CELL STRUCTURE

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CELL STRUCTURE
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WHAT WILL WE COVER?

• Cell theory
• Discovery of the microscopic world
• Microscopy
• Membrane structure and transport
• Differences between eukaryotic and bacterial
  membranes
• Prokaryotic cell structures
• Eukaryotic cell structures

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CELL THEORY

• Three main tenets of cell theory
• All living organisms are composed of one or more
  cells
• Cells are the basic structural and functional
  unit of organisms
• All cells come from preexisting cells

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DISCOVERY OF CELLS

• Robert Hooke (1665)
• England
• Constructed a compound microscope
• Magnification of 30X
• Viewed microscopic structure of cork
• Named the repeating units he viewed cells

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DISCOVERY OF CELLS

• Antony Van Leeuwenhoek (1676)
• Holland
• Constructed a microscope
• Single lens
• Magnified over 200X
• Viewed bacteria, protists, blood and sperm
  cells, etc.
• Observed motility in bacteria
• Animalcules

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MICROSCOPES

• Various types of microscopes are used to study
  cells and structures within cells
• Light microscopes are the most common

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MICROSCOPES

• The ability to view microscopic structures is
  dependent upon
• Magnification
• Resolving power
• Contrast
• Various techniques and types of microscopes can
  improve our ability to view microscopic
  structures by improving one or more of these
  parameters

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MICROSCOPES

• Magnification
• Objects are made to look larger
• Light microscopes use two lenses to increase
  magnification
• Ocular objective total
• e.g., 10X 100X 1,000X
• Leeuwenhoeks microscope magnified only 200 -
  300X
• Modern light microscopes commonly magnify 1000X
• Electron microscopes can magnify 100,000X

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MICROSCOPES

• Resolving power
• Resolution
• Minimum distance between two objects observed as
  separate entities
• Determines how much detail can be observed
• Limited by wavelength of light
• Maximum resolution for light microscope is 0.2 mm
• Maximum resolution for electron microscope is
  much smaller

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MICROSCOPES

• Contrast
• Number of visible shades in the specimen
• Black white high contrast
• Means of increasing contrast
• Certain types of light microscopes
• Staining

Confocal Microscopy
Fluorescence Microscopy
Dark-Field Microscopy
Gram Stain
Interference Microscopy
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MICROSCOPES
Bacterial conjugation
Sex chromosomes

• Modern microscopes
• Greater magnification
• Greater resolving power
• Ability to view incredibly small structures

Mitochondrion
Macrophage
T2 phage
Bacterium and bacteriophage
Euglena
Adenovirus
Respiratory cilia
Bacterial DNA
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CELL THEORY

• Three main tenets of cell theory
• All living organisms are composed of one or more
  cells
• Cells are the basic structural and functional
  unit of organisms
• All cells come from preexisting cells

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MICROORGANISMS

• Microorganisms appear, seemingly from nowhere
• Are these microorganisms spontaneously generated?
• Of course not
• Predominant view until 100 years ago
• Disproved by experiments of Pasteur (1861) and
  others

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PASTEURS EXPERIMENTS

• Louis Pasteur demonstrated that the air is filled
  with microorganisms
• Filtered air through cotton
• Viewed trapped microorganisms microscopically
• Addition of microorganisms to sterile
  nutrient-rich infusions results in visible growth

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PASTEURS EXPERIMENTS

• Pasteur demonstrated that nutrient-rich infusions
  remain sterile unless airborne microorganisms are
  allowed to enter
• All life arises from preexisting life

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THREE DOMAINS

• All living things can be grouped into three
  domains
• Groupings represent evolutionary relationships
• Major differences in cell structure between
  domains

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THREE DOMAINS

• Members of domain Eukarya are eukaryotic
• True nucleus
• Possess a membrane-enclosed nucleus and many
  membrane-enclosed structures
• Generally larger than prokaryotic cells
• Protists, fungi, animals, and plants

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THREE DOMAINS

• Members of domains Archaea and Bacteria are
  prokaryotic
• Before nucleus
• Lack a membrane-enclosed nucleus and most
  membrane-enclosed structures
• Generally smaller than eukaryotic cells

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THREE DOMAINS

• Prokaryotic domains Archaea and Bacteria
• Superficially similar appearance
• Fundamentally different prokaryotic groups
• Archaea is more closely related to domain Eukarya
  than to domain Bacteria

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PLASMA MEMBRANE

• All cells are enclosed by a plasma membrane
• Structurally and functionally similar in both
  prokaryotes and eukaryotes
• Some differences

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CELL MEMBRANE

• The cell membrane (plasma membrane) defines the
  outer boundary of the cell
• Surrounds the cytoplasm
• Some structures of cells exist external to the
  cell membrane
• e.g., Cell wall, etc.
• Many additional structures exist internal to the
  cell membrane
• e.g., DNA, organelles, etc.

