Chapter 5 flashcards
The collection of controlled biochemical reactions that take place w/in the microbe
Metabolism
Metabolic processes are guided by eight elementary statements
1) Every cell acquires nutrients (the chemicals necessary for metabolism)
2) Metabolism requires energy from light or from the catabolism of acquired nutrients
3) Energy is stored in the chemical bonds of adenosine triphosphate (ATP)
4) Using enzymes, cells catabolize nutrient molecules to form elementary building blocks called precursor metabolites
5) Using precursor metabolites, energy from ATP, & other enzymes, cells construct larger building blocks in anabolic reactions
6) Cells use enzymes & additional energy from ATP to anabolically link building blocks together to form macromolecules in polymerization reactions
7) Cells grow by assembling macromolecules into their cellular structures such as ribosomes, membranes, and cell walls
8) Cells typically reproduce once they have doubled in size
What is the first step of metabolism
The active & passive transport of nutrients into cells
Involves the transfer of electrons between molecules
Oxidation-reduction reactions
What are organic catalysts?
Enzymes, they make metabolism possible
Metabolism can be divided into two major classes of reactions
Catabolism, and anabolism. A series of such reactions is called a pathway
Cells have catabolic pathways which?
Break larger molecules into smaller products
Cells have anabolic pathways which?
Synthesis large molecules from the smaller products of catabolism
When catabolic pathways break down large molecules they?
Release energy, that is catabolic pathways are exergonic. Cells store some of this released energy in the bonds of ATP, though much of the energy is lost as heat. Another result of the breakdown of large molecules by catabolic pathways is the production of numerous smaller molecules, some of which are precursor metabolites of anabolism
Some organisms, such as Escherichia coli, can synthesis everything in their cells just from?
Precurser metabolites; other organisms must acquire some anabolic building blocks from outside their cells as nutrients
Catabolic pathways, but not necessarily individual catabolic reactions, produce?
ATP or metabolites or both
The breakdown of lipids into glycerol and fatty acids is an example of
Catabolic pathways
Because building anything requires energy, anabolic pathways are?
Endergonic, that is they require more energy than they release. The energy required for anabolic pathways usually comes from ATP molecules produced during catabolism
The synthesis of lipids for cell membranes from glycerol & fatty acids is an example of?
An anabolic pathway
A cell’s metabolism involves both catabolic pathways that _____ _____ macromolecules to supply molecular building blocks & energy in the form of ATP, and anabolic pathways that use the _______ _______ and ATP to synthesis macromolecules needed for growth and reproduction.
break down
building blocks
What is an electron donor
A molecule that donates an electron
What is an electron acceptor
A molecule that accepts an electron
Many metabolic reactions involve the transfer of electrons from an?
Electron donor to an electron acceptor. These are called oxidation-reduction reactions or redox reactions
An electron acceptor is said to be?
Reduced. They are reduced because their gain in electrons reduces their overall electrical charge (they are more negatively charged)
Molecules that lose electrons are said to be
Oxidized because frequently their electrons are donated to oxygen atoms.
An acronym to help you remember oxidation-reduction reactions in OIL RIG
O- oxidation I- involves L- loss R- reduction I- involves G- gain
Reduction & oxidation reactions always happen simultaneously because?
Every electron donated by one chemical is accepted by another chemical
During oxidation-reduction reactions, a chemical may be reduced by?
Gaining either a simple electron or an electron that is part of a hydrogen atom (composed of one proton and one electron)
A molecule may be oxidized in one of three ways
1) By losing a simple electron
2) By losing a hydrogen atom
3) By gaining an oxygen atom
Biological oxidations often involve the loss of hydrogen atoms; such reactions are also called?
Dehydrogenation reactions
Electrons rarely exist freely in cytoplasm; instead, they orbit atomic nuclei. Therefore, cells use electron carrier molecules to?
Carry electrons (often in hydrogen atoms) from one location in a cell to another
Three important electron carrier molecules, which are derived from vitamins, are?
1) nicotinamide adenine dinucleotide (NAD+)
2) nicotinamide adenine dinucleotide phosphate (NADP+)
3) flavin adenine dinucleotide (FAD)
Cells use each of the three electron carrier molecules (NAD, NADP, & FAD) in specific metabolic pathways to carry pairs of electrons. one of the electrons carried by either NAD+ or NADP+ is part of a ______ atom, forming?
FAD carries?
Hydrogen atom forming NADH or NADPH.
FAD carries 2 electrons as hydrogen atoms (FADH2).
Many metabolic pathways, including those that synthesis ATP, require such electron carrier molecules
Nutrients contain energy, but that energy is spread throughout their chemical bonds & generally is not concentrated enough for use in anabolic reactions. How do we get this energy?
