Microbiology Notes Exam 2 (Lectures 11 &12) – Flashcards

Not all mutations impact enzymes.

• The entire DNA does not code for enzymes. Some of it codes for structural proteins. 

• The reaction will proceed without the enzyme, but it will happen very, very, very slowly, so slowly as to be rather useless. 

• Glucose is converted into pyruvate via glycolysis
• There are 10 enzymes involved
• The number given in class has varied from 6-8

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Operons

• In genetics, an operon is a functioning unit of genomic DNA containing a cluster of genes under the control of a single promoter.
• The Lac operon, which controls for the production of enzymes enabling the metabolism of lactose in E. coli is shown below. 
• Notice that Z,Y and A, all code for enzymes which are related to this one process. Along with the promoter, repressor and operator, they are part of a single operon. 
• The regulatory genes are not part of the single operon
• The regulator does not have to be adjacent to other genes in the operon.

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Operons

• Bacterial genes are organized into operons, or clusters of coregulated genes. 
• In addition to being physically close in the genome, these genes are regulated such that they are all turned on or off together. 
• Grouping related genes under a common control mechanism allows bacteria to rapidly adapt to changes in the environment. 
• For example, the presence or absence lactose. When in the presence of lactose, they can turn on all the genes that enable them to metabolize it. 

• Operons are sections of the chromosome in bacteria. 
• Operons are clusters of coregulated genes made of DNA. 
• In addition to being physically close in the genome, these genes are regulated such that they are all turned on or off together. 

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P,O,G

Promotor region, Operator Region, & Gene Region

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• The promoter region is the first region of the operon.
• It is the region to which the Ribose backbone of what will become mRNA binds. 
• The textbook says, "...the promoter, is the region of DNA where RNA polymerase initiates transcription." 

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• The ribose backbone of mRNA attaches at the first region of the operon, the PROMOTER 

The OPERATOR, this is the second region, just after the promoter. 

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• The operator is the part of the operon that allows for the REGULATION of gene expression, that is, for the genes of the operon to be turned on or turned off.
• [image]

• The operator is the part of the operon that regulates gene expression, or whether that part of the DNA will be transcriped or not.  
• [image]

The second region of the operon, after the promoter, is the operator. This is the part of the operon that controls whether the genes are turned on or off.

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• GENES! Specifically genes that control one specific process, such as the metabolism of lactose. These are called structural genes. They code for proteins. 

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The genes on an operon code for one specific process. 

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• In transcription of an operon, the genes on a given operon are copied all at once. This is a means of efficiency and is possible because of the start and stop codes in the DNA, or the "punctuation". 

A start code. This is the genetic code's equivalent of a capital letter.

• Background: In the mRNA the start code reads: A-U-G or Adenine-Uracil- Guanine. [Meaning in the DNA it is TAC] 
• This code in the DNA says, "Hey, RNA polymerase! Start here! Transcribe some mRNA!" 
• Once that mRNA is at the ribosome, this sequence codes for the amino acid formylmethionine, though Prof. M said it was methionine[that's in humans]. p214

• NONE. This is the start code amino acid. 
• If such a code appears at the beginning of a sequence of mRNA, no amino acid is placed there. 
• The book says it's placed and later excised. [p. 216] In any case, it ends up not being there.

• NONE! Stop codes don't call for any amino acid. 
• They are nonsense codes or STOP CODONS. 
• They are the 3 of the 64 possible combinations of three nuecleotide bases that code for no amino acid. They tell protein synthesis to STOP, the gene is over. 

• The start code indicate that what follows will be the information for producing a protein. 

A nonsense code

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• On either side of each gene
• There is a start code to begin each gene and a stop code to end each gene. 
• In the image below, the start and stop code for the gene are shown as they would appear on the mRNA. 

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• The enzymes involved in glycolysis would be on what kind of operon?
• a. inducible
• b. repressible
• c. constitutive
• Note: This is because glycolysis is always happening at a base line level. 

• A constitutive enzyme, coded for by a constitutive operon. 

• Repressors: proteins that bind to operons at the operator region to inhibit the transcription of the operon.
• [image]

A repressor binds to the operator region of an operon

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• The repressor is a molecule that in binding to the operator region of an operon effectively turns that operon off. 
• [image]

• A repressor binds to the operator region of an operon, making the progession of transcription (and therefore translation) impossible. 
• According to lecture this is accomplished because the repressor misaligns the ribose backbone, moving it too far from the operon. 
• The image below indicates that the repressor makes the binding of RNA polymerase, the enzyme resposible for transcription, unable to progress.

