Cell Biology: Structure, Function, Metabolism, and Photosynthesis

Posted on Apr 2, 2025 in Biology

Cells (Chapter 4)

  • Cell Theory: 3 Main Points
    • All organisms are composed of cells.
    • Cells are the smallest living things.
    • Cells arise only from pre-existing cells.
  • Cell Size vs. Volume Ratio
    • An organism made of many small cells has an advantage over an organism composed of fewer, larger cells.
    • As a cell’s size increases, its volume increases much more rapidly than its surface area.
  • Microscopes: Functions and Types
    • Light Microscopes
      1. Use magnifying lenses with visible light.
      2. Resolve structures that are 200 nm apart.
      3. Limited to resolution using light.
    • Electron Microscopes
      • Use a beam of electrons.
      • Resolve structures that are 0.2 nm apart.
  • Cell Types: Prokaryotic and Eukaryotic
  • Prokaryotic Cells
    • Nucleoid, small ribosomes, flagella, cell wall, no chloroplasts or organelles.
    • Lack a membrane-bound nucleus.
    • DNA is present in the nucleoid.
    • May contain a cell wall or protein capsid outside of the plasma membrane.
    • Contain ribosomes but lack all membrane-bound organelles.
    • Two domains of prokaryotes:
      • Archaea
      • Bacteria
  • Eukaryotic Cells
    • Detailed study of structures and functions:
      • Cell membrane
      • Nucleus
      • Nucleolus
      • Nuclear envelope
      • Endoplasmic reticulum (smooth, rough)
      • Golgi body
      • Mitochondria
      • Chloroplasts
      • Centrioles
      • Lysosomes
    • Possess a membrane-bound nucleus.
    • More complex than prokaryotic cells.
    • Hallmark is compartmentalization:
      1. Achieved through the use of membrane-bound organelles and the endomembrane system.
    • Possess a cytoskeleton for support and to maintain cellular structure.
  • Endosymbiosis Theory
    • Origin of mitochondria and chloroplasts.
    • Proposes that some of today’s eukaryotic organelles evolved by a symbiosis arising between two cells that were each free-living.
    • One cell, a prokaryote, was engulfed by and became part of another cell, which was the precursor of modern eukaryotes.
    • Mitochondria and chloroplasts.
  • Cytoskeleton Fibers
    • Three types, size, and function of each.

Microfilaments (Actin Filaments)

  1. Two protein chains loosely twined together
    1. Movements like contraction, crawling, “pinching.”

Microtubules

  1. Largest of the cytoskeletal elements
    1. Dimers of α- and β-tubulin subunits.
    2. Facilitate movement of the cell and materials within the cell.

Intermediate Filaments

  1. Between the size of actin filaments and microtubules
    1. Very stable – usually not broken down.
  • Extracellular Matrix (ECM)
    • Composition and functions.
    • Animal cells lack cell walls.
    • Secrete an elaborate mixture of glycoproteins into the space around them.
    • Collagen may be abundant.
    • Forms a protective layer over the cell surface.
    • Integrins link ECM to the cell’s cytoskeleton
      1. Influence cell behavior.
  • Cell Junctions
    • Difference between tight junctions, desmosomes, gap junctions, and plasmodesmata.
      1. Tight Junctions
        • Connect the plasma membranes of adjacent cells in a sheet – no leakage.
      2. Anchoring Junctions
        • Mechanically attaches cytoskeletons of neighboring cells (desmosomes).
      3. Communicating Junctions
        • Chemical or electrical signal passes directly from one cell to an adjacent one (gap junction, plasmodesmata).

Cell Membranes (Chapter 5)

