Cell Structure and Function: Eukaryotic Nucleus

Cell Structure and Function

• Eukaryotic cells differ from prokaryotic cells in several ways, with eukaryotes displaying a cytologically distinct nucleus.
• The nucleus is the organizational and regulatory center for biochemical and hereditary processes in eukaryotes.
• The eukaryotic nucleus has a double-layered membrane with pores, with the outer surface containing tubules that transcend both membrane layers.

Eukaryotic Nucleus

• Eukaryotes, including protozoa, algae, fungi, and metazoans, have a discrete membrane-bound nucleus.
• Examples of eukaryotic cells with a nuclear membrane include mammalian cells, amoebeae, and myxomycetes.
• The eukaryotic nucleus has a nucleolus and ribosomes.

Bacterial Nucleoids

• In most bacteria, the DNA-containing region is folded into a cytologically distinct region without a nuclear membrane, known as the nucleoid.
• The nucleoid is not bound by a nuclear membrane and is generally smaller than the eukaryotic nucleus.

Comparison of Cell Components

• Eukaryotes have a true nucleus, nuclear membrane, nucleolus, and 40S, 60S/80S ribosomes.
• Prokaryotes lack a true nucleus, nuclear membrane, and nucleolus, and have 30S, 50S/70S ribosomes.
• Archaebacteria have characteristics distinct from both eukaryotes and eubacteria, including a lack of a cell wall peptidoglycan.

Cellular Structure and Function

• Eubacteria and archaebacteria differ in several characteristics beyond those listed in the table.
• Some species of eubacteria and archaebacteria have been shown to have a nuclear membrane.

Bacterial Nucleoids

• In most bacteria, the DNA-containing region (chromosome) is folded into a cytologically distinct region called the nucleoid.
• The nucleoid is not bound by a nuclear membrane.

Eukaryotic Cells

• Eukaryotic cells differ from prokaryotic cells in several major ways (Table 7-1).
• Lower eukaryotes (protozoa, algae, and fungi) lack some distinguishing features of metazoan cells.
• All eukaryotic cells appear to be similar versions of the same overall plan.

The Eukaryotic Nucleus

• Eukaryotes (Eukarya) display a cytologically distinct nucleus, which is the organizational and regulatory center for biochemical and hereditary processes.
• The eukaryotic nucleus has a well-defined nuclear membrane composed of at least two distinct layers.
• The outer surface of the nuclear membrane contains pores with tubules that transcend both membrane layers.

Cytoplasmic Membranes

• The cytoplasmic membrane of bacterial cells is a bimolecular lipid leaflet of phospholipid molecules aligned at their hydrophobic ends.
• The phospholipids are hydrophilic and face the external or outside of the membrane and the internal or cytoplasmic side of the membrane.
• The cell membrane serves as a permeability barrier, preventing most solutes from gaining entrance to the cytoplasm except through specific transport proteins present in the membrane layer.

Peptidoglycans of Bacterial Cell Walls

• Peptidoglycan is a heteropolymer of repeating units of β-1,4-N-acetylglucosamine (NAG) and N-acetyl-muramic acid (NAM).
• The glycan linkages of peptidoglycan are uniform in all bacteria, with every D-lactyl group of NAM being peptide-substituted.
• Glycans have short tetrapeptide units terminating with D-alanine or occasionally tripeptide units lacking the terminal D-alanine.
• The L-alanine at the N-terminus can be replaced by glycine.
• Interpeptide bridges linking peptidoglycans are of four major types.

Structure of Bacterial Cell Walls

• B. subtilis 168 has an amorphous wall fabric above the plasma membrane.
• E. coli has a thin peptidoglycan murein layer above the plasma membrane, over which lays a wavy outer membrane.
• Clostridium thermosaccharolyticum has a wall profile intermediate between gram-positive and gram-negative formats.
• Methanococcus voltae, an archaebacterium, has only a thin S-layer above the plasma membrane as its sole wall layer.

Yeast Cell Walls

• Yeast cell walls contain 29% β-glycans, 31% mannan, and 13% protein.
• The mannan-rich outer layer of the wall contains a higher proportion of 1,6-β-glycan.
• Yeast cell walls also contain small percentages of lipids and other materials.
• Chitin is present in small amounts in vegetative cells of yeast, being confined almost entirely to the ring encircling the septum of budding yeast.

Prokaryotic Cell Surfaces

• Peptidoglycan is the major backbone of the murein sacculus of the cell wall of both gram-positive and gram-negative bacteria.
• Archaea produce a pseudomurein and an associated surface layer (S-layer) composed of protein or glycoprotein.
• In many archaebacteria, the S-layer may represent the only surface component outside the plasma membrane.