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• Protein synthesis is energetically expensive for the cell.
• It uses a lot of amino acids. 

• Repressors may be: 
• The end product of another biochemical pathway
• Enviromental agents
• Produced by the cell itself 
•  by another operon

• All products of the cell, including repressors, are ORGANIC, meaning carbon based.
• All organic compounds degrade, or have a finite period of usefulness. 
• This includes repressor. 
• This is imporant because it tells us that all repressors degrade over time and must be replaced. 

• Another repressor is made and binds to the operator where the degraded repressor was. This is the normal process because in inducible system the default for the operon is the "off position". 

• The gene regulation system that is off unless there is the presence of some molecule is called an INDUCIBLE SYSTEM.
• It is off, but able to be induced or started. 
• A repressor bound to the operator of the operon is what keeps the system off. 
• The molecule that binds to the repressor, the inducer, is said to "induce expression". 

A repressor bound to the operator. 

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• In the lac operon, discussed as an example of an inducible enzyme system, the presence of lactose acts as an inducer.
•  In fact, it's allolactose but it amounts to the same thing.
• (Allo)Lactose binds to the repressor, distorting its shape and causing it to disengage with the operator. 
• Without the repressor to bar the transcription of mRNA from the operon, the enzymes to metabolize lactose are produced, at least in E. coli.
• [image]

• In an inducible system, an inducer binds to a repressor, disengaging it from the operator and enabling transcription.
• If another repressor is produced in the presence of the inducer, the inducer will bind to that repressor, making it unable to bind to the operator. 
• Once the inducer is no longer present, the repressor will again be able to bind with the operator and transcription will stop, and with it, the production of enzymes.  

• In the lac operon, when lactose binds to the repressor, the repressor cannot bind to the operator.

In an inducible operon, the inducer disables the repressor. 

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• In an inducible operon, when an inducer binds to the repressor at the operator, the repressor is disabled and the genes are able to be expressed. 
• That is, the RNA polymerase is able to proceed with transcription and the mRNA for those genes will be sent to the ribsomes initiating the process that will lead to their translation and expression. 

• The inducer binds to the new repressor so that it can not bind to the operator and the genes that the operon codes for continue to be transcribed, translated and expressed. 

• When a new repressor molecule is produced and the inducer is no longer present in the cell, the repressor binds to the operator region of the operon and gene expression is halted. 

• Inducible enzyme systems, wherein enzyme production is regulated by the presence or absence of an inducer. 
• Inducible operons are operons which are usually off but in which gene activity can be induced by the presence of an inducer.
• Repressible enzyme systems, wherein enzyme production is regulated by the presence or abesence of a repressor.
• Repressible operons are usually on but can be turned off by the presence of a repressor.

• A system of enzyme production [via an operon] that is usually off but which can be turned on.

Structural genes and regulatory genes

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Structural genes

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Structural genes are genes that code for some particular product of the CELL.

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Structural genes, because insulin regulates cellular activity.

Regulatory genes regulate DNA activity, not cellular activity. 

Regulatory genes regulate DNA 

[only DNA]

• Regulatory genes code for products that regulate DNA activity. 
• Regulatory genes code for inducers and repressors
• Someone asked if they code for the P[promoters] O,[operators] and the R [Repressors].
• Prof. said yes, though that doesn't exactly fit the definition as operators and promoters don't produce anything
• These two images indicate different understandings. 
• In the first it seems that the promoter and operator are distinct from the regulatory genes
• In the second it seems that the promoter and operator are part of a regulatory sequence.

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• No.
• The repressor, when its a product of the cell, may its own operon, which may be adjacent to the operon it regulates, but doesn't have to be. 
• Note that the lac pperon does not include the promoter, operator or structural gene for the repressor which controls it
• [image]

• No. Some operons have multiple regulatory genes and more than one repressor or inducer. Some, such as those that code for a constitutive enzyme, have none. 

• No. 
• Prof. McCleary noted that although they are not called operons, a similiar mechanism must exists because the expression of genes is clearly regulated. 

• Inorganic enviromental do not behave the same way as organic molecules, in particular because they do not degrade in the same way, meaning their effects can be permenant.
• E.g. They may bind to an operator, permanently repressing expression.

