Microbial Metabolism Flashcards
1
Q
,What is metabolism?
A
Metabolism: The sum of the chemical reactions that occur in an organism to sustain life
2
Q
Differentiate between Catabolism and Anabolism
A
Catabolism: chemical reactions that result in the BREAKDOWN of more complex organic molecules into simpler substances
Anabolism: Chemical reactions in which simpler substances are COMBINED to form more complex molecules
3
Q
What kind of reactions are Catabolic reactions? What do they involve and what are some examples?
A
Catabolic reactions:
-EXERGONIC (produce more energy than they consume)
-Often involve Hydrolytic reactions (cleavage of a compound by the addition of water )
Ex: Respiration (converting sugars to CO2 and H2O), convert Lipids to glycerols and fatty acids, fatty acids to acetate (Beta-oxidation)., proteins to amino acids
4
Q
Why are catabolic reactions necessary for anabolic reactions?
A
Catabolic reactions provide the Building Blocks and Energy needed for anabolic reactions
5
Q
What kind of reactions are anabolic reactions? Discuss what they involve and provide examples.
A
Anabolic reactions:
-ENDERGONIC (consume more energy than they produce)
-Often involve DEHYDRATION reactions (Release water)
Examples: form glucose from CO2, form glucose from pyruvate, make proteins from amino acids, polysaccharides from simple sugars, and nucleic acids from nucleotides
6
Q
What couples Anabolic and Catabolic reactions? Explain how the chemical composition of cell changes.
A
ATP couples anabolic and catabolic reactions
-In catabolic reactions, transfer energy from complex molecules to ADP, where heat will be released complex molecules break down to simple molecules (glucose, glycerol , fatty acids)
-In Anabolic reactions, transfer energy from ATP to complex molecules, heat released to make complex molecules (starch, proteins, lipids)
-Chemical composition of the cell is constantly changing: some molecules are broken down, while others are being synthesized
7
Q
What is the Metabolic pathway and what are their roles?
A
Metabolic pathway: a sequence of enigmatically catalyzed chemical reactions in a cell
-Metabolic pathways are determined by Enzymes (which are encoded by genes)
-Allows organisms to release and store energy in a series of controlled reactions rather than single burst
8
Q
What is Collision theory and what are the different types of collisions that occur?
A
Collision theory: states that atoms, ions and molecules must COLLIDE in order to react
-Collison energy can disrupt their chemical structures enough to Break (ineffective collision) or form new bonds (Effective collision)
9
Q
What 3 factors determine whether a chemical reaction will occur from the collision?
A
- Velocity of colliding particles (temp)
- Level of energy required for the chemical reaction
- orientation of colliding particles
10
Q
What is Activation energy?
A
Activation energy: The amount of collision energy necessary for a chemical reaction
11
Q
What is reaction rate? How can you increase reaction rates in a test tube?
A
Reaction rate: How fast or slow a reaction takes place (determined by the frequency of collisions containing sufficient energy to bring about a reaction)
To increase reaction rate in test tube:
-Increase Concentration
-Increase Temperature
Increase Pressure
(higher concentration of molecules, more collisions occur)
12
Q
How do enzymes affect activation energy and reaction rate in biological systems? Why is this ability critical in living systems?
A
In biological systems, enzymes LOWER the Activation Energy (and thereby INCREASE the reaction rate) without raising temperature
This is critical in living systems, because in living systems that you cannot really raise temperature that much (limited range of temp)
13
Q
What is an enzyme? Define its characteristics
A
Enzyme: biological molecule (usually a protein) produced by living cells that catalyzes a chemical reaction by lowering the activation energy
Enzyme characteristics:
-generally globular with characteristic 3-dimensional shapes
-each Usually acts on a specific substance, its substrate (s)
-each catalyzes only one reaction
-can operate at physiological temperatures
-Subject to various cellular controls (transcription of gene, translation of mRNA, phosphorylation)
14
Q
Explain how enzymes increases ability for successive reaction
A
An enzyme orients its substrate into a position that increases the probability of a successful reaction (enables collisions to be more effective, which lowers activation energy)
(enzymes have many other additional catalytic strategies)
15
Q
How is Enzyme Specificity achieved? Also discuss the lock and key model, and what dictates the configuration of each enzyme. How much can enzymes increase reaction rates?
A
Enzyme Specificity achieved by the Unique configuration of each enzyme that enables it to “find: the correct substrate
-Lock and Key model: describes the enzyme-substrate reaction, where the enzyme has an active site that is specifically shape to fit one specific substate. ( substrate is a key; enzyme is Lock)
-Configurations are dictated by the Primary, Secondary and Tertiary structures
- Enzymes can increase reaction rates from 10^8 to 10^10 higher than reactions without enzymes
16
Q
What is Turnover number/frequency/rate?
A
Turnover number/frequency/rate: max number of substrate molecules a single enzyme converts to product per second
-Examples: DNA polymerase I: 15, lactate dehydrogenase: 1,000; general range 1-10,000, some can go up to 500,000 (carbonic anhydrase0 (CO2+ H2O–> HCO3+ H+ )
17
Q
How are enzymes named? Describe the six classes of enzymes and the types of reactions they catalyze
A
Enzyme names usually end in -ase
-Enzymes are grouped in six classes based on the types of reactions they catalyze
1. Oxidoreductase: Oxidation-reduction reactions (cytochrome oxidase, alcohol dehydrogenase)
2. Transferase: Transfer functional groups (kinase, methlytransferase, deaminase)
3. Hydrolase: Hydrolysis (lipase)
4. Lyase: Removal of atoms without hydrolysis (Oxalate decarboxylase, isocitrate lyase)
5. Isomerase: Rearrangement of atoms (alanine racemase)
6. Ligase: Joining of molecules using ATP (DNA ligase, acetyl coA synthase)
18
Q
What are the components of a Holoenzyme? What is a coenzyme, cofactor?
A
Holoenzyme composed of Apoenzyme and Cofactor (whole enzyme is active)
Apoenzyme- Inactive protein portion; enzyme that is NOT bound to cofactor (but requires a cofactor)
-Cofactor: nonprotein portion that is the activator (it is required for action of enzymes as catalyst)
Most enzymes have cofactors (that can be organic (like coenzymes) or inorganic (metal ions)
-Coenzyme: organic molecule that binds loosely to active site of enzyme.
