High School Biology: Cell Reference
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The Cell

In 1665 Robert Hooke described what he saw as Microphagia. He described what a piece of cork looked like. He said it resembled a honeycomb and the pores or cells looked like little boxes.

In 1809 the French naturalist, Jean Baptiste Lamarck, wrote: Every living body is essentially a mass of cellular tissue in which more or less complex fluids move more or less rapidly.

German physiologist Theodor Schwann, b. Dec. 7, 1810, d. Jan. 11, 1882, and German botanist Matthias Jakob Schleiden, b. Apr. 5, 1804, d. June 23, 1881, are credited with formulating the cell theory.

Cell References
Cell Division
Cell Metabolism
Cell Reproduction
Cell Transport
Cloning
Molecular Biology
Onion Cell Lab
Osmosis
After studying medicine at the University of Berlin, Schwann began his most important work, the microscopic study of animal tissue, which led to his idea that all living things are made up of cells and that each cell contains essential components such as a nucleus. He published this idea in Microscopic Researches into Accordance in the Structure and Growth of Animals and Plants (1839).

After an education in law, Schleiden concentrated on botanical studies. In 1838, one year before Schwann, he developed the idea that the cell was the basic unit of plants and that growth consisted of production and development of new cells. Schleiden's two-volume text Principles of Scientific Botany (1842-43) was long a model for modern botanical works. The cell theory was extended by others and drew the attention of biologists to the study of cell contents.

The Cell Theory-Proposed by Schleiden & Schwann in 1839, stated All organisms are composed of one or more cells. and The cell is the basic organizational unit of life.

Later, in 1859, Virchow proposed that all living cells arise from pre-existing cells (except the very first cell!)

In 1862, Louis Pasteur proved Virchow's proposal by the long neck Flask experiment.

Today scientists know that living things are made up of cells that are made by chemical compounds, and yet they are able to proliferate and make new cells. There are, however, two classes of cells- The eucaryotes and procaryotes- the main difference being that procaryotes have no membrane bound organelles.

PROCARYOTES- Belong to the kingdom Monera with two series of Archaeobacteria and Eubacteria. These cells lack nuclear membrane, mitochondria, endoplasmic reticulum, golgi body and lysosomes. They replicate by binary fission. Procaryotes do not have centrosome. Procaryotes/bacteria, however, like eukaryotes, contain both DNA and RNA, ribosomes, digestive enzymes, and are able to generate ATP. The characteristics of bacteria are as follows:

1. Shape A. Bacilli- Rod shaped B. Cocci- Spherical C. Spirila- Helically coiled.

2. Cell Wall- Bacteria cell wall consists of Muriens, a polymer of polysaccharides, and the amino acid Muramic acid. The cell wall of the bacteria is the site where antibiotics work by promoting disassembly of the bacterial cell wall. Another characteristic of the cell wall is its chemical reactivity to various stains, which helps their classification and recognition.

Capsule- A mucoid polysaccharide that is secreted by some bacterial cells. It helps to protect the cell from the host's immune system in cases of infections.

Endospores- This is a form that a bacteria may take to protect itself from physical harm. The endospore contains both DNA and any other vital agents required for normal living. These endospores can tolerate extreme heat and dryness for long period of time.

3. Reproduction- Even though bacteria do not contain a nucleus, they have a nuclear regions or Nucleoid. Nucleoid is a site where the single strand of circular DNA-isolated chromosomes-is located. Bacteria reproduce at a very high rate (as low as once every 20 minutes) through binary fission. Reproduction is not by mitosis like in eucaryotic cells. The two new daughter cells have the same genetic information as the parental cell except that the daughter cells now have half of the original amount of cytoplasm and surface area.

4. Motility- Bacteria contain flagella for locomotion. This flagella has a rotatory motion as a result of the movement of H+ ions down their electrochemical gradient through specific channels at the base of the flagella. Bacterial flagella have no structural similarity to the eukaryotic flagella. Bacterial flagella arise from basal granules.

5. Pilli-Serves as an appendage on the surface of either motile or non-motile cells. Pilli function as either a grasping agents for the bacteria to the host cell or medium, or may function as conjugating tubes for transfer of DNA between two bacteria within the same species. Pilli also function in absorbing nutrition for the bacteria from the environment or the host cell. ...