Surface Layers of Bacteria

• Bacteria from all major phylogenetic groups produce a crystalline cell surface layer (S-layer) as the outermost component of the cell.

Cytoplasmic Membranes

• The cytoplasmic membrane of bacterial cells is a bimolecular lipid leaflet of phospholipid molecules aligned at their hydrophobic ends.
• The polar phospholipids are hydrophilic and face the external or outside of the membrane and the internal or cytoplasmic side of the membrane.
• The cell membrane serves as a permeability barrier, preventing most solutes from gaining entrance to the cytoplasm except through specific transport proteins present in the membrane layer.

Outer Membrane Structure

• The outer membrane of gram-negative bacteria appears as an asymmetric bilayer.
• The external layer is primarily composed of Lipopolysaccharides (LPS).
• LPS is composed of:
  • O-Antigen repeat
  • Core region (including GlcNAc, Glucose, Galactose, Heptose, and KDO)
  • Lipid A
• The inner layer is composed of phospholipids.

Outer Membrane Proteins

• OmpA:
  • Stabilizes outer membrane and mating aggregates in F-dependent conjugation.
  • Receptor for phage TuII.
• Murein lipoprotein (Braun's lipoprotein):
  • Most abundant surface protein in E. coli and S. enterica.
  • Major structural protein.
  • Stabilizes cell surface in conjunction with OmpA.
• Porins:
  • OmpB (porin): diffusion channel for various metabolites including maltose.
  • LamB (maltoporin): specific porin for maltose and maltodextrin; receptor for bacteriophage λ.
  • OmpC (porin): diffusion channel for small molecules; receptor for phages TuIb and T4.
  • OmpF (porin): diffusion channel for small molecules; receptor for phages TuIa and T2.
• Other proteins:
  • OmpT: protease.
  • PhoE (protein E): anion-selective diffusion channel induced under phosphate limitation.
  • Protein P: anion-selective diffusion channel in Pseudomonas aeruginosa; induced under phosphate limitation.
  • TolA: maintenance of OM integrity; activity of group A colicins.
  • TonA: ferrichrome siderophore uptake; receptor for phages T1, T5, 80, and colicin M.
  • TonB: siderophore-mediated iron transport; B12 transport.
  • Tsx: nucleoside-specific channel; receptor for T-even phages and colicin K.

Cytoplasmic Membrane

• The cytoplasmic membrane is a bimolecular lipid leaflet of phospholipid molecules.
• The polar phospholipids are hydrophilic and face the external or outside of the membrane and the internal or cytoplasmic side of the membrane.
• The cell membrane serves as a permeability barrier, preventing most solutes from gaining entrance to the cytoplasm except through specific transport proteins present in the membrane layer.

Cell Membrane Structure

• The outer membrane of gram-negative bacteria contains phospholipids and outer membrane proteins (OMPs), such as porins, which form large water-filled pores with diameters of 1-2 nm.
• The pores regulate the access of hydrophilic solutes to the cytoplasmic membrane.

Lipopolysaccharides (LPS)

• LPS consists of three basic components: O-antigen (region I), core region (region II), and lipid A (region III).
• The O-antigen region contains repeating carbohydrate units that determine the immunological specificity of the bacterium.
• The core region consists of an outer and an inner core, with the outer core showing high-to-moderate structural variability and the inner core showing very low variability.
• Lipid A is embedded in the outer membrane and consists of a chain of D-glucosamine disaccharide units with all hydroxyl groups substituted.
• The substituents on lipid A include core polysaccharide units and long-chain fatty acids, such as β-hydroxymyristic acid.

Lipopolysaccharide Structure

• The oligosaccharide subunits of the core region of E. coli and Shigella differ only slightly from those of Salmonella.
• The unique octose sugar, 2-keto-3-deoxyoctulosonic acid (KDO), is a common component of the core region of most gram-negative organisms.
• An average of three LPS subunits are linked together through pyrophosphate bridges between the lipid A molecules.

Outer Membrane Proteins (OMPs)

• OMPs, such as OmpA, are tightly associated with LPS and contribute to the stability of the outer membrane.
• OmpA spans the membrane and is cross-linked to the underlying peptidoglycan layer.
• OmpA is exposed at the surface, where it serves as a receptor for T-even phage and plays a role in conjugation and the action of colicins K and L.

Lipoteichoic Acids (LTAs)

• LTAs are membrane-associated polymers characteristic of gram-positive bacteria.
• LTAs are linear polymers of 16-40 phosphodiester-linked glycerol phosphate residues covalently linked to a membrane anchor.
• Physiological roles postulated for LTA include regulation of autolysin activity, scavenging of divalent cations, and interaction of bacteria with cells of infected hosts.