19
Q
List the different types of coenzymes/organic cofactors and Inorganic cofactors
A
Conenzymes/organic cofactors:
-nicotinamide adenine dinucleotide (NAD+) (catabolic reactions)
-Nicotinamide adenine dinucleotide phosphate (NADP+) (anabolic rxns)
-Flavin mononucleotide (FMN)
-flavin adenine dinucleotide (FAD)
-Coenzyme A (Krebs cycle)
Inorganic cofactors:
Metal ions of:
-iron
-copper
-zinc
-calcium
-cobalt
-manganese
-magnesium
(–>RNA, DNA)
20
Q
Explain the mechanism of Enzymatic Action. What allows the release of products?
A
Mechanism of Enzyme action:
Process:
1) The Substrate binds to active site of enzyme
2) This binding forms enzyme-substrate complex
3) The complex is then cleaved
4) substrate is cleaved forming products
5) The enzyme is back to normal position, without anything bound to active site
-Products are released since they no longer fit the active site
21
Q
What is the induced fit model and why is it significant?
A
Induced fit model of an enzyme substrate reaction proposes that the shape (conformation) of the active site within enzymes is Malleable and can be induced to fit the substrate and increase binding
This is considered the more Accurate model for enzyme-substrate complex than the more static, Lock and Key model.
22
Q
What are factors that influence enzyme activity?
A
-Temperature
-pH
-Substrate concentration
-inhibitors
23
Q
Explain how temperature affects the enzyme. What is denaturation? What temperature decreases reaction rate
A
At high temperatures, enzymes undergo Denaturation and lose their catalytic properties
Denaturation: the breaking of hydrogen and other non-covalent bonds, which Changes the folding of the structure)
- Active functional protein (normal shape, functioning) vs Dentured protein (inactive, and protein unfolds)
-At LOW temperatures, the reaction rate DECREASES.
24
Q
What other conditions will denature proteins? Is denaturation partially or fully reversible?
A
Other conditions that will denature proteins:
High or Low pH
- Heavy metal Ions (Pb, Hg) (that compete with disulfide bonds)
-Salts (that compete with ionic bonds)
-Alcohol (compete with Hydrogen bonds)
YES, they are reversible, as long as protein is soluble, you can refold it
25
Discuss the relationship between temperature and enzymatic activity. What is the optimal temperature for particular enzyme? Is the optimal temperature for DNA polymerases that bacteria have the Same?
Temperature vs Enzymatic activity
-The enzymatic activity (rate of reactions catalyzed by enzyme) increases with increasing temperature. This will occur until the enzyme is denatured by heat and inactivated. You will eventually reach a a peak, where enzyme activity will drop because the temp is too high
-Optimal temp for enzyme; 37 degrees celsius
-All bacteria have DNA polymerases. NO, these enzymes do not have same optimal temperature, because each enzyme have different amino acid composition
some might be more heat stable, while others operate at low temperatures.
26
How does pH affect enzymes?
pH changes alter an enzyme's 3-D structure because:
1) H+ (and OH-) compete for hydrogen bonds
2) pH dictates the Protonation state of amino and carboxyl groups; the changes alter ionic interactions between amino acids
27
How does Substrate concentrate affect enzyme activity? Are enzymes typically saturated under normal cellular conditions?
Substrate concentration
-The rate of reaction increases with increasing substrate concentration, until the active sites on enzyme molecules are filled
-At this point the enzyme is said to be SATURATED
-NO, enzymes are Not typically saturated under normal cellular conditions
28
How are enzyme inhibitors classified?
Enzyme inhibitors classified as either..
-Competitive inhibitors
-Non-competitive inhibitors
29
Describe what occurs in competitive inhibition and how it differs from normal substrate-enzyme reaction.
Normally in a substrate-enzyme reaction, the substrate binds to active site of enzyme (or enzyme binds substrate) , causing enzyme to release products
Competitive inhibition: The inhibitor fits the active site of the enzyme, but does NOT undergo a reaction to produce products
The inhibitor competes with substrate for bind to enzymes (blocks access of normal substrate to active site of enzyme)
30
Explain how competitive inhibitors can be either reversible or non-reversible
-Some competitive inhibitors bind IRREVERSIBLY to amino acids at the active site, preventing further interaction with the normal substrate
-Reversible competitive inhibitors occupy and can leave the site
You can alleviate the effects of inhibitor by increasing the amount of substrate (more substrate concentration)
31
What are examples of competitive inhibitors?
SULFANILIAMIDE is an example of a competitive inhibitor (Sulfa drug)
Sulfanilamide is has similar structure to PABA (para-aminobenzoic acid; which is involved in synthesis of folic acid
(sulfonamide chemical group - R1-S=O=O-N-R3-R2)
32
Describe the folic acid synthesis in bacteria and how competitive inhibitors can affect the pathway.
Folic acid synthesis in bacteria;
Para-aminobenzoic acid (PABA) (is an intermediate) that will convert to dihydrofolic acid through enzyme Dihydropteroate synthase
The Dihydrofolic acid will then use dihydrofolate reductase enzyme to form Tetrahydrofolic acid which will convert to Purines and then to DNA.
However, competitive inhibitor like Sulfonamides will compete with PABA (by interacting with enzyme that converts PABA into dihydrofolic acid). Sulfonamides will inhibit the enzyme
Also, another competitive inhibitor called Trimethoprim will compete with substrate to inhibit dihydroflate acid reductase enzyme (that converts dihydrofolic acid to tetrahydrofolic acid)
33
Why isn't Sulfanilamide toxic to mammals?
Sulfanilamide is Not toxic to mammals because mammals cannot synthesize folic acid ourselves
-We must ingest it when it is already formed (we get folic acid from our Diet)
34
Why don't bacteria use folic acid from their environment to avoid toxicity?
Because Folic acid cannot cross bacterial membranes by diffusion or active transport. Therefore, bacteria must synthesize their folic acid starting with PABA
35
What is Noncompetitive inhibition and what does it involve?
Noncompetitive Inhibition: when an inhibitor molecule binds to a part of the enzyme other than the active site (Allosteric site). This inhibitor will then prevent the binding of the substrate, by changing the shape of the active site in enzyme.
-normally, substrate binds to active site of enzyme , and a reaction occurs, forming new products
36
What is the other site on an enzyme called? Can non-competitive inhibition be classified as either reversible or irreversible? Can these interactions also activate enzymes ?
ALLOSTERIC SITE (other site on enzyme, besides active site)
- YES, non-competitive inhibition can be classified as reversible or irreversible; it depends on whether the active site can return to its original shape
-Yes, these interactions can also activate enzymes
37
What are enzyme poisons?
Enzyme poisons: Substances that permanently inactivate enzymes (ex; Cynaide [Fe] and fluoride [Ca2+/Mg]
this is a form of IRREVERSIBLE non-competitive inhibition
Cynaide can bind to iron and irreversibly inhibit it.
