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BIOL 2107
Fall '23 CRN86772

Home -Syllabus

Schedule
Lectures: (1)
- Lecture 1
- Lecture 2
- Lecture 3
- Lecture 4
- Lecture 5
- Lecture 6 -Quiz 1
- Lecture 7
- Lecture 8
- Lecture 9
- TEST 1
- Lecture 10
- Lecture 11
- Lecture 12
- Lecture 13
- Lecture 14
- Lecture 15 -Quiz 2
- Lecture 16
- -
- Quiz 1 Grades
- Quiz 2 Grades
- Quiz 3 Grades
- -
- Test 1 Grades
- Test 2 Grades
- Grade Summary
Lectures: (2)
- Lecture 17
- Lecture 18
- TEST 2
- Lecture 19
- Lecture 20
- Lecture 21
- Lecture 22
- Lecture 23 -Quiz 3
- Lecture 24
- Lecture 25
- Lecture 26
- FINAL
- -
- Quiz 1 Answers
- Quiz 2 Answers
- Quiz 3 Answers
- -
- Test 1 Answers
- Test 2 Answers
Courses

BIOL 2107 Principles of Biology I

home page: CRN86772

schedule:

BIOL 4564/6564 Advanced Genetics

home page

schedule

BIOL 4905 Biotech. - ON LINE

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schedule

BIOL 4905 Biotech. Laboratory

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schedule

BIOL 8510/8710 Concepts in Mol. Genetics

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schedule

BIOL 8620 Molecular Genetics of Eukaryotes

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schedule

BIOL 8700 Molecular Genetics of Eukaryotes

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schedule

BIOL 8970 Instruments in Biotechnology

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Resources
General Resources
- Biology Department
- ABCore facility

Lecture 19: Cell Metabolism -REDOX and Water

pdf download      video w/o sound
 

             
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Term Paper: DUE November 18th.
1. "Evolution is a man-made myth"
2. "An understanding of Genetics is fundamental to our understanding of how an organism works."
        
3. "Virus(es) are alive"
 
Choose one of the statements above, and provide two arguments for me; one for and one opposed to the statement that you chose. 
Minimally, each of your arguments should be half a page of 11pt, single-spaced writing (450 words). 
Maximally, each of your arguments should be no more than one page of 11pt, single-spaced writing (900 words). 
In addition: you will need to put down references for all the sources of information that you cite.
 
You will submit your paper as a typed document (E-MAIL)...  by November 18th!!  
When you do e-mail me your paper, please ensure that you give the title "BIO2107 Term Paper" in the subject line of the email.
Example: Term Paper
___________________
ATP is Adenosine Triphosphate, the ultimate, "Universal Source" of useable energy in biological systems, as it can can be hydrolyzed to yield ADP an inorganic phosphate ion (Pi, short for HPO42-) and...  
            ...ENERGY
  
  
ATP hydrolysis releases energy -making it available for the cell to use elsewhere.....
ATP consists of the nitrogenous base adenine bonded to ribose. Carbon 5 of the ribose has three phosphate groups attached.
ATP can be hydrolyzed to yield ADP and an inorganic phosphate ion (Pi, short for HPO42-).
 
ATP + H2O ----> ADP + Pi + free energy. 
 
The change in free energy (  G) ~ 7.3 kcal/mol at a living cell’s typical temperature and pH.
The equilibrium for this reaction is far to the right of the equation shown above, gavouring the production of ADP ; so much so that there are approximately 1 x 107 ADP molecules to each remaining ATP. 
Making ATP from ADP involves overcoming repulsive negative charges on the phosphates to be joined. 
The energy that is necessary to do this in humans and many other living cells is generally stored as glucose (or condensed derivatives thereof....) or other fuel molecules and is released in the ensuing endergonic process. 
 Fats, a variety of sugars, and proteins can also be consumed for energy. However, a great many organisms (not all) preferentially use glucose as their primary fuel molecule.
 As a consequence, almost all foods that are eventually used for energy are converted to glucose or to an intermediate metabolic product of its breakdown.
 When burned in a flame, glucose releases heat, carbon dioxide, and water.
 
C6H12O6 + 6 O2 ---> 6 CO2 + 6 H2O + energy (heat and light).
 
