Functional Anatomy of Prokaryotic and Eukaryotic Cells

Biol 3400

Tortora et al – Chap 4

Functional Anatomy of Prokaryotic and Eukaryotic Cells

I.Introduction

Prokaryotic and eukaryotic cells are similar in a number of ways including

Chemically similar – contain macromolecules: Nucleic acids, proteins, lipids and polysaccharides’
Similar metabolic reactions to metabolize food, synthesis proteins and nucleic acids and store energy
Contain a membrane, cytoplasm, DNA and ribosomes

Prokaryotic and eukaryotic cells differ in a number of ways (Table 4.2) including

Prokaryotic cells

DNA is usually in the form of a single circular dsDNA chromosome and not enclosed in a membrane
DNA is not associated with histones; other proteins are associated with DNA
They lack membrane bound organelles
Usually divide by binary fission

Eukaryotic cells

DNA is usually in the form of multiplelinear dsDNA chromosomes found in a membrane bound nucleus
The DNA is consistently associated with chromosomal proteins called histones and with nonhistone proteins
They may have a number of membrane bound organelles, including endoplasmic reticulum, Golgi complex, lysosomes, vacuoles, mitochondria and chloroplasts
Cell division usually involves mitosis

Prokaryotic cells: Archaea (member of Archaeal domain = archaeon) and Bacteria (member of Bacterial domain = bacterium)

Prokaryotic cell structures include the following (Fig. 4.6; Note: Underlined structures are found in all prokaryotic cells):

Plasma membrane
Cytoplasm
Nucleoid region
Ribosomes
Cell wall (and periplasmic space)
Flagellum
Pili and Fimbriae
Inclusions
Gas vacuole
Capsule and slime layers
Endospores

Eukaryotic cells: Protozoa, Fungi and Algae

Eukaryotic cell structures include the following (Fig. 4.22; Note: not all cells possess all of these structures at all times):

Plasma membrane

Cell wall

True nucleus - membrane bound nucleus

Ribosomes

Membrane bound organelles

chloroplast

mitochondrion

endoplasmic reticulum

vacuoles

golgi apparatus

lysosomes

peroxisomes

Cytoskeleton

Flagellum/Cilium

II.Cell Morphology

A. Prokaryotic Cells

Two most common cell shapes

coccus (pl.cocci) e.g.,
bacillus (pl. bacilli) e.g.,

Other shapes include:

spirillum (pl. spirilli) e.g.,
Mycelial – e.g., Actinomycetes
Stalked – e.g., Caulobacter, Hypomicrobium
Plates
Star shape

Some prokaryotes are variable in shape and lack a single characteristic form = pleomorphic

e.g.,

B. Eukaryotic Cells

Highly variable: cell shapes vary in shape from sphere and cylinders to very irregular nerve cells.

C. Cell Size

Cells come in a variety of sizes & shapes
Size limit is set by the logistics required to carry out metabolism

The smallest cells are nanobacteria (diameter of 0.05 to 0.2 µm).
Mycoplasmas = 0.2 µm in diameter

What factors constrain the lower size limit of cells?

Most bacterial cells are 10 times larger than mycoplasmas (1 to 10 µm in diameter)

Eukaryotic cells are typically 10 times larger than bacteria (10 - 100 µm in diameter).

What factors constrain the upper size limit of cells?

Generally prokaryotic cells are smaller than eukaryotic cells. But there are exceptions.

e.g., Epulopisciumfishelsonisize up to 80 x 600 µm

Thiomargaritanamibiensissize up to 750 µm in diameter

Nanochlorumeukaryotum1 to 2 µm in diameter

Generally cells are microscopic. But there are exceptions

Loligo - Atlantic squid has neurons with axon diameters as large as 1.0 mm.

Ostrich egg

IIICell Components

A. Plasma membrane

Every cell is surrounded by a plasma membrane (also known as a cytoplasmic or cell membrane)
Encloses the cytoplasm
This is an important feature distinguishing archaea from bacteria and eukaryotes

Membranes are selectively permeable barriers - Why?

What is the function of the plasma membrane?