Organelles
?
Cell membrane
?
?
Cell wall
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MEMBRANE FUNCTION

• The plasma membrane is selectively permeable
• Semipermeable
• Regulates movement to and from the cell
• Allows some substances to cross the membrane
• Prevents some substances from crossing the
  membrane
• Maintains cells internal environment separate
  from the external environment
• Fundamental characteristic of life

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MEMBRANE STRUCTURE

• Phospholipids are the main component of
  membranes
• Amphipathic
• Form a phospholipid bilayer
• Two layers (leaflets) of phospholipids
• Hydrophobic regions hidden from water
• Hydrophilic regions in contact with water

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MEMBRANE STRUCTURE

• Other amphipathic molecules are embedded within
  this phospholipid bilayer
• Cholesterol
• Integral membrane proteins
• Additional biological molecules are attached to
  the surface of the membrane
• Sugar groups
• Peripheral proteins

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MEMBRANE STRUCTURE

• Fluid mosaic model of membranes
• The membrane is a two-dimensional fluid structure
  containing a mosaic of embedded proteins

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MEMBRANE STRUCTURE

• The membrane is a fluid and dynamic structure
• Most lipids can move laterally within the
  membrane
• Very rarely move from one phospholipid layer
  (leaflet) to the other
• Some proteins can also move laterally within the
  membrane
• Larger, therefore move more slowly
• Some are attached to the cytoskeleton and are
  virtually immobile

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MEMBRANE STRUCTURE

• Fluidity is required for proper membrane function
• Movement of molecules within the membrane is
  required for many membrane functions
• Selective permeability depends upon membrane
  fluidity
• Solidification of the membrane is fatal to cells
• Permeability is altered
• Enzymatic proteins become inactive
• etc.

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MEMBRANE STRUCTURE

• The temperature at which a membrane solidifies is
  dependent upon the types of lipids it contains
• Unsaturated hydrocarbon tails inhibit close
  packing and solidification

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MEMBRANE STRUCTURE

• The temperature at which a membrane solidifies is
  dependent upon the types of lipids it contains
• Lipid concentration can change as an adjustment
  to changing temperature
• Many plants able to tolerate extreme cold
  increase their percentage of unsaturated
  phospholipids in the fall
• e.g., Winter wheat, etc.

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MEMBRANE STRUCTURE

• The temperature at which a membrane solidifies is
  dependent upon the types of lipids it contains
• Cholesterol also inhibits close packing and
  solidification at low temperatures
• Membrane antifreeze
• Decreases fluidity at high temperatures
• Temperature buffer

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MEMBRANE STRUCTURE

• Cholesterol is present in the plasma membrane of
  animal cells
• 20 of membrane lipids in humans
• Many other eukaryotes possess similar sterols
• e.g., Ergosterol is possessed by fungi and some
  protists such as trypanosomes
• Most bacterial membrane lack sterols
• Present in some species of Mycoplasma

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MEMBRANE STRUCTURE

• Fluid mosaic model of membranes
• The membrane is a two-dimensional fluid structure
  containing a mosaic of embedded proteins

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MEMBRANE STRUCTURE

• A mosaic of different types of proteins are
  embedded within cell membranes
• Different types of cells possess different types
  of membrane proteins
• Different membranes within a cell also possess
  different types of membrane proteins
• Membrane proteins determine most of the
  membranes specific functions

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MEMBRANE STRUCTURE

• Two main groupings of membrane proteins
• Integral membrane proteins
• Penetrate the hydrophobic core of the
  phospholipid bilayer
• Most are transmembrane proteins
• Completely span the membrane
• Peripheral proteins
• Not embedded within the bilayer
• Loosely bound to the membranes surface
• Often to exposed parts of integral proteins

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MEMBRANE STRUCTURE

• Transmembrane proteins are amphipathic
• Hydrophobic regions consist of one or more
  stretches of nonpolar amino acids
• Generally a-helices
• Hydrophilic portions are exposed to water on
  each side of the membrane

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MEMBRANE STRUCTURE

• Six major functions of membrane proteins

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MEMBRANE STRUCTURE

• Carbohydrate groups protrude from the external
  side (outer leaflet) of the cell membrane
• Generally short branched sugar chains
• Some are covalently linked to lipids
• Glycolipids
• Most are covalently linked to proteins
• Glycoproteins

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MEMBRANE STRUCTURE

• Carbohydrate groups protrude from the external
  side of the cell membrane
• Vary between species
• Vary between types of cells within a
  multicellular organism
• Important in cell-cell recognition
• e.g., Formation of tissues and organs in embryo
• e.g., Recognition of microorganisms by your
  immune system
• Carbohydrate groups are often antigenic

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MEMBRANE TRANSPORT

• The plasma membrane controls movement into and
  from the cell
• Small molecules and ions continually move across
  the membrane in both directions
• Nutrients continually enter the cell
• Waste products continually leave the cell
• etc.

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MEMBRANE TRANSPORT

• The plasma membrane is selectively permeable
• Some small molecules are transported
• Other small molecules are excluded
• Substances move across the membrane at different
  rates

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MEMBRANE TRANSPORT

• Most of the thickness of the plasma membrane is
  hydrophobic
• Hydrophobic molecules can dissolve in the lipid
  bilayer
• e.g., Hydrocarbons, CO2, O2, etc.
• Readily cross the plasma membrane
• Membranes hydrophobic core impedes movement of
  polar and charged (hydrophilic) molecules

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MEMBRANE TRANSPORT

• Membranes are permeable to a variety of polar
  molecules
• Cannot cross the membrane directly
• Pass through transport proteins embedded within
  the membrane
• Avoid contact with the bilayers hydrophobic core

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MEMBRANE TRANSPORT

• Transport proteins
• Embedded within the plasma membrane
• Specific for the transported substance
• e.g., Glucose transporter will transport glucose,
  but not the chemically similar fructose
• e.g., Sodium channel will not transport
  potassium
• Channels or carrier proteins

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MEMBRANE TRANSPORT

• The selective permeability of a membrane is
  dependent upon two main factors
• The hydrophobic barrier of the phospholipid
  bilayers
• The types of specific transport proteins present

