Lecture 2: Structure and Function of Prokaryotes PDF

Lecture 2 Structure and Function of Prokaryotes © Jason Rothman Introduction Most bacteria share similar fundamental traits Thick, complex outer region Compact genome under intense selection for efficiency Tightly coordinated cell functions Archaea, like bacteria,...

Lecture 2 Structure and Function of Prokaryotes © Jason Rothman Introduction Most bacteria share similar fundamental traits Thick, complex outer region Compact genome under intense selection for efficiency Tightly coordinated cell functions Archaea, like bacteria, are prokaryotes (but they aren’t bacteria!) Unique membrane and envelope structures Eukaryotes, in contrast to prokaryotes, have a nucleus and extensive membranous organelles © Jason Rothman The Bacterial Cell: An Overview In the early twentieth century, the cell was envisioned as a bag of “soup,” full of floating ribosomes and enzymes. Modern research shows that the cell’s parts fit together in a structure that is ordered, though flexible. © Jason Rothman  Structural differences between Prokaryotes and Eukaryotes Prokaryotes have no defined organelles DNA is not bounded by a membrane (the nucleus in eukaryotes) Prokaryotes are generally much smaller in size Equivalent to about the size of the mitochondrion in eukaryotes © Jason Rothman Cell structures Eukaryotes Prokaryotes © Jason Rothman Bacterial Cells are Smaller than Eukaryotes © Jason Rothman  Surface area vs volume Larger surface / volume ratios allow for faster growth rates This is an important concept throughout biological systems Rapid transport rates: Import of nutrients Removal of waste products Enzymes are located on the cell membrane Larger membrane area allows more active metabolism © Jason Rothman Bacterial Cell Shapes Cocci Cocci (coccus) - spheres Bacilli Bacilli - rods Vibrios - bent rods Spirochetes - helical structure Vibrio Irregular - everything else Spirochete Irregular © Jason Rothman Bacterial Cellular Morphology Cells can come in pairs, clusters, or chains © Jason Rothman The bacterial cell Cytoplasm surrounded by the cell envelope The DNA is contained in the nucleoid – non- membraned, looped coils of DNA Cell membrane – encloses the cytoplasm © Jason Rothman The cell envelope Cell envelope: The cell membrane, the cell wall, and the outer membrane (if present). © Jason Rothman Bacterial cytoskeleton Shape-determining proteins: FtsZ = forms a “Z-ring” in spherical cells MreB = forms a coil inside rod-shaped cells CreS “crescentin” = forms a polymer along the inner side of crescent- shaped bacteria © Jason Rothman The bacterial nucleoid Single loop of double-stranded DNA Single molecule of compact, supercoiled, DNA, usually ~4M basepairs. Non-membraned, attached to the cell envelope. Not separated from the cytoplasm! Replicates once per cell division Forms loops of DNA called domains Within domains, DNA is supercoiled and compacted by DNA-binding proteins © Jason Rothman What’s happening in the nucleoid? Remember the nucleoid isn’t separated from the rest of the cell Within this region, RNA Polymerase transcribes DNA to mRNA Then ribosomes are translating RNAs to proteins © Jason Rothman Cell division and replication Cell elongates as it grows Adds new wall at cell equator DNA replicates to make 2 chromosomes DNA replicates bidirectionally Can begin next replication before cell divides Cell undergoes septation Usually at equator Each daughter has same shape © Jason Rothman  Cell Membrane Double layer of phospholipids – lipid bilayer Separate cytoplasm from outside environment: Permeability barrier Fluid mosaic model – integral proteins embedded in the lipid membrane Transport materials Generate energy Sense environmental changes Have hydrophilic and hydrophobic regions that lock the protein in the membrane © Jason Rothman Phospholipid Bilayer General structure of biological membranes Composed of fatty acids (hydrophobic) and glycerol-phosphate (hydrophilic). Hopanoids are molecules that strengthen the lipid membrane Cholesterol is the reinforcing agent in eukaryotes Probably the most abundant organic compounds on Earth Hydrophilic region Hydrophobic region Hydrophilic region © Jason Rothman Transport across the cell membrane Transporters: Structures that move things into/out of the cell Passive transport follows concentration gradients Active transport moves some sugars Pumps: Transporters that use energy Either use ATP or the Proton Motive Force Move things against their concentration gradient © Jason Rothman Transport across the cell membrane Proton pumps: Push protons out of the cell Generates the Proton-Motive Force (PMF) This pushes protons (H+) against their concentration gradient The gradient than moves back through a different protein (ATP synthase) to make ATP © Jason Rothman Breathe. © Jason Rothman  Bacterial cell wall (sacculus) Rigid structure that lies just outside the cytoplasm membrane Enable bacteria to withstand turgor pressure due to dissolved solutes in the cells Two (2) major types Gram positive (thick) Gram negative (thinner) © Jason Rothman  Bacterial cell wall (sacculus) Sacculus made of peptidoglycan (murein): A polymer unique to bacteria. Single interlinked molecule Sugar chains wrapped in circles around cell Sugar chains linked to each other by short peptides polysaccharide (sugar) chains peptide (amino acid) crosslinks © Jason Rothman  Monomeric units of peptidoglycan in bacteria Peptido = peptide links A peptide with four amino acids linked by peptide bonds. Glycan = NAM+ NAG disaccharide NAM: N-Acetylmuramic acid NAG: N-Acetylglucosamine © Jason Rothman Bacteria have two different ways to crosslink peptidoglycan units Gram negative: Direct cross-linking Thin layer Gram