• Their DNA integrates into the host DNA, distorting the expression or repression of said DNA.

A repressible system

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• In a repressible system, the repressor is USUALLY the end-product of some biochemical pathway. 

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• In a repressible system the repressor is usually the end product of some biochemical pathway.

• The system is shut down or repressed by the accumulate of the end product. 
• Prof McCleary used the example of an assembly line backing up. If the assembly line shut off when more of the product was being generated than could be processed, it would be very much like a repressible system. 

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• In a repressible system, as the end product  of the process accumulates in excess, it acts as a repressor until levels are normalized. 

• Repressors can be produced by the cell. 
• They can be the end product of a pathway. (usually)
• They can be an enviromental agent. 

• Most commonly, they are something added from the outside, such as lactose. They could be produced by the cell as well. 

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• Types of operons:
• Constitutive: always on, at least at a baseline level
• Inducible: usually off, but can be turned on by an inducer
• inducer is usually external agent, not produced by cell e.g. lactose
• Repressible: usually on, but can be turned off by a repressor
• repressor is usually the end product of a biological pathway or process. 

• A frameshift mutation would alter an organism's
• a. phenotype
• b. genotype and potentially phenotype
• c. neither. 
• Why?
• A frameshift mutation is a mutation in DNA, mutations are by definition permenant and heritable, therefore it would impact the genotype and potentially the phenotype. 

• A point substituation mutation would alter
• a. the phenotype
• b. the genotype and therefore potentially the phenotype
• c. neither
• Why?
• A point substitution mutation occurs in the DNA during replication. By definition such a change is "permenant and heritable" therefore it will effect the genotype, and potentially the phenotype. See p.223

• Transduction, transformation and conjugation would alter an organism's:
• genotype and therefore potentially phenotype
• phenotype
• neither
• These are all methods by which new bacterial DNA is introduced into the organism and integrated either into its chromosome or plasmid. Because each contributes to the organisms permenant and heritable DNA (though plasmid based information is not always replicated) each (potentially) adds to the genotype. 

• Prof. M indicated that we should be able to answer this question for a variety of situations. I'M NOT SURE IN THIS SITUATION.

• The repression or induction of repressible or inducible genes on a given operon effects the organism's:
• a. phenotype
• Prof. M indicated that a phenotype is all of the genes that an organism is currently expressing, which would lead me to believe that a phenotypic change occurs when a given operon is induced or repressed. 
• b. genotype, and therefore potentially phenotype
• It certainly wouldn't effect the genotype 
• c. neither
• If all organisms of a given genotype have the ability to express or repress a certain gene, I don't know if it qualifies as a phenotypic difference.  It's certaintly not comparable to the expression of the gene for eye color. 

• Genes are made up of sets of 3 nucleotide bases called triplets. These triplets allow the production of amino acids. The stringing together of which leads to the production of proteins, both structural proteins and enzymes. 

Inhibitors [ Competitive & Allosteric-or-noncompetitive]

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• Competatitve inhibitors: 
• fill the active site of an enzyme and compete with the normal substrate for the active site
• Allosteric or noncompetative inhibitors: 
• do not compete with the substrate for the enzme's active site; instead the inhibitor binds to a site on the enzyme other than the substrate's binding site. This binding causes the active site to change shape, rendering it nonfunctional

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• ONE! Enzymes are HIGHLY SPECIFIC and will only interact with a single substrate

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A substrate.

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NO! Enzymes are strictly rate alterers.

They DO NOT make a reaction happen. 

• Enzymes. 
• Enzymes speed up chemical reactions in the cell by lowering their activation energy.
• This is accomplished because the enzyme orients the substrate into a position that increases the probability of a reaction. 
• [image]

• NO. Enzymes DO NOT make reactions happen. They are not a magic wands. 
• They only increase the probability that a reaction will happen. 

• Without the effecting enzyme, the reaction will still occur, but at a rate which is of limited to no benefit to the organism. 
• That is, without the enzyme, the rate of the reaction is too slow to support life. 

A competitive inhibitor

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Competitive inhibition

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• Competitive inhibitors reduces the efficiency of the enzyme it inhibits. 
• By introduction of a molecule that is not the substrate, but which fits in the enzyme, the enzyme's likelihood of binding with its actual substrate is reduced, reducing the overall benefit of the normal reaction.

