Exam 2 Flashcards
Compare and contrast anabolic and catabolic reactions.
Anabolic reactions involve the building of larger, complex molecules from smaller, simpler ones, and require an input of energy. (requires energy, builds larger, complex molecules from smaller, simpler ones and forms chemical bonds between molecules)
Catabolic reactions are the opposite of anabolic reactions, and break the chemical bonds in larger, more complex molecules. (releases energy, breaks down large, complex molecules into smaller, simpler ones and breaks chemical bonds within molecules)
Describe the two ways energy harvested from catabolic reactions can be stored. Know the oxidized and reduced forms of NAD+/NADH and FAD/FADH2 and where the energy is store in the ATP molecule
Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules, which are used to drive anabolic pathways.
NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule.
The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2.
A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell.
This chemical energy is stored in the pyrophosphate bond, which lies between the last two phosphate groups of ATP.
Be able to explain the following enzyme related term: enzyme
Enzymes: major cellular catalysts
typically proteins (some R N A s)
highly specific as a result of structure
Be able to explain the following enzyme related term: substrate
in reaction, enzyme combines with reactant (substrate: chemical reactants of an enzymatic reaction), forming enzyme-substrate complex, releasing product and enzyme
Be able to explain the following enzyme related term: active site
active site: region of enzyme that binds substrate
Be able to explain the following enzyme related term: allosteric site
an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate.
allosteric site: location within an enzyme, other than the active site, to which molecules can bind, regulating enzyme activity
Describe how enzymes speed up reactions in terms of activation energy and how temperature and pH affect enzymes.
An enzyme functions by lowering the activation energy of a chemical reaction inside the cell. Activation energy is the energy needed to form or break chemical bonds and convert reactants to products. Enzymes lower the activation energy by binding to the reactant molecules and holding them in such a way as to speed up the reaction.
Enzymes are subject to influences by local environmental conditions such as pH, substrate concentration, and temperature. Although increasing the environmental temperature generally increases reaction rates, enzyme catalyzed or otherwise, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, losing their three-dimensional structure and function. Enzymes are also suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature. Active-site amino-acid side chains have their own acidic or basic properties that are optimal for catalysis and, therefore, are sensitive to changes in pH.
Some energy must be added to the system to get the reaction started:
Called activation energy
Increased temperature or inappropriate pH can denature enzymes.
Enzymes are essential to life so changes in temp or pH can kill organisms.
Explain how substrate concentration affects the rate of enzyme reactions.
substrate concentration: Enzyme activity is increased at higher concentrations of substrate until it reaches a saturation point at which the enzyme can bind no additional substrate. Overall, enzymes are optimized to work best under the environmental conditions in which the organisms that produce them live.
Substrate concentration: Increasing substrate concentration also increases the rate of reaction to a certain point. Once all of the enzymes have bound, any substrate increase will have no effect on the rate of reaction, as the available enzymes will be saturated and working at their maximum rate.
Compare and contrast competitive and non-competitive enzyme inhibitors. Describe feedback inhibition as an example of non-competitive inhibition.
competitive inhibitor is a molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding. For a competitive inhibitor to be effective, the inhibitor concentration needs to be approximately equal to the substrate concentration. Sulfa drugs provide a good example of competitive competition.
a noncompetitive (allosteric) inhibitor binds to the enzyme at an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate. Because only one inhibitor molecule is needed per enzyme for effective inhibition, the concentration of inhibitors needed for noncompetitive inhibition is typically much lower than the substrate concentration.
Feedback inhibition involves the use of a pathway product to regulate its own further production. The cell responds to the abundance of specific products by slowing production during anabolic or catabolic reactions.
Compare and contrast autotroph vs. heterotroph and phototroph vs. chemotrophs.
Autotrophs convert inorganic CO2 to organic compounds.
Heterotrophs get their carbon from complex organic compounds (often from autotrophs)
Phototrophs get their energy from electron transfer from light.
Chemotrophs get their energy from electrons by breaking chemical bonds
Identify organisms based on how they get carbon and how they get energy.
For chemotrophs, there are chemoautotrophs(energy: chemical, carbon: inorganic) [examples: Hydrogen-, sulfur-, iron-, nitrogen-, and carbon monoxide-oxidizing bacteria]or chemoheterotrophs(energy: chemical, carbon: organic compounds) [examples: All animals, most fungi, protozoa, and bacteria]
For phototrophs, there are photoautotrophs(energy: light, carbon: inorganic) [examples: All plants, algae, cyanobacteria, and green and purple sulfur bacteria] or photoheterotrophs(energy: light, carbon: organic compounds) [examples: Green and purple nonsulfur bacteria, heliobacteria]
Identify the three different types of ATP production.