6. Photosynthesis- Chemosynthetic bacteria acquire their energy through oxidizing inorganiccompounds-like sulfur, nitrite, and ferrous ion. The nitrifying bacteria belong to this group and it has an important function in the nitrogen cycle. However, some of the bacteria are autotrophic-namely they acquire energy via photosynthesis. These are:

A. Green And Purple Bacteria- Anaerobic bacteria that have light trapping compounds in their Chromatophores. This chromatophore provides energy for the bacteria via Photosystem I. Green and Purple bacteria carry their "Dark" reaction photosynthesis in the cytoplasm.

B. Halophillic Archeo Bacteria-These are bacteria that live in the salt lakes and brines. They use Rhodopsin-like pigments instead of chlorophyll in their plasma membrane. In an anaerobic condition these pigmented molecules in the presence of light release the internal H+, hence creating a H+ gradient that will produce ATP. This ATP is then used for bacterial energy.

C. Cyanobacters- These are photosynthetic bacteria with their chlorophyll A within the Thylakoid membranes. Oxygen is the end product of their photosynthesis. Cyanobacters are thought to be the father of eucaryotic chloroplasts.

Note:The characteristic color of Blue-Green bacteria is due to the presence of Phycoerythin (red) and phycocyanin (blue).

D. Nutrition- Bacteria are mostly heterotrophs, namely they are either parasitic or saprophytic. A majority of bacteria are Aerobic, namely they require O2 for their final electron acceptor in their electron transport system. Note: The Electron Transport System (ETS) of bacteria are held on the inside plasma membrane or on its invagination. ...

Cell Metabolism

A. Metabolism- It is the total energy that is released and consumed by a cell. Metabolism is the sum of the total energy of catabolism and anabolism.

1. Catabolism- The energy releasing process in which a chemical (food) is broken down, via decomposition or degradation, into its smaller constituents. An example is the breakdown of glucose into CO2 and water and 38 molecules of ATP.

2. Anabolism- Anabolism is the opposite of catabolism. In this class of metabolism, the cell consumes energy to produce larger molecules via smaller ones. An example is the synthesis of glycogen from glucose and ATP.

Note: The produced energy in catabolism may be used to provide heat energy for other cellular catabolism or anabolism. Yet, some of the energy that is used by anabolism may be used later for catabolism. Example. glycogen is an storage site for both glucose and ATP since, when glucose is released from glycogen, the sugar molecule can be used by the cell to produce 38 ATP via catabolism.

B. Respiration- Is the energy releasing process whereby sugar molecules are broken down via 3 consecutive steps (1. glycolysis, 2 Kreb's cycle and 3. Electron transport system) to CO2 and water and 38 ATP molecules.

C. Redox Reaction- This is a simultaneous oxidation-reduction process whereby cellular metabolism occurs. It is:

ENERGY RICH MOLECULES- In a cellular respiration there are three kinds of energy rich molecules. These are ATP, NADH2 and FADH2. However, for NADH2 and FADH2 molecules to be useful by the cell they are both converted, via other mechanisms, into ATP.

1. Adenosine Triphosphate-This is the most common energy carrier molecule in respiration. It is used in cellular respiration, metabolism, catabolism, neuron action potentials and muscle contractions as examples. Its structure is :

The ATPase is consumed and can be broken down into ADP and AMP via hydrolysis;

Phosphorylation of adenosine monophosphate is a process whereby the low energy AMP formed creates a higher energy bond ADP and ATP.

2. Flavin Adenine Dinucleotide (FAD)-Another molecule that is used by cellular respiration to carry energy from one place to another. FAD is used in the Kreb's Cycle.

Every molecule of FADH2 has the energy equivalent of 2 molecules of ATP.

3. Nicotinamide Adenine Dinucleotide (NADH)-After ATP, NADH is the second most commonly used energy carrier.

Every molecule of NADH2 has enough energy to promote 3 molecules of ATP.

RESPIRATION- Respiration is the process whereby a sugar molecule is broken down into CO2, H2O and 38 ATP via 3 consecutive steps. These are 1. Glycolysis, 2. Kreb's cycle, and 3. Electron Transport System.