Competitive inhibitors are substrate concentration dependent.

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Competitive inhibitors are substrate concentration dependent.

                          ^{(two words)}

• When the quanitiy of substrate is increased, the efficiency of a competitive inhibitor 
• a. increases
• b. initially increases, then decreases
• c. decreases
• d. stays the same
• Because there is less competitive inhibitor in proportion to substrate, the original enzymatic reaction will occur more frequently; inhibition of this reaction is thereby decreased.

• 50% The enzyme will be half as efficeint. It has a 50% chance of interacting with its substrate and catalyzing the specified reaction, and a 50% chance of interacting with the competitive inhibitor, creating no reaction.

• It is not reasonable to use a competitive inhibitor to inhibit a reaction with a substrate that is the end product of another process or reaction because unless that process is also inhibited the normal substrate will continue to build in the organism, increasing the concentration of  the substrate and increasing the efficiency of the enzyme intended for inhibition. 

• Competitive inhibition by look-a-like competitive inhibitors is substrate concentration dependent. 

• When the concentration of the normal substrate is increased,  the efficiency of the competitive inhibitor is decreased. 

An allosteric or noncompetitive inhibitor

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• An inhibitor that binds to the enzyme at a site other than the active site in such a way that it either distorts or blocks the active site.

• An allosteric inhibitor inhibits a reaction at the active site by distorting or blocking the active site. 

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• NO. It does not bind to the active site. It will inhibit the binding of the substrate regardless of how many of that substrates are present.

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• Beta blockers work by blocking the effects of the hormone epinephrine, which is a neurotransmitter. They bind to the receptor that epinephrine would normally bind to. With the binding space occupied, the epinephrine can not stimulate the nerve. This reduces stimulatation, which is advantageous in certain illnesses such as high blood pressure. 
• This is functionally similar to the way that allosteric inhibitors make it impossible for the normal substrate to bind to the enzyme, although they do not inhabit the active site. [image]

• Prof. McCleary said that this drug acted like an allosteric inhibitor, however, it binds to the active site, and numerous literature notes it as a competitive inhibitor.  
• In the second panel below, you can see Neostigmine, in the active site, being represented as a competitive inhibitor.

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• NONE. Competitive inhibitors effect neither genotype or phenotype.
• The enzyme is made [DNA expression- phenotype].
• The DNA that codes for the enzyme production is unaltered [genotype].

• NONE. Allosteric inhibitors effect neither phenotype or genotype. 
• The individuals DNA [genotype] remains the same. Nothing is added, moved or substrated.
• The expression of the gene [phenotype] remains the same, the enzyme is still formed. 

• Catabolism
• Catabolism is one aspect of metabolism; it results in the release of energy. 

• Anabolism, the enzyme regulated energy-requiring reactions that build complex organic molecules from simplier ones. 

• There really is no process which starts metabolism. 
• Professor McCleary said that it's like a water wheel. She also said that metabolism "you start with the breakdown of larger molecules"
• Metabolism is a cycle in which catabolism, [the breakdown of complex organic molecules into simplier ones] and anabolism, [the building up of complex organic molecules from simplier ones] are occuring simultaneously and continually.

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• We make nonessential amino acids by a combination of catabolism [the breakdown of large organic molecules] and anabolism [ the build up of complex organic molecules. 

• Catabolism, the break down of large organic molecules into simplier ones, resulting in the release of energy. 

• Adenosine Triphosphate or ATP is the gas that runs the biological show.
• ATP is formed from ADP + and an inorganic phosphorus during catabolism
• ATP is broken down into ADP and inorganic phosphorus during anabolism.

• The basis of most organic molecules is a "carbon skeleton" which is a framework of covalently bonded carbon atoms with other atoms or functional groups attached to it.  
• Here is glucose. C₆H₁₂O_6. The carbon skeleton is in grey.

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In bonds. 

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Energy is released, and stored as ATP .

• Cellular respiration is a catabolic or exergonic process, which breaks molecular bonds, releasing energy, which is stored as ATP. One of the bonds in ATP is then broken to provide the energy to build up new bonds in anabolic process.

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Adenosine Triphosphate.

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Andosine diphosphate (see molecule at bottom of image)

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• ATP is what forms when energy created by breaking chemical bonds is used to bond a third inorganic phosphate to ADP 
• When ATP is hydrolysised the bond between the third inorganic phosphate an the second breaks, releasing energy. ADP is formed.  