A T P generated through 1 of 3 mechanisms
Substrate-level phosphorylation: energy-rich substrate bond hydrolyzed directly to drive A T P formation (e.g., hydrolysis of phosphoenolpyruvate)
Oxidative phosphorylation: Movement of electrons generates proton motive force (electrochemical gradient) used to synthesize A T P
Photophosphorylation: light used to form proton motive force
Compare and contrast aerobic respiration, anaerobic respiration, and fermentation.
Respiration:
Aerobic respiration:
Terminal acceptor is oxygen
Anaerobic respiration:
Alternative terminal electron acceptors
NO3-, SO4-2, CO2
Lower energy yields than O2
Fermentation (anaerobic):
Organic substrate for NADH oxidation
Low energy yield
Know the 4 phases of respiration, what goes in, what comes out, where it occurs, and if oxygen is required.
Four Phases:
Glycolysis: Energy is added to a glucose molecule by adding a phosphate group to each end.
Carbon-carbon bond is broken, 2 NAD+ are reduced, and 2 inorganic phosphates are added.
Phosphates are transferred from carbon to ADP to form ATP (staring material: glucose, products: 2 NADH, 2 ATP(net), and 2 pyruvate, this takes place in cytoplasm and no oxygen is required)
Transition reaction:
Starting materials: 2 pyruvate
Products:
2 NADH
2 CO2
2 acetyl CoA
Takes place in: Mitochondrial matrix
Oxygen required? YES
Krebs cycle (also known as Citric acid cycle or TCA cycle): Krebs Cycle
Starting materials: 2 acetyl CoA
Products:
4 CO2
6 NADH
2 FADH2
2 ATP
Takes place in: mitochondria
Oxygen required? YES
Electron transport chain:
Starting materials: NADH, FADH2, O2
Products: ATP:
3 from each NADH
2 from each FADH2
H2O
Takes place in: mitochondria
Oxygen required: yes
Understand the reasons organisms might use fermentation instead of respiration.
When certain organisms can’t do cellular respiration, they do glycolysis, followed by fermentation instead.
Many cells are unable to carry out respiration because of one or more of the following circumstances:
Lacking enough of any appropriate, inorganic, final electron acceptor to carry out cellular respiration. (TEMPORARY)
Lacking genes to make appropriate complexes and electron carriers in the electron transport system. (PERMENANT)
Lacking genes to make one or more enzymes in the Krebs cycle. (PERMENANT)
Understand the steps of fermentation starting with glycolysis.
Uses glycolysis to make 2 ATP, but then what?
Electron transport chain will not function to oxidize NADH as we have no oxygen
Make lactic acid from pyruvate
Accepts the electrons from NADH oxidizing it to NAD+
Now NAD+ is available for more rounds of glycolysis
What would happen if NAD+ is not regenerated?
If NAD was not regenerated for the Krebs cycle then there would be a collapse of the total energy obtained from the breakdown of fats, proteins and carbohydrates.
List other organic molecules that organisms can use besides carbohydrates.
Lipids:
Enzymes used to break down lipids can be part of disease progression
For example, Staphylococcus aureus uses phospholipases to attack host cells, then use the lipids for energy.
Proteins:
Enzymes used to break down protein can be part of disease progression
Pseudomonas aeruginosa has the ability to break down casein which helps identify it.
Be able to explain the 2 phases of photosynthesis, their reactants, products, and major steps.
Light-dependent reactions:
Energy from sunlight is captured by photopigments and stored as chemical energy.
The light-dependent reactions produce ATP and either NADPH or NADH to temporarily store energy. These energy carriers are used in the light-independent reactions to drive the energetically unfavorable process of “fixing” inorganic CO2 in an organic form, sugar.
Light-independent reactions:
Chemical energy from the light-dependent reaction is used to build sugar molecules from CO2
The light-independent reactions (Calvin cycle) use the chemical energy from the light-independent reactions and uses it to build CO2 into sugar.
CO2+H2O –> C6H12O6+O2
Know the difference between oxygenic and anoxygenic photosynthesis.
Oxygenic:
Water is source of e- and H+
O2 is released
Anoxygenic:
Compounds other than water are the electron and proton donor
Purple non-sulfur bacteria use dissolved organic material like succinate or malate or hydrogen gas
(1. Sunlight/energy
2. Light-dependent reactions
3. Light-independent reactions)
Understand how chemoautotrophs get their energy.
Chemoautotrophs get their energy from inorganic molecules instead of light.
Use the oxidation of reduced inorganic chemicals to generate energy
Hydrogen sulfide, ammonia, H2, ferrous iron, elemental sulfur
Often found in harsh environments.