I. Glycolysis- Or anaerobic respiration, is the process that occurs in either the absence or presence of oxygen molecules in the cytoplasm of a cell. The process starts when a glucose molecule is phosphorylated and is broken down into two 3 carbon molecules of pyruvic acid. In this process 2 molecules of ATP start the hydrolysis and via subsequent steps 2 molecules of ATP and 2 molecules of NADH2 are produced, resulting in total production of 2 ATP molecules to be used by the cells energy. Note: The energy stored in NADH2 (equivalent to 6 ATP molecules) is used again by the Kreb's cycle itself. Thus this energy is not counted toward glycolysis energy release. Glycolysis is as follows:

II. Fermentation- This step occurs in eucaryotes only when there is a shortage of oxygen. It occurs in anaerobic and facultative aerobic bacteria, for instance.

1. In Muscle Cells- During extraneous activities, the oxygen in the muscle tissue is decreased to an extent that aerobic respiration does not occur at a sufficient rate. Hence;

2. In Yeast- The fermentation end product is ethyl alcohol;

Note: In fermentation, pyruvic acid is the final electron acceptor. Also, when oxygen is present in the lactic acid accumulated muscle cells, then, via the enzyme lactate dehydriogenase the lactic acid is converted back into pyruvic acid to be used again in oxidation respiration.

III. Aerobic Metabolism- Or aerobic respiration, is the process that occurs only in the mitochondria. This is the most energy yielding chemical reaction within the cell. Namely 36 of 38 ATP are produced in the mitochondria, hence its nick name " The cell's Powerhouse". There are three stages where oxidation respiration occurs. 1. Production of Acetyl-COA from pyruvic acid. 2. Tricarboxylic acid cycle. 3. Electron Transport system

1. Acetyl-Coa Pathway- This is a cycle where a single molecule of pyruvic acid is bonded to a molecule of coenzyme-A, and the released energy forms a molecule of NADH2+. Yet, the pyruvic acid in the process has lost its carboxylic acid end in the form of CO2 gas. The end product is called Acetyl-COA.

Note: The prefix 2 is written because a 6 carbon sugar molecule yields 2 molecules of pyruvic acid. Thus, from here on the prefix 2 represents the total molecules in each step produced from theoriginal single molecule of glucose.

2. Tricarboxylic Acid Cycle (Tca)- Or the Kreb's or Citric Acid Cycle. This is the cycle where Acetyl-COA binds to an Oxaloacetic acid (from the cycle) to form a citric acid, the initiating molecule of the TCA cycle. The TCA cycle produces 24 ATP molecules. The cycle is as follows:

SUMMARY: The three stages of energy liberating pathway of glucose metabolism can be written in the form: ...

IV. Electron Transport System (ETS)- This is a system that is the most complicated of all, whereby the energy stored in the NADPH2+ and FADH2+ molecule is released via different steps so that molecules of ADP and Pi are combined to form ATP molecules. All of the processes in this system occur within the inner mitochondrial membrane, via various enzymes and protein changes. It should be noted that the whole process is to use the energy stored in either NADH2+ and FADH2+ and consume it to create a concentration gradient of H+ between the outer mitochondrial membrane compartment (higher H+ concentration) and inner mitochondrial membrane compartment. The process is as follows:

1. When NADH2+ binds to the flavoprotein (FP) it reduces an e- and a H+. Two H+ are released into the outer mitochondrial matrix, while the electron moves along the proteins of the inner mitochondrial membrane.

2. Two electrons are bounded to the flavoprotein then these two electrons move from FP to the protein containing iron and sulfur (FeS + FeSB), then to the cytochrome b. Cytochrome b gives the e- to the coenzyme Q (Q).

3. Coenzyme Q is an enzyme that moves across the inner matrix membrane when it carries an e- within . This movement also transports 2H+ to the outer matrix membrane. Again e- moves from Q to cytochrome b2----> Cyt e-------> Cyt a and Cyt a3.

With the exception that 2H+ molecules are imported into the outer membrane matrix from inner membrane matrix. B. The electron when it reaches Cyt a3 is absorbed by highly electronegative oxygen and 2 H+ to form a water molecule.

4. Due to the consumption of energy by ETS the e- has the highest energy when it is at FP, and it loses energy as it goes down the ETS until it reaches the Cyt a3.

5. ATP permease- This is a pump that is used by the inner matrix membrane to bring H+ and ADP+ Pi into the inner matrix from outer matrix, and yet the ATP permease functions in exporting the newly synthesized ATP + OH- from the inner matrix to the outer matrix.

6. The last but the most important enzyme on the pathway is the F complex or the ATP permease. This enzyme uses the electrochemical gradient between the outer membrane matrix and inner membrane matrix to synthesize ATP from ADP + Pi. For every inflow of a pair of H+ there will be a new ATP synthesized.