Fluid mosaic model (Fig 4.14)

S.J. Singer and G. Nicolson (1972)
Dynamic structure
bifacial quality – sidedness
5 – 10 nm thick

1. Membrane components

i. Lipids

backbone or basic fabric
often as a lipid bilayer (amphipathic)

hydrophobic core

hydrophilic exterior surfaces

ii. Proteins

integral (70 to 80 % of the membrane proteins)
peripheral (20 to 30% of the membrane proteins)

Functions

Transport – import and export
Enzymes
Receptors
Intracellular junctions
Cell to cell recognition
Metabolic processes

iii. Carbohydrates

Usually associated with the outer surface of the membrane

2. Differences between bacterial, eukaryotic and archaeal membranes

i. Bacterial membranes

Like eukaryotes, most of the membrane lipids are phospholipids
unlike eukaryotes bacteria lack sterols such cholesterol but contain sterol like compounds called hopanoids. The role of hopanoids is likely similar to steroids – stabilized membranes.
Some bacteria may have extensive in folding of the plasma membrane to increase membrane surface area for the purpose of greater metabolic activity

Glycerol diesters(phospholipids)

Glycerol bonded to phosphate (negatively charged) and two fatty acids
Linkage between fatty acids and glycerol is an ester linkage

Ester linkageR-O-C-(CH2)n CH3

Environmental conditions affect fatty acid composition of membranes

Fatty acids are generally unbranched and 16 to 18 carbons long

e.g.,palmitic acid CH3(CH2)14 COOH

stearic acid - 18 carbons

Fatty acids may be saturated or unsaturated

Membrane composition also varies with species and these differences can be used to identify bacteria (Fatty acid methyl ester analysis - FAME).

ii. Eukaryotic membranes

generally the same structure as bacterial membranes including phospholipids but differs in the major lipids: phospholipids, sphingolipids and cholesterol.
Microdomains that differ in protein and lipid composition may be found – lipid rafts – span membrane and appear to be involved in a variety of cellular processes (e.g., signal transduction and cell movement)

Sterols

compounds consisting of carbon skeleton of 4 interconnected rings
targets for polyene antibiotics - damage cell membranes
Mycoplasmas acquire sterols from eukaryotic cells

iii. Archaeal membranes

Many are thought to be “Extremophiles”
Membranes are distinctive
Phospholipids are not the main structural components
Have branched chain hydrocarbons attached to glycerol by ether linkages

Glycerol diethers

Ether linkageR-C-O-C-R

Bilayers

glycerol bound to branched hydrocarbons (e.g., phytanyl) by ether linkage
glyceroldiethers

Monolayers

diglyceroltetraether
often found in extreme thermophiles

Phosphate, sulfur and sugar containing groups are attached to the third carbon of glycerol resulting in a polar lipids that are the predominant lipids (70 – 93%) in the membrane
Nonpolar lipids (squalene derivatives) make up the rest of the membranes

3. The movement of materials across membranes

Review this material on your own – it is largely review from Biol 1010. You should be familiar with the following

Passive Transport

Simple diffusion
Facilitated diffusion
Transporter proteins
Osmosis
Aquaporin
Osmotic pressure

Active Transport

Group translocation

B. Cell walls

1. Bacterial cell walls

Functions

Define cell shape
Protection from osmotic shock (turgor pressure) and toxic substances
Point of anchorage for flagella
May contribute to pathogenicity
Most bacteria have cell walls but there are exceptions – e.g., mycoplasmas
Forms a strong, protective layer that is relatively porous, elastic and somewhat stretchable

Gram positive and Gram negative (Fig. 4.13)

Can be differentiated through the Gram stain - an important diagnostic tool.

Gram negative
Gram positive
Gram variable

i. Peptidoglycan (murein)

Components

a. Polysaccharide

1,4 linkages between N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) monomers

(Fig 4.12).

Note: N-acetylmuramic acid is found only in Bacteria
Polymers 10 to 65 monomers long

...NAM – NAG- NAM- NAG- NAM- NAG...

b. Peptide chains

Tetrapeptide chains linked to M residues - composed of unusual amino acids (D- amino acids) – Why?