  • Fluid Mosaic Model
    • Membrane structure.
    • Cellular membranes have 4 components:
      1. Phospholipid bilayer
        • Flexible matrix, barrier to permeability.
      2. Transmembrane proteins
        • Integral membrane proteins.
      3. Interior protein network
        • Peripheral or Intracellular membrane proteins.
      4. Cell surface markers
        • Glycoproteins and glycolipids.
  • Membrane Components
    • Arrangement of chemical components (phospholipids, cholesterol, proteins, glycoproteins).
    • What contributes to the fluidity and mosaic nature of membranes? = cholesterol.
    • Environmental influences on fluidity:
      1. Saturated fatty acids make the membrane less fluid than unsaturated fatty acids
        • “Kinks” introduced by the double bonds keep them from packing tightly.
        • Most membranes also contain sterols such as cholesterol, which can either increase or decrease membrane fluidity, depending on the temperature.
  • Membrane Proteins
    • Types of membrane proteins.
  • Membrane Transport
    1. Passive Transport
      • Definitions, meanings, and applications of the following: diffusion, osmosis, facilitated diffusion (carrier vs. channel proteins).
    2. Passive transport is the movement of molecules through the membrane in which:
      1. No energy is required.
      2. Molecules move in response to a concentration gradient.
    3. Diffusion is the movement of molecules from high concentration to low concentration
      1. Will continue until the concentration is the same in all regions.
    4. Facilitated diffusion
      1. Molecules that cannot cross the membrane easily may move through proteins.
      2. Move from higher to lower concentration
        1. Channel proteins
          • Hydrophilic channel when open.
        2. Carrier proteins
          • Bind specifically to molecules they assist.
    5. Membrane is selectively permeable.
  • Tonicity
    1. Iso-, hypo-, hypertonic solutions.
    2. Hypertonic
      1. Movement of water out of the cell.
      2. Cell shrivels.
    3. Hypotonic
      1. Movement of water into the cell.
      2. Cell swells.
    4. Isotonic
      1. No net water movement.
      2. No cellular change.
  • Active Transport
    1. Know the sodium-potassium pump, 3 types of “port” systems.
  • Requires energy – ATP is used directly or indirectly to fuel active transport.
  • Moves substances from low to high concentration.
  • Requires the use of highly selective carrier proteins
    • Uniport – move one molecule at a time.
    • Symport – two molecules in the same direction.
    • Antiport – two molecules in opposite directions.
  • Sodium-potassium (Na+–K+) pump.
  • Direct use of ATP for active transport.
  • Uses an antiport to move 3 Na+ out of the cell and 2 K+ into the cell
    1. BOTH against their concentration gradient.
  • ATP energy is used to change the conformation of the carrier protein
    1. Bulk Transport
      • Endocytosis (phagocytosis, pinocytosis), exocytosis.
  • Endocytosis
    1. Movement of substances into the cell.
  • Phagocytosis – cell takes in particulate matter.
  • Pinocytosis – cell takes in fluid (containing small solutes).
  • Exocytosis
    1. Discharge of materials out of the cell.
    2. Requires energy!
    3. Used in plants to export cell wall material.
    4. Used in animals to secrete hormones, neurotransmitters, digestive enzymes.

Energy & Metabolism (Chapter 6)

  • Energy (E)
    • Free energy, entropy, enthalpy.
  • Calorie vs. calorie
  • Heat is the most convenient way of measuring energy.
  • 1 calorie = heat required to raise 1 gram of water 1ºC.
  • calorie or Calorie?
    1. Redox Reactions
      • Know redox reactions.

Oxidation

  • Atom or molecule loses an electron.

Reduction

  • Atom or molecule gains an electron.

Oxidation-Reduction Reactions (Redox)

  • Reactions always paired.
  1. First Law of Thermodynamics
    • Conservation of energy, heat loss.
    • Energy cannot be created or destroyed.
    • Energy can only change from one form to another.
    • The total amount of energy in the universe remains constant.
    • During each conversion, some energy is lost as heat.
  2. Second Law of Thermodynamics
    • Entropy (disorderliness).
    • Entropy (disorder) is continuously increasing.
    • Energy transformations proceed spontaneously to convert matter from a more ordered/less stable form to a less ordered/ more stable form.
    1. Activation Energy
      • What is activation energy?
    2. Extra energy required to destabilize existing bonds and initiate a chemical reaction.
  2. Endergonic vs. Exergonic Reactions
    • Endergonic Reactions
      1. Not spontaneous.
      2. Requires input of energy.
    • Exergonic Reactions
      1. Spontaneous.
      2. Releases energy.
  • ATP
    • What is ATP? What are the parts? What makes it easy to breakdown?
    • Adenosine triphosphate.
    • Chief “currency” of all cells.
    • Composed of:
      1. Ribose – 5 carbon sugar.
      2. Adenine.
      3. Chain of 3 phosphates
        • Key to energy storage.
        • Bonds are unstable.
        • ADP – 2 phosphates.
        • AMP – 1 phosphate – lowest energy form.
  • Enzymes
    • Biological catalyst, protein structure, shape important, active site, functions to lower energy of activation, lock and key shapes for high specificity, induced fit model for activation.

Biological Catalysts

  • Most enzymes are protein.
  • The shape of the enzyme stabilizes a temporary association between substrates.
  • The enzyme is not changed or consumed in the reaction.

Active Site

  • Pockets or clefts for substrate binding.
  • Forms enzyme–substrate complex.
  • Precise fit of substrate into active site.
  • Applies stress to distort a particular bond to lower activation energy
      1. Induced fit.

Enzyme Function

  • The rate of enzyme-catalyzed reaction depends on concentrations of substrate and enzyme.
  • Any chemical or physical condition that affects the enzyme’s three-dimensional shape can change the rate.
  • Optimum temperature.
  • Optimum pH.
  • Enzyme Inhibitors
    • Competitive vs. noncompetitive inhibitors.
    • Inhibitor – a substance that binds to an enzyme and decreases its activity.
    • Competitive Inhibitor
      1. Competes with the substrate for the active site.
    • Noncompetitive Inhibitor
  1. Binds to the enzyme at a site other than the active site.
  2. Causes a shape change that makes the enzyme unable to bind the substrate.