positive: Peptide interbridge Thick layer © Jason Rothman Overall structure of Gram Positive peptidoglycan layers © Jason Rothman Gram-Positive Cell Wall A thick layer of peptidoglycan Teichoic acid - threads through multi-layers of peptidoglycan to reinforce cell wall Lipoteichoic acid: links cell wall to cell membrane – helps maintain cell structure Absent in Gram negative bacteria © Jason Rothman The Gram-Positive Envelope Capsule (not all species) Polysaccharide coat S Layer (not all species) Made of protein (numerous functions) Thick cell wall Amino acid crosslinks in peptidoglycan Teichoic acids for strength Plasma membrane © Jason Rothman Gram-Negative Cell Wall A thin layer of peptidoglycan Surrounded by outer membrane © Jason Rothman Gram-Negative Envelope Capsule (not all species) Polysaccharide coat Outer Membrane Thin cell wall 4-amino acid crosslinks in peptidoglycan Thick periplasm Plasma membrane © Jason Rothman Gram-Negative Outer Membrane Outer membrane - protection barrier Maintains permeability barrier Asymmetric: Inward-facing leaflet is a phospholipid monolayer. Outward-facing leaflet consists of lipopolysaccharide (LPS) © Jason Rothman  Gram-Negative Outer Membrane Proteins associated with the outer membrane: Porins: proteins for transport of materials Murein lipoproteins: link to the peptidoglycan © Jason Rothman Lipopolysaccharide (LPS) Conserved sequence of major components: Lipid A – core polysaccharide– O-specific polysaccharide. Core Polysaccharide: about 5 sugars. O-specific Polysaccharide: can be as many as 200 sugars. Vary between species. A protective layer and stabilizing layer for Gram-negatives outside © Jason Rothman inside  Other outer coverings S-layers: Archaea and many Gram-positive bacteria Layers of protein or glycoprotein Protection against pH, viral infection, extracellular enzymes Glycocalyx: Network of polysaccharides extending from cell surface Used for survival, attachment, virulence Capsule: well organized glycocalyx; difficult to remove © Jason Rothman Gram Stain The composition of the bacterial cell wall can be used to categorize groups of bacteria Developed by Hans Christian Gram in 1884 Differential Stain: Does not stain all cells equally Based on differences in composition of cell wall Gram-positive bacteria stain purple. Gram-negative bacteria stain pink. © Jason Rothman The Gram Stain Procedure Cells are fixed to a microscope slide Crystal violet and iodine are added, which stains the peptidoglycan in the cell wall purple © Jason Rothman  The Gram Stain Procedure Alcohol is added, which removes the stain from Gram- but not Gram+ cells It probably removes the outer lipid membrane, allowing the Crystal Violet-Iodine complex to leave the cell wall © Jason Rothman The Gram Stain Procedure Cells are counter-stained with the lighter stain safranin This colors all Gram- cells pink Gram+ cells retain their darker crystal violet stain and remain purple © Jason Rothman The Gram Stain Procedure Gram-positive bacteria stain purple. Gram-negative bacteria stain pink. © Jason Rothman Breathe. © Jason Rothman  Cell Division The bacterial cell needs to divide to reproduce… Binary fission Cell elongates as it grows Adds new wall at cell equator DNA replicates to make 2 chromosomes DNA replicates bidirectionally Can begin next replication before cell divides Cell undergoes septation Usually at equator Each daughter has same shape Cell-surface structures: Pili and fimbriae vs flagella Rigid structure that lies just outside the cytoplasm membrane Enable bacteria to withstand turgor pressure due to dissolved solutes in the cells Two (2) major types Gram positive (thick) Gram negative (thinner) © Jason Rothman Cell-surface structures: Pili and fimbriae vs flagella Both long and thin cell surface structures Both comprised of repeating protein monomers (pilin or flagellin) Anchored to cell envelope Pili can be more numerous Attachment and motility Flagella are usually longer Used for motility Specialized cell attachment structures Fimbriae and pili Thin, hair-like protein filaments Twitching: individual movement on solid surface Secretion systems attach cells to prey Conjugation (mating) – sex pili transfers DNA between cells Bacterial Motors Flagella Long protein filaments. Swimming: individual movement in liquid Swarming: multicellular movement on solid surface  Flagella structure Whip-like appendage attached to the cell at the poles or over the whole cell It’s a motor for bacterial motility The whip is comprised of monomers of flagellin protein A hook links the filaments to the ring structures Ring structures anchor the flagella to the cell envelope Flagella rotate to propel cell Video: https://www.youtube.com/watch?v=xEVq7jCT4kw Flagella types Monotrichous (Polar) Flagella Single flagellum attached to one end Lophotrichous Flagella A group of flagella is attached to one or both ends Peritrichous Flagella Flagella are arranged on all sides  Movement of polar flagella Polar flagella: reversible and unidirectional Cell stops, reorients (tumble), restarts rotation and movement Movement of peritichous flagella Peritrichous flagella – bundles or disaggregation Counterclockwise bundles cause smooth swimming, more or less in a straight line Clockwise disaggregation causes tumble and allows reorientation  Directing movement Chemotaxis: Movement in response to a chemical gradient Attractants, attract: Cells move up a gradient of these molecules (nutrients) Repellents, repel: Cells move down a gradient of these molecules (wastes or toxic chemicals) Directing movement Runs + tumbles cause “random walk” Directing movement Attractant concentration increases and prolongs run Biased random walk Net movement of bacteria toward attractants