L-alanine
D-glutamic acid
L-lysine (Gram positive) or diaminopimelic acid (DAP; Gram negative)
D-alanine

There are either peptide interbridges (G-G-G-G-G: Gram positive) or direct peptide linkages (Gram negative) between tetrapeptides Results in a strong multilayer sheet or sacculus

Autolysins - enzymes used by the bacteria to recycle, reshape or restructure cell wall

Lysozyme

Hydrolyes the 1,4 linkages between M and G monomers

Sources of lysozyme

predators
tears
saliva
chicken egg white

spheroplast - partial removal of cell wall

protoplast - complete removal of cell wall

Penicillin

Prevents formation of peptides cross linkages between tetrapeptides
Penicillin binds to transpeptidase
Not effective against bacteria lacking cell walls such as mycoplasmas

ii. Gram positive cell wall

Up to 20% of the organism
peptidoglycan represents 50-90% of this structure
relatively thick (ca. 40 nm – ranges from 20 to 80 nm)
a thick peptidoglycan layer is more resistant to desiccation
Polysaccharides such as teichoic acids (e.g., glycerophosphate or ribitol phosphate residues – negatively charged) or teichuronic acids are bonded to the peptidoglycan or plasma membrane lipids
Putative function- bind to cations and regulate movement into and out of the cell

- Prevent extensive cell wall lysis

Responsible for cell wall’s antigenicity

e.g., Bacilli, Staphylococci, Streptococci

iii. Gram negative cell envelope

more complex than Gram positive cell wall

Cell wall

thin layer of peptidoglycan (ca. 2 to 7 nm)
1 - 10 % of the cell wall
lipoproteins instead of teichoic acids

Outer membrane - lipid bilayer

phospholipids
proteins - e.g., porins
lipoproteins – anchored to peptidoglycan
The outer membrane may be linked to the plasma membrane in a number of places
lipopolysaccharides (LPS)

composed of i) lipid A, ii) the core polysaccharide and iii) the O polysaccharide side chain.
main structural component of outer half of outer membrane believed to aid in creating a permeability barrier as well as contributes to negative charge of the cell surface.
Protects pathogenic bacteria from host defenses
The LPS (Lipid A componenet in particular) is frequently toxic to animals and known as endotoxin (i.e., because it is still attached to cell).
O polysaccharide is an antigen that is used to distinguish species of bacteria

The outer membrane is more permeable than the plasma membrane to most small molecules due to the presence of porin proteins
Less permeable than the plasma membrane to hydrophobic and amphipathic molecules - makes cells less susceptible to certain antibiotics.
Keeps periplasmic enzymes from diffusing away.

Periplasmic space (30 - 70 nm wide)

Gel-like in consistency due to abundance of proteins

Import region where number of chemical reactions occur:

oxidation-reduction reactions
osmotic regulation
solute transport
hydrolysis
protein secretion

2. Archaeal cell wall

No peptidoglycan, in particular lacking in N-acetylmuramic acid
May be composed of

Pseudopeptidoglycan – N-acetylglucosamine and N-acetyltalosaminuronic acid linked by 1,3 linkages
Protein or glycoproteins - most common form of cell wall
Polysaccharide

NOTE: Some Bacteria and Archaea do not have cell walls

e.g.,mycoplasma

Thermoplasma

3. Eukaryotic cell wall

Like Bacteria and Archaea, not all eukaryotes have cell walls

Algal cell wall

Polysaccharides are the major components

e.g., cellulose

May contain high concentrations of calcium or silicon - diatoms

Fungi

Many contain chitin - polysaccharide consisting of N-acetylglucosamine monomers.
Composition is used in classification schemes

e.g., primitive Chytridiomycetes fungal cell walls lack chitin but contain cellulose

Protists

Many protists have a pellicle for support – rigid layer of components beneath the plasma membrane.
Pellicle is composed of protein

C.Layers External to the Cell Wall

Prokaryotes

Prokaryotes have a variety of layers outside the cell wall

Functions

protection

ingestion

dehydration

loss of nutrients

attachment
pathogenicity

Form thick or thin, rigid or flexible layers depending upon composition
Variable composition – glycoproteins and polysaccharides

