Chapter 7 Notes: A Tour of the Cell

HOW WE STUDY CELLS

Microscopes provide windows to the world of the cell

• Light microscopes (LMs) – light is passed through the specimen and then through glass lenses
• Lenses refract light so that image of specimen is magnified
• Resolving power – measure of the clarity of the image
• Minimum distance two points can be separated and still distinguished as two separate points
• Organelles – subcelluar structures
• Electron microscope (EM) – focuses bean of electrons through specimen or onto surface
• Transmission electron microscope (TEM)
• Studies internal structure of cells
• Scanning electron microscope (SEM)
• Studies surface of specimen
• Electron microscopy kills cells

Cell biologists can isolate organelles to study their functions

• Cell fractionation – take cells apart to study major organelles
• Centrifuge (ultracentrifuges)

1. homogenate – break cells apart without damaging organelles
2. differential centrifugation – heavier organelles at bottom, lighter on top
3. allows organelles to be collected according to size

A PANORAMIC VIEW OF THE CELL

Prokaryotic and eukaryotic cells

• All cells have several basic feature in common:
• Bounded by a membrane – plasma membrane
• Cytosol – semifluid substance where all organelles are
• Contain chromosomes - DNA
• Ribosomes – make proteins from instructions from DNA
• Prokaryotic cell – DNA concentrated in nucleoid, but no membrane
• Eukaryotic – nucleus bounded by membranous clear envelope
• Region between nucleus and membrane – cytoplasm
• Suspended in cytosol are organelles (not in prokaryotic cells)
• Eukaryotic cells bigger than prokaryotic
• Metabolic requirements impose limits on size that is practical for a cell, large size harder to maintain
• Plasma membrane – selective barrier that allows passage of oxygen, nutrients, waste
• Too large of a cell = rate of chemical exchange not fast enough
• So large organisms only have more cells, not larger cells

Internal membranes compartmentalize the functions of an eukaryotic cell

• Eukaryotic cell has internal membranes, compartments
• Compartments provide different local environments that facilitate specific metabolic functions
• Incompatible processes can go on simultaneously

THE NUCLEUS AND RIBOSOMES

The nucleus contains a eukaryotic cell’s genetic library

• Nucleus – contains genes in the eukaryotic cell
• Nuclear envelope = double membrane
• Each membrane a lipid bilayer
• Has pores, regulate entry and exit of large particles
• Lined by nuclear lamina – netlike array of protein filaments
• Maintain shape of nucleus
• DNA organized along with proteins into chromatin
• When cell divides, thin chromatin fibers coil up à thick into chromosomes
• Nucleolus – RNA – ribosomal RNA is synthesized and assembled with proteins into ribosomal subunits
• Subunits then pass to cytoplasm, combine to form ribosomes
• Nucleus directs protein synthesis by making mRNA and sending it to cytoplasm through nuclear pore
• mRNA reaches cytoplasm à ribosomes translate genetic message

Ribosomes build a cell’s proteins

• Ribosomes – particles made of ribosomal RNA and protein, carry out protein synthesis (two subunits)
• Build proteins in two places:
• Free ribosomes – suspended in cytosol
• Proteins made here will function in cytosol
• Bound ribosomes – attached to the outside of endoplasmic reticulum or nuclear envelope
• Proteins made used for insertion into membranes, packaging within organelles, or export from cells

THE ENDOMEMBRANE SYSTEM

Endomembrane system – different membranes of eukaryotic cell

Vesticles – sacs made of membrane, membrane segments

The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions

• Endoplasmic reticulum (ER) – accounts for more than half of total membrane
• Latin – little net within the cytoplasm
• Network of tubes and sacs (cisternae)
• Separates internal compartment of ER (cisternal space) from cytosol
• Smooth ER – cystoplasmic surface no ribosomes
• Rough ER – ribosomes stud the surface

