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126 Cards in this Set
- Front
- Back
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What is metabolism?
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the sum of all chemical reactions in an organism
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What is anabolism?
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building up macromolecules and their precursors - requires energy
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What is catabolism?
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breaking down nutrients - yields energy
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Anabolic Reactions
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-are involved in the building up of biological molecules (DNA, proteins, lipids, polysaccharides, and precursor molecules)
-produce the complex molecules that cytoplasm is made of -are involved with growth -consume energy in the form of ATP |
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Catabolic Reactions
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-release energy that is used to produce ATP
-are involved in the breaking down of complex molecules to yield simple molecules that the cell can use as synthetic raw material -pp 126-127 in book |
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What is chemoheterotrophy?
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energy and carbon derived from organic compounds
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Terminal electron acceptors in Aerobic Respiration
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oxygen
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Terminal electron acceptor in Anaerobic Respiration
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an oxidized mineral
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Terminal electron acceptor in Fermentation
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an organic compound
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What is the terminal electron acceptor?
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the oxidized compound that gets reduced by the energy-producing metabolic reactions
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What is photoautotrophy?
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energy from light, carbon from CO2
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What is the reaction for photosynthesis?
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6CO2 + 6H2O + light --> C6H12O6 + 6O
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What is chemoautotrophy?
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energy from inorganic redox reaction, carbon from CO2
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Types of metabolic reactions in chemoautotrophs
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iron oxidation
iron reduction sulfate reduction sulfide oxidation methanogenesis |
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Types of metabolic pathways for chemoheterotrophs
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aerobic respiration
anaerobic respiration fermentation |
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Types of metabolic pathways for photoautotrophs
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photosynthesis
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What is the chemotrophic ways of making energy use?
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some reduced compound plus some oxidized compound and materials for a redox reaction that yields energy
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What is an enzyme?
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a biological catalyst
most are proteins, some RNA molecules made of living cells that require growth impairment can cause death |
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What is a catalyst?
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a substance that helps a chemical reaction to proceed at a faster rate
can not make an unfavorable reaction occur |
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How do catalysts quicken reaction rates?
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by reducing the activation energy barrier
this is done by destabilizing chemical bonds in the substrate and by stabilizing the activated complex, a state that is in-between the substrate and the product |
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Are catalyst consumed in the reaction?
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no
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A typical enzyme can make a biochemical reaction go how much faster?
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100 million times faster
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A typical cell has how many different enzymes?
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2000-3000
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What is the active site on an enzyme?
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catalytic site
usually a pocket or cleft where substrate binds |
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What role do functional groups play with the activation site?
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found on amino acid side chains that surround the active site and create conditions that stress the chemical bonds found in the substrate molecule and encourage the formation of a new set of chemical bonds that lead to formation of the product
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What is a substrate?
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the reactant in a biochemical reaction that is catalyzed by an enzyme
some enzymes convert a single substrate to a single product but many enzymes use two more substrates and produce two or more products |
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What are the three general areas in or around the cell where enzymes are found?
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-outside the cell, in the culture media
-embedded within the cytoplasmic membrane -in the cytoplasm of the bacterial cells |
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What enzymes are found outside the cell, in the culture media?
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excreted enzymes, called exoenzymes i.e. hemolysin
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What do exoenzymes do?
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some help to digest large molecules such as starch to release smaller molecules like sugars that can be absorbed by the cell; can be toxins
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What do the enzymes found embedded in the cytoplasminc membrane do?
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some involved in respiration; some pump ions across the membrane; some actively pump nutrients in and waste out; some cause metabolic changes
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What do enzymes found in the cytoplasm do?
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some synthesize amino acids, proteins, nucleotides, nucleic acis, sugars, etc; some break down nutrients to simple compounds forming ATP
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There are more than (blank) different enzymes at work in the cytoplasm?
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1000
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What is the first of the general steps of an Enzyme Catalyzed Biochemical Reaction?
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substrate(s) bind to the enzyme at the action site
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What is the second general step of an Enzyme Catalyzed Biochemcial Reaction?
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flexing of the enzyme produces a strain/distortion of some of the chemical bonds that are found in the substrate molecules
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What is the third general step of an enzyme catalyzed biochemical reaction?
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substrates are chemically changed into products
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What is the fourth general step of an enzyme catalyzed biochemical reaction?
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product is released
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What is the fifth general step in an enzyme catalyzed biochemical reaction?
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the enzyme emerges from the reaction unchanged and ready to bind and change another molecule of substrate
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What is the lock and key model?