During catabolism, organisms release energy from nutrients that can be concentrated & stored in high-energy phosphate bonds of molecules such as ATP. This happens by a general process called phosphorylation, in which inorganic phosphate is added to a substrate. For example cells phosphorylate adenosine diphosphate (ADP), which has two phosphate groups, to form adenosine triphosphate (ATP), which has three phosphate groups
Cells phosphorylate ADP to form ATP in three specific ways
1) Substrate-level phosphorylation, which involves the transfer of phosphate to ADP from another phosphorylated organic compound
2) Oxidative phosphorylation, in which energy from redox reactions of respiration is used to attach inorganic phosphate to ADP
3) Photophosphorylation, in which light energy is used to phosphorylate ADP with inorganic phosphate
After ADP is phosphorylated to produce ATP, anabolic pathways use some energy of ATP by breaking a?
Phosphate bond (which re-forms ADP)
How does ATP molecules store energy?
ATP stores energy from light (in photosynthetic organisms) & from catabolic reactions & then release stored energy to drive cellular processes (including anabolic reactions, active transport, & movement). ADP molecules can be “recharged” to ATP again & again
In catabolic reactions, a bond must be?
Destabilized before it will break, whereas in anabolic reactions reactants collide with sufficient energy for bonds to form between them
In anabolism, increasing either the concentrations of reactants or ambient temperatures increases the number of collisions & produces more chemical reactions; however in living organisms, neither reactant concentration nor temp. is usually high enough to ensure that bonds will form. Therefore, the chemical reactions of life depend upon?
Catalysts, which are chemicals that increase the likelihood of a reaction but are not permanently changed in the process
The names of enzymes usually end with the suffix “ase”, and the name of each enzyme often incorporates the name of that enzymes?
Substrate, which is the molecule the enzyme acts upon.
Based on their mode of action, enzymes can be grouped into six basic categories
1) Hydrolases
2) Isomerases
3) Ligases, or polymerases
4) Lyases
5) Oxidoreductases
6) Transferases
Hydrolases catabolize molecules by?
Adding water in a decomposition process known as hydrolysis. Hydrolases are used primarily in the depolymerization of macromolecules
Isomerases rearrange the atoms within a?
Molecule bu do not add or remove anything (so they are neither catabolic nor anabolic)
Ligases, or polymerases, join?
Two molecules together (and are thus anabolic). They often use energy supplied by ATP.
Lyases split?
Large molecules (and are thus catabolic) without using water in the process
Oxidoreductases remove?
Electrons from (oxidize) or add electrons (reduce) various substrates. Used in both catabolic & anabolic pathways
Transferases transfer?
Functional groups, such as an amino group, a phosphate group, or a two-carbon (acetyl) group, between molecules. Can be anabolic
Many protein enzymes are complete in themselves, but others are composed of both protein & nonprotein portions. The proteins, called _______, are inactive if they are not bound to one or more of the nonprotein substances called _______
apoenzymes
cofactors
What are cofactors?
Either organic ions (such as iron, magnesium, zinc, or copper ions) or certain organic molecules called coenzymes.
All coenzymes are either?
Vitamins or contain vitamins, which are organic molecules that are required for metabolism but cannot be synthesized by certain organisms (like mammals)
Some apoenzymes bind with inorganic cofactors, or coenzymes, or both. The binding of an apoenzyme & its cofactor(s) forms an active enzyme, called a?
holoenzyme
Not all enzymes are proteinaceous; some are RNA molecules called?
Ribozymes
In eukaryotes, ribozymes process other RNA molecules by removing?
Sections of RNA & splicing the remaining pieces together.
Within cells, enzymes catalyze reactions by?
Lowering the activation energy, which is the amount of energy needed to trigger a chemical reaction.
Heat can provide energy to trigger reactions, the temps. needed to reach activation energy for most metabolic reactions are often too high to allow cells to survive, so what is needed?
Enzymes are needed if metabolism is to occur. This is true regardless of whether the enzyme is a protein or RNA, or the chemical reaction is anabolic or catabolic
The activity of enzymes depends on the?
Closeness of fit between functional sites of an enzyme & its substrate
The shape of an enzymes functional site, called its _____ ____, is complementary to the shape of the?
active site
substrate
What determines the shape of an enzyme’s active site
The shapes & locations of only a few amino acids or nucleotides. A change in a single component (mutation) can render an enzyme less effective or even completely nonfunctional
Enzyme-substrate specificity is critical to enzyme activity & has been likened to the fit between a?
lock & key. This analogy is not completely apt, because enzymes change shape slightly when they bind to their substrate, almost as if a lock could grasp its key once it had been inserted. This description is called the induced-fit model
In some cases, several different enzymes possess active sites that are complementary to various portions of a single substrate molecule. For example, the precursor metabolite called phosphoenolpyruvic acid (PEP) is the substrate for at least 5 enzymes, and depending on the enzyme involved, various products are produced from PEP. In one catabolic pathway, PEP is converted to pyruvic acid, whereas in a particular anabolic pathway, PEP is converted to the amino acid ____________
Phenylalanine
How do enzymes lower activation energy?