Metabolism

  • Definition, types.
  1. Catabolism
    • Decomposition processes.
    • Harvest energy by breaking down molecules.
    • Starvation = breakdown muscle
  2. Anabolism
    • Synthesis processes.

Expend energy to build up molecules Anabolic Steroids=build muscle

  • Biochemical Pathways
    • What is a biochemical pathway? Negative vs. positive feedback loops.
    • Chemical reactions that create/store or produce other chemical products for daily function.
    • Reactions occur in a sequence.
    • The product of one reaction is the substrate for the next reaction.
    • Negative Loop
      1. Most common control type.
      2. Downstream product increases, this increase level of product tells an upstream factor that there is enough and it slows or stops the reaction.
        • Blood pressure: stand up fast, HR increases to keep you from passing out, then HR returns to normal.
    • Positive Loop
      1. Very few examples in normal physiology that have a good outcome.
      2. Downstream product tells the upstream system that more needs to be produced.
        • Childbirth: control of the contractions, the harder the babies head pushes on the cervix causes hormones to be produced that increase the muscle contraction. This continues until the baby and placenta are delivered.

Cellular Respiration (Chapter 7)

  • Autotrophs vs. Heterotrophs
    • Organisms can be classified based on how they obtain energy:
    • Autotrophs
      • Able to produce their own organic molecules through photosynthesis.
    • Heterotrophs
      • Live on organic compounds produced by other organisms.
  • All organisms use cellular respiration to extract energy from organic molecules.
  • NAD
    • What is NAD? Why is it important?
    • Nicotinamide adenosine dinucleotide (NAD+).
    • An electron carrier.
    • NAD+ accepts 2 electrons and 1 proton to become NADH.
    • The reaction is reversible.
  • Glycolysis
    • What comes in, what goes out.
    • Converts 1 glucose (6 carbons) to 2 pyruvate (3 carbons).
    • 10-step biochemical pathway.
    • Occurs in the cytoplasm.
    • Net production of 2 ATP molecules.
    • 2 NADH produced by the reduction of NAD+.
    • Only process that occurs in red blood cells since they do not have mitochondria!
  • Aerobic Respiration vs. Fermentation
  • Fate of Pyruvate
  • DEPENDS ON OXYGEN AVAILABILITY
    • When oxygen is present, pyruvate is oxidized to acetyl-CoA which enters the Krebs cycle
      • Aerobic respiration.
    • Without oxygen, pyruvate is reduced in order to oxidize NADH back to NAD+
      • Fermentation.
  • For the process to continue, NADH must be recycled to NAD+ by either:
  1. Aerobic respiration.
  1. Fermentation.
    • Definitions.
    • Aerobic or anaerobic?
    • What comes in, what comes out.
    • Which one is more efficient?
    • Number of ATPs produced?

Photosynthesis (Chapter 8)

  • Definition, Overall Equation
    • The ultimate source of energy is the Sun and is captured by plants, algae, and bacteria.
    • 6CO2 + 12H2O → C6H12O6 + 6H2O + 6O2
  • Chloroplast
    • Structure, identify where specific processes occur, thylakoid, stroma.
    • Thylakoid membrane – internal membrane
      1. Contains chlorophyll and other photosynthetic pigments.
      2. Pigments clustered into photosystems.
    • Grana – stacks of flattened sacs of thylakoid membrane.
    • Stroma lamella – connect grana.
    • Stroma – semiliquid surrounding thylakoid membranes.
  • Light-Dependent vs. Carbon Fixation Reactions
    • Difference between light-dependent and carbon fixation reactions.
    • Light-dependent reactions
      • Require light.
      • Capture energy from sunlight.
      • Make ATP and reduce NADP+ to NADPH.
    • Carbon fixation reactions
      • Do not require light.
      • Use ATP and NADPH to synthesize organic molecules from CO2.
  • Light and Pigments
    • Photons, visible light, colors of light, absorption and action spectra.
    • Molecules that absorb light energy in the visible range.
    • Light is a form of energy.
    • Photon – particle of light
      1. Acts as a discrete bundle of energy.
      2. The energy content of a photon is inversely proportional to the wavelength of the light.
    • When a photon strikes a molecule, its energy is either lost as heat, OR
      1. Absorbed by the electrons of the molecule.
    • Absorption Spectrum – range and efficiency of photons molecules is capable of absorbing.
    • Action Spectrum
    • Relative effectiveness of different wavelengths of light in promoting photosynthesis.
    • Corresponds to the absorption spectrum for chlorophyll.
  • Chlorophyll
    • Chlorophyll a & b, carotenoid.
    • Chlorophyll a
      • Main pigment in plants and cyanobacteria.
      • Only pigment that can act directly to convert light energy to chemical energy.
      • Absorbs violet-blue and red light.
    • Chlorophyll b
      • Secondary pigment absorbing light wavelengths that chlorophyll a does not absorb.