Biochemistry book

• Prokaryotes are the most numerous and widespread organisms on earth, and are so classified because they have no defined membrane-bound nucleus
• Prokaryotes

  • Bacteria (or eubacteria)
  • Archaea (or archaebacteria)
• Prokaryotic cell


  • No membrane-bound nucleus
  • Surrounded by a plasma membrane
  • No subcellular organelles, only infoldings of the plasma membrane called mesosomes
  • DNA condensed within the cytosol to form the nucleoid
• Peptidoglycan cell wall

  Protects the prokaryotic cell from mechanical and osmotic pressure
• Some antibiotics, such as penicillin, target enzymes involved in the synthesis of the cell wall
• Gram-positive bacteria


  • Thick cell wall surrounding the plasma membrane
• Gram-negative bacteria

  • Thinner cell wall and an outer membrane, between which is the periplasmic space
• Bacterial flagella


  • Tail-like structures used for movement
  • Rotation of flagella allows bacteria to move through their surrounding media in response to chemicals (chemotaxis)
  • Made of the protein flagellin that forms a long filament attached to the flagellar motor by the flagellar hook
• Bacterial flagella


  • Made of the protein flagellin
  • Rotate rather than bend
• Bacterial flagella movement


  1. Rotation

  2. Allows bacteria to move towards attractants and away from repellents (chemotaxis)
• Flagellar filament


  • Thin helical filament, 15 nm in diameter and 10 µm long
  • Contains 11 subunits in two helical turns
  • Appears as an 11-bladed propeller with a hollow central core
• Flagella growth


  1. New flagellin subunits added to the end away from the cell

  2. New subunits diffuse through the central core
• Flagellar hook


  • Short, curved structure composed of 42 kDa hook protein subunits
  • Connects the flagellar filament to the basal body
• Flagellar motor


  • Intricate assembly of proteins in the plasma membrane
  • Rotation driven by a flow of protons through an outer ring of proteins (the stator)
• Flagellar motor


  Similar proton-driven motor found in the F1F0-ATPase that synthesizes ATP
• Prokaryotes generally range in size from 0.1 to 10 µm, and have one of three basic shapes: spherical (cocci), rod-like (bacilli) or helically coiled (spirilla)
• Prokaryotic cell


  • Bounded by a plasma membrane
  • May have infoldings of the plasma membrane called mesosomes
  • Mesosomes may be sites of DNA replication and specialized enzymatic reactions
  • Photosynthetic bacteria have mesosomes containing proteins and pigments for light trapping and ATP generation

  
• Prokaryotic chromosome


  Single circular DNA molecule condensed into a nucleoid
• Prokaryotic cell wall


  • 3-25 nm thick
  • Composed of peptidoglycan, a complex of oligosaccharides and proteins
  • Oligosaccharide component is linear chains of alternating N-acetylglucosamine and N-acetylmuramic acid
  • Attached to the N-acetylmuramic acid are D-amino acid-containing tetrapeptides
  • Adjacent peptidoglycan chains are covalently cross-linked through the tetrapeptides
  • Extensive cross-linking gives the cell wall strength and rigidity
• 1. amino acids in peptidoglycan


  • Render the cell wall resistant to proteases
  • Provide a target for certain antibiotics like penicillin
• Gram staining


  Classifies bacteria as Gram-positive or Gram-negative
• Gram-positive bacteria


  • Have a thick (25 nm) peptidoglycan cell wall surrounding the plasma membrane
• Gram-negative bacteria


  • Have a thinner (3 nm) peptidoglycan cell wall and an additional outer membrane
• Outer membrane of Gram-negative bacteria


  Very permeable to large molecules (>1000 Da) due to porin proteins forming pores
• Periplasmic space


  Space between the outer membrane and cell wall of Gram-negative bacteria, containing secreted proteins
• Endoplasmic reticulum


  The site of phospholipid biosynthesis, and is where a number of detoxification reactions take place
• Golgi apparatus


  A system of flattened membrane-bound sacs, is the sorting and processing center of the cell
• Golgi apparatus


  1. Membrane vesicles from the RER, containing membrane and secretory proteins, fuse with the Golgi apparatus and release their contents into it

  2. On transit through the Golgi apparatus, further post-translational modifications to these proteins take place and they are then sorted and packaged into different vesicles

