Study Questions:

1. Describe glycolysis.

2. What is the purpose of fermentation, and under what environmental condition does it occur?

3.  What happens in the gateway step?

4.  What happens in the krebs cycle?

5. What happens in the elctron transport chain?  Explain chemiosmosis.

6. How is oxygen invovled in the process of aerobic respiration?

8. How are nucleotides linked together into a nucleic acid strand (draw it).

9. Draw a DNA double helix with three base pairs, at the level of detail shown in class.

Cell Biology Unit

I. Membranes: How Things Get in and Out of Cells

II. Harvesting Energy

A. Photosynthesis

B. Respiration

1. Glycolysis

    2. Anaerobic Respiration

glycolysis first.... then one of the following to recycle the NADH and produce the NAD needed for glycolysis

    a. In plants, fungi, and bacteria:

                The C₃ pyruvates are broken into a C₂ molecule and CO₂.  The NADH releases its electron and hydrogen to the C₂ molecule, forming ETHANOL (alcohol).

    b. In animals:
 
                The NADH transfers its electron and H+ directly to the C₃ pyruvates.  This converts them into lactic acid.  Typically, this type of respiration in animals can only occur for short periods because the energetic demands for ATP will eventually exceed the rate of production from glycolysis, alone.  At this point, oxygen concentrations must rise again so that the lactic acid can be converted back to pyruvate and metabolized by aerobic respiration.

    3. Aerobic Respiration

       a. Overall Process:

       - Glycolysis  

- Pyruvates are broken down into Carbon Dioxide
         - Energy that is released for the complete breadown of the C-C bond is used to make ATP (38).
         - When bonds are broken, electrons are released. They have to be accepted by another molecule. They are initally accepted by NAD and FAD, which then take their "high energy" forms of NADH and FADH2.  Ultimately, they transfer this energy to ATP, give up their electrons and H+, and are recylced as NAD and FAD. (That's important, remember?  We need to recycle that NAD so glycolysis - the first step in this whole process - can continue.)
         - Ultimately, the electrons are passed to Oxygen O--, which then binds two hydrogen ions to balance charge (forming water).
         - Aerobic respiration is a more complete breakdown of glucose, so it yields more ATP than glycolysis, alone
         - In eukaryotes, this occurs in a three step process in the Mitochondria of cells.

        b. Mitochondrial Structure:

        - Double membrane system, with intermembrane space and matrix within inner membrane.
        - Has its own DNA, and replicates itself. Cells don't make mitochondria, per se, mitochondria replicate themselves.
        - Given these observations, Lynn Margulis hypothesized that these similarities were due to common ancestry, rather than common environment.  She raised this hypothesis as the Endosymbiotic hypothesis of eukaryote evolution, hypothesizing that eukaryotes acquired their organelles by engulfing free-living bacteria and, rather than digesting them, simply engulfed them and consumed their products (in this case the ATP that the bacteria produce.  The relationship is called symbiotic, because Margulis hypothesized that the bacteria would also benefit by being in a stable environment where the concentration of glucose was high (inside the cell).
        - The most direct test of a hypothesis of relatedness is DNA similarity.  DNA only comes from parents, so similarities imply a common source. When these tests were performed in the 1970's, her hypothesis was confirmed.  Additional tests with choloplasts and basal bodies (other organielles in eukaryotes) also showed strong patterns of relatedness with free-living bacteria.  As such, we now refer to this tested model as the Endosymbiotic Theory
        - We will describe this theory in more detail later in the term...

        c. The Details:

            1. 'Gateway' Step:

         - Pyruvates cross both membranes into the mitochondria and enter matrix
         - Each reacts with a Coenzyme A molecule, and is split into a C₂-CoA molecule and CO₂. (One C broken off).
         - The electrons and energy released are accepted by NAD, forming 1 NADH for each pyruvate used. (I said ATP in class...that was wrong.)

            2. Citric Acid (Krebs) Cycle:

         - each C₂-CoA reacts with a C₄ molecule (oxaloacetate)
         - the C₂ acetate transferred to a C₄ molecule, forming a C₆ molecule of citrate. (CoA is released and recycled).
         - through a series of reactions, the 2 'extra' C's are broken off as a CO₂ molecules and the C₄ molecule is regenerated (Cycle).
         - Some of the energy released by the breaking of the C-bonds is used to make 1 ATP, 3 NADH, and 1 FADH₂.