Functions of Smooth ER

• Functions in metabolic processes: synthesis of lipids, metabolism of carbohydrates, detoxification of drugs and poisons
• Enzymes of smooth ER important to synthesis of lipids
• Sex hormones of vertebrates, steroid hormones
• Carbohydrate metabolism
• Liver cells – store carbohydrate in glycogen
• Hydrolysis of glycogen releases glucose, but first releases glucose phosphate (which can’t leave the cell)
• Enzyme in ER removes phosphate from glucose
• Detoxify drugs and poisons
• Adds hydroxyl groups to drugs
• E.g. barbiturates – induce proliferation of smooth ER and detoxification enzymes
• Leads to increased tolerance to the drugs
• Increased proliferation of smooth ER in response to one drug can increase tolerance to other drugs
• Muscle cells
• ER membrane pumps calcium ions from cytosol into cisternal space
• Muscle cell simulated, calcium rushes back to cytosol, triggers muscle contraction

Rough ER and the Synthesis of Secretory Proteins

• Produces proteins that are secreted by cells
• Pancreas secrete protein insulin
• Polypeptide chain grow from bound ribosome
• Threaded into cisternal space through pore formed by protein in ER membrane
• Most secretory proteins – glycoproteins – covalently bonded to carbohydrates
• Carbohydrate (oligosaccharide) attached to protein in ER
• ER membrane keeps fully formed secretory proteins apart from proteins that remain in cytosol
• Depart from ER wrapped in membranes of vesicles – transport vesicles

Rough ER and Membrane Production

• Membrane factory that grows by adding proteins and phospholipids
• Polypeptide destined to be membrane proteins grow from ribosomes
• Inserted into ER membrane, anchored by hydrophobig portions
• Makes its own membrane phospholipids
• Membrane can expand and be transferred

The Golgi apparatus finishes, sorts, and ships cell products

• Transport vesicles go to Golgi apparatus
• Center of manufacturing, warehousing, sorting, and shipping
• Consists of many flattened cisternae – separates internal space from cytosol
• Two poles:
• Trans: receiving and shipping department
• Cis: located near ER
• Transport vesicles move material from ER to Golgi
• Vesicles from ER fuses to cis face’s Golgi membrane
• Trans face gives rise to vesicles which go off elsewhere
• Products are modified as they go from cis pole to trans pole
• Eg produces large variety of oligosaccharides by changing sugars
• Manufactures some macromolecules such as polysaccharides
• Sorts and targets them for various parts of cell
• Molecular identification tags – phosphate groups

Lysosomes are digestive compartments

• Membrane-bounded sac of hydrolytic enzymes, used to digest macromolecules
• Works best at pH of 5 – pumps hydrogen ions from cytosol
• Enzymes made by rough ER
• Phagocytosis – engulfs smaller food particles
• Recycles cell’s organic material – autophagy
• Programmed destruction of cells (tadpole à frog)
• Lysomal storage disorder – enzymes become engorged with indigestible substrates

Vacuoles have diverse functions in cell maintenance

• Membrane-bounded sac
• Food vacuoles
• Contractile vacuoles – pumps excess water out of cell
• Central vacuole – enclosed by membrane called tonoplast
• Coalescence of smaller vacuoles
• Hold reserves of important organic compounds
• Main repository of inorganic ions
• Disposal sites for by-products
• Contain pigments
• Protect against predators (contain poisonous compounds)

OTHER MEMBRANOUS ORGANELLES

Mitochondria and chloroplasts are the main energy transformers of cells

• Convert energy to forms that cells can use for work
• Mitochondria – sites of celluar respiration
• Generates ATP by extracting energy from sugars, fats, etc with oxygen
• Chloroplasts (plants and algae) – sites of photosynthesis
• Convert solar energy to chemical energy
• Absorbs sunlight and use It to drive synthesis of organic compounds
• Not part of endomembrane system
• Membrane proteins made by free ribosomes or from within themselves
• Contain some DNA – programs synthesis of proteins made on their own ribosomes

Mitochondria

• Enclosed by two membranes of phospholibid bilayers
• Outer membrane is smooth
• Inner membrane is convoluted, foldings called cristae
• Divides mitochondrion into two internal compartments
• First is region between inner and outer membranes
• Second is mitochondrial matrix – enclosed by inner membranes
• Enzymes, DNA, ribosomes
• Cellular respiration here

Chloroplasts

• Part of plastids
• Contains green pigment chlorophyll
• Two membranes with intermembrane space
• Flattened sacs called thylakoids
• Stacked = granum
• Fluid outside thykaloid = stroma (DNA, ribosomes, enzymes)