Lipoteichoic Acid Synthesis

• The synthesis of LTA occurs in three phases: the glycolipid anchor, the poly(glycerophosphate) component, and the D-alanyl esters linked to poly(glycerophosphate).
• The diglucosyldiacylglycerol moiety of LTA functions as the membrane anchor in S. aureus.

Cell Membrane Structure

• The outer membrane of gram-negative bacteria contains phospholipids and outer membrane proteins (OMPs), such as porins, which form large water-filled pores with diameters of 1-2 nm.
• The pores regulate the access of hydrophilic solutes to the cytoplasmic membrane.

Lipopolysaccharides (LPS)

• LPS consists of three basic components: O-antigen (region I), core region (region II), and lipid A (region III).
• The O-antigen region contains repeating carbohydrate units that determine the immunological specificity of the bacterium.
• The core region consists of an outer and an inner core, with the outer core showing high-to-moderate structural variability and the inner core showing very low variability.
• Lipid A is embedded in the outer membrane and consists of a chain of D-glucosamine disaccharide units with all hydroxyl groups substituted.
• The substituents on lipid A include core polysaccharide units and long-chain fatty acids, such as β-hydroxymyristic acid.

Lipopolysaccharide Structure

• The oligosaccharide subunits of the core region of E. coli and Shigella differ only slightly from those of Salmonella.
• The unique octose sugar, 2-keto-3-deoxyoctulosonic acid (KDO), is a common component of the core region of most gram-negative organisms.
• An average of three LPS subunits are linked together through pyrophosphate bridges between the lipid A molecules.

Outer Membrane Proteins (OMPs)

• OMPs, such as OmpA, are tightly associated with LPS and contribute to the stability of the outer membrane.
• OmpA spans the membrane and is cross-linked to the underlying peptidoglycan layer.
• OmpA is exposed at the surface, where it serves as a receptor for T-even phage and plays a role in conjugation and the action of colicins K and L.

Lipoteichoic Acids (LTAs)

• LTAs are membrane-associated polymers characteristic of gram-positive bacteria.
• LTAs are linear polymers of 16-40 phosphodiester-linked glycerol phosphate residues covalently linked to a membrane anchor.
• Physiological roles postulated for LTA include regulation of autolysin activity, scavenging of divalent cations, and interaction of bacteria with cells of infected hosts.

Lipoteichoic Acid Synthesis

• The synthesis of LTA occurs in three phases: the glycolipid anchor, the poly(glycerophosphate) component, and the D-alanyl esters linked to poly(glycerophosphate).
• The diglucosyldiacylglycerol moiety of LTA functions as the membrane anchor in S. aureus.

Outer Membrane Structure

• The outer membrane of Gram-negative bacteria consists of an outer layer containing lipopolysaccharides (LPS) and an inner layer containing primarily phospholipids.
• Outer membrane proteins (OMPs), called porins, form large water-filled pores with diameters of 1 to 2 nm that traverse the membrane and regulate the access of hydrophilic solutes to the cytoplasmic membrane.

Lipopolysaccharides (LPS)

• LPS consists of three basic components or regions: the O-antigen region, the core region, and lipid A.
• The O-antigen region (Region I) contains repeating carbohydrate units that represent the “O” antigen, which determines the immunological specificity of the bacterium.
• The core region (Region II) consists of an outer and an inner core, with the inner core showing very low structural variability.
• Lipid A (Region III) is embedded in the outer membrane and has been extensively studied in Salmonella.
• The chemical composition of lipid A consists of a chain of D-glucosamine disaccharide units with all of the hydroxyl groups substituted with long-chain fatty acids.

Lipid A Structure

• The most commonly observed fatty acid in lipid A is β-hydroxymyristic acid (3-hydroxy-tetradecanoic acid), a C14 saturated fatty acid.
• The hydroxyl groups of lipid A are also esterified with other long-chain fatty acids such as lauric, myristic, and palmitic acids.
• An average of three lipid A subunits are linked together through pyrophosphate bridges.

Outer Membrane Proteins (OMPs)

• OMPs play a variety of overlapping roles in the physiology of the cell, including regulation of the access of hydrophilic solutes to the cytoplasmic membrane.
• OmpA is a major OMP that contributes to the stability of the outer membrane, spans the membrane, and is cross-linked to the underlying peptidoglycan layer.
• OmpA is exposed at the surface, where it serves as a receptor for T-even phage and plays a role in conjugation and the action of colicins K and L.

