigen or O polysaccharides

Gram negative outer membrane

O antigen: – Functions as antigen. It elicits the immune

response but bacteria developed ways to vary it thus avoiding the immune response

– Gives negative charge to bacterial surfaces

– It stabilizes the outer membrane– Restricts entry of antibiotics and toxic

substance that kill the bacteria

Gram negative outer membrane

Core: • The Core domain always contains an

oligosaccharide component that attaches directly to lipid A

Lipid A:• Lipid portion of LPS is called lipid A

and is an endotoxin that causes fever and shock

Gram negative outer membrane

Functions of the outer membrane:– Helps the cell to avoid phagocytosis and

complement– Impermeable to certain antibiotic (e.g.

penicillin) and digestive enzymes, detergents, heavy metals, bile salts and certain dyes.

– Allows nutrients and other substances to enter the cell through PORINS that form channels.

Damage to cell wall

Without the cell wall, bacterial cell will undergo lysis in hypotonic solutions

While bacterial cell will shrivels if it is in hypertonic solution (plasmolysis).

Osmotic pressure summary

Damage to cell wall

Lysozyme attack peptidoglycan by hydrolyzing the bond that connect the NAG and NAM destroys the cell wall.

Lysozyme treatment of gram positive in presence of hypotoinc solution - result in complete loss of the cell wall with the formation of protoplasts.

Protoplast –removal of cell wall by enzymatic digestion resulting in spherical cells

Lysozyme treatment of gram negative- destruction is partial, the peptidoglycan is lost but the outer membrane remains and spheroplasts are formed. In hypotonic solution

In hypotonic solution both spheroplasts and protoplast rupture = osmotic lysis.

Cell Walls of Archaea

No peptidoglycanTypically no outer membranePseudomurein

– Polysaccharide similar to peptidoglycan Composed of N-acetylglucosamine and N-acetyltalosaminuronic acid

Cell walls of some Archaea lack pseudomurein

Pseudomurein

Archaeal cell wall

Some archaea resemble gram positive but they contain pseudomurine, as structure similar to peptidoglycan that contain 1) L-amino acid rather than D. 2) β(1-3) glycosidic bond rather than and β(1-4).

Some archaea resemble gram negative have a layer of glycoprotein on the outside

Archaeal cell wall

S-layer consists of proteins or glycoprotein

Bacterial structure

Cell Surface Structures Capsules and Slime Layers

– Polysaccharide layers May be thick or thin, rigid or flexible

– Assist in attachment to surfaces

– Protect against phagocytosis– Resist desiccation– May be TOXIC and may stop

immune system from working properly (important in virulence اختباء

– Can be used as a source of nutrition

Cell Surface Structures

Fimbriae– Filamentous protein structures – Enable organisms to stick to surfaces

or form pellicles

Cell Surface Structures Pili

– Filamentous protein structures – Typically longer than fimbriae– Assist in surface attachment– Facilitate genetic exchange between cells

(conjugation)– (1-10 per cell) hairlike structure – Type IV pili involved in twitching motility

Flagella and motility

Protein rods (hollow) that provide means for movement to motile bacteria.

Go through the cell wall and at the base they have MOTOR that is driven by FLOW OF PROTONS.

The number and position of flagella is part of the species genetic characteristics.

The movement is described as RUN and TUMBLE

Flagella

A: Monotrichous- one flagellum B: Lophotrichous- a cluster of flagella at one or both ends C: Amphitrichous-single flagellum at each pole D: Peritrichous- flagella are spread over the whole cell

Structure and function of the flagellum in gram-negative Bacteria

L ring connected to LPS

P ring connected to the peptidoglycan

Ms ring connected to the inner membrane (periplasmic side)

C ring connected to the inner membrane (cytoplasmic side)

