Chapter 8- Microbial metabolism Flashcards
Metabolism
Describes all of the chemical reactions inside a cell
Exergonic reactions
Reactions that are spontaneous and release energy
Endergonic reactions
Reactions that require energy to proceed
Anabolism
Refers to endergonic metabolic pathways involved in biosynthesis, where simple molecular building blocks are converted into complex molecules, through the use of cellular energy. Molecular energy is stored in the bonds of complex molecules and can be harvested to produce high energy molecules that are used to drive anabolic pathways
Catabolism
Refers to exergonic pathways that break down complex molecules into simpler ones. Molecular energy is stored in the bonds of complex molecules and is released in catabolic pathways
Autotrophs
Organisms that convert inorganic carbon dioxide into organic carbon compounds. Plants and cyanobacteria are examples
Heterotrophs
Use complex organic carbon compounds as nutrients, which are provided to them by autotrophs. This includes many organisms, like humans and many prokaryotes like E. coli
Phototrophs
Organisms who use light as their energy source. They get their energy from electron transfer from light
Chemotrophs
Obtain energy for electron transfer by breaking chemical bonds. Includes organotrophs and lithotrophs
Organotrophs
Chemotrophs that obtain energy from organic compounds. Humans, fungi, and many prokaryotes are examples
Lithotrophs
Chemotrophs that get energy from inorganic compounds, like hydrogen sulfide and reduced iron. Only microbes get their energy this way
Oxidation reactions
Reactions that remove electrons from donor molecules- this means the donor molecules are oxidized. Transferring energy in the form of electrons allows energy to be transferred incrementally
Reduction reactions
Reactions that add electrons to acceptor molecules, reducing them
Redox reactions
Electrons move from one molecule to another, so oxidation and reduction occur together. These pairs of reactions are called oxidation-reduction reactions
Electron carriers
A class of compounds that bind to and shuttle high energy electrons between compounds in pathways. The 3 main electron carriers are from the B vitamin group and are derivatives of nucleotides. They include nicotinamide adenine dinucleotide (NAD), nicotine adenine dinucleotide phosphate (NADP), and flavin adenine dinucleotide (FAD).
NAD+/NADH
The most common mobile electron carrier used in catabolism. NAD+ is the oxidized form of the molecule, NADH is the reduced form of the molecule. It is typically used in energy extraction from sugars during catabolism in chemoheterotrophs
NADP+/NADPH
NADP+ is the oxidized form of an NAD+ variant that contains an extra phosphate group. It is another important electron carrier than forms NADPH when reduced. It plays an important role in anabolic reactions and photosynthesis
FAD/FADH2
FAD is the oxidized form and FADH2 is the reduced form. It is typically used in energy extraction from sugars during catabolism in chemoheterotrophs
Adenosine triphosphate (ATP)
Used as the energy currency of the cell. Living cells use ATP to safely store energy released during catabolism and release it for use as needed.
Adenosine monophosphate (AMP)
A molecule located at the heart of ATP. It is composed of an adenine molecule bonded to a ribose molecule and a phosphate group. Ribose is 5 carbon sugar found in RNA, and AMP is one of the nucleotides in RNA
Adenosine diphosphate (ADP)
A molecule formed when a second phosphate group is added to AMP. Adding a phosphate group is done through a process called phosphorylation, which requires energy
High energy phosphate bonds
Phosphate groups are negatively charged and therefore repel one another when they are arranged in series, like they are in ATP and ADP. This makes ATP and ADP inherently unstable, so the bonds between the phosphate groups are considered high energy
What happens when the high energy phosphate bonds are broken?
When one phosphate is released, it is considered inorganic phosphate. Two connected phosphate groups, called pyrophosphate, can also be released from ATP in the process called dephosphorylation. During dephosphorylation, energy is released to drive endergonic reactions
Catalysts
A substance that helps speed up a chemical reaction. Catalysts are reusable because they are not used or changed during reactions
Enzymes
Proteins that act as catalysts for biochemical reactions inside cells. They play a role in controlling cellular metabolism
Activation energy
The energy needed to form or break chemical bonds and convert reactants to products. Enzymes work by lowering the activation energy of a chemical reaction, by binding to reactant molecules and holding them in a way that speeds up the reaction
Substrates
The chemical reactants that an enzyme binds to
Active site
The location within the enzyme where the substrate binds
Induced fit of an enzyme
The amino acids near an enzyme’s active site create a specific chemical environment that makes it suitable for a substrate to bind. This makes an enzyme very specific. When an enzyme binds to the substrate, the structure of the enzyme changes slightly to create a good fit between the intermediate (transition) state and the the active site. The enzyme essentially molds itself to fit the substrate. There is a specifically matched enzyme for each substrate and therefore each chemical reaction, but some enzymes can act on several different structurally related substrates
How does temperature influence enzyme activity?
Increasing temperature can increase reaction rates, but high temperatures can cause enzymes to denature. Increasing or decreasing the temperature outside of a specific range can affect the chemical bonds within the active site, making them less likely to bind to substrates
How does pH influence enzyme activity?
Enzymes function best in a certain pH range. If the pH is too acidic or basic, the enzyme can denature. Amino acid side chains have acidic or basic properties that are best for catalysis, so they are sensitive to pH changes
How does substrate concentration influence enzyme activity?
Enzyme activity increases when the concentration of substrates is higher. Activity will increase until it reaches a saturation point, where there is no more substrate for the enzyme to bind to. Enzymes are optimized to work best in the conditions that their organisms live. Human enzymes work best at 37 degrees Celsius
Cofactors and coenzymes
Cofactors are inorganic ions like iron and magnesium that help stabilize enzyme conformation and function. DNA polymerase, which helps build DNA molecules, requires a zinc ion to function. Coenzymes are reusable organic helper molecules that are required for enzymes to function. Dietary vitamins are examples
Apoenzyme
An enzyme that lacks a necessary cofactor or coenzyme, and is therefore inactive. An apoenzyme becomes a holoenzyme once it’s bound to a cofactor or coenzyme.
Holoenzyme
An enzyme with a necessary associated cofactor or coenzyme, which is therefore active. It is able to bind to a substrate
Competitive inhibitor
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. The inhibitor concentration needs to be about equal to the substrate concentration for it to be effective. Sulfa drugs are one example. They bind to the active site of an enzyme in the bacterial folic acid synthesis pathway, blocking folic acid synthesis. Bacteria can’t grow because the need folic acid to make DNA, RNA, and proteins. Humans aren’t affected because we get folic acid from our diets
Allosteric site
A location on an enzyme other than an active site
Noncompetitive (allosteric) inhibitor
Binds to the enzyme at an allosteric site and still manages to block substrate binding at the active site by inducing a conformational change. This reduces the affinity of the enzyme for its substrate. Only one inhibitor molecule is needed for effective inhibition of the enzyme, so the concentration of inhibitors needed for allosteric inhibition is lower than the concentration needed for competitive inhibition
Allosteric activators
Bind to locations on an enzyme other than the active site, inducing a conformational change that increases the affinity of the enzyme’s active site for the substrate
Feedback inhibition of enzyme activity
Involves the use of a pathway product to regulate its own further production. When the cell senses an abundance of specific products, it slows down production during anabolic or catabolic reactions. Allosteric control is an important mechanism used to accomplish this.