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• A molecule of adenosine, and three inorganic phosphate groups. 
• There is also a ribose molecule, though this wasn't mentioned. 

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• In order to obtain energy from ATP, the high energy phosphate bond between the second (?) phosphate and the third (?) phosphate is broken. 
• Energy is released and the molecule ADP [Adenosine Diphosphate] and a molecule of inorganic phosphate result. 

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• YES! With the release of energy during catabolic reactions [or other cellular process] ADP can bind with a third inorganic phosphate group [a process called phosphorulation] becoming a ATP.
• [image]

• No. Not all bacteria use all processes. Some bacteria can use multiple processes, some only one. 

• Cellular Respiration.
• Glycolosis
• Kreb's cycle
• Electron Transport Chain

• The three stratigies that organisms have to satisfy their need for carbon skeletons are: Cellular Respiration, Fermentation & Photosynthesis

Genetics. The energy producing and carbon generating pathway  of any given organism is coded for in its DNA.

• No. Some organism are capable of more than one pathway (e.g. Cellular respiration and fermentation). Some are only capable of one. 

PHOTOSYNTHESIS

• Rhodospirillum uses a light sensitive pigment which makes them red when exposed to light.
• Rhodospirillum has the ability to live through cellular respiration, fermentation, photosynthesis, or photoautotrophic growth.

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•  We can perform cellular respiration and fermentation. 

• Gylcolysis
• Glycolysis is the metabolic pathway that converts glucose  into pyruvate
• The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

• Glycolysis is an anaerobic process. This means that no oxygen is required to turn 1 molecules of glucose into 2 pyruvate and 2 ATP plus 2 NADH.  
• I believe this means that any bacteria, independent of oxygen preference should be able to run this part of cellular respiration. p122

Glucose

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• Glycolysis or the oxidation of glucose to pyruvic acid, starts out with  1 molecules of glucose and ends with two molecule (s) of pyruvate/pyruvic acid .

• According to lecture, the first reaction in glycolysis is the formation of glucose-6 phosphate from the original glucose and the phosphate of an ATP molecule. 
• One  molecule of ATP is used in this first step, forming ADP. 
• Glucose 6-phosphate is produced by phosphorylation  of glucose (attachment of a phosphate) on the sixth carbon. This is catalyzed by the enzyme hexokinase in most cells. One molecule of ATP is consumed in this reaction.

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• None. The transformation of glucose 6 phosphate to fructose 6 phosphate is a remodelling process enabled by an ezyme.
• No expenditure of ATP is required. 

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• 2 molecules of ATP are consumed during glycolysis. 
• The first is used when glucose is transformed into glucose 6 phosphate. 
• The added phosphate came from a molecule of ATP
•  The second is used when the  molecule fructose 6 phosphate is transformed into fructose 1,6 biphosphate. 
• The 1 & 6 indicate that there is a phosphate group on the 1st and 6th carbon of the fructose molecule. This new phosphate came from a molecule of ATP

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• 1. Glucose becomes Glucose 6 phosphate (1ATP > 1ADP)
• 2. Glucose 6 phosphate becomes Fructose 6 phosphate 
• 3.Fructose 6 phosphate becomes Fructose 1,6 phosphate (1ATP > 1ADP) 
• Yes, 1 ATP is used in this transformation
• NOTE: Enzymes which enable these reactions or transformations are in red. 

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• Before reaction: NAD+
• After reaction: NADH
• In metabolism, NAD+ is involved in redox (electron gaining) reactions, carrying electrons from one reaction to another. The coenzyme is, therefore, found in two forms in cells: NAD+ is an oxidizing – it accepts electrons from other molecules and becomes reduced (reduction is a gaining of electrons). 
• This reaction forms NADH, which can then be used as a reducing agent to donate electrons. 
• These electron transfer reactions are the main function of NAD+.
• NAD+ is a derivative of the B vitamin Niacin 

• 2 pyruvates or pyruvic acids
• 2 ATP (4 ATP generated  - 2 ATP spent)
• 2 NADH

• 4 molecules of ATP are generated during glycolysis, however 2 are used. 
• The process, therefore, nets 2 ATP.