The exact ways are not known, it appears that several mechanisms are involved. Some appear to bring reactants into sufficiently close proximity to enable a bond to form, whereas others change the shape of a reactant, including a bond to be broken. Enzymes increase the likelihood that bonds will form or break
Many factors influence the rate of enzymatic reactions, including?
Temperature, pH, enzyme & substrate concentrations, & the presence of inhibitors
Higher temps. tend to do what to most chemical reactions?
What about enzymes?
Increase the rats of most chemical reactions because molecules are moving faster & collide more frequently, which encourages bonds to form or break. This isn’t entirely true of enzymatic reactions, because the active site of enzymes change shape as temp. changes. If the temp. rises too high or falls too low, an enzyme is often no longer abel to achieve a fit with its substrate
Each enzyme has an optimal temp. for its activity.
The optimum temperature for the enzymes in the human body is 37 degrees C which is normal body temp.
Organisms that grow best at temperatures above 80 degrees C
Hyperthermophiles
If temps. rises beyond a certain critical point, the non covalent bonds within an enzyme (such as the hydrogen bonds between amino acids) will break, & the enzyme will?
Denature
Denatured enzymes lose their?
Specific three-dimensional structure, so they are no longer functional
Denaturation is said to be permanent when?
An enzyme cannot regain its original three-dimensional structure once conditions return to normal, much like the irreversible solidification of the protein albumin when egg whites are cooked & then cooled
When is denaturation reversible?
The denatured enzyme’s non covalent bonds reform upon the return of normal conditions
Extremes of pH also denature enzymes when?
Ions released from acids & bases interfere with hydrogen bonding and distort and disrupt an enzymes secondary and tertiary structures. Therefore each enzyme has an optimal pH
Changing pH provides a way to control the growth of unwanted microorganisms by?
Denaturing their proteins. For example, vinegar acts as a preservative in dill pickles, and ammonia can be used as a disinfectant
Another factor that determines the rate of enzymatic activity within cells is the concentration of substrate present
As substrate concentration increases, enzymatic activity increases as more & more enzyme active sites bind more and more substrate molecules. When all enzyme active sites have bound substrate, the enzymes have reached their saturation point, and the addition of more substrate will not increase the rate of enzymatic activity
The rate of enzymatic activity is also affected by the concentration of enzyme within cells. One way that organisms regulate their metabolism is by controlling the quantity & timing of enzyme synthesis. Explain
Many enzymes are produced in the amounts & at the times they are needed to maintain metabolic activity.
Eukaryotic cells control some enzymatic activities by?
Compartmentalizing enzymes inside membranes so that certain metabolic reactions proceed physically separated from the rest of the cell. For example, white blood cells catabolize phagocytized pathogens using enzymes packaged within lysosomes
Enzymatic activity can be influenced by a variety of inhibitory substances that block an enzyme’s active site. Enzymatic inhibitors, which may be either _________ or _________, do not _______ enzymes
competitive or noncompetitive
denature
What are competitive inhibitors?
They are shaped such that they fit into an enzyme’s active site & thus prevent the normal substrate from binding. Such inhibitors do not undergo a chemical reaction to form products. They can bind permanently or reversibly to an active site. Permanent binding results in permanent loss of enzymatic activity; reversible competition can be overcome by an increase in the concentration of substrate molecules, which increases the likelihood that active sites will be filled with substrate instead of inhibitor
What are noncompetitive inhibitors?
Do not bind to the active site but instead prevent enzymatic activity by binding to an allosteric site located elsewhere on the enzyme. Binding at an allosteric site alters the shape of the active site so that substrate cannot bound.
Allosteric control of enzyme activity can take two forms
Inhibitory and excitatory
Excitatory allosteric control, the binding of certain activator molecules (such as a heavy-metal ion cofactor) to an allosteric site causes?
A change in shape of the active site, which activates an otherwise inactive enzyme
Some enzymes have several allosteric sites, both inhibitory and excitatory, which allows?
Their function to be closely regulated
Cells often control the action of enzymes through feedback inhibition (also called negative feedback or end-product inhibition). Allosteric feedback inhibition functions in much the same way a thermostat controls a heater, explain.
As the room gets warmer, a sensor inside the thermostat changes shape & sends an electrical signal that turns off the heater. Similarly, in metabolic feedback inhibition, the end-product of a series of reactions is an allosteric inhibitor of an enzyme in an earlier part of the pathway. Because the product of each reaction in the pathway is the substrate for the next reaction, inhibition of the first enzyme in the series inhibits the entire pathway, thereby saving the cell energy
