Microbial Metabolism Flashcards
,What is metabolism?
Metabolism: The sum of the chemical reactions that occur in an organism to sustain life
Differentiate between Catabolism and Anabolism
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
What kind of reactions are Catabolic reactions? What do they involve and what are some examples?
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
Why are catabolic reactions necessary for anabolic reactions?
Catabolic reactions provide the Building Blocks and Energy needed for anabolic reactions
What kind of reactions are anabolic reactions? Discuss what they involve and provide examples.
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
What couples Anabolic and Catabolic reactions? Explain how the chemical composition of cell changes.
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
What is the Metabolic pathway and what are their roles?
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
What is Collision theory and what are the different types of collisions that occur?
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)
What 3 factors determine whether a chemical reaction will occur from the collision?
- Velocity of colliding particles (temp)
- Level of energy required for the chemical reaction
- orientation of colliding particles
What is Activation energy?
Activation energy: The amount of collision energy necessary for a chemical reaction
What is reaction rate? How can you increase reaction rates in a test tube?
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)
How do enzymes affect activation energy and reaction rate in biological systems? Why is this ability critical in living systems?
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)
What is an enzyme? Define its characteristics
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)
Explain how enzymes increases ability for successive reaction
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)
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?
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
What is Turnover number/frequency/rate?
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+ )
How are enzymes named? Describe the six classes of enzymes and the types of reactions they catalyze
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)
What are the components of a Holoenzyme? What is a coenzyme, cofactor?
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.
List the different types of coenzymes/organic cofactors and Inorganic cofactors
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)
Explain the mechanism of Enzymatic Action. What allows the release of products?
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
What is the induced fit model and why is it significant?
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.
What are factors that influence enzyme activity?
-Temperature
-pH
-Substrate concentration
-inhibitors
Explain how temperature affects the enzyme. What is denaturation? What temperature decreases reaction rate
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.
What other conditions will denature proteins? Is denaturation partially or fully reversible?
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
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.
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
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
How are enzyme inhibitors classified?
Enzyme inhibitors classified as either..
-Competitive inhibitors
-Non-competitive inhibitors
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)
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)
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)
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)
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)
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
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
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
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.
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*
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)
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.
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
-
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
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.
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.
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)
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)
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)
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
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.
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”