• Both reactions start with a molecue in which the number of phosphates is indicated in the name. Both end with a molecule whose name indicates that one phosphate group has been removed. That phosphate group went to an ADP to form ATP. 
• Because there are two of each of these molecules the total production of ATP is 4 molecules. 
• These are the reations in which ATP is generated.
• 1,3 Biphosphoglycerate >phophoglycerate kinase  > Phosphoglycerate  
• Biphos indicates two phosphate groups
• Phosphenolpyruvate >pyruvate kinase >Pyruvate
• Notice the phos is removed from the pyruvate. 

• Single molecules of glucose DO NOT NECESSARILY run all the way through cellular respiration from glycolysis to the electron transport chain.
• This is because the cell removes intermediary products as needed; the cell may take out any byproduct of cellular respiration at any time. 

They all have carbon skeletons. 

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• Phosphoenolpyruvate. This is because this a 3 carbon molecule, the one just prior to pyruvate. 
• The other molecule, Fructose 6 phosphate, is a 6 carbon molecue, therefore the cell would have to do more work to utilize it. 
• Prof. M. noted that the cell is only as ambitious as it has to be. 

• No. New molecules are constantly being fed into the system. Any molecule removed is quickly replaced when another molecule is converted. 

• When intermediary products of glycolysis are removed for their carbon skeletons less than maximal energy (in the form of ATP) is produced by the cell.  

• Total ATP production would be reduced because the molecule from which the amino acid was made will no longer contribute to that pathway. 

• ATP production does not occur in glycolysis until after the use of the electron carrier NAD+.
• This is after 2 ATP have already been invested 
• Note the red arrows and highlighted ATP molecules below.

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NAD+ 

• Note: Without NAD+ to accept the 2 electrons that result from the breaking down of the 2 Glyderaldhyde 3 phosphate by the enzyme glyeraldehyde phosphate dehydrogenase, pyruvate would never be produced. 

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• 2 ATP must be invested in glycolysis before any ATP or NADH are produced. 

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• No. The production of four molecules of glucose is (2 net) is a best case scenario. The cell may use some of the intermediary products of glycolysis for other purposes (for their carbon skeletons).
• A cell that does this may only produce 3 ATP (net 1) or 2 ATP (net 0) per molecule of glucose fed into the process.  

• Glycolysis. Although not a product of glycolysis, the cell can pull an intermediary of that process and use its carbon skeleton in the production of nonessential amino acids. 

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• We recylce what we have. The NAD+ used as electron carriers in glycolysis ; the Kreb's Cycle (becoming NADH) donate their electrons at the cell membrane to power the Electron Transport Chain. 
• They are then (as NAD+) reused in the glycolysis or the Kreb's Cycle. 

• Something that a cell or organism needs that is in shortest supply. [NAD+ in glycolysis]
• "It's what you're going to run out of first."

• NEVER. Glucose is never a limting factor in glycolysis because even if one has no glucose as such, one can make glucose from fatty acids and amino acid via gluconeogenesis.

• Because organisms have the ability to make glucose from non-glucose precursors (fatty acids and amino acids). 
• This is called gluconeogenesis.

• 4 are produced. (2 are used, therefore there is a net profit of 2)
• This is the language that Prof. McCleary uses to discuss these amounts. 

• Substrate-level phosphorylation
• This is a type of phosphorylation in which the phosphoryl group is transferred from a donor compound (a phosphorylated reactive intermediate) to the recipient compound
• In substrate-level phosphorylation, the PO₄^3- from a phosphorylated substrate [an organic molecule to which a phosphate group has been added] is transferred to ADP to form ATP. 
• The enzymes phosphorylases and kinases catalyse this process. 

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substrate-level phosphorylation

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• Substrate-Level Phosphorylation in the production of ATP 
• Substrate level phosphorylation is used to produce ATP in the GLYCOLYSIS ; KREBS CYCLE portions of cellular respiration. 

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Substrate-level phosphorylation

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Substrate phosphorulated ATP

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They have one of their carbons removed by oxidative decarboxylation

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• Oxidative decarboxylation reactions are oxidation (loss of electrons) reactions in which a carboxylate group is removed [The carboxyl group is an organic functional group consisting of a carbon atom double bonded to an oxygen atom and single bonded to a hydroxyl group.], forming carbon dioxide. 
• Oxidative decarboxylation is part of the preperation that enables the molecules of pyruvate gleaned from glycolysis (transformed into Acetyl-CoA) to enter the Kreb's Cycle

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• There are 3 carbons in pyruvate. There are 2 in Acetyl CoA. 
• One carbon is lost in oxidative decarboxylation. This carbon leaves the cell in the form of CO₂.