1. Capsule

Rigid – tight matrix that excludes particles
protein or polysaccharide

2. Slime layer

loosely bound layer – easily deformed

3. Extracellular Polymeric Substance (EPS)

glycocalyx that helps cells bind to surfaces and other cells – formation of biofilm

Glycocalyx – term that collectively refers to both capsule and slime layer

3. Surface layer (S-layer)

nearly all bacteria and Archaea
crystalline protein layer
unknown function – may function as permeability or protective barrier

D.Genetic Information

Deoxyribonucleic acid (DNA) - macromolecule consisting of nucleotide monomers

Backbone = 5'...-Phosphate-Sugar-Phosphate-Sugar -Phosphate-Sugar-…3'

Nucleotide = nucleoside plus phosphate

Nucleoside = deoxyribose + nitogenous base

Purines – adenine & guanine

Pyrimidines - cytosine & thymine

Review structure of DNA – Chapter 2

1. Bacterial and Archaeal DNA

These organisms do not have a nucleus – the bulk of the genetic material is found in the nucleoid region

Chromosome

single double stranded DNA molecule in the form of a covalently closed circular chromosome – also known at the genophore
Exceptions: Borreliaburgdorferi and some Streptomyces spp. have a linear chromosome; Rhodobactersphaeroides has two circular chromosomes

usually only one chromosome and it may be present as multiple copies in rapidly growing cells

DNA arranged into supercoiled domains that are stabilized with structural proteins

In some Archaea – DNA is extensively complexed with proteins that closely resemble histone proteins of eukaryotic organisms

Plasmids

autonomously replicating units that usually contain only a few genes (< 30; 1 – 5% of the size of the chromosome). Most the bacterial and archaeal genomes sequenced contain plasmids
Usually covalently closed circles (CCC) but may be linear
May contain one to many plasmids
Range in size from several kbp to Mbp

Examples of plasmid coded factors (Table 3.3)

R-plasmids - antibiotic resistance genes
Bacteriocins
Conjugal factors
Metabolic factors - substrate utilization or fixation
Virulence factors - toxin production

2. Eukaryotic DNA

Most possess a nucleus that contains the bulk of the genetic material
Nucleus contains a number of linear chromosomes
Chromosomes composed of DNA complexed with protein  chromatin
DNA associated with Histones in structural subunits called nucleosomes

Chloroplasts and mitochondria also contain small circular genomes

E.Ribosomes

Sites of protein synthesis

Approximately 20 - 25 nm in diameter
Large numbers may be present in cells (>10,000 in bacterial cells and more in eukaryotic cells)
Number varies depending on the level of protein synthesis going on in the cell.

Bacteria andEukarya

Archaea

Ribosome70 S*80S

Large subunit50 S60S

23S rRNA and 5S rRNA25 - 28S rRNA and 5.8S rRNA

Large number of proteinsLarge number of proteins

e.g., 34 proteins in E. coli

Small subunit30S40S

16S rRNA18S rRNA

Large number of proteinsLarge number of proteins

e.g., 21 proteins in E. coli

* Svedberg units (S)

Eukaryotic organisms have 70S ribosomes in their mitochondria and chloroplasts

Implications in the endosymbiotic theory

Practical implications of ribosome structural differences

Antibiotic treatment

chloramphenicolall bind 70S bacterial

tetracyclineribosomes and disrupt protein

kanamycinsynthesis

erythromycin

streptomycin

diptheria toxinbind 70S archaeal and 80S eukaryotic ribosomes and

anisomycindisrupts protein synthesis

F.Cytoskeleton

Prokaryotic Cells

For many years it was thought that prokaryotic cells lacked cytoskeletal elements. Recently homologues have been discovered for all three elements of the eukaryotic cytoskeleton

e.g., FtsZ – tubulin homologue; widely observed in Bacteria and Archaea

MreB – actin homologue; Many rod shaped cells

Crescentin – intermediate filament proteins; Caulobacter

Eukaryotic Cells

Have a well developed three dimensional network of fibrous proteins (microtubules, microfilaments and intermediate filaments
Microtubules and microfilaments are very dynamic structures – can be quickly disassembled and assembled elsewhere