Lipoteichoic Acids (LTAs)

• LTAs are membrane-associated polymers characteristic of Gram-positive bacteria.
• LTAs are linear polymers of 16 to 40 phosphodiester-linked glycerol phosphate residues covalently linked to a membrane anchor (generally a glycolipid or glycophospholipid).
• Physiological roles postulated for LTA include regulation of autolysin activity, scavenging of divalent cations, electromechanical properties of the cell wall, and interaction of bacteria with cells of infected hosts.

Peptidoglycan Structure

• Peptidoglycan is a heteropolymer composed of repeating units of β-1,4-N-acetylglucosamine (NAG) and N-acetyl-muramic acid (NAM)
• Glycan linkages of peptidoglycan are uniform in all bacteria
• Every D-lactyl group of NAM is peptide-substituted
• Glycans have short tetrapeptide units terminating with D-alanine or occasionally tripeptide units lacking the terminal D-alanine

Peptidoglycan Interpeptide Bridges

• Interpeptide bridges linking peptidoglycans are of four major types
• The proportion of peptide cross-linking varies between bacteria

Bacterial Cell Walls

• The cell wall of B. subtilis 168 has an amorphous wall fabric that lies directly above the plasma membrane
• E. coli has a thin peptidoglycan murein layer above the plasma membrane, with a wavy outer membrane above it
• The region between the outer and plasma membranes is called the periplasm or periplasmic space

Cytoplasmic Membranes

• The cytoplasmic membrane is a bimolecular lipid leaflet of phospholipid molecules aligned at their hydrophobic ends
• The polar phospholipids are hydrophilic and face the external and internal sides of the membrane
• Various proteins and other components of the cell may be partially or wholly embedded in the membrane layer
• The cell membrane serves as a permeability barrier, preventing most solutes from entering the cytoplasm except through specific transport proteins

Cell Wall Polymers

• Chemical structures of cell wall polymers include cellulose, chitin, glucan, and mannan
• Yeast cell walls contain 29% β-glycans, 31% mannan, and 13% protein

Prokaryotic Cell Surfaces

• Peptidoglycan is the major backbone of the murein sacculus of the cell wall of both gram-positive and gram-negative bacteria
• Archaea produce a pseudomurein and an associated surface layer (S-layer) composed of protein or glycoprotein
• The S-layer may represent the only surface component outside the plasma membrane in many archaebacteria

Surface Layers of Bacteria

• Bacteria from all major phylogenetic groups produce a crystalline cell surface layer (S-layer) as the outermost component of the cell
• The S-layer can be attached to the peptidoglycan-containing sacculus or the outer membrane in different bacteria

Peptidoglycans of Bacterial Cell Walls

• Peptidoglycan is a heteropolymer of repeating units of β-1,4-N-acetylglucosamine (NAG) and N-acetyl-muramic acid (NAM).
• Glycan linkages of peptidoglycan are uniform in all bacteria with every D-lactyl group of the NAM being peptide substituted.
• All glycans have short tetrapeptide units terminating with D-alanine or occasionally tripeptide units lacking the terminal D-alanine.
• L-alanine at the N-terminus can be replaced by glycine.
• Interpeptide bridges linking peptidoglycans are of four major types.

Cell Wall Structure

• Cell wall profile of B. subtilis 168 shows amorphous wall fabric directly above the plasma membrane.
• Escherichia coli has a thin peptidoglycan murein layer above the plasma membrane, overlaid by a wavy outer membrane.
• Clostridium thermosaccharolyticum has a wall profile intermediate between gram-positive and gram-negative formats, with a peptidoglycan layer and a proteinaceous S-layer.
• Methanococcus voltae has a thin S-layer as its sole wall layer.

Cytoplasmic Membranes

• Cytoplasmic membrane is a bimolecular lipid leaflet of phospholipid molecules aligned at their hydrophobic ends.
• Polar phospholipids are hydrophilic and face the external and internal sides of the membrane.
• Various proteins and components may be embedded in the membrane layer.
• Cell membrane serves as a permeability barrier, preventing most solutes from entering the cytoplasm except through specific transport proteins.

Cell Wall Polymers

• Chemical structures of cell wall polymers include cellulose, chitin, glucan, and mannan.
• Yeast cell walls contain 29% β-glycans, 31% mannan, 13% protein, and small percentages of lipids and other materials.

Prokaryotic Cell Surfaces

• Peptidoglycan is the hallmark of eubacteria, forming the major backbone of the murein sacculus of the cell wall.
• Archaea produce a pseudomurein and an associated surface layer (S-layer) composed of protein or glycoprotein.
• In many archaebacteria, the S-layer may represent the only surface component outside the plasma membrane.

Surface Layers of Bacteria

• Bacteria from all major phylogenetic groups produce a crystalline cell surface layer (S-layer) as the outermost component of the cell.
• S-layer may be attached to the peptidoglycan-containing sacculus or the outer membrane.