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• Acetyl or an a acetyl group.
• The CoA [derivative of vitamin A] is ultimatly added to this to make Acetyl CoA, which is fed into the Krebs cycle.

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• The Acetyl group joins with Coenzyme A, a derivative of vitamin A, to form Acetyl CoA.
• Acetyl CoA enters the Krebs Cycle

• NADH is produced during the transformation of pyruvate by the actions of an enzyme called alcohol dehydrogenase.
• The hydrogen freed by that enzyme attaches to an NAD+ forming NADH.
• This step occurs prior to the introduction and joining with Coenzyme A. 
• One NADH is formed for each molecule of pyruvate transformed. 
• 2 NADHs are formed
• NOTE: Prof. McCleary did not do over energy production during this stage, or the enzyme mentioned. 

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10!

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• "A rearrangement ... and reduction of the carbon molecules" . - Prof. M.
• The 2 carbons that enter the cycle with each Acteyl CoA, leave in the form of CO₂
• Along the way each molecule of Acetyl CoA generates energy in the following forms:
• NAD> 1 NADH  (x3) = 3 for each Acetyl CoA
• Prof. M only mentioned one but all other sources say 3.
• ADP via substrate phosphorulation> 1 ATP
• FAD >1 FADH₂ 

Substrate Phosphorulation or Substrate Level Phosphorulation (same thing)

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• The answer to this question, posed by Prof. M, was a little tricky.
• She noted that if an organism doesn't have NAD+ for glycolysis, that organism will never get to the Kreb's cycle. 
• [That begs the question: If one had enough NAD+ to run glycolysis but not enough to run Krebs would that process stop? I'm going to ask]

In the cytoplasm

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• FOUR
• Three move protons, in the form of hydrogen, outward across the  membrane. The final one moves hydrogen back into the cytoplasm of the cell. 

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HYDROGEN or H+

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• NADH> becomes NAD+ . The NAD+ is recylced. 
• It can be utlized in glycolysis again or in the Kreb's cycle. 

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• The offloading of an electron by NADH activates the first pump of the electron transport chain. 

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• The hydrogen ions are pumped into the periplasmic space or intermembrane space. This is the space between the cell membrane and the cell wall. 

[image]

• The offloading of an electron at the first pump of the electron transport chain.
• starts the pump.
• frees up the NAD+ that carried in the electron to go and get another electron

2 each, for a total of 6. p.127-9

[image] 

• FADH₂ offloads an electron, becoming FAD+ at the second proton pump in the electron tranport chain.

[image] 

• Two hydrogens, or a pair, are pumped into the periplasmic space at the second pump, just as they are at the first.

[image]

• 2 Hydrogen ions are pumped into the periplasmic space at the third proton pump, just as two are pumped into the perisplasmic space for each of the pervious pumps. [image]

• 6 hydrogen ions are pumped into the periplasmic space per electron entered into the electron transport chain, 2 for each of the first three pumps. 

[image]

• The electrons that power the electron transport chain power three pumps before they are deposited on a terminal electron acceptor.
• In the image below the terminal electron acceptor is oxygen. This occurs just below the skull and cross bones. 

[image]

SINGLET OXYGEN!

[image]

• Oxygen has the highest affinity for electrons; if it is present, electrons will be drawn to it like a magnet. 

• Superoxide Free Radical is formed when an oxygen acts as a terminal electron acceptor. 
• The enzyme superoxide dismutase is used to make this free radical into the less harmful but still toxic hydrogen perxoide [and oxygen]. 

• Superoxide Dismutase
• Catalase 
• Peroxidase

• NO₂ nitrogen dioxide
• SO₂  sulfur dioxide
• Both can act as terminal electron acceptors in the absence of oxygen. 

• There is a chemical gradient, which, because the concentration of hydrogen ions is greater outside the plasma membrane than inside it, wants the hydrogen to move into the cytoplasm, towards equilibrium
• There is an electrical gradient, which, because the charge outside the plasma membrane is highly positive when compared to inside the plasma membrane, also wants the hydrogen to move into the cytoplasm. 

[image]

• A double gradient is created in the electron transport chain by the ion HYDROGEN.

