Biology of the Cell Lecture Course

BIOL 1013 - BIOLOGY OF THE CELL

The following text and material represent a copy of some of my notes that formed the basis of some of my lectures given during the third portion of the Biology of the Cell (BIOL 1013) course. Please refer to your own notes, handouts, and to the textbook (essential cell biology, 2nd edition, by Alberts, et al. 2004 - reading assignments are in the syllabus) for additional information. If you note any errors in the following document, I'd appreciate it if you would bring this to my attention. READING ASSIGNMENTS listed from Chapters 11, 12, 13, and 14 coincide with the textbook essential cell biology, 2nd ed., by Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts, & Walter, 2004, published by Garland Science - Taylor & Francis Group.

For some very helpful information visit the following Web Site: Biology I Animations, Movies & Interactive Tutorial Links. Visit the categories: Cell Transport, Cellular Respiration, and Photosynthesis. In particular, check out the animations from McGraw-Hill Publisher's posted at this site. You may find it quite informative.

MEMBRANE STRUCTURE AND FUNCTION

Biological membranes are made up of a phospholipid (hydrophobic tails - fatty acids and hydrophilic heads - phosphate group) bilayer and proteins (peripheral and integral or transmembrane) proteins ==> Fluid mosaic model of membrane structure.

If fatty acid tails are unsaturated they become bent and this increasing the fluidity of the membrane making it more unstable. Other lipids, such as cholesterol (animals) and ergosterol (fungi) become integrated into the membrane.

Properties of biological membranes

membranes are oily and can change structure by sliding the phospholipid layers over one another.
membranes are different on one side than on the other - this contributes to ASYMMETRY.
proteins attached to carbohydrates = glycoproteins are involved in cell to cell communication and enhancing asymmetry because of their position on the outer side (exoplasmic face) of the cell membrane.
membranes are semipermeable or differently permeable (large uncharged polar molecules like glucose, and ions don't pass through membrane, but hydrocarbons, water, oxygen and carbon dioxide go straight through).

Function of membranes

movement of water and solutes into and out of cells and organelles.
differential permeability.
ion pump - K⁺ and H⁺ are moved through the membrane at the cost of ATP.
enzyme activity due to presence of certain proteins, for example, site of ATP synthesis.
electron transport system occurs across membranes found inside the mitochondria and chloroplasts.
cellular communication - binding of certain chemicals to cell membrane, initiate metabolic changes inside cell.

Movement of water and other molecules across membranes

diffusion - random movement of molecules in a fluid or gas from a region of high concentration to a region of low concentration. [EXAMPLES: dye in water, perfume in the air]
diffusion occurs along a concentration gradient. To go against a concentration gradient always requires the input of energy.

OSMOSIS

Thought experiment: A beaker containing 2% sucrose is gently placed into a larger beaker containing distilled water. Sucrose will tend to diffuse out of the small beaker into the larger beaker along a concentration gradient. Water will also tend to diffuse into the beaker from a region of high concentration (surrounding distilled water) to a region of low concentration (the water displaced by the presence of a solute - sucrose).

If you place a semipermeable membrane (i.e., permeable to water, but impermeable to sucrose) over the surface of the small beaker, then sucrose cannot cross the barrier but water can! Osmosis is the movement of water across a differentially permeable membrane along a concentration gradient.

Potential (stored) energy of water = water potential expressed in units of pressure (bars or megapascals - Mpa). When water tends to move from a region of higher concentration (higher potential) to a region of lower concentration (or lower potential), this is referred to as water potential. Add a membrane, this is called osmotic potential.

TONICITY (tonos = tension)

Hypotonic - low solute concentration relative to another solution.
Hypertonic - high solute concentration relative to another solution.
Isotonic - solute concentration is the same as that of another solution.

The use of these terms is always in relationship to another solution. For example:

Distilled water =========>2% NaCl ==============> 5% NaCl

hypotonic =============> hypertonic

hypotonic ============> hypertonic

hypotonic =================================> hypertonic

TURGOR PRESSURE - Water moving into cell pushes the cell membrane up against the cell wall causing turgor pressure. Loss of water from the vacuole/cytoplasm causes shrinkage of cellular contents, or PLASMOLYSIS. Loss of water from plant cells results in wilted tissue!

Red blood cells or RBCs or Erythrocytes:

If external solution is isotonic (0.9 % sodium chloride solution) ==> no change in cell volume.
If external solution is hypertonic ==> cells shrivel (Hence the saying, if lost at sea with no drinkable water, "Water water everywhere, but not a drop to drink!").
If external solution is hypotonic ===> cells swell and explode!

TRANSPORT PROTEINS

Facilitated diffusion occurs by means of a channel or carrier protein, gate open and closes, or gate stays continuously open. Process works along a concentration gradient and requires no input of energy ==> PASSIVE TRANSPORT!.