38
Explain how allosteric (non-competitive) inhibitors are important in feedback (end-product) inhibition
Generally first enzyme of the pathway is INHIBITED to shut down the entire pathway
-As the end product is used by the cell, the allosteric site of the first enzyme becomes unbound more frequently
(binding of end-product to allosteric site will slow down or stop the enzyme's activity, so little or no end-product is formed)
*** Needs to be reversible***
39
Discuss the history and role of Ribozymes
Ribozymes
-It was discovered in the 1980s that some RNAs can act as enzymes
-They catalyze covalent changes in the structure of substrates (which are mostly restricted to other RNA molecules)
40
Why is the ribosome considered a ribozyme?
Ribosome is considered a ribozyme because it was believed that linkage of amino acids is due to Ribosomal RNA. It seems to be most important for peptidyl transferase activity that links amino acids together.
41
Explain the concept of oxidation-reduction. Also discuss with a Redox reaction is.
Oxidation: Removal of electrons, a reaction that often produces energy
-Reduction; GAIN of electrons
-Redox reaction; An oxidation reaction paired with a reduction reaction
-
42
Describe the kind of oxidations that occur in biological systems. Where does the energy released by oxidation-reduction reactions go?
In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often DEHYDROGENATIONS
ex; Organic molecule that includes two H+ atoms and NAD+ coenzyme (electron carrier) react, the organic molecule will lose e- and the NAD+ carrier will accept the e+ in form of H+. This results in products of oxidized organic molecule and NADH+ + H+ (proton); reduced electron carrier (since it gained e-).
***Much of the energy released by metabolic oxidation-reduction reactions in the cell is TRAPPED by the formation of ATP
43
Explain what occurs in the formation of ATP. Why is ATP so important? How many mechanisms are used to generate ATP?
Formation of ATP:
ADP (adenosine + 2 phosphates) + Energy + Phosphate --> Adenosine-P-P-P (ATP)
-ATP is the MOST ABUNDANT Energy carrier molecule in cells (molecules whose breakdown is directly coupled to endergonic reactions)
-THREE mechanisms of Phosphorylation are used to generate ATP from ADP.
44
What occurs in substrate level phosphorylation?
Substrate level Phosphorylation: A high-energy phosphate from an intermediate in catabolism (substrate) is directly transferred to ADP.
This will be used to make ATP
-The phosphorylated substrate itself generally has acquired its energy during an earlier reaction in which it was oxidized.
45
What is oxidative Phosphorylation? what is the terminal electron acceptor in microbes?
Oxidative Phosphorylation: electrons from molecules are used to reduce electron carriers (ex; NAD+ and FAD) that pass their electrons and protons to the electron transport chain. This chain passed electrons from donors to acceptors, and transports protons across a membrane. The proton gradient is used to generate ATP.
-In microbes, the terminal electron acceptor can be either Oxygen or other organic or inorganic compounds
pathway of oxidative phosphorylation (NADHQ-Reducatase--> Q --> cytochrome reductase--> Cytochrome C --> Cytochrome oxidase (and then into matrix)
46
What occurs in Photophorylation?
Photophosphorylation: describes when light energy is converted to the ehcemical energy of ATP
-occurs only in PHOTOSYNTHETIC cells
(uses PSII, PSI, ferredoxin reductase, atp synthase and cytochrome; photolysis )
(end up forming NADPH and ATP)
47
Explain how energy is released from organic molecules. What would happen if energy was released all at once?
Describe the two different arrows that are in reactions and what they mean
Energy is extracted from organic molecules by a series of Controlled reactions (metabolic pathway)
-If the energy was released all at once as a large amount of heat, it could NOT readily drive chemical reactions and would DAMAGE the cell.
ex: (NAD+ to NADH+ + H+ is coupled to reaction of A--> B ; ADP + P--> ATP coupled with C--> D)
-The single arrows in a reaction, represent reactions moving forward in one direction. The double arrows represent how substrates can convert back and forth from one to the other (E--->D and D-->E)
48
Explain what occurs in Carbohydrate Catabolism. What is the most common carbohydrate used by cell?
Carbohydrate Catabolism:
-Most microbes oxidize carbohydrates as there primary source of energy
-GLUCOSE is the most common carbohydrate used by cells
49
What are the two major types of glucose catabolism?
Two major types of glucose metabolism:
-Respiration: glucose is COMPLETELY broken down to CO2+ H2O
-Fermentation: Glucose is Partially broken down.
50
What is glycolysis and what are the products produced? What is another name used for Glycolysis pathway?
Glycolysis: The Oxidation of glucose to PYRUVIC acid, produces 2 ATP and 2 NADH
both glucose respiration and Fermentation start with Glycolysis
-The Embden-Myerhof-PARNAS pathway is referred to as "Glycolysis"
51
What does the word "Glycolysis" mean? What are the two main stages in the Glycolysis pathway?
Glycolysis: means the Cleavage of sugar
-The pathway consists of two basic stages, the PREPARATORY Stage and an ENERGY CONSERVING stage
52
Discuss what occurs in the Preparatory Stage of Glycolysis
Preparatory Stage of Glycolysis (also called "Energy-requiring", priming, or "investment stage")
- 2 ATP are used
-Glucose is phosphorylated, isomerize, phosphorylated again, then split to form 2 glyceraldehyde-3-phosphate molecules
("glucose is trapped, destabilized and split")
(form glucose, G6P, then F6P, F,1,6 DP, then DHAP and G3P)
53
What occurs in the Energy-Conserivng stage of Glycolysis?
Energy Conserving Stage of Glycolysis:
(also called "harvesting", "energy-trapping", energy generation", "energy releasing" or "Pay-off stage)
-2 glycerladehyde-3-phosphates are oxidized to 2 pyruvic acid
-4 ATP is produced
-2 NADH is produced
(In some textbooks, the glycolytic pathway is NOT divided into stages, while in others it is presented in THREE stages)
(in this stage, G3P forms 1,3 dP acid--> 3 phophoglyceric acid--> 2-phosphoglyceric acid-->PEP-->pyruvate)
-substrate phosphorylation (remove phosphate from 1,3 DP to form 3 phosphogylceric acid; form ATP from ADP)
54
What is the reaction for Glycolysis? how many ATP molecules are you gaining for each molecule of glucose?
Glycolysis:
-Glucose + 2 ATP + 2 ADP + 2 PO4- + 2NAD+ --> 2 pyruvic acid + 4 ATP + 2 NADH + 2 H+
A net gain of TWO molecules of ATP for each molecule of glucose
55
In addition to glycolysis, what other glucose oxidation pathways are sometimes present?