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refers to the need for structural compatibility between the substrate and the enzyme; enzymes are specific catalysts; given enzyme will recognize only one type of substrate molecule and convert it to only one particular type of product; shape of the pocket that contains the active site of an enzyme is perfectly complementary to the shape of the substrate molecule
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What is an example of the lock and key model?
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enzyme that attaches alanine to a tRNA molecule needs a pocket where alanine can bind, but the enzyme that attaches lysine to a tRNA molecules needs a pocket big enough for lysine
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What is a metabolic pathway?
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a conceptual tool to help visualize relationships between some of the biochemical reactions that go on in a cell
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True/False
There is a physical track in the cytoplasm that acts as a road for the movement of metabolic intermediates. |
FALSE
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How many steps are involved in converting amino acid asparate to methionine?
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six
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What is a metabolic intermediate?
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a transitory product that is made from the starting material and is quickly converted to the next product; found in cytoplasm in low concentrations
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What is a simple protein?
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just a chain of amino acids
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What is a conjugated enzyme?
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consists of protein plus additional organic or inorganic molecules that are closely associated with the protein
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What is an example of a conjugated enzyme?
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succinate dehydrogenase; removes two hydrogen atoms from succinate to produce fumarate; reaction is part of the tricarboxylic acid cycle, aka kreb's cycle
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What is an apoenzyme?
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protein portion of a conjugated enzyme without any cofactors; apoenzyme of succinate dehydrogenase consists of two peptide chains or subunits
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What is a cofactor?
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small molecule that binds to an enzyme and helps to produce the catalytic activity
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What is an enzyme cofactor called if it is an organic molecule?
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coenzyme
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Explain the succinate dehydrogenase reaction
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requires several cofactors; uses a coenzyme flavone adenine dinucleotide (FAD) as the acceptor of the two hydrogens; metal ions are the other important group of enzyme cofactors; succinate dehydrogenase requires several iron ions, in what are called iron-sulfur clusters
succinate + FAD --> fumarate + FADH2 |
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What is FAD?
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flavone adenine dinucleotide; coenzyme
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What role do iron-sulfur clusters play in succinate dehydrogenase?
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involved in electron transfer steps
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What are conditions that can affect the activity of an enzyme?
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-protein denaturation
-temperature -pH -substrate concentration -presence of competitive inhibitors -allosteric inhibitors or activators -feedback inhibition (regulation of activity) |
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Explain denaturation of proteins
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for an enzyme to be active, the protein must be in the native globular shape; when the protein is in a random coil conformation the shape of the active site is disrupted and the catalytic activity is lost
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Explain the effect of temperature and pH on the activity of and enzyme
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all enzymes have an optimum temperature and pH for maximun activity (not too high of a temp, neutral pH)
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Explain the effect of substrate concentration on enzyme activity
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a higher concentration of substrate gives a faster rate of product formation
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Explain the presence of competitive inhibitors on enzyme activity
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competitive inhibitors slow the rate of product formation; they are chemically and structurally similar to the substrate and bind to the enzyme at the active site. blocking catalytic activity of the enzyme
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Explain allosteric inhibitors or activators on enzyme activity
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they bind to an enzyme at some specific site other than the active site; causes a change in the shape of the enzyme that inactivates or activates the catalytic site; if inhibitor is bound, active site changes shape and ends activity; ex asparate methionine reaction
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What can enzymes DO?
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make biochemical reactions go faster by reducing the activation energy barrier by stabilizing the transition state
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What can enzymes NOT DO?
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-change the nature of the reactants or products
-change the chemical potential energy of the substances -change the Free Energy of a Reaction -make unfavorable reactions favorable |
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What is ATP?
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the energy molecule of cells; adenosine triphosphate; bonds between phosphate groups are unstable and contain a lot of chemical potential energy; energy is released when ATP looses a phosphate to form ADP plus free phosphate
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What is ADP?
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adenosine diphosphate
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How does a cell store energy for a short while?
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energy from a catabolic reaction can be trapped by the cell and used to attach to a ADP to make ATP
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What does a cell use ATP for?
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an energy source to drive unfavorable biosynthetic reactions; i.e. the formation of a phosphoester bond between glucose and a phosphate to make glucose-6-phosphate (unfavorale reaction)
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True/False
hydrolysis of ATP is a favorable reaction? |
true
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How do you make phosphorylation of glucose favorable?
