Unit 2 Flashcards
Metabolism
The sum of all chemical reactions within a living organism.
*Can be viewed as an energy-balancing act.
Role of an Enzyme
Enzyme catalyzes reaction for specific molecule called substrate, producing new products.
*This means enzymes accelerate (bio)chemical reactions BY lowering their activation energy AND increasing the number of reactants that attain sufficient activation energy to react AT a temperature compatible with the normal functioning of the cell.
Role of a Cofactor/ Coenzyme (nonprotein component required for the activation of an apoenzyme)
Cofactors can help catalyze a reaction by forming a bridge between an enzyme and its substrate.
Coenzyme may assist the enzyme by accepting atoms removed by the substrates.
Catabolism (Exergonic)
The breakdown of macromolecules into simple component parts, releasing energy.
*Catabolic reaction are hydrolytic reactions (reactions which use water and in which chemical bonds are broken), and they PRODUCE MORE energy than they consume.
Anabolism (Endergonic)
The building of macromolecules by combining simpler molecules, using energy.
*Anabolic reactions involve dehydration synthesis reaction (reactions that release water), and they CONSUME MORE energy than they produce.
Example of anabolic/ biosynthetic reactions:
The formation of proteins from amino acids, nucleic acids from nucleotides, and polysaccharides from simple sugars.
Example of an catabolic/ degradative reaction:
The process in which cells break down sugars into carbon dioxide and water.
(activation energy)
the energy needed to disrupt the stable electronic configuration of any specific molecules so that the electrons can be rearranged.
NAD+ (nicotinamide adenine dinucleotide) & NADP+ (nicotinamide adenine dinucleotide phosphate)
These are coenzymes and derivatives of the B vitamin niacin (nicotinic acid). Both function as electron carriers.
NAD+ involved in catabolic (energy-yielding) reactions, NADP+ involved in anabolic (energy-requiring) reactions.
The mechanism of enzymatic action
1) The substrate will bind to the enzyme at the active site
2) A temporary intermediate compound forms, called enzyme-substrate complex. The enzyme orients the substrate into a position that increases the probability of reaction, which enables the collisions to be more effective
3) The substrate molecule is transformed by the rearrangement of existing atoms, the breakdown of the substrate molecule, or in combination with another substrate molecule.
4) The transformed substrate molecules, the products of the reactions, are released from the enzyme because they are no longer fit in the active site
5) The unchanged enzyme are now free to react with other substrate molecules.
List the factors that influence enzymatic activity
1) Temperature:
- Elevation beyond the optimal temperature drastically reduces the rate of reaction because of the enzyme’s denaturation, the loss of its characteristic three-dimensional structure (tertiary configuration).
2) pH
- Extreme change in pH can cause enzyme’s denaturation.
3) Substrate Concentration
- Under conditions of high substrate concentration, an enzyme is said to be in saturation (active site is always occupied). On the other hand, many of the enzyme molecules are inactive for lack of substrate.
4) Inhibitors
- Two types of inhibitors that bind to enzymes, preventing the interaction with the substrates (or slow it down): Competitive inhibitors and Noncompetitive inhibitors.
Competitive inhibition
The filling of competitive inhibitor in the active site of the enzyme, preventing further interaction with the substrate
Noncompetitive inhibition
The binding of the noncompetitive inhibitor to the site other than the substrate’s binding site (allosteric sites). This binding causes the active site to change its shape, making it nonfunctional.
Feedback inhibition
Inhibition of an enzyme in a particular pathway by the accumulation of the end-product of the pathway; also called end-product inhibition.
Oxidation (loss of e-)
The removal of electrons (e-) from an atom or molecule, a reaction that often produces energy.
- Often involved with the removal of H+ (or proton) and e-
- Molecule A has undergone oxidation (meaning that it has lost one or more electrons)
Reduction (gain of e-)
The gaining of electrons of an atom or molecule, requiring energy (?)
- Often involved in the gaining of H+ and e- (?)
