Metabolism Flashcards
What are the essentials for all microorganisms?
-Hydrogen
-carbon
-nitrogen
-oxygen
-phosphorus
-sulfur
-selenium
What are the types of energy sources?
-chemical = chemotrophy
-light = phototrophy
What are the types of chemical (chemotrophy) source?
-chemoorganotrophs
-chemolithotrophs
chemoorganotrophs
uses organic compounds
chemolithotrophs
uses inorganic chemicals
What is a type of light (phototrophy) source? and what does it produce?
-phototroph (light)
-produces ATP
Catabolic reaction (catabolism)
Breaking down available nutrients to extract energy and to provide simple organic building blocks for synthesizing new cell components.
Anabolic reactions (anabolism)
using simple organic building blocks to produce more complex components = biosynthesis
What increases a rate of a biological reaction?
Enzymes
Enzymes
-are NOT consumed or altered in the reaction
-do NOT determine the direction of the reaction
-increase the frequency of the substrate reaching the transition state
-have an active site
-may undergo a conformational change during catalysis
Lysozyme
-kills bacteria
-found in saliva
Lysozyme and Peptide pathway
- Substrate is bound to enzyme active site
- enzyme substrate complex form
-when it binds it bends - Strain is placed on bond
- products are released
- enzyme is ready to begin new catalytic cycle
What might enzymes have?
a prosthetic group
Prosthetic Group
-covalently bound to enzyme
-heme and Fe-S cluster never come off
Coenzymes
-move between enzymes and are recycled
-NAD+
-FAD
-coenzyme A
The electron donor becomes…
oxidized
The electron acceptor becomes…
reduced
A reducing agent (or reductant) donates electrons and becomes…
oxidized
An oxidizing agent (or oxidizer) accepts electrons and becomes…
reduced
Frequently, donors release not only electrons but also … and acceptors receive both electrons and …
protons
The Redox Tower
-all electrons have reduction potentials
-A donor can only give up electrons to an acceptor that is lower on the redox tower than itself
-Energy is released in the transfer
-An acceptor in one reaction can be a donor in another
In the cell, electron transfer are generally facilitated by electron carries
-NAD+ (NADP+ is the same but with an extra phosphate)
-FAD+
-These are coenzymes that interact with enzymes that catalyze redox reactions, accept electrons and can then diffuse to another site in the cell and donate electrons to an acceptor that is lower on the redox tower
NAD+ reduction steps
- enzyme 1 reacts with e- donor and oxidized from coenzyme, NAD+
- NADH and reaction product are formed
- enzyme 2 reacts with e- acceptor and reduced form of coenzyme, NADH
- NAD+ is released
What does this mean ~ ?
anhydride bond
Is ATP a high energy source?
Yes
What does the transfer of a high energy phosphate bond form?
A biochemical intermediate to ADP, forming ATP
What are the two ways to make ATP?
-substrate-level phosphorylation
-oxidative phosphorylation
What does PMF stand for?
proton motor force
Can a cell exists with a hole in its membrane?
No
Oxidative Phosphorylation
the production of ATP from a proton motive force that is formed by electron transport reactions driven by the oxidation of an electron and reduction of an external electron acceptor
Substrate-level Phosphorylation
the production of ATP by the direct transfer of an energy-rich phosphate molecule from a phosphorylated organic compound to ADP
Glycolysis/Embden - Meyerhof Pathway
-glucose catabolism
-parts of the pathway occur in ALL living cells
-This process does not require oxygen
-Glycolysis produces energy (ATP and reduced coenzymes) AND essential precursor molecules for biosynthesis pathways
-net 2 ATP via substrate level phosphorylation
Glycolysis Products
-Yeast = Glucose -> 2 ethanol +2CO2
-Lactic Acid = glucose -> 2 lactate
Recycling reduction coenzymes: Method #1: Fermentation
-permits recycling of reduced coenzymes
-requires no electron transport chain (no external electron acceptors)
-produces commercially useful products
What MUST organisms do if they do not have a good terminal electron acceptor (like O2)? (this is frequently under anaerobic conditions)
recycle reduced coenzymes by fermentation
How much ATP is yielded from catabolism of glucose with fermentation?