Other glucose oxidation pathways in addition to glucose glycolysis:
-Entner-Doudoroff pathway (some prokaryotes)
-Pentose phosphate pathway (all organisms) (hexose monophosphate shut phosphogluconate pathway)
56
Explain what occurs in the Entner-Doudoroff pathway and how it differs from EMP pathway
Entner-Doudoroff pathway:
Prokaryotes with this pathway can carbolize glucose to pyruvate without EMP pathway (Embden-myerhof paras)
-A few enzymes are different from those in the EMP pathway
-Produces ONE ATP, ONE NADPH, and ONE NADH for each glucose
(whereas, 2 ATP are produced for each molecule in EMP)
Present in some gram-negative bacteria, but not generally found in gram-positive bacteria
**The Entner-Duodoroff pathway is an OVERLOOKED glycolytic route in Cyanobacteria and plants (2016)
comparison to EMP: Entner-Doudoroff uses different enzymes and has different substrates( 6P-gluconic acid, KDPA)
EMP requires more enzymes to convert.
57
What was the purpose of Phylogenetic analysis of the EMP and ED pathways?
REVIEW
The phylogenetic analysis of EMP and ED pathways:
-Glycolytic strategy as a tradeoff between energy yield and protein cost
-this was a way of looking for genes that encode enzymes
(in phylogeny, 43% EMP, 13% ED, 14% both EMP and ED, and 30% unknown)
58
What occurs in the Pentose Phosphate Pathway (PPP)?
Pentose Phosphate Pathway:
-may be used simultaneously with the EMP pathway or Entner-Doudroff pathways
-Breaks down 5-carbon sugars, as well as glucose
-***Produces TWO NADPH for each glucose
-Neither consumes nor produces ATP (book states 1 ATP is generated)
- **A source of four and 5 carbon skeletons that can be used for synthesis of amino acids, nucleic acids, and other macromolecules
59
What is primary role of pentose phosphate pathway? What is another name for it? which molecule is shunted from glycolysis?
Although it involves oxidation of glucose, its primary role is ANABOLIC, rather than catabolic
pentose phosphate pathway (aka hexose monophosphate shunt phosphogluconate pathway)
-it is an alternative pathway to glycolysis, and produces ribose 5-phosphate and NADPH .
Glucose-6-phosphate is SHUNTED from glycolysis
60
What happens to pyruvate produced in the EMP and ED pathways?
Pyruvate will be channeled to either Fermentation or Cellular Respiration
61
What are two major functions of Cellular Respiration? What are the two types of respiration?
Cellular Respiration
Two functions:
-dispose of electrons produced during the catabolism of energy sources
-produce efficient yields of ATP by oxidative phosphorylation
Two types of respiration
-Aerobic: terminal electron acceptor is O2
-Anaerobic: a terminal electron acceptor Other than O2 is used. Utilized by many species of bacteria and can include nitrate, sulfate, and carbon dioxide.
62
What eventually happens to pyruvic acid in respiration ?
Respiration
-Pyruvic acid (from oxidized glucose) is further oxidized and decarboxylated
Pyruvic acid will convert to Acetyl coA, release CO2 and NAD+ --> NADH
-recall that each glucose oxidized produces 2 pyruvate
**Acetyl CoA enters the Krebs Cycle****
63
What is the Krebs cycle? What molecules are produced?
The Krebs cycle:
- A series of oxidation and reduction reactions that release the potential energy of Acetyl-CoA step by step
-NADH (chiefly) and FADH2 are produced
-ATP is also produced by substrate level phosphorylation
64
What are the general categories that Kreb's cycle reactions fall into?
Krebs Cycle:
Reactions fall into general categories:
1) Decarboxylation: conversion of all 6 glucose carbons to CO2 (seen in prep+ steps 3 and 4 of Krebs cycle)
2) Oxidation-reduction: hydrogen atoms are transferred to NAD+ and FAD [ Steps 3, 4, 6, and 8]
3) Isomerizations: 2 and 7
4) Substrate level phosphorylation : 5
intermediates also play roles in other pathways.
65
What are the major steps in Krebs cycle?
Process of Krebs cycle:
1. Acetyl CoA (2c) will combine with oxalacetate (4c) to form citric acid (6c)
2. Citric acid will then isomerize to come isocitric acid
3. NAD+ will then be reduced to NADH, decarboxylation also happens and causes Isocitric acid to be converted to alpha-ketoglutaric acid
4. another reduction, NAD+ --> NADH occurs, and decarboxylation, as well as CoA attaching to from succinyl-CoA
5. Succinyl coA undergoes substrate level phosphorylation (where energy released from CoA) and converts ADP + Phosphate --> ATP, forming succinic acid.
6. FAD is then reduced to FADH2 (accept 2 e- and 2H+ causing succinic acid to form Fumaric acid)
7. Fumaric acid is isomerize to malic acid
8. Malic acid undergoes Reduction (NAD+ --> NADH) to form oxaloacetic acid.
66
What is the final output of every two acetyl-CoA molecules?
Final output for every 2 acetyl CoA molecules:
4 CO2, 6 NADH, 2 FADH2, and 2 ATP
67
What is the Electron Transport Chain?
Electron Transport Chain:
A series of electron carrier molecules)NADH, FADH2) that are, in turn, oxidized and reduced as electrons are passed down the chain
-The energy released can b sued to produce ATP by CHEMIOSMOSIS
68
List ehe major classes of carriers in the electron transport chain
Classes of Carriers in the Electron transport chain:
-Flavoproteins: contain flavin (coenzyme derived from riboflavin) . One important flavin coenzyme is flavin mononucleotide (FMN--> FMNH--> FMNH2)
(cofactor for NADH and succinate dehydrogenase complexes I, II of ETC)
-Cytochromes: proteins with an iron-containing group (heme) with reduced (Fe2+) and Oxidized (Fe3+) forms (cofactor for cytochrome bc1 and cytochrome c oxidases, complex III and IV)
-Ubiquinoes (Q): small non-protein carriers.
All of these carriers can be reduced then oxidized.
69
Describe what occurs in the Chemiosmotic Generation of ATP, including the different functions of the complexes.