 The same equation applies for the biological, metabolic use of glucose. This process, however, has many steps and is carefully controlled.
 
 When glucose is used up by the cell -as might be expected- about half of the energy is collected and "banked" in the cell's currency, ATP.
 
 The change in Gibb's Free energy for the complete conversion of glucose is approximately - 686 kcal/mol.
 
 The overall reaction is, therefore, highly exergonic,and it can consequently be used to drive the endergonic formation of a number of ATP's.
 and    
 Some kinds of 
                      cells metabolize glucose down to a 3 carbon alphae keto acid, PYRUVAT.  Others ado a much more efficient job and metabolize it COMPLETELY                  
 The incomplete breakdown is called fermentation and is ANAEROBIC (no oxygen). 
The complete capture of the energy in the hydrocarbon bonds of glucose requires oxygen -through what is termed AEROBIC respiration.
 The two main 
                            metabolic processes for complete use of glucose are glycolysis and cellular respiration.
The entire Glycolytic process is a series of reactions that takes glucose (a six carbon 
                            sugar) to produce some usable energy and two molecules of a three-carbon sugar - pyruvate.
 Cellular respiration 
                            occurs in aerobic (oxygen-containing) environments. Pyruvate can then 
                            be converted in to CO2 and H2O, with the energy resulting being used to make ATP molecules. 
 If cellular 
                            respiration does not occur, then fermentation ususally does.
 Fermentation 
                            occurs when the environment is anaerobic (lacking gaseous oxygen).
                              
                            
 In fermentation, lactate or ethanol and CO2 are produced, but far less energy is extracted from glucose. 
How is this all 
                            brought about?    Essentially it all involves reactions 
                            called                           
"Redox reactions" which involve that rather important element "hydrogen" and the transfer of the energy of reactions, as they transition from one form to another.                          
                          
                          
                          
 A gain of one or more electrons or hydrogen atoms is 
                            called reduction.
 The loss of one or more electrons or hydrogen atoms is called oxidation.
 Whenever one 
                            material is reduced, another is oxidized. 
 
 If 
                            a carbon compound gains a bond with hydrogen, the compound is reduced.
                            
                          
 If 
                            a carbon compound loses a bond with hydrogen, the compound is oxidized.
                              
                            

                          
 
Reaction 1 of the above diagram is oxidation because the changed carbon loses a bond with hydrogen.
 
Reaction 2 is also oxidation because the central carbon in the reactant loses a hydrogen bond (even though the compound as a whole still has the same amount of hydrogens).
 As a result of all this.....
An oxidizing agent accepts an electron OR a hydrogen atom (a proton + electron).
 A reducing agent donates an electron OR a hydrogen atom (a proton + electron).
The ultimate redox reaction  (in the biological world) is the formation of..... WATER 
 
H2 +  1/2 O2  --->H2O
 
 If this reaction were allowed to occur in one step....it would be... explosive.  
Moreover, the cell doesn't have any Hydrogen molecules hanging around (or else we would all float  away....). Even so, the cell is able to harness the energy of 
sugar metabolism to create an almost equivalent reaction.........to produce (of all molecules......) WATER!
During both the process of burning glucose and the metabolism of glucose, glucose is the reducing agent (and is oxidized), while oxygen (being the ultimate oxidation state) is the oxidizing agent (and itself is reduced).
C6H12O6 + 6 O2 ---> 6 CO2 + 6 H2O + energy (heat and light).
 
 The overall DELTA G (change in free energy) of a biologically related redox reaction should be -and is - negative. (i.e. it gives off energy!!!).
Most of the time, the "energy" of reactions does not go to ATP formation directly, but goes to an "energy production line" by being transferred in hydrogens (hydrogren ions) to another molecule -a coenzyme- named NAD, which can carry H+s (in its reduced form) and which can easily be converted to H2O -in the presence of O2
     
 The molecule NAD is an essential electron carrier in cellular redox reactions.
 NAD is short for nicotinamide adenine dinucleotide.
 NAD exists in an oxidized form, NAD+, and a reduced form, NADH + H+.
 
 
NAD+ + 2e- + H+   ---->  NADH
 
The reduced form (NADH + H+) can be converted back into the oxidized form in the presence of oxygen: 
 
NADH + H++ 1/2 O2  ---->  NAD+ +   H2O
 
 The ∆Go'  of this oxidation reaction is -52.4 kcal/mol. (For comparisons sake, remember that the ∆Go' of the ATP to ADP reaction is ~7.3 kcal/mol.)
 