2
How much ATP is yielded from catabolism of glucose with aerobic respiration?
-36-38 ATP
-going in an oxygen rich atmosphere can be very useful.
What is first step in the glucose metabolism in the present of oxygen?
- the citric acid cycle (CAC) begins when the two-carbon compound acetyl-CoA condenses with the four-carbon compound oxaloacetate to form the six-carbon compound citrate
What is second step in the glucose metabolism in the present of oxygen?
- Through a series of oxidations and transformations, citrate is ultimately converted back to the four-carbon compound oxaloacetate, which then begins another cycle with addition of the next molecule of acetyl-CoA
What is third step in the glucose metabolism in the present of oxygen?
two redox reactions occur but no CO2 is released from succinate to oxaloacetate
What is fourth step in the glucose metabolism in the present of oxygen?
Oxaloacetate can be made from C3 compounds by the addition of CO2.
Electron Transport Chain
-electrons enter the chain from a primary electron donor
-when FMNH2 reduces an Fe/S protein (an electron-only carrier) protons are extruded
-electrons exit the chain by reducing the terminal electron acceptor (O2)
What are the 5 principles of electron transport chain and respiration?
- oxidize and recycle NAD and FAD
- Electrons and protons move DOWN the redox tower
- E- carries are quinones, cytochromes, iron-sulfur proteins FMN, Fe S, and Hemes are protein prosthetic groups
- Protons are moved from the inside to the outside GENERATE PMF!
- O2 is the terminal electron acceptor, produces water
Electron/Proton Carries
-Coenzymes (NAD+, NADP+, FAD+, Quinones)
-prosthetic groups
-accept and donate electrons/or protons
What are examples of prosthetic groups?
-FMN= flavin mononucleotide
-Heme, a porphyrin, contains iron, found in cytochrome proteins
-FeS cluster = iron sulfur clusters, found in complex 1 and 3
ATP synthase: F0 and F1
-movement of protons DOWN the gradient (from outside to inside) provides the energy for synthesis of ATP.
-The enzyme is often called “ATPase” because it was first discovered an enzyme present in cell extracts that could break down ATP. The reaction is reversible.
-cells that only carry out fermentation run this reaction in reverse to generate PMF
Where are F0 and F1 found?
-F0 is found in the membrane
-F1 is found in the cytoplasm
Glycolysis
-Glucose -> pyruvate (ATP via substrate -level)
-Pyruvate -> Fermentation or CO2
-Pyruvate -> Fermentation (fermentation products acids or alcohols)
-Pyruvate -> CO2 (TCA cycle and respiration)
Energy Production
-substrates -> catabolism -> exergonic reaction
-ATP -> proton motive force (and substrate level phosphorylation)
-Monomers -> Anabolism (Biosynthesis) -> Macromolecules and other cellular constituents
Catabolism
energy generation
Anabolism
energy consumption
exergonic reaction
produce energy
endergonic reaction
use energy
Anabolic Metabolism = Biosynthesis
-biosynthesis of sugar (and polysaccharides), amino acids (and proteins), nucleotides (nucleic acid) and fatty acids (and lipids)
Anabolic Metabolism = Biosynthesis (Sugars)
-biosynthesis of sugars
-not all organisms grown on sugar sources
Anabolic Metabolism = Biosynthesis (amino acids)
-biosynthesis of amino acids
-Transaminases = move amino groups between molecules
-citric acid cycle = glutamate and aspartate family
-glycolysis = aromatic family
Anabolic Metabolism = Biosynthesis (nucleotides)
-carbon and nitrogen atoms from amino acids
-single carbons from CO2 and folic acid (a vitamin that cycles single carbons for this purpose)
Anabolic Metabolism = Biosynthesis (fatty acids)
-ACP = acyl carrier protein, the carrier on which the fatty acid is built
-the reaction is repeated, lengthing the chain by 2 c in each step
-The 16 c chain is eventually transferred to glycerol to produce the lipid