ACTIVE TRANSPORT ==> transport of a substance across the membrane against the concentration gradient and requires the input of energy (high energy bond from ATP).

The setup for cotransport usually requires an investment of energy by the cell. Channel protein allows one substance through that pulls another through. Both substances may move across the membrane together (symport) or in opposite directions of one another (antiport).

Ion pumps use and electrochemical gradient to drive substances across the membrane.

EXOCYTOSIS - bypasses membrane transport and allows for movement of large molecules and quantities across membrane into the cell .

ENDOCYTOSIS

Phagocytosis - occurs in amoeba and white blood cells to capture bacteria and other microbes.
Pinocytosis - nonspecific uptake of bits of liquid and dissolved molecules.
Receptor-mediated endocytosis - specific uptake of substances that are recognized by receptor proteins on the plasma membrane.

CELLULAR RESPIRATION

Cellular respiration - the conversion of chemical energy (found in the chemical bonds that hold the glucose molecule together) into chemical bonds that hold the phosphate groups to adenosine triphosphate (ATP). The process is a step by step degradation of sugar mediated at each step by a specific enzyme.

ATP = energy currency. Analogous with situation that if glucose were a one dollar bill, ATP would be a bunch of nickels or pennies.

Cellular respiration can occur in the presence or absence of oxygen:

Anaerobic metabolism (absence of oxygen) = fermentation (alcoholic or lactic acid fermentation).

Aerobic metabolism (presence of oxygen is required) = oxidative phosphorylation.

Both anaerobic and aerobic metabolism or respiration begin with breaking a six-carbon sugar (glucose) into two molecules of a three carbon compound called pyruvate. This process is called GLYCOLYSIS (SUGAR-BREAKING REACTIONS) and begins in the cytoplasm, Two ATP are necessary to get glycolysis going and 4 are produced as a result, making the net yield of ATP equal to 2 ATP. Pyruvate can be used for aerobic respiration (with oxygen) to yield many ATP molecules (34 ATP) or in fermentation (yielding only 2 ATP + 2 NADH). Only organisms that possess eukaryotic cells containing mitochondria are capable of respiring in the presence of oxygen. Certain types of bacteria and yeasts can transform pyruvate into ethanol (alcohol) and a carbon dioxide molecule (found in beer, wine, and rising bread dough). Other types of bacteria and animal cells can transform pyruvate into lactic acid (found in yogurt, sauerkraut, and overworked muscles). Because glucose is only partially broken down, little energy is captured in the form of ATP (a net total of 2 ATP and 2 NADH). We know this because if you burn alcohol, energy is released in the form of heat and light.

The overall equation for aerobic respiration is:

C₆H₁₂O₆ (glucose) + 6O₂ (from the air) ===> 6CO₂ + 6H₂O + 36 ATP (usable energy)

Pyruvate (a 3 carbon compound) produced by glycolysis is further degraded by other enzyme-mediated chemical reactions until it is broken down into nothing more than water and carbon dioxide. This occurs during a process called the KREBS'S CYCLE (also called the TCA cycle - tricarboxylic acid cycle, and citric acid cycle ). During this process molecules of 6NADH, 2FADH₂, and 2ATP are generated. The chemical reactions of the Krebs's cycle produce products that continue to feed on itself, as long as a continuous supply of acetyl CoA generated from pyruvate (producing one NADH) are available at the beginning of the process. The products of the Krebs's cycle (NADH, FADH₂) are used to feed the next step of respiration, which is Electron Transport Oxidative Phosphorylation. Electrons and hydrogen ions are liberated (yielding NAD⁺, FAD⁺). The electrons are moved from one electron acceptor molecule to another. These electron acceptors are imbedded in the inner membrane of the mitochondrion. As these move back and forth across the membrane, the energy contained in these electrons are used to shuttle additional hydrogens across the membrane into the outer compartment. Hydrogens liberated from NADH and FADH₂, increase this concentration still further. Hydrogen ions are removed from the inner compartment, when these combine with electrons and oxygen (the final electron acceptor) yielding water. Consequently an electrochemical concentration gradient develops between the outer and inner compartments of the mitochondrion. These ions eventually are allowed to diffuse back into the inner compartment through the membrane by passing through the a channel protein (ATPase or ATP synthase) - this process is called chemiosmosis As hydrogen ions pass through this channel protein, they couple a chemical reaction between ADP and Pi to produce ATP. It is estimated that each NADH molecule is responsible for generating 3 ATP molecules; FADH₂ = 2 ATPs.

PHOTOSYNTHESIS

Autotrophs - "self feeder". Examples include photosynthetic organisms (e.g., cyanobacteria, green algae and plants).

Heterotrophs - "other feeder". Examples include bacteria, some protists (e.g., amoebae, paramecia, slime molds), fungi, non-photosynthetic parasitic plants (e.g., dodder, Indian pipe) and animals.