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BROWNIAN MOTION

• All molecules are in a constant state of motion
• Brownian motion or Brownian movement
• Temperature is a measure of this movement
• Measure of the average kinetic energy of
  molecules
• No movement only at absolute zero (-273oC)

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DIFFUSION

• When molecules collide, their velocity and
  direction of movement are altered
• Molecules tend to move from an area of high
  concentration to an area of low concentration
• Molecules move down their concentration gradient
• Diffusion

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DIFFUSION

• Diffusion is a spontaneous process
• Happens without an input of work
• Driven by a decrease in free energy and an
  increase in entropy
• The concentration gradient itself represents
  potential energy

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MEMBRANE TRANSPORT

• Most of the traffic across cell membranes occurs
  by diffusion
• Molecules diffuse across the membrane down their
  concentration gradients
• Passive transport
• No energy is expended by the cell
• Potential energy is inherent in the concentration
  gradient

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MEMBRANE TRANSPORT

• Oxygen transport into a cell is accomplished by
  passive transport
• O2 is a nonpolar molecule
• O2 readily diffuses across the bilayer into cells
• Movement is down its concentration gradient
• Cellular respiration consumes O2 as it enters
• The concentration gradient is maintained
• Diffusion into the cell continues

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MEMBRANE TRANSPORT

• Hydrophilic molecules and ions do not readily
  diffuse across the bilayer
• Their movement across the bilayer is aided by
  transport proteins
• Allows movement down their concentration
  gradient
• Passive transport aided by membrane proteins is
  termed facilitated diffusion
• No energy is expended by the cell

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MEMBRANE TRANSPORT

• Simple diffusion and facilitated diffusion are
  examples of passive transport
• No energy is expended by the cell
• Movement is down a concentration gradient

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MEMBRANE TRANSPORT

• Molecules can be transported against (up) their
  concentration gradients by active transport
• Requires an energy expenditure by the cell
• Energy generally supplied by ATP
• Always mediated by a carrier protein
• Sometimes mediated by the same carrier involved
  in facilitated diffusion
• Important in maintaining an internal environment
  distinct from the external environment

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MEMBRANE TRANSPORT

• The proton pump actively transports H out of a
  variety of cells
• Energy supplied by hydrolysis of ATP
• Generates chemical and electrical
  (electrochemical) gradient
• Stores potential energy that can later be
  tapped for cellular work

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MEMBRANE TRANSPORT

• Energy is not always supplied directly by ATP
• The downhill movement of one substance is coupled
  to the uphill transport of another substance
• Cotransport
• Symport
• Driven by the potential energy stored in a
  preestablished chemical gradient
• Active transport

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MEMBRANE TRANSPORT

• The uptake of many nutrients is accomplished by
  cotransport
• e.g., Uptake of sugars, amino acids, etc.
• Typically coupled to H or Na

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MEMBRANE TRANSPORT

• The sodium-potassium pump is found in most
  animal cells
• Group of membrane proteins
• Uses ATP to actively transport Na and K
• Na is pumped out
• K is pumped in
• Both are moved against their concentration
  gradients
• Active transport

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MEMBRANE TRANSPORT

• The sodium-potassium pump is involved in various
  processes in multiple animal systems
• Muscle contractions
• Neuronal signals
• Fluid balance
• Electrolyte balance

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MEMBRANE TRANSPORT
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CYSTIC FIBROSIS

• Cystic fibrosis is a genetic disorder
• Affected individuals are defective in chloride
  ion transport
• Mutated genes encode a defective (or absent)
  channel protein

X
X
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CYSTIC FIBROSIS

• Lack of channels results in abnormally high
  extracellular chloride ion concentrations
• Mucus coating cells becomes thicker and stickier
• Builds up in lungs, pancreas, digestive tract,
  etc.
• Multiple phenotypic effects
• Poor nutrient absorption
• Chronic bronchitis
• Recurrent bacterial infections
• Premature death
• Before age 5 if untreated
• Late 20s / 30s if treated
• etc.

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MEMBRANE TRANSPORT

• Some items are too large to cross a membrane
  through a transport protein
• e.g., Proteins, polysaccharides, entire cells,
  elephants, etc.
• Movement of such items is accomplished though
  bulk transport
• Requires the expenditure of energy
• Bulk transport is a form of active transport

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MEMBRANE TRANSPORT

• Endocytosis involves the uptake of large
  substances by surrounding them with vesicles
  newly formed from the plasma membrane
• Three different types of endocytosis
• Phagocytosis (cell eating)
• Pinocytosis (cell drinking)
• Receptor-mediated endocytosis

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MEMBRANE TRANSPORT

• Phagocytosis
• Material is surrounded by pseudopodia
• Pseudopodia fuse to engulf material
• Material enclosed within membrane-bound vacuole

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MEMBRANE TRANSPORT

• Pinocytosis
• Small area of the plasma membrane sinks inward
• Pocket is formed
• Membranes fuse to pinch off pocket
• Vesicle formed contains material previously
  outside of the cell

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MEMBRANE TRANSPORT

• Receptor-mediated endocytosis
• Numerous receptors embedded within membrane
• Clustered in coated pits
• Specific extracellular substances bind to
  receptors
• Membrane sinks inward and forms vesicle

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MEMBRANE TRANSPORT

• Not all organisms can perform endocytosis
• Rigid cell walls outside the cell membrane
  prevent cells from engulfing extracellular
  material
• e.g., Bacteria, fungi
• Many such organisms release hydrolytic enzymes
  into the environment
• Breakdown of large molecules is external
• Smaller molecules are transported into cell
• Often important decomposers