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adding the hydrolysis of ATP to ADP
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Explain the two ways to make ATP
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1) H+-ATPase (proton-ATPase)
2) Substrate-level phosphorylation |
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Explain H+-ATPase pathway for ATP production
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uses the potential energy of the proton motive forces (PMF); also known as the chemoosmotic theory and oxidative phosphorylation; for this pathway ther must be a membrane separating 2 compartments that have a difference in the concentrations of protons; protons flow through the portal from the side with the highest concentration to the side with the lowest; energy from the flow of protons can be used to synthesize ATP; proton gradients can be established using the chemical reactions of respiration via the electron transport chain, or through a photoactivated electron transport chain
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Explain the Substrate-level phosphorylation pathway for ATP production
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energy to form a high energy phospho-anhydride bond can come from the hydrolysis of a higher energy bond such as a mixed anhydride bond (carboxylic acid-phosphate) or a phospho-enol bond; requires the sacrifice of a chemical bond that has a higher energy than the high energy bond of ATP
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What are some of the ways that a cell uses ATP?
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-substrate activation
-power cellular motion -pump ions or other molecules across a membrane |
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What is substrate activation?
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-for glucose to be broken down it must be activated by the attachment of two phosphates; cell converts glucose to glucose-1,6-biphosphate, which can then be broken down to yeild energy and form ATP
-ATP and similar nucleotide triphosphates are the activated building blocks of nucleic acid biosynthesis -energy from ATP is used to attach amino acids to tRNA molecules; key energy consuming step in protein synthesis |
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What is cellular motion?
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-energy from ATP is used to make flagella rotate and muscle fibers contract
-energy from the hydrolysis of a similar compound, GTP, is used to make a ribosome move along a strand of mRNA in a specific direction -energy from ATP can be used to make GTP |
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What is a redox reaction?
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=oxidation-reduction reactions
-involves a transfer of electrons from one atom to another; do NOT always require the involvement of oxygen -electrons are not destroyed, just transferred from on type of atom to another -when one compound is oxidized (loss of electrons)some other compound has to be reduced (gain of electrons) |
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In biochemistry, an oxidation usually involves what?
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adding oxygen or removing a pair of hydrogens from a compound
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In biochemistry, a reduction usually involves what?
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addition of two hydrogen atoms or the removal of an oxygen atom from a compound
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Are sugars oxidized or reduced?
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they are exactly mid-way between being completely oxidized (CO2) or completely reduced (a saturated alkane)
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What are oxidation-reduction and glycerol derivatives?
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-glycerol
-glyceraldehyde -glyceric acid -glycerate -3-phospho-glyceraldehyde -1,3-biphosphoglycerate |
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What is the reaction of oxidation of glucose?
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C6H12O6 + 6O2 --> 6CO2 + 6H2O
-releases energy into the cell -essentially the same as the combustion of wood which is mostly cellulose, a polymer of glucose -oxidation of glucose in a cell releases just as much energy as oxidation of glucose in a fire, but in a cell the reaction takes place at 37*C, the fuel is dissolved in water and some of the energy released is used to make ATP -20 steps, releases energy slowly |
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How many metabolic pathways are involved in the oxidation of glucose?
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3
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What are the three metabolic pathways involved in the oxidation of glucose?
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-glycolysis
-kreb's cycle -electron transport chain (oxidative phosphorylation) |
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What is the reaction taking place in glycolysis?
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glucose is converted to 2 pyruvate in 10 steps
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For each glucose molecule converted to 2 molecules of pyruvate, you also make what?
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-2 ATPs are required to start the process
-4 ATPs are produced by substrate-level phosphorylation -2 molecules of NAD+ are reduced to NADH + H+ |
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What is the first, second, third steps of glycolysis?
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glucose is activated by the attachment of two phosphates to form fructose-1,6-bisphosphate (costs 2 ATP)
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What are the fourth, fifth steps of glycolysis?
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fructose-1,6-bisphosphate breaks down to form 2 molecules of 3-phosphoglyceraldehyde
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What is the sixth and seventh step of glycolysis?
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conversion of glceraldehyde-3-phosphate to 3-phosphoglycerate
oxidation of carbon 1 from an aldehyde to a carboxylic acid electron carrier NAD gets reduced, some of the energy is released by this to produce ATP through SLP |
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What are the eigth, ninth, tenth steps in glycolysis?
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3-phosphoglycerate is converted to phosphoenolpyruvate (PEP) in two steps
as PEP is converted to pyruvate, ATP is made carbon 2 is oxidized from the alcohol level to the keton level carbon 3 is reduced from the alcohol level to the alkyl level |
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What are the other names for the kreb's cycle?