Chemiosmotic Generation of ATP
- mammalian mitochondrial Electron transport chain (ETC occurs in innermebrane space of mitochondria)
Chemiosmosis: the movement of ions (particularly Hydrogens) across the membrane, resulting in an electrochemical gradient that drives ATP synthesis
Ubiquinone (Q) and cytochrome c are mobile electron carriers
Complex I (NADH dehydrogenase) - accepts two high energy electrons from NADH that was made in Krebs cycle earlier and uses those 2 e- to convert ubiquinone to ubiquinol (also pump 4 H+ from maxtrix to intermembrane space)
Complex II (Succiante dehydrogenase; Krebs cycle enzyme) succinate DH is part of Krebs cycle as FAD is reduced to FADH2 and succinate is converted into fumarate. In ETC, the Succinate DH accepts electrons from FADH and transfers it to Q to eventually enter complex III (complex II does NOT pump protons)
Complex III (cytochrome bc1 complex) -transfers the electrons across the inter membrane space to cytochrome c (these electrons are carriers to complex 4 by mobile carrier, cytochrome c also pumps protons)
Complex III has two cytochromes: Cytochrome c and cytochrome b1
Complex IV (Cytochrome c oxidase) -transfers electrons from cytochrome C to Oxygen (final electron acceptor) and reduce O2 to water, help generate proton gradient.
note: cytochrome c can only accept electrons one at a time
(complex 1, 3, 4, transfer electrons and pump portions, resulting in protein gradient on one side of membrane)
ATP synthase (considered completely V)-proton gradient produced by proton pumping in ETC, allows H+ protons to pass through ATP synthase and spin the complex, converting ADP + Phosphate to ATP.
70
Where is ETC in mitochondria vs bacteria?
(ETC is in the inner membrane of mitochondria; and ETC is in plasma membrane in bacteria)
71
Describe how ETC (Electron transport chain) differs in prokaryotes.
Generalized ETC in prokaryotes
-The ETC is more flexible and varied because there are several different electron donors and acceptors
- ***Electron can enter and exit the chain at different positions (depending on bacteria) ***
(Donors can be Dehydrogenase, quinone and cytochrome; acceptors can be oxidase (reductase)
(The electron acceptor in mitochondria, O2 is final acceptor and accepts from cytochrome c oxidase
With bacteria, it can accept electrons from different complexes )
72
How is ATP generated using the electron transport chain?
- The phospholipid membrane is normally impermeable to protons
-complexes I, III and IV actively transport protons across the membrane
-An electrochemical gradient is formed (proton motive force)
-Protons can only diffuse across membrane through channels containing an ATP synthase (V)
-energy is released and used by the enzyme to synthesize ATP from ADP
73
Discuss the overview of Respiration that includes the three major pathways.
Overview of Respiration:
1) Glycolysis produces ATP and reduces NAD+ to NADH, while oxidizing glucose to pyruvic acid. In respiration, the pyruvic acid is converted to soothe first reactant in krebs cycle (acetyl-coA)
2) The Krebs cycle produces ATP and reduces NAD+ (and another electron carrier called FADH2) while giving off CO2. The NADH and FADH2 from both processes carry electrons to the electron transport chain
3) In the electron transport chain. the energy of the electrons is used to produce a great deal of ATP.
74
Describe the total amount of energy produced form-complete oxidation of one glucose, using aerobic respiration
Energy produced from complete oxidation of one glucose using aerobic respiration:
-Glycolysis; 2 ATP, 2 NADH, 0 FADH2 produced
-Intermediate step (convert pyruvate to acetly-CoA): 0 ATP produced, 2 NADH produced, 0 FADH2 produced
-Krebs cycle: 2 ATP produced, 6 NADH produced, 2 FADH2 produced (since 2 acetyl coA made)
****Total : 4 ATP, 10 NADH, and 2 FADH2.
75
How many ATP is generated from 1 NADH and 1 FADH2? How many ATP are produced in Eukaryotes vs Prokaryotes?
1 NADH generates 3 ATP
1 FADH2 generates 2 ATP
Prokaryotes- proudce 38 ATP
Eukaryotes produce 36 ATP
76
Why do eukaryotes only produce a total of 36 ATP?
Eukaryotes only produce 36 ATP because 2 ATP are required to shuttle 2 NADH (not electrons) that are produced in glycolysis across the mitochondrial membrane to ETC.
C6H12O6 + 6 O2 + 38 ADP + 38 Pi--> 6 CO2 + 6 H2O + 38 ATP
(prokaryotes do not have to cross the membrane)
77
Discuss where each aerobic respiration pathway is located, in prokaryotes vs eukaryotes
Glycolysis occurred in the Cytoplasm for Eukaryotes (except Pyruvate and NADH that were in mitochondria) and Prokaryotes
Intermediate Step (pyruvate--> Acetyl-CoA) occurred in Mitochondrial matrix for Eukaryote, and in Cytoplasm for Prokaryotes
Krebs cycle occurs in mitochondrial matrix for Eukaryotes and in cytoplasm for prokaryotes.
ETC occurs in Mitochondrial inner membrane for Eukaryotes and Plasma membrane for prokaryotes.
78
How does pyruvate arrive in mitochondrial matrix?
Pyruvate is cotransported with H+ across the inner mitochondrial membrane into the matrix.
79
What occurs in Anaerobic respiration and how does it differ form aerobic respiration?
Anaerobic Respiration:
-An inorganic electron acceptor is used in the electron transport chain, NOT O2.
-Yields LESS energy than aerobic respiration because:
-NOT all carriers in electron transport participate
*** The Terminal electron acceptors have SMALLER reduction potentials than O2... they're less oxidizing than O2(has +0.82 value for redox potential)
-Only part of the Krebs cycle operates during anaerobic conditions. The TCA cycle is NOT universal- Not all Prokaryotes have the full cycle
80
What are the final electron acceptors and products in anaerobic respiration ?
Final Electron acceptor Products
-NO3- NO2- , N2+ H2O
- SO4- H2S + H2O
- CO2 CH4 + H2O
81
What is a redox potential? Describe the redox potential for microbial respiration (anaerobic)
Redox potential: a measure of how easily a metal (or other ion) will give up electrons or retain electrons
redox potentital for electron acceptors in microbrial respiration are NOT as high, as in aerobic respiration and less energy is produced .
electrons flow from negative to positive
-The greater (more POSITIVE) the redox potential, the more readily an electron will be reduced (accept electrons)
82
What is Fermentation? Describe the range of definitions that are used
What is Fermentation?
-Any spoilage of food by microorganisms (general use)
-Any process that produces alcoholic beverages or acidic dairy products (general use)
-Any large-scale microbrial process occurring with or without air (common definition used in industry)
83
What is the scientific definition of Fermentation? What molecules are involved?