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MEMBRANE TRANSPORT

• Exocytosis involves the bulk export of materials
  from a cell
• Involves the fusion of a membrane-bound vesicle
  with the cell membrane
• Vesicles contents are secreted from the cell
• Endocytosis in reverse

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OSMOSIS

• Transport of water across a membrane is readily
  accomplished by passive transport
• Water does not readily diffuse across the bilayer
• Movement of water across the bilayer is aided by
  transport proteins known as aquaporins
• Allows movement down its concentration gradient
• Transport via facilitated diffusion

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OSMOSIS

• Some membranes are permeable to water but
  impermeable to solute molecules such as sugars
• Osmosis is the passive diffusion of water across
  a semipermeable membrane
• Water moves across the membrane in both
  directions
• Water displays a net movement down its
  concentration gradient

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OSMOSIS

• Two solutions with equal solute concentrations
  are termed isotonic
• Water concentrations are also equal
• Water will flow across a semipermeable membrane
  separating two isotonic solutions
• Movement will be equal in both directions
• No net flow of water will occur

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OSMOSIS

• Two solutions with unequal solute concentrations
  are not isotonic
• Solution with more solute is hypertonic
• More solute less solvent (water)
• Solution with less solute is hypotonic
• Less solute more solvent (water)
• Remember, the prefixes hyper- and hypo- refer to
  the amount of solute, not the amount of water
  (the solvent)

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OSMOSIS

• Water will flow across a semipermeable membrane
  separating two solutions of different tonicities
• Movement will not be equal in both directions
• A net flow of water will occur down its
  concentration gradient

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OSMOSIS

• Solute concentration affects the concentration of
  water molecules available to cross a membrane
• Water molecules tightly cluster around
  hydrophilic solute molecules
• These water molecules are not available to
  diffuse across the membrane
• Increasing the amount of solute dissolved in a
  solution decreases the effective concentration
  of water

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OSMOSIS

• Animal cells are stable in isotonic solutions
• Not net flow of water across the membrane
• Animal cells swell burst in hypotonic solutions
• Net flow of water into the cells
• Animal cells shrivel in hypertonic solutions
• Net flow of water from the cell

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OSMOSIS

• How can cells live in a hypotonic environment?
• Many cells possess a rigid cell wall external to
  the cell membrane
• e.g., Plants, fungi, bacteria, some protists,
  etc.
• Resists osmotic pressure from inflow of water
• Prevents excessive expansion of membrane

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OSMOSIS

• How can cells live in a hypotonic environment?
• Some cells possess contractile vacuoles
• e.g., Paramecium
• Net flow of water into cell is not prevented
• Active transport of water from cell counters
  influx

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BACTERIAL MEMBRANE

• The bacterial cell membrane is fundamentally
  similar to its eukaryotic counterpart
• Semipermeable barrier regulating movement into
  and from the cell

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BACTERIAL MEMBRANE

• The bacterial cell membrane differs from its
  eukaryotic counterpart in certain ways
• Different phospholipid composition
• Lacks sterols
• Involved in energy transformations
• Heavily infolded

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BACTERIAL MEMBRANE

• Bacterial membrane lipid composition
• Phospholipids often have different chemical
  groups attached
• e.g., Sugar groups, etc.
• Immunologically important
• Lack sterols
• Possessed by some species of Mycoplasma

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BACTERIAL MEMBRANE

• Energy transformations
• Conversion of energy to a usable form
• Critical to respiration and photosynthesis
• Accomplished by organelles in eukaryotes
• Mitochondria and chloroplasts
• Is there a connection here?
• Stay tuned Same Bat-time Same Bat-channel

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BACTERIAL MEMBRANE

• The bacterial membrane is commonly highly
  infolded
• Increases surface area
• Facilitates transport and energy transformations
• In contrast, eukaryotic cells often have
  outfoldings termed microvilli

Microvilli (eukaryotic)
Bacterial membrane infoldings
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CELL ORGANIZATION

• All cells are enclosed by a plasma membrane
• Some structures are present outside of the
  membrane
• e.g.,. Cell wall, etc.
• The semifluid substance enclosed by this membrane
  is the cytosol
• Various molecules and structures are present
  within the cytosol
• e.g., Chromosomes, ribosomes, etc.

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CELL ORGANIZATION

• The organization of prokaryotic and eukaryotic
  cells have many differences
• Both will be discussed

84
BACTERIAL CELL SHAPES

• Most common bacteria have one of two different
  shapes
• Spherical bacteria
• Coccus/cocci
• Rod shaped bacteria
• Bacillus/bacilli
• There are many variations of these basic cell
  shapes

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BACTERIAL CELL SHAPES

• Variations of basic cell shapes
• Coccobacilli
• Very short rods
• Easily mistaken for cocci
• Vibrio
• Short curved rod

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BACTERIAL CELL SHAPES

• Variations of basic cell shapes
• Spirillum
• Long curved rod forming spirals
• Spirochete
• Long helical cell
• Flexible cell wall
• Unique motility

87
BACTERIAL CELL SHAPES

• Variations of basic cell shapes
• Coccobacilli
• Vibrio
• Spirillum
• Spirochete
• etc.