7. If you add the highlighted number of H+ in the paragraphs 1 and 3 you will see that a single molecule of NADH2+ initiates the release of 6H+ from the inner membrane matrix to the outer membrane matrix. Thus when 3 pairs of H+ are imported back from the outer membrane matrix there will be 3 ATP molecule synthesized.

8. In the case of FADH2, the lower energy FADH2 molecule will bind the electron transport system at coenzyme Q. This results in the export of 2 pairs of H+ from the inner matrix to the outer matrix (4H+ in paragraph 3 only). As a result there will be only 2 ATP produced. Note: The inner matrix membrane without its ATP permease and ATP synthase is not permeable to the passage of H+. Thus the outer membrane matrix is positively charged with an electrochemical gradient and osmotic pressure with respect to the negatively charged inner matrix....

Respiration links
Respiration - The Basic Reaction
O2 + Carbohydrate & Other
Organic Compounds* 		+ --- Living Cells --- ATP
& Heat*		 + CO2 + Water

Overview of Respiration (See Lewis fig. 7.5)

Organic Compounds*
From Food		 --- Glycolysis
(Enzyme
Reactions
in Cytoplasm)		 --- Pyruvic
Acid*
some ATP*		 ---------
Krebs Cycle
(Enzyme Reactions
in Mitochondria)		 --- NADH*
& CO2		 --- Proton
Gradient*		 --- Lots
of
ATP*
Mitochondrion Structure (see Lewis, figures 7.7 & 7.14) Anaerobic Fermentation (see Lewis, figure 7.17 & 7.19)
Cells as the "Basic Unit of Life"Prokaryotic Cells

Eukaryotic Cells

Cell Organelles

Nucleus This is where the DNA is kept and RNA is transcribed. RNA is transported out of the nucleus through the nuclear pores. Proteins needed inside the nucleus are transported in through the nuclear pores. The nucleolus is usually visible as a dark spot in the nucleus (note the dark nucleolus in this electron microscope photo of a nucleus), and is the site of ribosome formation.

Ribosomes Ribosomes are the sites of protein synthesis, where RNA is translated into protein. Protein synthesis is extremely important to cells, and so large numbers of ribosomes are found throughout cells (often numbering in the hundreds or thousands). Ribosomes exist floating freely in the cytoplasm, and also bound to the endoplasmic reticulum (ER). ER bound to ribosomes is called rough ER because the ribosomes appear as black dots on the ER in electron microscope photos, giving the ER a rough texture. These organelles are quite small, made up of 50 proteins and several long RNAs intricately bound together. Ribosomes have no membrane. Ribosomes disassemble into two subunits when not actively synthesizing protein..

Mitochondria Mitochondria (singular: mitochondrion) are the sites of aerobic respiration, and generally are the major energy production center in eukaryotes. Mitochondria have two membranes, an inner and an outer, clearly visible in this electron microscope photo of a mitochondrion. Note the reticulations, or many infoldings, of the inner membrane, This serves to increase the surface area of membrane on which membrane- bound reactions can take place. The existence of this double membrane has led many biologists to theorize that mitochondria are the descendants of some bacteria that was endocytosed by a larger cell billions of years ago, but not digested. This fascinating theory of symbiosis, which might lend an explanation to the development of eukaryotic cells, has additional supporting evidence. Mitochondria have their own DNA and their own ribosomes; and those ribosomes are more similar to bacterial ribosomes than to eukaryotic ribosomes..

Chloroplasts These organelles are the site of photosynthesis in plants and other photosynthesizing organisms. They also have a double membrane. There is a more complete description of the chloroplast here, in the chapter on photosynthesis..

Endoplasmic Reticulum (ER) The ER is the transport network for molecules targeted for certain modifications and specific final destinations, as opposed to molecules that are destined to float freely in the cytoplasm. There are two types of ER, rough and smooth. Rough ER has ribosomes attached to it, and smooth ER does not.

Golgi apparatus This organelle modifies molecules and packages them into small membrane bound sacs called vesicles. These sacs can be targetted at various locations in the cell and even to its exterior.

Lysosome This organelle digests waste materials and food within the cell, breaking down molecules into their base components with strong digestive enzymes. Here we can see an advantage of the compartmentalization of the eukaryotic cell: the cell could not support such destructive enzymes if they were not contained in a membrane-bound lysosome.

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