Functions

Support
Maintenance of cell shape
Cell movement - e.g., muscle cell contraction, amoeboid movement, cilia
Cell division (mitosis, cytokinesis and meiosis)
Cell wall deposition
Provides spatial organization and movement of organelles and cytosolic enzymes
Regulation of biochemical activities in the cell – mechanical signaling

Cytoskeleton components

a) Microtubules

thickest cytoskeletal elements - hollow rods - 25 nm
found in the cytoplasm of all eukaryotes
composed to and tubulindimers
readily assembled and disassembled
grow by addition of subunits to ends
centrosome - microtubule organizing centre (MOC) important in cell division
a pair ofcentioles (9 sets of microtubule triplets) often found in the centrosome region of animal cells. Replicate during cell division. May function in cell division but not necessary as they are generally not found in plant cells.

Functions

compression resisting function
cell motility (flagella and cilia)
chromosome movement
organelles movement
cell shape

b) Microfilaments

thinnest cytoskeletal element - 7 nm in diameter
composed of protein called actin
readily assembled and disassembled

Functions

tension bearing function
muscle contraction (myosin motors molecules-burn ATP)
cytoplasmic streaming (myosin motors molecules-burn ATP)
cell motility (pseudopodia)
cell division
cell shape – three dimensional network just inside the plasma membrane

c) Intermediate filaments

8 to 12 nm in diameter
diverse class composed of different protein subunits including keratins
more permanent structures not readily assembled and disassembled like microtubules and microfilaments

Functions

tension bearing function
maintenance of cell and organelle shape e.g. nuclear lamina
fixing positions of certain organelles

G.Motility

Bacterial and Archaeal Movement

1. Flagellum (pl. flagella)

one to many flagella
up to 60 cell lengths/s

Atrichous – no flagella

Monotrichous - single polar flagellum

Amphitrichous - single flagellum at each pole

Lophotrichous - polar tuft of flagella

Peritrichous - multiple flagella disgributed over the entire cell

Parts of a prokaryotic flagellum (Fig 4.8)

i. filament - whiplike extension that rotates - helical in shape – 15 to 20 µm long

composed of flagellin – highly conserved in bacteria

ii.curvedhook - single protein - connects filament to motor

iii.Basal apparatus or motor composed of many proteins (~30)

central rod  a series of rings embedded in the cell wall, plasma membrane and outer

membrane (Gram negative cells). This structure is around 20 nm in diameter

Mot proteins drive the flagellar motor - energy comes from proton motive force (about 1000

H+/rotation)

Fli proteins act as a switch

> 40 genes (fla, fli, flg) required for synthesis and motility (structural, export of components

and timing of synthesis)

2. Gliding

cells glide along a surface.
Mechanism is unknown but there are several models

a)excreted slime adheres to surface pulls cells along - cyanobacteria

b)movement of surface proteins - Flavobacterium

3. Gas Vesicles

confer buoyancy on cells and allow to move up and down in a water column
composed of two types of protein (97% of the gas vacuole is composed of GvpA (-sheets). The remainder is made of GvpC (-helix) that acts like a cross linker between the GvpA molecules

4. Behavioural Responses to Stimuli

In a heterogenous environment prokaryotes are capable of movement (taxis; pl. taxes) towards or away from stimuli (light, heat, chemicals and electricity)

Chemotaxis

movement towards or away from a chemical stimulus (chemoattractant or chemorepellent).
Respond to temporal gradient
Respond to very low levels of some materials – 10-8 M for some sugars

Types of Taxes

phototaxis - light stimulus

scotophobotaxis - entering darkness has a negative effect on a cell

geotaxis - gravitational stimuli

magnetotaxis - magnetic stimuli

aerotaxis – oxygen stimulus

osmotaxis – high osmotic strength stimulus

Bacteria lack spatial sensing capabilities- they are too small to sense a gradient along the cell length. Consequently they respond in a temporal fashion.

1.Periodically sample environment e.g., chemoreceptors – sensory proteins

2. Process information through a signal transduction pathway