88
BACTERIAL CELL GROUPINGS

• Cells often adhere following division
• Cell arrangements depend on planes of division
• Some bacteria divide in only a single plane
• Many cocci divide in more than one plane

89
BACTERIAL CELL GROUPINGS

• Cells dividing in only one plane form chains of
  varying lengths
• e.g., Neisseria gonorrhoeae characteristically
  forms diplococci
• e.g., Streptococcus species characteristically
  form long chains

90
BACTERIAL CELL GROUPINGS

• Some cocci divide in two or three perpendicular
  planes to form cubical packets
• e.g., Members of the genus Sarcina

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BACTERIAL CELL GROUPINGS

• Some cocci divide in several planes at random to
  form clusters
• e.g., Members of the genus Staphylococcus
  characteristically form grapelike clusters

92
BACTERIAL CELL GROUPINGS
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BACTERIAL CELL GROUPINGS

• Cell groupings are sometimes described with a
  Latin word
• Chains of cocci may be called streptococci
• Cubical packets may be called sarcinae
• Clusters may be called staphylococci
• These same Latin words are also used as genus
  names
• Use of these terms as descriptors can cause
  confusion with genus names

94
BACTERIAL CELL GROUPINGS

• Some types of bacteria live as multicellular
  associations
• Myxobacteria form swarms that move as a pack
• Form macroscopic fruiting bodies when nutrients
  are scarce
• Many types of bacteria like on surfaces in
  associations termed biofilms
• e.g., Dental plaque
• etc.

Biofilm
Fruiting body
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BACTERIAL CELL STRUCTURE

• Appendages
• Flagella
• Pili
• Surface layers
• Sheath
• Glycocalyx
• Cell wall
• Cell membrane
• Cytoplasm
• DNA
• Ribosomes
• Gas vesicles
• Granules
• Endospores

96
BACTERIAL CELL WALL

• The bacterial cell wall is a rigid structure
  external to the cell membrane
• Determines the shape of the organism
• Restricts water uptake
• Prevents bursting due to osmotic pressure
• Composed of unique structures and molecules
• e.g., Peptidoglycan is unique to bacteria
• Some are recognized by our immune system
• Some antimicrobial compounds target some of
  these unique structures

97
BACTERIAL CELL WALL

• The bacterial cell wall is a rigid structure
  external to the cell membrane
• Determines the shape of the organism
• Restricts water uptake
• Prevents bursting due to osmotic pressure
• Composed of unique structures and molecules
• e.g., Peptidoglycan is unique to bacteria
• Some are recognized by our immune system
• Some antimicrobial compounds target some of
  these unique structures

98
BACTERIAL CELL WALL

• Two main bacterial groups are distinguished by
  their cell wall structure
• Gram-positive bacteria
• Gram negative bacteria

99
BACTERIAL CELL WALL

• The bacterial cell wall contains peptidoglycan
• Contains a linear polymer of two alternating
  sugars
• N-acetylmuramic acid (NAM)
• N-acetylglucosamine (NAG)
• ? Glycan chain

100
BACTERIAL CELL WALL

• The bacterial cell wall contains peptidoglycan
• Tetrapeptides are attached to NAM
• Form cross-linkages between glycan chains
• Joined directly in Gram-negative cells
• Generally joined through short peptide
  interbridges in Gram-positive cells

101
BACTERIAL CELL WALL
102
GRAM-POSITIVE CELL WALL

• The gram-positive cell wall contains a relatively
  thick layer of peptidoglycan
• May contain up to 30 interconnected layers/sheets
  of glycan chains
• 40 80 of cells dry weight
• Remains permeable to many substances
• e.g., Sugars, amino acids, and ions

103
GRAM-POSITIVE CELL WALL

• The gram-positive cell wall contains a relatively
  thick layer of peptidoglycan
• Techoic acid is covalently linked to NAM
• Polymers of phosphorylated sugars
• Some are linked to the cell membrane
• Lipotechoic acids
• Antigenic

104
GRAM-NEGATIVE CELL WALL

• The gram-negative cell wall is more complex than
  the gram positive cell wall
• Contains only a thin layer of peptidoglycan
• Possesses an additional membrane external to the
  peptidoglycan
• Outer membrane
• The region between the two membranes is termed
  the periplasm

105
GRAM-NEGATIVE CELL WALL

• The outer membrane of gram-negative cells is
  selectively permeable
• Movement of various small molecules and ions is
  aided by porin channels
• Excludes many molecules, including some
  antibiotics

106
GRAM-NEGATIVE CELL WALL

• The structure of the outer membrane of
  gram-negative cells is unique
• Outer leaflet is composed of lipopolysaccharides
  rather than phospholipids
• LPS layer
• Functions as an endotoxin

107
BACTERIAL CELL WALL

• Some antibacterial compounds interfere with cell
  wall synthesis or integrity
• Penicillin (and derivatives)
• Lysozyme

108
BACTERIAL CELL WALL

• Penicillin binds and inactivates proteins
  involved in cell wall synthesis
• Prevents cross-linking of adjacent glycan chains
• Most effective on Gram-positive cells
• Excluded by Gram-negative outer membrane
• Some derivatives are modified to pass through
  porin channels

109
BACTERIAL CELL WALL

• Lysozyme is an enzyme present in many body fluids
• e.g., Tears, saliva, etc.
• Destroys the structural integrity of glycan
  chains
• Breaks the bond between NAM and NAG
• Helpful in removing peptidoglycan in the
  laboratory

110
GRAM STAINING

• Gram-positive and -negative bacteria can be
  identified using a Gram stain

111
GRAM STAINING

• Gram-positive and -negative bacteria can be
  identified using a Gram stain

112
BACTERIAL CELL WALL

• Some bacteria naturally lack a cell wall
• e.g., Mycoplasma pneumoniae
• Possess sterols in their cytoplasmic membrane
• Stabilize membrane, making it stronger
• Not sensitive to penicillin or lysozyme
• Why not?