Fermentation (scientific definition)
-Releases energy from oxidation of sugars or OTHER ORGANIC molecules
-Doesn't require oxygen (but can occur in its presence- microbe dependent )
-Does NOT use Krebs cycle or ETC
-Uses an organic molecule as the final electron acceptor
(**polyols, organic acids, amino acids, and purines/pyrimidines)
(E.coli can only ferment if NO O2 is available)
84
Explain the process of Fermentation and how much ATP is produced.
Fermentation: uses glycolysis to extract energy in form of ATP
It converts 1 glucose to 2 pyruvic acids, while also reducing NAD+ to NADH and forming 2 ATP, and 2 NADH
NADH regeneration will also occur, as NADH will convert back to NAD+ (to be recycled for glycolysis) , as Pyruvic acid forms fermentation end products.
85
What are the End products of Pyruvic acid Fermentation? Which organisms produce these products?
End products of Pyruvic Acid Fermentation:
-Lactic acid (produced by Streptococcus, Lactobacillus)
-Ethanol and CO2 (produced by Saccharomyces (yeast) )
-Propionic acid, acetic acid, CO2, and H2 (produced by Propionibacterium)
-Butryic acid, butanol, acetone, isopropyl alcohol and CO2 (produced by Clostridium)
-Ethanol, lactic acid, succinic acid, acetic acid, CO2 and H2 (produced by Escherichia, Salmonella)
-Ethanol, lactic acid, formic acid, butanediol, acetone, CO2, and H2 ( produced by Enterobacteria)
86
What occurs in Lactic acid fermentation ? Differentiate between Homolactic and Heterolactic fermentation
Lactic acid fermentation; Lactic acid is produced
(after glycolysis, when 2 pyruvic acids are produced, NADH is Oxidized to NAD+, and pyruvic acid is reduced to lactic acid). You also produce 2 ATP and 2 NADH
-Homolactic fermentation: produces Lactic Acid ONLY
-Heterolactic fermentation: produces lactic acid and other compounds
87
Why is Lactic acid fermentation important? What are two important microorganisms in this process?
Lactic acid fermentation is important in the Food industry: -cause of food spoilage
Produce....
-yogurt from milk
-Sauerkraut from cabbage
Two important genera...
-Streptococcus and Lactobacillus
88
What occurs in Ethanol Fermentation? What products are made? Which microorganisms play a role in this proceess?
Ethanol Fermentation:
-Produces Ethanol and CO2.
-Performed by a number of bacteria and yeasts
-The yeast Saccharomyces cerevisiae is commercially important for ethanol production
-ethanol for alcoholic beverages, fuel, disinfectants, etc.
-CO2 causes dough to rise
process: (2 pyruvic acids (from glycolysis) will first undergo decarboxylation and produce Acetalaldehyde. NADH will also be oxidized to NAD+ and the acetaldehyde will then be reduced to ethanol (2)
89
is ethanol a waste product for yeast cells?
YES, Ethanol is a waste product for yeast cells because
if you give yeast excess amount of glucose, they will ferment the glucose.
In the environment, there is a lot of competition for usage of glucose with yeast and other organisms. So if Yeast will want to rapidly use up glucose and convert it to ethanol for COMPETITIVE ADVANTAGE ; since other organisms cannot use ethanol and it will kill them.
When there is no glucose, they can take the ethanol and use it for respiration.
The ethanol they produce, with O2 round can be respired, and get additional ATP.
90
What occurs in lipid Catabolism and how are microbes involved?
Lipid Catabolism
-Micorbes produce extracellular enzymes called LIPASES to break down Triacylglycerols into fatty acids and glycerol
-bacteria can help clean up oil spills (some bacteria use oil as carbon source)
Fatty acid can also be broken down to Acetyl CoA (though Beta oxidation) which can be used in Krebs cycle and Glycerol can be broken down to substrates of Gylcolysis (DHAP (dihydroxyacetone phosphate) , G3P (glycerladheyde 3-phosphate) to undergo glycolysis form pyruvic acid.
(Triacylglycerols: 1 glycerol and 3 fatty acids)
91
What occurs in Protein Catabolism?
Protein Catabolism:
- 1) Describes how extracellular proteases/peptidases break down proteins to Amino acids (also peptidases break down protein to peptides )
-These peptides and amino acids can then undergo
2) Deamination, Deacarboxylation, dehydrogenation, desulfylation, which will produce Sulfur, CO2 that will go to Glycolysis or Krebs cycle.
91
What occur
92
What occurs in the Catabolism of Organic Food Molecules?
Catabolism of Organic food Molecules:
Proteins are broken down to amino acids which can combine with pyruvic acid (from glycolysis), acetyl CoA or Krebs cycle
-Carbohydrates can be broken down to sugars to tenter glycolysis and produce pyruvic acid--> Acetyl CoA--> Krebscyclol and then all the way to ETC.
-Lipids can also break down to glycerol, and fatty acids.
The glycerol can go back and be used for glycolysis; while fattyl acids broken down to Acetyl CoA for Krebs cycle.
93
What is purpose of biochemical tests?
Biochemical tests- used to identify different enzymes in bacteria.
- **tests ability to use or produce specific chemicals
- **can be used for bacterial identification
94
What is involved in a Fermentation test and how does it work?
Fermentation test;
Test medium contains protein, a single carbohydrate (mannitol in this experiment), a pH indicator and an inverted Durham tube (see if gas is produced from tube)
**This test is used to detect the presence of ACID production and GAS production which is indicative of fermentation of single carbohydrate (mannitol in this case) ***
SIDE NOTE:
(Process:
if acid is produced, it will reduce pH, causing pH indicator to turn yellow (yellow color indicates presence of acid)
-if durham tube starts to produce bubbles in tub, indicates gas is produced.
(mannitol is used for fermentation. Protein is used as alternative carbon source that bacteria will grow on if cannot ferment)
(in experiment, 4 cultures were used, including S. epidermis, S. aureus, E. coli) If tube is not yellow color or any bubbles, likely not ferment mannitol)
95
Describe the process of a protein Catabolism test
Protein Catabolism Test: used to look for DECARBOXYLATION of an amino acid
if you have an enzyme that can Remove the CO2 group from amino acid, there will only be AMINE group left, which will raise the pH. A purple indicator means the pH has been increased
Test medium contains glucose, a pH indicator and a specific amino acid
-indicator turns yellow when acid is produced from glucose (ferment glucose)
-Alkaline products from decarboxylation turn indicator purple
96
What is another Protein Catabolism Test that can occur when it comes to sulfur?
Protein Catabolism Test: used to ask whether a Sulfur group can be removed (Desulfurlyation)
(have cysteine (amino acid) that can be desulfurylated to form H2S)
-Test medium contains Peptone IRON agar
-If H2S is liberated, it combines with the iron in medium to form an iron sulfide
The iron sulfide is visualized as black predicate in the medium.