            3. Electron Tranport Chain:

         - proteins nested in the inner membrane of the mitochondria accept the electrons from NADH and FADH₂
         - the electrons are passed from molecule to molecule and some of the energy released is used to pump H+ ions across the inner membrane from the matrix to the intermembrane compartment
         - a steep concentration gradient of H+ ions is formed... this represents chemical potential energy.
         - When the ions flow through protein channels associated with ATP-synthesizing enzymes in the membrane, this potential energy is transformed into chemical energy in bonds between ADP and P, making ATP. (This is chemiosmosis - see fig 7.12)
         - When the electrons reach a low energy state, they are accepted by oxygen in the matrix and H+ ions react with the O-- to form water.  This is the ONLY use of oxygen in the process - as an electron acceptor.

         - 34 to 36 ATP are made from the energy tranferred from NADH and FADH₂ molecules produced in the Krebs Cycle.

    4. Summary of Glucose Metabolism

    5. Metabolizing other Biomolecules

a. Fats:
- Glycerol broken from fatty acids; glycerol (3C) fed into glycolysis and are modified into pyruvates (C₃). - the Fatty Acids are broken down into C₂ groups that are modified to react with CoA - they are shuinted to the Krebs Cycle - these reacts are reversible, so if there is a surplus of C₂-CoA, it can react to form fatty acids ---> energy consumed in carbo's can be stored as bonds in fat.

b. Proteins:
- Broken into Amino Acids which, depending on their structure, can be shunted into glycolysis, modified into pyruvate, or broken into acetate (C₂). - In all cases, the amine groups are cleaved, producing ammonia (NH₃) as a toxic waste. In mammals, this is converted into urea which must be diluted in water for removal from the body (urine). Reptiles and birds convert it to uric acid, which is expelled as a paste that does not require as much water for dilution.

c. Nucleic Acids: - ribose can be metabolized after coversion to glucose.
 

III. "Spending" Energy I: Protein Synthesis

Through the process of respiration, all living cells on earth harvest energy from the organic molecules they absorb (heterotrophs) or make (autotrophs - photosynthetic and chemosynthetic organisms). Now we will look at two processes that cells use this energy for - protein synthesis and mitosis. As we have already mentioned, proteins are extraordinarily variable and perform a wide variety of functions. We have already seen proteins involved in the functions of the cell membrane (transport proteins), in photosynthesis (photosystems, electron transport chains, and the enzymes in the Calvin cycle), and in respiration (enzymes catalyze all the reactions mentioned, and comprise the electron transport chain here, too). Since proteins DO so much, making proteins is central to what a cell does. The proteins made by a cell are determined by the genes that are 'on' in that cell. DNA is simply a recipe for making proteins. So, to understand protein synthesis, we must first understand the structure of DNA (and RNA).

 

A. Nucleic Acids and Chromosome Structure

1. Nucleic Acid Structure

a. Monomers - nucleotides

1. Pentose Sugar - ribose and deoxyribose
2. Phosphate group (PO4) attached to #5 carbon
3. Nitrogenous base attached to #1 carbon
                a. purines (double ring): Guanine Adenine
                b. pyrimidine (singel ring): Cytosine Thymine Uracil

b. Polymers - RNA and DNA

- Linking Nucleotides to form Polynucleotide Helices
        1. Dehydration Synthesis Reactions
        2. Polymerization links hydroxyl group on #3 carbon to Phosphate group of next nucleotide.
        3. So, a single helix of nucleic acid has a 'polarity' to it - there is a free hydroxyl group at one end (3' end) and a reactive phosphate group at the other (attached to the #5 carbon and thus referred to as the 5' end of the helix).
        4. Although the nucleotides have one phosphate group when they are linked into the helix, they contain 2 additional phosphate groups as a 'reactant'.  The double-phosphate is cleaved, releasing some energy used to link the remaining phosphate/nucleotide to the hydroxyl group of the existing helix, thus binding this new nucleotide to the existing helix.
 

- RNA:  exists as single-stranded molecules (except in some viruses)
         - three types:
             - m-RNA:  "copy" of a DNA gene
             - r-RNA: RNA that functions in Ribosomes to "read" the m-RNA
             - t-RNA: RNA that is bound to single amino acids.... it "transfers" the amino acid to the site of protein synthesis (ribosome).
         - ALL 3 types of RNA are made by TRANSCRIPTION... they are copied from DNA sequences.  However, only m-RNA represents the instructions for making a protein.  The other types are functional as RNA (they don't 'code' for anything else...)

- DNA:
    - is a biopolymer that consists of 2 helices, bound together, in a complementary and antiparallel arrangement. .
        1. Antiparallel (opposite 3-5 polarity)
        2. Complementary (A-T and C-G pairings across the double helix)