Mycoplasma pneumoniae
113
ARCHAEA CELL WALL

• Cell wall structure is more variable in domain
  Archaea
• Not surprising, since they inhabit a wide range
  of extreme environments
• None possess peptidoglycan
• Some possess the similar pseudopeptidoglycan
• Much more poorly studied than bacteria

114
GLYCOCALYX

• Many bacteria are enveloped by a glycocalyx
• Gel-like layer external to cell wall
• Colonies appear glistening
• Most are formed of polysaccharides
• A few are formed of polypeptides
• Two main forms
• Distinct and gelatinous capsule
• Diffuse and irregular slime layer

Capsule
Slime layer
115
GLYCOCALYX

• Some types of glycocalyx enable bacteria to
  adhere to surfaces
• e.g., Teeth, rocks, other bacteria
• Often enable organisms to grow as a biofilm
• e.g., The capsule of Streptococcus mutans allows
  it to adhere and grow on teeth
• Other bacteria adhere to this layer
• Acid production by the bacteria of this biofilm
  damages the tooth surface

116
GLYCOCALYX

• Some capsules enable bacteria to avoid innate
  defense systems
• e.g., Streptococcus pneumoniae can only cause
  disease if it has a capsule
• Unencapsulated cells are quickly engulfed and
  killed by body defenses

117
SHEATH

• Some aquatic bacteria are surrounded by a sheath
• Tube surrounding a linear chain of cells
• Provides a protective function
• Helps bacteria attach to solid objects in
  favorable environments

118
FILAMENTOUS APPENDAGES

• Many bacteria have filamentous protein appendages
  
• Anchored in the membrane
• Protruding from their surface
• Two different types
• Flagella
• Pili

119
BACTERIAL FLAGELLA

• Flagella are cell appendages responsible for
  bacterial motility
• Number and location are variable
• Can be used to characterize flagellated bacteria

120
BACTERIAL FLAGELLA

• Bacterial flagella have three basic parts
• Filament
• Long, slender, and hollow
• Composed of the protein flagellin
• Twists into a helical structure
• Hook
• Curved structure connecting filament to cell
  surface
• Basal body
• Anchors flagellum to cell wall and cell membrane

121
BACTERIAL FLAGELLA

• The structure of bacterial flagella is far
  different from that of eukaryotic flagella
• Not surrounded by a membrane
• Do not contain microtubules

122
BACTERIAL FLAGELLA

• Bacterial flagella function in a manner far
  different from eukaryotic flagella
• Bacterial flagella rotate
• Capable of gt100,000 rotations per minute
• 20 body lengths per second
• Akin to 80 mph for humans

123
BACTERIAL FLAGELLA

• The flagella of Helicobacter pylori have an
  atypical function
• Causative agent of gastric ulcers
• Flagella allow the cells to burrow into the
  viscous mucus coating stomach epithelium

124
CHEMOTAXIS

• Chemotaxis is the movement in response to a
  chemical stimulus
• Attractant or repellant
• Movement is indirect, involves runs and tumbles
• Counterclockwise rotation ? propelled forward
  (run)
• Clockwise rotation ? reversal of rotation causes
  tumble

125
CHEMOTAXIS

• Movement toward an attractant or away from a
  repellant inhibits tumbles, promotes runs
• Result is staggering directional movement

126
_______-TAXIS

• Phototaxis
• Movement in response to light
• Aerotaxis
• Movement in response to O2 concentrations
• Magnetotaxis
• Movement in response to Earths magnetic field

127
PILI

• Pili are composed of helically arranged protein
  subunits
• Form a long, hollow cylinder
• Much shorter and thinner than flagella
• Various types and functions

128
PILI

• Pili are of various types and functions
• Fimbriae are pili that enable attachment to
  surfaces
• Some pili play a role in twitching or gliding
  movement
• Sex pili facilitate conjugation
• Transfer of DNA from one cell to another

129
BACTERIAL DNA

• Bacteria possess chromosomal DNA
• Essential
• One double-stranded, circular chromosome
• 1 mm in length
• Supercoiled (condensed)
• Not enclosed within a nucleus
• Forms the nucleoid region of a cell
• 10 of the cell volume

130
BACTERIAL DNA

• Bacterial chromosomal DNA contains essentially no
  repetitive junk DNA
• Virtually all of the DNA is functional
• Very different from most eukaryotes

131
BACTERIAL DNA

• Bacteria often possess plasmid DNA
• Nonessential
• Not always present
• Often present in multiple copies
• Circular double-stranded molecules
• Smaller than the bacterial chromosome
• 0.1 - 10
• Often contain antibiotic resistance genes
• Readily transferred between bacteria, even of
  different species
• Very useful in manipulating and transferring
  genes in the laboratory

132
BACTERIAL DNA

• Plasmids often contain antibiotic resistance
  genes
• Readily transferred between bacteria, even of
  different species
• Important factor in the rapid evolution of
  antibiotic resistance in bacteria

133
BACTERIAL DNA

• Plasmids are very useful in manipulating and
  transferring genes in the laboratory
• One aspect of biotechnology
• Genes can be readily transferred between species
  for various purposes
• Glowing tobacco plant
• Bacteria producing human insulin
• Mammals producing and secreting pharmaceutical
  proteins in their milk