-bacteria will stab the iron agar
***readily distinguishes Salmonella species from E.coli
(only one of the organisms has that enzyme) ***
(peptone- animal protein that is digested with trypsin or pepsin to make peptide; bacteria use it as carbon source)
97
What occurs in a Urease Test?
Urease Test: Urea is broken down to NH3+ CO2
-Many gastrointestinal or urinary tract have pathogens produce urease, enabling the detection of urease to be used as a diagnostic to detect presence of pathogens
-In a positive test, bacterial urease hydrolyses urea producing ammonia . Ammonia raises the pH and the indicator in media turns pink/purple
98
What is Photosynthesis? What do the two words in photosynthesis mean?
Photosynthesis: The conversion of light energy into chemical energy (ATP)
-Synthesis: Fixing CO2 into organic. molecules
99
Differentiate between the Oxygenic and Anoxygenic photosynthesis. What do they have in common.
Oxygenic Photosynthesis: (plants, algae and Cyanobacteria) [ Photosystems I and II]; they produce O2, and electrons come from water.
6 CO2 + 12 H2O + Light energy is converted to C6H12O6 + 6 H2O + 6 O2
Anoxygenic (purple sulfur and green sulfur bacteria) [ Photosystem I only] ; this will NOT produce O2; will get electrons from H2S.
6 CO2 +12 H2S + Light Energy---> C6H12O6 + 6 H2O + 12S
In Both cases, electrons are taken from hydrogen atoms and incorporated into sugar.
100
What are the two stages of Photosynthesis?
Photosynthesis occurs in two stages:
Light Dependent reactions (photophosphorylation): light energy is used to convert ADP and P into ATP
Light Independent reactions (The Calvin-Benson Cycle): electrons and ATP are used to reduce CO2 to sugar.
101
What can Photophosphorylation also be classified as?
Photophosphorylation can also be classified as...
-Noncyclic photophosphorylation (oxygenic)
-Cyclic photophosphorylation (anoxygenic)
(photophosphorylation: process of phosphorylating ADP to ATP)
102
What occurs in Noncyclic Photophosphorylation? What molecules are involved?
Noncyclic Photophosphorylation:
-Photosystem II regains electrons by splitting water, leaving O2 gas as a by-product
-Electrons do NOT return to the chlorophyll, they incorporate into the NADPH
-Energy from electron transfer is converted to ATP and NADPH
When the photosystem absorbs a photon of light, it ejects a high energy electron
(although not illustrated, the proton gradient is only obtained when electrons flow from photosystem II to I)
103
Where is the proton gradient formed in Noncyclic Phosphorylation?
In Noncyclic Phosphorylation, the proton gradient forms in the Thylakoid interior space of choloroplast
104
What occurs in Cyclic phosphorylation?
In Cyclic phosphorylation:
-Electrons return to the bacteriochlorophyll
-As the electron is passed along the electron transport chain, energy is provided to produce a proton gradient across the membrane which can be used for the ADP to ATP conversion
-Favored in ANAEROBIC conditions
(Photosystem I will absorb photon of light, eject electrons that will pass down ETC and energy be converted to ATP and will also come back to bacteriochlorophyll)
105
How is the NADPH that is necessary for CO2-fixation generated? What happens with Purple and green Non-sulfur bacteria?
Purple and green SULFUR bacteria use electron donor that have a HIGHER reduction potential than NADPH (like H2S), a source of electrons to reduce NADP+ to NADPH
-Purple and Green NON-SULFUR bacteria obtain most (or all) their carbon from Organic compounds rather than fix CO2. (Phototropic, but not photosynthetic)
phototropic- use light energy to generate cellular energy (ATP)
photosynthetic: use light energy to generate nutrients, ATP form CO2 and water.
106
Explain what occurs in the The Calvin-Bension Cycle. what molecules are produced? where is the enzyme that produces Ribulose diphosphate (sugar) stored in?
Light Independent reactions; the Calvin-Benson Cycle
-A cyclic pathway in which **CO2 is "fixed"- used to synthesize sugars **
-3 turns of the cycle produces one glyceraldehyde-3-P
-6 turns is required to produce one glucose molecule
-1 glucose molecule requires 6 CO2, 18 ATP, and 12 NADPH.
(side note: 1 turn of cycle will use 6 co2, 9 ATP, and 6 NADPH )
The enzyme that produces Ribulose diphosphate is stored in CARBOXYSOMES
107
Explain how Microbes are distinguished?
Microbes are distinguished by their Great metabolic DIVERSITY
-Some can sustain themelseves on inorganic compounds that plants and animals Cannot use (H2, NH3, NO2, H2S, CO, Fe++)
108
How can all organisms be classified metabolically? Describe the different forms
by their Energy and Carbon sources
Energy
-Chemotrophs: Use energy from organic or inorganic compounds (chemicals)
-Phototrophs: Use light as primary energy source
Carbon:
-Autotrophs: Use CO2 for their principle carbon source
-Heterotrophs: Require an organic carbon source (feed on others)
109
Describe how Chemoheterotrophs obtain their energy source. How can chemoheterotrophs be further classified?
Chemoheterotrophs:
-Energy and carbon sources are not so easy to categorize because they are usually the same organic compound (ex: glucose)
- **Specifically, they use electrons from Hydrogen atoms in ORGANIC compounds as their energy source **
-Chemoheterotorphs can be further classified based on organic molecule source:
-Saprophyte; Live on DEAD organic matter
-Parasites: Derive nutrients from a living host
110
How do chemoautotrophs obtain their energy? What is an example of a microorganism who does this?
Chemoautotrophs:
-Use energy from reduced INORGANIC compounds (ex; H2, NH3, NO2, H2s, CO, Fe++)
-Thiobacillus ferrooxidans (obtains its energy source from oxidation of ferrous ions (Fe3+ and reduced sulfur compounds)
-Use the Calvin-Benson cycle to fix CO2 (self-feeder)
111
What are Photoheterotrophs? How do they obtain their energy source? What are examples?
Photoheterotrophs;
Use light as primary energy source
-CANNOT convert CO2 to sugar. Require an organic carbon source
-Green non sulfur bacteria and purple NONSULFUR bacteria (anoxygenic)
112
Differentiate between the two groups of photoautotrophs and discuss how they work
Two groups of photoautotrophs (based upon how CO2 is reduced)
-Oxygenic (cyanobacteria, algae and plants)
-electrons from water are used to generate NADPH and Oxygen is given off
-Anoxygenic (green and purple SULFUR bacteria)
-Anaeorobic bacteria that cannot use water to reduce CO2
-Instead use sulfur, sulfur compounds or H2 to generate NADPH to reduce CO2.