- Molecule B has undergone reduction (meaning that it has gained one or more e-)
(phosphorylation)
the addition of P (a phosphate group) to a chemical compound
Substrate-level phosphorylation
- ATP is generated when a high-energy (P) is directly transferred from a phosphorylated compound (a substrate) to ADP.
- Generally, the (P) has acquired its energy during an earlier reaction in which the substrate itself was oxidized.
Oxidative phosphorylation
- Electrons are transferred from organic compounds to one group of electron carriers. Then electrons are passes through a series of different electrons carriers to molecules of oxygen or other oxidized inorganic or organic molecules.
- The sequence of electron carriers used in oxidative phosphorylation is called an electron transport chain (system).
Distinguish Cellular respiration & Fermentation
Cellular respiration:
- require O2
- undergo Krebs Cycle and the electron transport chain
- 38 ATP is produced from one glucose molecule
- final electron acceptor is O2
Fermentation:
- does not require O2
- does not require the use of the citric acid (Krebs) cycle or an electron transport chain
- 2 ATP is produced only during glycolysis
- final electron
acceptor is an organic molecule (pyruvic acid)
- Fermentation reaction on its own does NOT generate ATP
Cellular respiration
- Glycolysis produces ATP and reduces NAD+ to NADH while oxidizing glucose to pyruvic acid.
=> In respiration, the pyruvic acid is converted to the first reactant in the Krebs Cycle, acetyl CoA - The Krebs cycle produces some ATP by substrate-level phosphorylation, reduced the electron carriers NAD+ and FAD, and gives off CO2.
=> Carriers from both glycolysis and the Krebs cycle donate electrons to the electron transport chain. - In the electron transport chain, the energy of the electrons is used to produce a great deal of ATP by oxidative phosphorylation.
- In respiration, the final electron acceptor (O2) comes from outside the cell.
Fermentation
- Does not require O2, but can occur in its presence.
- During glycolysis, a molecule of glucose is oxidized to two molecules of pyruvic acids. This oxidation generates the energy that is used to form the two molecules of ATP.
- In the second step, the reduced coenzymes from glycolysis (NADH) or its alternative (NADPH) donate their electrons and hydrogen ions to pyruvic acid or a derivative to form a fermentation end-product and reoxidize the NADH to be available for glycolysis.
@ Step 2 in Lactic acid fermentation:
- 2 molecules of pyruvic acid are reduced by two molecules of NADH to form 2 molecules of lactic acid, the end-product of the reaction.
@Step 2 in Alcohol fermentation:
- 2 molecules of pyruvic acid are converted to 2 molecules of acetaldehyde and 2 CO2. The two molecules acetaldehyde are reduced by 2 molecules of NADH to form 2 molecules of ethanol.
3 Principal stages of the respiration of glucose: 1) Glycolysis 2) Krebs Cycle 3) Electron Transport Chain (Need revision)
1) Glycolysis:
- The enzymes of glycolysis catalyze the splitting of glucose, a six-carbon sugar, into 2 three-carbon sugars. These sugars are then oxidized, releasing energy, and their atoms are rearranged to form 2 molecules of pyruvic acid. During glycolysis NAD+ is reduced to NADH, and there is a net production of two ATP molecules by substrate-level phosphorylation.
2) Krebs Cycle:
- (Pyruvate Oxidation)
Pyruvic acid is oxidized, losing 1 CO2 and becoming two-carbon compound. Two-carbon compound (acetyl group) then attaches to coenzyme A through a high-energy bond, resulting a complex known as Acetyl CoA.
- The Acetyl CoA enters the Krebs Cycle: Start with 2 acetyl CoA; end with 4 CO2, 6 NADH, 2 FADH2, and 2 ATP.
- All of the 6 C atoms in the glucose are released as CO2 by the Krebs Cycle.
3) Electron Transport Chain:
- Consists of a sequence of carrier molecules that are capable of oxidation and reduction. As electron are passed through the chain, there occurs a stepwise release of energy, which is used to drive the chemiosmotic generation of ATP.