Peroxisomes generate and degrade H₂O₂ in performing various metabolic functions

• Specialized metabolic compartment bounded by single membrane
• Enzymes that transfer hydrogen from substrates to oxygen, producing hydrogen peroxide (by-product)
• Breaks down fatty acids so they can be transported to mitochondria as fuel
• Detoxify in liver by transferring hydrogen from poisons to oxygen
• Contains enzyme that converts H₂O₂ to water
• Grow by incorporating proteins and lipids made in cytosol

THE CYTOSKELETON

Cytoskeleton – a network of fibers extending throughout cytoplasm

Providing structural support to the cell, the cytoskeleton also functions in cell motility and regulation

• Mechanical support to cell, maintain shape
• Balance between opposing forces by its elements
• Anchorage for organelles
• Cell motility – movement
• Cilia and flagella
• Contraction of muscle cells
• Transportation vesicles
• Transmit mechanical forces from surface of cell to interior

Microtubules

• Wall made of globular protein – tubulin
• Two polypeptide subunits – alpha and beta tubulin
• Grows by adding tubulin dimmers to the end
• Shape and support cell
• Serve as tracks that organelles can move on
• Guide separation of chromosomes during cell division

Centrosomes and centrioles

• Microtubules grow out from centrosome (near nucleus)
• Compression-resisting microtubules girders of cytoskeleton
• Within centrosome are a pair of centrioles (nine sets of triplet microtubules arranged in a ring)

Cilia and Flagella

• Flagella
• Longer than cilia
• One or few per cell
• Undulating snakelike motion, generates force in same direction as flagellum axis
• Cilia
• Large numbers on cell’s surface
• Work like oars, generates force perpendicular to cilium’s axis
• Common ultrastructure
• Core of microtubules
• 9 doublets in a ring
• 9 + 2 pattern
• Wheels of proteins connect doublets to each other and central 2 microtubules
• Anchored in cell by basal body, identical to centriole
• Dynein – large protein arms respondible for bending movement
• Dynein walking –
• Arms of one doublet attach to adjacent doublet and pull so that the doublets slide past each other in opposite directions. The arms then release from the other doublet and reattach a little further along its length.

Microfilaments (Actin Filaments)

• Built from molecules of actin, a globular protein
• Twisted double chain of actin subunits
• Role is to bear tension
• Supports cell’s shape
• Cell motility
• Contractile apparatus of muscle cells
• Myosin – motor molecule, arms that walk along actin filaments
• Contraction of muscle cells from actin and myosin filaments sliding past another, shortening the cell
• Pseudopia extend and contract
• Through assembly of actin subunits into microfilaments
• Cytoplasmic streaming – circular flow of cytoplasm within cell

Intermediate Filaments

• Bearing tension
• Belongs to family of proteins called keratins
• Diverse, different molecular subunits
• Permanent fixtures, reinforces shape of a cell and fixing position of certain organelles
• E.g. nucleus sits in a cage of intermediate filaments

CELL SURFACES AND JUNCTIONS

Plant cells are encased by cell walls

• Protects plant cells, maintains shape, prevents excessive intake of water
• Hold plant up against force of gravity
• Made of cellulose, embedded in matrix of other polysaccharides and protein
• Young plant cell first has thin and flexible wall called primary wall cell
• Between primary walls is middle lamella – think layer rich in sticky polysacchrides called pectins (glues the cells together)
• Cell matures, hardens its walls
• Either by secreting hardening substances
• Or add secondary cell wall

The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and regulation

· Mainly made of glycoproteins

o Mainly collagen, forms strong fibers outside the cell

o Embedded in network from proteoglycans (glycoproteins of another class)

o Cells attach to ECm through other kinds of glycoproteins – fibronectins

§ Bind to receptor proteins called integrins in plasma membrane

· Regulate a cell’s behavior by communicating with it through integrins

· Can influence the activity of genes in the nucleus

Intercellular junctions help integrate cells into higher levels of structure and function

• Plant cell walls perforated with plasmodesmata
• Cytosol passes from one cell to another
• In animals three types of intercellular junction
• Tight junction: membranes of neighboring cells are fused
• Prevents leakage of extracellular fluids
• Desmosomes: rivets, fastening cells together into strong sheets
• Gab junctions: provides cytoplasmic channels between adjacent animal cells
• Salt ions, sugars, amino acids etc can pass through
• Flow of ions coordinate contraction of cells