134
BACTERIAL RIBOSOMES

• Bacteria possess ribosomes
• Organelles facilitating protein synthesis
• 7,000 25,000 per cell (E. coli)
• Comprised of ribosomal RNA and proteins
• Smaller than eukaryotic ribosomes
• 70S (bacterial) vs. 80S (eukaryotic)
• Composed of two subunits

135
HIGHLY CONSERVED GENES

• The function of ribosomes is critical to life
• Mutations in rRNA genes are frequently lethal
• Genes encoding rRNA are evolutionarily highly
  conserved
• Relatively few differences between species
  compared to less critical genes

136
HIGHLY CONSERVED GENES

• Highly conserved genes are commonly used to
  determine or verify evolutionary relationships
• Number of differences between species is a
  measure of the evolutionary distance between
  these species

137
STORAGE GRANULES

• Storage granules are accumulations of high
  molecular weight polymers
• Synthesized by a nutrient present in excess
• Stored for later hydrolysis and use

138
STORAGE GRANULES

• Storage granules are accumulations of high
  molecular weight polymers
• Often a carbon/energy source
• e.g., Glycogen
• e.g., Poly-b-hydroxybutyrate
• Used to make biodegradable plastic
• Sometimes other nutrients
• e.g., Volutin, a storage form of phosphate
• Phosphate-storing bacteria are useful in
  wastewater treatment

139
GAS VESICLES

• Some aquatic bacteria produce gas vesicles
• Small, rigid, protein-bound compartments
• Provide buoyancy to the cell
• Organism can float or sink to its ideal position
  in the water column
• e.g., Photosynthetic bacteria float close to the
  surface

140
ENDOSPORES

• Some bacterial species produce dormant cells
  termed endospores
• e.g., Bacillus, Clostridium
• Able to remain dormant for long periods of time
• gt100 years
• Very resistant to adverse conditions
• e.g., Boiling, desiccation, ultraviolet light,
  etc.
• Can germinate to form vegetative cells able to
  multiply

141
ENDOSPORES

• Endospores can be found virtually everywhere
• Common in soil
• Often problematic in laboratories, hospitals,
  food, medical devices, etc.
• Very resistant to destruction
• Several endospore-forming bacteria cause disease
• e.g., Clostridium botulinum ? botulism
• e.g., Clostridium tetani ? tetanus
• e.g., Clostridium perfringens ? gas gangrene
• e.g., Bacillus anthracis ? anthrax

142
ENDOSPORES

• Endospore formation (sporulation) is promoted
  by a lack of nutrients
• Highly ordered sequence of changes

143
ENDOSPORE FORMATION

• Steps in endospore formation
• DNA is replicated
• Septum forms between chromosomes
• Cytoplasm divides unequally
• Larger compartment engulfs smaller
• Mother cell engulfs forespore
• Smaller compartment is enclosed by two membranes
• Ultimately forms core of endospore
• Peptidoglycan is formed between membranes
• Core wall
• Mother cell makes spore coat
• Mother cell is degrades
• Endospore is released

144
ENDOSPORE GERMINATION

• Endospore germination can be triggered by a brief
  exposure to heat or certain chemicals
• Endospore takes on water and swells
• Spore coat and cortex crack open
• Vegetative cell grows out

145
CELL ORGANIZATION

• The organization of eukaryotic cells differs from
  that of prokaryotes
• Eukaryotic cells are highly compartmentalized by
  internal membranes

146
ORGANELLES

• Eukaryotic cells possess numerous organelles
• Subcellular structures with specialized functions
• Most are surrounded by an internal membrane

147
NUCLEUS

• The nucleus is generally the most conspicuous
  organelle
• Boundary defined by a double membrane
• Nuclear envelope
• Perforated by nuclear pores
• 100 nm diameter
• Relatively large
• Regulate macromolecule movement

148
NUCLEUS

• The nucleus contains the cells genetic material
• Linear double-stranded DNA molecules
• Organized into chromosomes
• DNA is intimately associated with histones and
  other proteins
• 4 pairs for fruit files
• Drosophila melanogaster
• 23 pairs for humans

149
NUCLEUS

• The nucleus directs protein synthesis
• mRNA is produced from DNA instructions (genes)
• This mRNA is transported to the cytoplasm through
  nuclear pores
• Ribosomes in the cytoplasm assemble proteins
  according to the instructions on the mRNA

150
NUCLEUS

• Eukaryotic genomes are larger than prokaryotic
  genomes
• Some of this variation is correlated to
  complexity
• e.g., Multicellular organisms have genomes larger
  than unicellular organisms
• Much of this variation is correlated to
  repetitive DNA sequences
• Sequences present in multiple copies per genome
• Much of this is typically termed junk DNA
• Sometimes as much as 80
• Repetitive DNA is absent in prokaryotes

151
NUCLEOLUS

• The nucleolus is a darkly staining region within
  the nucleus
• Not surrounded by its own membrane
• One or slightly more than one
• Adjoins part of the chromatin
• Site of rRNA synthesis
• Site of partial assembly of ribosomes
• Final assembly occurs in cytoplasm

152
RIBOSOMES

• Ribosomes are organelles not surrounded by a
  membrane
• Facilitate protein synthesis
• Assemble proteins based upon instructions in the
  mRNA
• Comprised of ribosomal RNA (rRNA) and proteins
• Larger than bacterial ribosomes
• 80S vs. 70S
• Composed of two subunits

153
RIBOSOMES

• Ribosomes are present in large numbers
• e.g., Millions present within many human cells