 Think of NADH + H+, therefore, as a pre-packaged form of available "potential" energy source, that can eventually be turned into ATP and used to do work!!!
There is also and alternative hydrogen carrier, called FAD (Flavin Adenine Dinucleotide) that is not quite as efficient as NAD, but can also be used to carry Hydrogen in the cell.
 
  
 
FAD +   H2 ----> FADH2 
 
FADH2 + 1/2 O2 ----> FAD +   H2O
 
But what 
                            about the actual metabolism of Glucose:  
It generally occurs in three stages
Glycolysis: From Glucose to Pyruvate
 To get energy 
                            out of this overall reaction, energy first must be invested in the process.
 In separate 
                            reactions, two ATP molecules are used to make chemical modifications 
                              to glucose.
 Phosphates from 
                            each ATP are added to the carbon 6 and carbon 1 of the glucose molecule.
 The figures below show for the details 
                            of this part of glycolysis.
              
In this part of the 
                          pathway most of the energy that is derived as ATP involves the direct synthesis of ATP directly in various reactions called substrate-level phosphorylation.
>Some cells under anaerobic conditions continue glycolysis and produce a 
                          limited amount of ATP by the process fermentation.
...There is a NET GAIN  of TWO ATP's per glucose molecule -through fermentation.
This form of anaerobic respiration produces incompletely broken down carbon skeletons such as lactic acid and alcohol
  &
In the ABSENCE of oxygen the 
                          reduced form of NAD+ (NADH + H+) builds up and becomes a cellular toxin.... 
It therefore needs to be RECYCLED..... 
Hence the formation of a reduced carbon intermediate : LACTIC ACID build up in muscle tissue feel the burn.
 
In the presence of oxygen, however, the 
                          reduced form of NAD+ (NADH + H+) can be converted back into 
                          the oxidized form ......
 
NADH + H++ 1/2 O2  ---->  NAD+ +   H2O
 
....and just like the normal reaction this is an ENERGY yielding reaction... with almost the same energy yield.
 
 
H2 +  1/2 O2  --->H2O
 
Pyruvate
                          Oxidation -Dehydrogenase.   In
                          this reaction, the 3 carbon pyruvate is converted to a 2-carbon Acetyl
                          group attached to a Coenzyme A configuration.   A molecule of NADH + H+ is generated during this reaction.                        
  
 
From there the acetylCoA gets involved with a "production line" system called.....
The Citric 
                          Acid Cycle / TCA cycle (Tri-Carboxylic Acid Cycle / Kreb's Cycle
                        
   
 
The cycle begins when the two carbons from the acetate are added to oxaloacetate, a four-carbon molecule, to generate citrate, a six-carbon molecule.(2 + 4 = 6, so we're
                          now back to 6!!)
 
Summary:
 
Glucose (6 carbon)---> Pyruvate (3 Carbon)                                            Net yield = 1 ATP and 1 NADH + H+
                                     ---> Pyruvate (3 Carbon)                                        Net yield = 1 ATP and 1 NADH + H+
Pyruvate (3 Carbon) ---> Acetyl CoA (2 Carbon) + CO2                           Net yield = 1 ATP and 1 NADH + H+          
Pyruvate (3 Carbon) ---> Acetyl CoA (2 Carbon) + CO2                            Net yield = 1 ATP and 1 NADH + H+      
 
Acetyl~ CoA (2 Carbon) + Oxaloacetate (4 Carbon)    ----->    Oxaloacetate (4 Carbon) + 2 CO2                
                                                                                                                     Net yield = 1 ATP,  1 FADH2 and  3NADH + H+                        
Acetyl~ CoA (2 Carbon) + Oxaloacetate (4 Carbon)    ----->    Oxaloacetate (4 Carbon) + 2 CO2                
                                                                                                                       Net yield = 1 ATP,  1 FADH2and  3NADH + H+
                                              Total Net yield = 4 ATP,   2 FADH2and  10 NADH + H+
 
The question now is, how exactly does the cell make use of all these  hydrogens that are interacting with the various hydrogen carriers?  It passes them on to the....
 
 

  