Flagella and Motility

Flagellar Structure– Consists of several components – Filaments are hollow , cylinders and made out of

subunits called the flagellin , it ends with a capping protein

– Hook and the basal body are wider– The basal body is the most complex and consists to

four rings connected to central rod– Move by rotation

Gliding Motility

Gliding Motility– Flagella-independent motility– Slower and smoother than swimming– Movement typically occurs along long axis

of cell– Requires surface contact– Mechanisms

Excretion of polysaccharide slimeType IV piliGliding-specific proteins

Microbial Taxes

Taxis: directed movement in response to chemical or physical gradients

حركة الوسواط– Chemotaxis: response to chemicals– Phototaxis: response to light– Aerotaxis: response to oxygen– Osmotaxis: response to ionic

strength– Hydrotaxis: response to water

Endospores

Spores are tough, dormant خاملة structure Bacteria form endospores when

environmental conditions become stressful (lack of nutrients, lack of water etc)

Mostly found in bacteria of the soil Formed during sporulation. Highly resistant

to heat, radiations, and chemicals. Can survive for a very long time (100,000 y)

It is a proper process of differentiation. The vegetative cell converts to endospore in stages.

The bacterial endospore

The life cycle of an endospore-forming bacterium

Sporulation can take up to 8 hours. Germination is much faster than sporulation

and takes only a few minutes

Endospores

Endospores.

Endospores are composed of many layers. The outermost layer is called exosporium (thin

protein cover. Under there are spore coats (endospore-specific proteins), cortex (peptidoglycan), and core.

Nucleoid is located in the core The DNA is protected by endospore-specific

proteins (SASP – small acid soluble protein)- used as a carbon source during germination

Dipicolinic acid synthesis result in increase resistance to heat and promoting dormancy

https://www.youtube.com/v/7zCQLITFEb0

Sporulation and germination

Endospores

Protein secretion

The membrane of procaryotes present a considerable barrier to movement of large molecules in or out of the cell.

However, many structures of considerable size are found outside the wall.

Also exoenzymes and other proteins are released by the cell in their environment.

The process of releasing molecules outside the cell is called protein secretion.

Sec-dependent pathway

Major pathway in both Gram positive and Gram negative bacteria

It translocates proteins across the membrane or integrates them in the membrane itself.

The machinery of the Sec pathway recognizes a hydrophobic N-terminal leader sequence (signal peptide) on proteins destined for secretion, and translocates proteins in an unfolded state, using ATP hydrolysis and a proton gradient for energy

while in Gram-negative bacteria they are responsible for export of proteins into the periplasm

Sec-dependent pathway

Two-arginine secretion (Tat)

The machinery of the Tat secretion pathway recognizes a motif rich in basic amino acid residues (S-R-R-x-F-L-K) in the N-terminal region of large co-factor containing proteins and translocates the proteins in a folded state using only a proton gradient as an energy source

Tat pathway moves proteins across the plasma membrane then deliver it to type II, it transports folded protein

Secretion in gram negative bacteria Six different secretion system have been

identified in Gram-negative bacteria In Gram-negative bacteria, some secreted

proteins are exported across the inner and outer membranes in a single step via the type I, type III, Type IV or type VI pathways

Other proteins are first exported into the periplasmic space via the universal Sec or two-arginine (Tat) pathways and then translocated across the outer membrane via the type II, type V or less commonly, the type I or type IV machinery

Bacterial secretion system

Summary of known bacterial secretion systems. In this simplified view only the basics of each secretion system are sketched. HM: Host membrane; OM: outer membrane; IM: inner membrane; MM: mycomembrane; OMP: outer membrane protein; MFP: membrane fusion protein. ATPases and chaperones are shown in yellow.

Transport and Transport Proteins

ABC (ATP-Binding Cassette) Systems >200 different systems identified in prokaryotes– Often involved in uptake of organic

compounds (e.g., sugars, amino acids), inorganic nutrients (e.g., sulfate, phosphate), and trace metals

– Typically display high substrate specificity

– Contain periplasmic binding proteins

Mechanism of an ABC transporter