154
ENDOPLASMIC RETICULUM

• The endoplasmic reticulum (ER) is an extensive
  network of membranes
• Accounts for over half of the membrane in many
  cells
• Continuous with the nuclear membrane
• ER lumen continuous with space between nuclear
  membranes
• Two distinct regions differing in structure and
  function
• Smooth endoplasmic reticulum (SER)
• Rough endoplasmic reticulum (RER)

155
RIBOSOMES

• Ribosomes may be free or attached to the rough
  endoplasmic reticulum
• Most proteins made by free ribosomes function in
  the cytosol
• ER-bound ribosomes generally produce proteins
  destined for organelles, insertion into
  membranes, or secretion

156
ENDOPLASMIC RETICULUM

• The smooth endoplasmic reticulum functions in
  diverse metabolic processes
• Lipid synthesis
• Oils, phospholipids, and steroid hormones
• Carbohydrate metabolism
• Detoxification of drugs and poisons
• Storage of calcium ions

157
ENDOPLASMIC RETICULUM

• Primary functions of the smooth endoplasmic
  reticulum differ in different cell types
• e.g., Cells in the testes and ovaries produce and
  secrete steroid hormones
• These cells are rich in SER
• e.g., Phenobarbitol and other drugs are
  metabolized by SER in liver cells
• e.g., Release of calcium ions from the SER of
  muscle cells triggers muscle contraction

158
ENDOPLASMIC RETICULUM

• Ribosomes stud the surface of the rough
  endoplasmic reticulum and the nuclear envelope
• Gives rough appearance

159
ENDOPLASMIC RETICULUM

• Ribosomes bound to the rough endoplasmic
  reticulum generally produce proteins destined for
  regions other than the cytoplasm
• e.g., Organelles, integral membrane proteins,
  secreted proteins
• These proteins enter the lumen of the RER

Lumen
160
ENDOPLASMIC RETICULUM

• Proteins are modified within the lumen of the
  rough endoplasmic reticulum
• Addition of carbohydrate groups
• Addition of phosphate groups
• Removal of amino acid residues

Lumen
161
ENDOPLASMIC RETICULUM

• Membrane-bound vesicles bud from the rough
  endoplasmic reticulum
• Synthesized proteins are present within these
  vesicles
• Many travel to the Golgi apparatus

162
ENDOPLASMIC RETICULUM

• The rough endoplasmic reticulum also functions as
  a membrane factory
• Phospholipid synthesis
• This function is in common with the SER
• (Protein synthesis and modification are not
  functions in common with the SER)

163
GOLGI APPARATUS

• The Golgi apparatus consists of a series of
  membrane-bound flattened sacs
• The cis face of the Golgi receives many of the
  transport vesicles budded from the RER
• Fuse with Golgi membrane
• Contents enter lumen of the Golgi

164
GOLGI APPARATUS

• Proteins are transferred through the Golgi
  apparatus from the cis face to the trans face
• Proteins are modified further
• Modification of carbohydrate groups
• Addition of phosphate groups
• Chemical tags functioning as zip codes are
  added
• 90210 ? Beverly Hills, CA (plasma membrane)
• 55113 ? Roseville, MN (lysosome)

165
GOLGI APPARATUS

• Vesicles containing modified proteins bud from
  the trans face of the Golgi apparatus
• Shipped to proper locations

166
LYSOSOMES

• A lysosome is a membranous sac containing
  hydrolytic enzymes
• e.g., Proteases, nucleases, etc.
• Formed by budding from Golgi complex
• Digests macromolecules
• Acidic pH (pH 5)
• Maintained by a proton pump
• Enzymes are active at this acidic pH

167
LYSOSOMES

• Lysosomes degrade various materials
• Fuse with food vacuoles to degrade phagocytized
  materials
• Fuse with organelles to recycle cellular materials

168
LYSOSOMES

• The membrane enclosing a lysosome sequesters its
  hydrolytic enzymes
• Enzymes released from a ruptured lysosome are
  inactive in the neutral pH of the cytoplasm
• Damage can result from the rupture of several
  lysosomes

169
LYSOSOMES

• Deficiencies in lysosomal enzymes cause lysosomal
  storage diseases
• e.g., Tay-Sachs disease
• A normal lipid cannot be broken down in brain
  cells
• Lipid accumulation results in mental retardation
  and death

170
PEROXISOMES

• Peroxisomes generate hydrogen peroxide (H2O2)
• Byproduct of fatty acid catabolism
• Byproduct of the detoxification of ethanol and
  other harmful compounds
• e.g., In human kidney and liver cells
• H2O2 is itself toxic
• The peroxisomal enzyme catalase detoxifies H2O2
• H2O2 ? H2O O2

171
MITOCHONDRIA

• Mitochondria are found in most eukaryotic cells
• Present in multiple copies
• Site of the majority of cellular respiration
• Krebs Cycle and Electron Transport Chain

172
MITOCHONDRIA

• Mitochondria are surrounded by two membranes
• Outer membrane in typical eukaryotic membrane
• Inner membrane is highly infolded
• Inner membrane is involved in energy
  transformations
• Electrochemical gradient ? ATP generation
• Does this remind you of something?

173
CHLOROPLASTS

• Chloroplasts are found in algae and plants
• Present in multiple copies
• Site of photosynthesis

174
CHLOROPLASTS

• Chloroplasts are surrounded by two membranes
• Outer membrane in typical eukaryotic membrane
• Inner membrane is highly infolded
• Thylakoids
• Inner membrane is involved in energy
  transformations
• E