113
What distinguishes green and purple sulfur bacteria from each other?
Although BOTH use bacteriochlorophyll...
- green sulfur bacteria: located in vesicles called CHLOROSOMES underlying and attached to plasma membrane
-Purple sulfur bacteria: located in invaginations called CHROMATOPHORES.
***Distingusih by LOCATION of stored sulfur***
*** Distinguish by 16S rRNA sequence ***
(example: Rhodospirlum rubrum can grow chromatophores )
114
what are three membranes that are used in photosynthesis?
1) Thylakoid (for chlorophyll a)
2) Chlorosomes
3) Chromatophores
(Cyanobacteria: have choloropyll in thylakoids; Green and Purple bacteria use bacteriochlorophylls for chlorosomes and chromoatorphores (intracytoplasmic membranes)
115
Why are the sulfur bacteria called Green or purple? How do they actually appear?
They are called green or purple depending on their CARONTENOID content
- **Purple bacteria appear purple or reddish brown
- **Green bacteria appear as yellow green, green orange or brown*
116
What other names can autotrophs and heterotrophs be referred as? Almost all medically important microbes belong to which class?
Autotrophs are also referred to as LITHOTROPHS (rock eating)
Heterotrophs are also referred to as ORGANOTROPHS
-they belong to CHEMOHETEROTROPHS
117
Differentiate between Photoautotropoh, Photoheterotroph, chemoautotroph, and chemoheterotroph in terms of energy source, Carbon source and examples.
Nutritional type Energy source Carbon Source
-Photoautotroph Light CO2
Photoheterotorph. Light Organic compounds
Chemoautotroph Chemical. CO2
Chemoheterotroph Chemical. Organic compounds
Examples
Photoautotrophs:
Oygenic: Cyanobacteria plants; Anoxygenic: green, purple bacteria
Photoheterotrophs: Green, purple, non-sulfur bacteria
-Chemoautotrophs: iron-oxidizing bacteria
-Chemoheterotrophs: Fermentative bacteria, animals, protozoa, fungi, bacteria
118
During the complete oxidation of glucose to Co2 and H2O, how much energy is trapped in the bonds of ATP? How much is lost as heat?
55% goes to ATP and 45% is lost off as Heat.
119
Besides other production of new cellular components, what other cellular processes use this ATP?
Active Transport and Flagellar motion
120
What occurs in Polysaccharide Biosynthesis?
Polysaccharide Biosynthesis:
The carbon used to synthesize glucose is derived from intermediates produced during other processes (glycolysis, Krebs cycle, lipid, amino acids)
-ADPG (Adenosine diphosphoglucose) is the glucose that is stored as Glycogen in Bacteria
-UDPG (Uridine diphosphoglucose) is the glucose that is stored as glycogen in ANIMALS
both ADPG and UDPG stem from Glucose-6-phosphate in Glycolysis
-UDPNac (UDP-N-acetlyglucosamine) is stored as peptidoglycan in bacteria
This UDPNac stems from fructose-6-phospate in glycolysis
121
How are Polysaccharides used in the cell?
For cell wall synthesis, forming glyoclaylx, and LPS
122
What occurs in Lipid biosynthesis? What are the different types of lipids?
Lipid Biosynthesis
-Lipids vary considerably in composition and thus are synthesized by various routes.
- Simple lipids can be synthesized from intermediates like Acetyl CoA that will form Fatty acids and convert to lipids
- Glycerol from DHAP (dihydroxyacetone phosphate) in Pentose Phosphate pathway can also make simple lipids. In glycolysis: intermediates like G3P (glyeralddehyde 3 phosphate) can be converted to DHAP or be converted into Pyruvic acid to form acetyl CoA
hence DHAP can convert to Glycerol, and Acetly CoA can form fatty acids which both lead to formation of simple lipids
Types of lipids
-phospholipids
-Cholesterol (eukaryotic cells)
-Waxes (acid fast bacteria)
-carotenoids (pigments)
123
Describe the pathways of Amino acid Biosynthesis and how microbes are involved.
Pathways of Amino acid biosynthesis
-Some microbes can make all the amino acids from glucose and inorganic salts
-other microbes requires some preformed amino acids
Pathways:
The Pentose Phosphate Pathway can lead to formation of amino acids
-Acetyl CoA can be used in Krebs cycle to undergo Amination or transamination to forma amino acids
3) Entner-Duodoroff pathway (bacterial respiration (breakdown glucose to pyruvate) can also form amino acids.
124
Explain how Amination or transamination play a role in Amino acid Biosynthesis. Discuss the additional aminations that occur.
Amination or TRANSAMINATION of Krebs cycle intermediates
Transamination (transfer amino group to ketoacid to form a new amino acid)
-Glutamic acid + Oxaloacetate acid can undergo transamination to form alpha-ketoglutaric acid (CH2-CH2) and Aspartic acid (NH2)
in addition;
Transamination of pyruvate yields alanine
Transamination of aspartate yields asparagine
Transamination of Alpha-ketoglutarate yields glutamate
Transamination of Glutamate yields glutamine
125
what intermediates are seen in the Purine and pyrimidine Nucleotide Biosynthesis?
Purine and Pyrimidine Nucleotide Biosynthesis
1) Gylcolysis: Glucose 6-phosphate can go through the Pentose phosphate pathway or Entner-Duodoroff pathway to make Pentose (5-carbon sugar). This Pentose can then be converted to purine nucleotides and pyrimidine nucleotides
2) an intermediate named Phophoglyceric acid in glycolysis can also go through ED (Enter-Duodoroff) pathway and form glycine which will form purine nucleotide
3) The Krebs cycle can form Glutamine which are part of Purine nucleotides and also Aspartic acid which are part of pyrimidine nucleotides
(Purines: Adenine, Guanosine) Pyrimidines; (Cytosine, Thymine)
126
Explain how metabolism is integrated. What are Amphibolic pathways? What are examples of anabolic pathways?
The integration of Metabolism:
-Anabolic and catabolic reactions are integrated through a group of common intermediates
- Amphibolic pathways: Metabolic pathways that have both catabolic and anabolic functions (dual purpose)
examples: Glycolysis(anabolic pathway of ATP, lipids, amino acids; catabolic: break down of glucose ) and Krebs cycle (since they play role in catabolic (fatty acids, amino acids) and anabolic (amino acids, nucleotides)
KREBS Cycle: MAJOR amphibolic pathway