Aerobic respiration v.s. Anaerobic respiration
- In aerobic respiration, O2 is the final electron acceptor.
- In anaerobic respiration, the final electron acceptor is an inorganic molecule other than O2 or, rarely, organic molecule.
The use of Biochemical test in bacterial identification
- Biochemical tests are designed to detect the presence of enzymes, and to identify bacteria that cause disease.
@One type of biochemical tests detects amino acid catabolizing enzymes involved in decarboxylation and dehydrogenation
@Another biochemical test is a fermentation test. The test medium contains protein, a single carbohydrate, a pH indicator, and an inverted Durham tube indicates gas formation.
@The oxidase test is used to detect the presence of an enzyme that oxidizes cytochrome c in bacteria. For example, Neisseria gonorrhoeae is positive for cytochrome oxidase, Pseudomonas is oxidase-positive, and Escherichia is oxidase-negative
@Use of peptone iron agar to detect the production of H2S, released when bacteria remove sulfur from amino acids.
Photosynthesis
- The conversion of light energy from the sun into chemical energy. Plants and many microbes synthesize complex organic compounds from simple organic inorganic compounds in the presence of sunlight.
6 CO2 + 12 H2O + light energy => C6H12O6 (glucose) + 6H2O + 6O2
2 Stages of Photosynthesis:
@ Light-dependent reactions (light reactions):
- Light energy is absorbed by chlorophyll molecules in the photosynthetic cell, exciting some of the molecules’ electrons. The excited electrons jump from the chlorophyll to the first of a series of carrier molecules. As electrons are passed along the series of carriers, protons are pumped across the membrane, and ADP is converted to ATP by chemiosmosis.
Electrons released from photosystem II and photosystem I will be incorporated into NADPH. The electrons lost from chlorophyll are replaced by electrons from H2O.
@light-independent reactions (dark reactions)
- 3 molecules of CO2 are fixed and one molecule of glyceraldehyde 3-phosphate is produced and leave the cycle. Two molecules of glyceraldehyde 3-phosphate are needed to make one molecules of glucose. The cycle turns 6 times for each glucose molecule produced, requiring a total investment of 6 molecules of CO2, 18 molecules of ATP, and 12 molecules of NADPH.
photosystems
Photosystem is a package of chlorophyll and other pigments in the thylakoids.
@ Photosystem II:
- contain chlorophyll that is sensitive to wavelength of light of 680 nm.
@ Photosystem I:
- contain chlorophyll that is sensitive to wavelength of light of 700 nm.
Phototrophs (Energy)
- Organisms that use light as their primary energy source
Chemotrophs (Energy)
- Organisms that depends on oxidation-reduction reactions of inorganic or organic compounds for energy.
Autotrophs (Carbon)
- (Self-feeder)_Organisms use carbon dioxide for carbon source
- Also referred to as lithotrophs (rock eating)
Heterotrophs (Carbon)
- (Feeders on others)_Organisms require an organic carbon source
- Also referred to as organotrophs
Photoautotrophs
- Use light as their source of energy and CO2 as a chief source of carbon.
Ex: photosynthetic bacteria, algae, and green plants.
Oxygenic photosynthesis
In the photosynthetic reactions, the hydrogen atoms of water are used to reduce carbon dioxide, and oxygen gas is given off.
* noncyclic phosphorylation
Anoxygenic photosynthetic
- Found in bacteria that cannot use H2O to reduce CO2 and cannot carry on photosynthesis when oxygen is present (must carry out in an anaerobic environment).
=> Consequently, their photosynthesis does not produce O2.
*Typical of cyclic phosphorylation
Parasite
An organism that derives nutrients from a living host
Aerobe
An organism that requires molecular O2 for growth.
Anaerobe
An organism that does not require molecular O2 for growth.
Saprophyte
Organism that live on dead organic matter
Parasite
Organism that derive nutrients from a living host