  3. These vesicles bud off from the Golgi apparatus and are transported through the cytosol, eventually fusing either with the plasma membrane to release their contents into the extracellular space or with other internal organelles

  
• Mitochondrion


  • Has an inner and an outer membrane between which is the intermembrane space
  • The outer membrane contains porin proteins which make it permeable to molecules of up to 10 kDa
  • The inner membrane, which is considerably less permeable, has large infoldings called cristae which protrude into the central matrix
  • The inner membrane is the site of oxidative phosphorylation and electron transport involved in ATP production
  • The central matrix is the site of numerous metabolic reactions including the citric acid cycle and fatty acid breakdown
  • Also within the matrix is found the mitochondrial DNA which encodes some of the mitochondrial proteins
• Chloroplast


  • Has inner and outer membranes
  • Has an extensive internal membrane system made up of thylakoid vesicles (interconnected vesicles flattened to form discs) stacked upon each other to form grana
  • Within the thylakoid vesicles is the green pigment chlorophyll, along with the enzymes that trap light energy and convert it into chemical energy in the form of ATP
  • The stroma, the space surrounding the thylakoid vesicles, is the site of carbon dioxide (CO2) fixation – the conversion of CO2 into organic compounds
  • Chloroplasts, like mitochondria, contain DNA which encodes some of the chloroplast proteins

  
• Lysosome


  • Has a single boundary membrane
  • The internal pH is mildly acidic (pH 4–5), maintained by integral membrane proteins which pump H+ ions into them
  • Contains a range of hydrolases that are optimally active at this acidic pH and are involved in the degradation of host and foreign macromolecules into their monomeric subunits
• Peroxisome


  • Has a single boundary membrane and contain enzymes that degrade fatty acids and amino acids
  • A byproduct of these reactions is hydrogen peroxide, which is toxic to the cell
  • The presence of large amounts of the enzyme catalase in the peroxisomes rapidly converts the toxic hydrogen peroxide into harmless H2O and O2
• Cytosol


  • The part of the cytoplasm not included within any of the subcellular organelles, and is a major site of cellular metabolism, containing a large number of different enzymes and other proteins
  • Is not a homogeneous 'soup' but has within it the cytoskeleton, a network of fibers criss-crossing through the cell that helps to maintain the shape of the cell
  • Also found within the cytosol of many cells are inclusion bodies (granules of material that are not membrane-bounded) such as glycogen granules in liver and muscle cells, and droplets of triacylglycerol in the fat cells of adipose tissue

  
• Plant cell wall


  • Surrounding the plasma membrane of a plant cell, imparts strength and rigidity to the cell
  • Built primarily of cellulose, a rod-like polysaccharide of repeating glucose units linked β(1–4)
  • Cellulose molecules are aggregated together by hydrogen bonding into bundles of fibers, and the fibers in turn are cross-linked together by other polysaccharides
  • In wood another compound, lignin, imparts added strength and rigidity to the cell wall
• Plant cell vacuole


  • Used to store nutrients (e.g. sucrose), water, ions and waste products (especially excess nitrogen-containing compounds)
  • Like lysosomes in animal cells, vacuoles have an acidic pH maintained by H+ pumps in the membrane and contain a variety of degradative enzymes
  • Entry of water into the vacuole causes it to expand, creating hydrostatic pressure (turgor) inside the cell which is balanced by the mechanical resistance of the cell wall
• Microtubules


  Formed by the addition of α- and β-tubulin molecules to pre-existing filaments or nucleation centers
• Microtubules


  • One end is usually attached to a microtubule-organizing center called a centrosome
  • Drugs like colchicine and vinblastine inhibit polymerization, blocking cell processes like cell division
  • Compound taxol stabilizes tubulin and promotes polymerization, used as anticancer drug
• Molecular motors


  Accessory proteins that associate with the cytoskeleton, bind to a cytoskeletal filament and use ATP hydrolysis to move along it, converting chemical energy into motion
• Types of motor proteins


  • Myosins (bind to actin filaments)
  • Kinesins (bind to microtubules)
  • Dyneins (bind to microtubules)
• Muscle structure


  • Composed of multinucleate cells with parallel myofibrils
  • Functional unit is the sarcomere which repeats along the fibril axis
  • Contains thick filaments of myosin and thin filaments of actin, tropomyosin and troponin