Metabolism - ability to acquire and use energy.

Each time an energy transfer takes place, some energy is lost in the form of heat.

Photosynthesis - a set of enzyme-mediated reactions in which light energy from the sun is converted into the chemical bond energy of glucose and ATP.

The overall chemical reaction for photosynthesis is:

6CO₂ + 12H₂O + sunlight energy =======> C₆H₁₂O₆(glucose) + 6H₂O + 6O₂

In eukaryotes, the organelle associated with photosynthesis is the chloroplast. Chlorophylls a and b, the light absorbing pigments (along with accessory pigments such as the carotenoids) are embedded in the thylakoid membrane that form the grana and membrane system (thylakoid interior - pH of 5.0) within the chloroplast. The grana and thylakoid membrane system are surrounded by the stroma (pH of 8.0).

Why are plants green? The presence of the pigment chlorophyll (a and b) in the thylakoid makes the chloroplast appear green in color. Sunlight, within the visible spectrum of the electromagnetic spectrum, is composed of different wavelengths or colors of light. When light hits a leaf, some of the light is absorbed, some passes or is transmitted through the leaf (like light through a filter), and the rest is reflected away. The reason that leaves are green is due to the fact that colors like red and blue are absorbed, while green and yellow are reflected back to you. When light lands on the retina of your eye, your brain perceives this as the color green. This phenomenon also explains why we see any object as being one color versus another. Objects that are red reflect the red wavelengths of light and absorb all other wavelengths; objects that are black reflect little light back, most light is absorbed; while those objects that appear to be white reflect most of the light away, little light is absorbed.

Sunlight contains energy, which under the right conditions can be converted to other forms of energy: e.g., chemical bond energy, electricity, kinetic energy, heat, etc...

Light possesses both wave-like and particle-like properties. Packets of energy called photons. The shorter the wavelength of light, the more energy it contains per photon. The longer the wavelength of light, the less energy it contains per photon. Wavelengths of light are measured in very small units called nanometers.

Photosynthesis proceeds in two major steps: (1) During the light dependent reactions, light energy is captured by pigments in chloroplasts and water is split to yield hydrogen ions, electrons, and oxygen. When light strikes the electrons of the magnesium atom, it gets excited. Electrons are jumped to a higher energy level and the energy transferred by fluorescence (via photons of longer wavelengths and less energy) from one pigment molecule to the next in an antennae complex until it is "captured" at the reaction center. This energetic electron is funneled to electron transport system imbedded in the thylakoid membrane of the chloroplast. The electrons originate from the breakdown of water (photolysis), which liberates hydrogen ions and oxygen. The electrons move from one electron acceptor to another in the thylakoid membrane, starting at Photosystem II (P680) and moving through Photosystem I (P700). The energetic electrons and hydrogen ions are used to generate ATP by noncyclic photophosphorylation and chemiosmosis (hydrogen passing through the channel protein, ATPase or ATP synthase) and NADPH (from NADP⁺). The energy originally in light, is now present in the chemical bonds associated with ATP and NADPH. The aforementioned method (noncyclic photophosphorylation) occurs in eukaryotic plants - algae, mosses, ferns, conifers, and flowering plants. Cyclic photophosphorylation occurs in prokaryotes (cyanobacteria) with electrons being used over and over again. Note that in cyclic photophosphorylation that no oxygen or NADPH are generated.

(2) The light dependent reactions are associated with the thylakoid membrane system. The energy in ATP and NADPH is used during the light independent reactions, to "fix" the carbon in CO₂ by producing a more complex carbohydrate. The series of enzyme-mediated chemical reactions responsible for the capture and incorporation of "gaseous carbon" into "solid" carbon compounds is called the CALVIN-BENSON CYCLE (also referred to as C₃ photosynthesis). The enzyme that initially starts off the process by reacting with CO₂is called ribulose bisphosphate carboxylase. This is the most abundant naturally-occurring protein produced on the earth.

In leafy plants, glucose is used to stored as sucrose or starch. Glucose is transported through phloem (food-conducting vascular tissue). Another type of vascular tissue found in the leaves, stems and roots is the xylem, which conducts water. Plants have a body design that enhances and coordinates the process of photosynthesis. Above ground, these plants are highly branched to increase the surface area for the absorption of sunlight and CO₂. Below ground, plants have a highly branched root system to anchor the plant and increase the surface area for the absorption of water. Glucose and the stored chemical energy it contains are used to build more complex organic compounds (e.g., polysaccharide, lipids, proteins, nucleotides). Energy, when needed (e.g., germination of seeds and growth, at night when no photosynthesis is possible, in underground roots), contained in glucose is liberated by mitochondria through aerobic respiration.

This web page is maintained by Dr. Martin Huss, who can be reached by E-mail at mhuss@astate.edu.