[image]

• The electrical and chemical gradients created by the hydrogen ions in the electron transport chain ultimatly push the hydrogen back through the plasma membrane via a special protein channel that contains the enzyme ATP synthase, and which generates ATP from ADP and P_i [inorganic phosphate] via oxidative phosphorulation. 

[image]

Chemiosmotic Gradient & Electrochemical Gradient

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• Where is the concentration of hyrogen ions the highest as a result of the proton pumps of the electron transport chain?
• In the cytoplasm
• Outside of the cell
• In the periplasmic space
• In the cell membrane. 

• What do we call the gradient that is generated by the electron transport chain? 
• Select all that apply.
1. Chemical gradient
2. Electrochemical gradient
3. Proton gradient
4. Electrosmotic gradient
5. Chemiosmotic gradient
6. Electrical gradient

• The electrochemical or chemiosmostic gradient creates a movement of substances (protons in this case) that generates energy. 
• This energy pushes hydrogen ions back into the cytoplasm through a protein channel. 
• As they move through this protein channel they activate ATP synthase, which generates new ATP by oxidative phosphorulation.  

[image]

What process generates the most ATP?

a. Glycolysis

Net 2 per glucose molecule*

b. Kreb's cycle & Oxidatative Decarboxylation of Pyruvate

Net 2. No ATP is produced in the decarboxylation of pyruvate, only 2 NADH per glucose molecule*

c. Proton pumps

Proton pumps don't generate any ATP

d. Chemiosmosis

This is the gradient that activates the ATP synthase in the Electron transport chain. It produces 34 ATP - 3 for each of the 10 NADH produced and 2 for each of the 2 FADH₂ produced. Again, this is per glucose molecule.*

e. Substrate level phosphorulation

This type of phosphorulation is active in both glycolysis and the Kreb's cycle. It is responsbile for the generation of 4 ATP per glucose molecule*

 *All number are best case scenarios. 

• The enzyme is called "ATPase" or ATP synthase. 
• It brings together ADP and an inorganic phosphate, generating ATP by OXIDATIVE PHOSPHORULATION.

[image]

• The maximum number of ATP per glucose molecule for a bacteria is 38.
• Glycolysis - net 2
• Krebs - 2
• Electron Transport Chain - 34

• Humans can produce 36* molecules of ATP per molecule of glucose at most. 
• *There are two schools of thought on this and the number 38 is often reported as well. 

• FADH₂ offloads its electron at the second proton pump in the electron transport chain. Upon doing this it becomes FAD+ and returns to the cytoplasm where it can carry another electron from the Kreb's cycle.

[image]

• FADH₂ offloads at the second pump, therefore it enables the pumping out of 2 pairs of hydrogen ions, one pair at that second pump, and one at the third pump. 
• One FADH₂ generates 2 molecules of ATP, one per pair of hydrogen ions pumped into the periplasmic space.
• A total of 4 ATP are generated by FAD+ per molecule of glucose.

[image]

• NADH, which offloads at the first pump, generates 3 pairs of hydrogen ions [1 pair per pump] in the periplasmic space. 
• Those 3 pairs generate 3 ATP, one ATP per pair. 
• Because 10 NADH [2 from glycolysis, 2 from the oxidative decaroxylation of pyruvate, and 6 from the Kreb's Cycle] enter the Electron Transport Chain and three are generated for each, 30 ATP are generated by NADH

[image]

• Oxidatative phosphorulation produces the ATP generated in the ELECTRON TRANSPORT CHAIN.
• [image]

There is no energy value difference between ATPs generated by different methods.

They are chemically identical.

• Oxidative phosphorylation is the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH 2 to oxygen [or other organic or inorganic oxidized molecules] by a series of electron carriers. 

NAD+ is a derivative of the B vitamin niacin. 

FAD+ is a derivative of the B vitamin riboflavin. 

Both are coenzymes and electron carriers. 

• Aerobes, anaerobes and facultative anaerobes can run cellular respiration. 

• Anaerobes and aerobes use different terminal electron acceptors during cellular respiration. Aerobes use oxygen. 
• Anaerobes use another inorganic molecule. 

• Anaerobic organisms 
• if no oxygen is present and an alternate nonorganic terminal electron is
• Aerobic organisms 
• if oxygen is present
• Facultative anaerobes
• if oxygen is present