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-tricaboxylic acid cycle
-the citric acid cycle |
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What is the pyruvate dehydrogenase reaction?
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pyruvate is converted to acetyl coA
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What is the kreb's cycle?
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a series of reactions that results in the complete oxidation of pyruvate to carbon dioxide
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What happens when 2 molecules of pyruvate are oxidized to six molecules of carbon dioxide?
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-8 molecules of NAD+ are reduced to NADH + H+
-2 molecules of FAD are reduced to FADH2 -2 ATPs are produced by the SLP |
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What is oxidative phosphorylation?
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a series of redox reactions involving membrane bound enzymes and electron carriers that results in the reoxidation of NADH + H+ back to NAD+, the reduction of O2 to H2O and the production of about 34 ATPs per glucose
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what is the electron transport chain?
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series of enzymes and electron carriers embedded in a membrane; is located in the mitochondrial membrane in eukaryotic cells and in the cytoplasm membrane in bacteria
-NADH + H+ is oxidized to NAD+ -electrons are passed from carrier to carrier, protons are pumped across the membrane -oxygen is reduced to water, in aerobic respiration oxygen is the terminal electron acceptor -protons flow through ATP synthase and generate ATP from ADP + Pi |
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What is the general mechanism for SLP?
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S~P + ADP --> S + ATP
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What are kinases?
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enzymes that catalyze the transfer of the phosphate groups in SLP, which takes place in the cytoplasm and involves water-soluble enzymes
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What is aerobic respiration?
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oxidation of glucose to carbon dioxide and water
ATP is generated via PMF |
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How many ATPs does aerobic respiration produce?
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34
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When are most ATPs made in aerobic respiration?
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ETC and OP
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What is fermentation?
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ATP generated by SLP
terminal electron acceptor is organic ex: lactic acid fermentation, ethanol fermentation yeilds 2 ATPs |
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What happens during lactic acid fermentation?
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glucose is partially oxidized to pyruvate via the reactions of glycolysis, then the NADH is oxidized back to NAD by the reduction of pyruvate to lactic acid
2 ATP/glucose molecule |
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What happens during ethanol fermentation?
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glucose is partially oxidized to pyruvate via the reactions of glycolysis, then the pyruvate is decarboxylated to yeild acetaldehyde; the NADH is oxidized back to NAD by the reduction of the actealdehyde to ethanol
2 ATP/glucose molecule |
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Examples of Fermentation Products
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-lactic acid
-ethanol -carbon dioxide -acetic acid -proprionic acid -butyric acid, acetone, isopropyl, butanol, butyraldehyde -2,3-butanediol |
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how is lactic acid made?
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by a variety of bacteria, including Lactobacilli, lactococcus, that are used in cheese and yogurt production and streptococcus that play a role in tooth decay
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how is ethanol made?
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by bacteria and fungi, especially yeasts
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how is acetic acid made?
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in mixed acid fermentation by many bacteria and made by actobacter and gluconobacter strains that are used to produce vinegar
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How is vinegar produced?
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1. yeast are used anaerobically to produce ethanol from sugar in the apple juice
2. gluconobacter and acetobacter carry out a form of incomplete aerobic respiratory metabolism, they use oxygen, buth they do not fully oxidize then ethanol |
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what is propionic acid?>
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three carbon fatty acid found in small amounts in swiss cheese
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how is 2,3-butanediol made?
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by many species of bacteria, detected by vogues-proskaur test
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what are oxidizing agents in anaerobic respiration?
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nitrate, nitrite, sulfate, sulfite, carbonate
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what are waste products of anaerobic respiration?
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nitrite, nitrous oxide, sulfite, hydrogen sulfide, methane
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what is photoautotrophic metabolism?
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photosynthesis
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What are the basics of photosynthesis?
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process by which light energy is trapped and converted to chemical energy
light energy is used to excite electrons that are taken from water electron transfer generates a PMF ATP is synthesized using the PMF NADP is reduced to NADPH using the excited electrons APT and NADPH are used to reduce CO2 to glucose |
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What is the calvin cycle?
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used for the fixation of carbon in both photoautotrophic and chemoautotrophic microorganisms
conversion of carbon dioxide to sugar requires the input of energy from ATP and reducing power from NADPH |
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what is lithotrophy?
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form of metabolism where bacteria acquire energy from the oxidation of inorganic substances and carbon from CO2
lithos = stone |
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What is nitrifying bacteria?
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found in the soil
i.e. nitrosomonas, nitrobacter they oxidize ammonia to nitrate using oxygen as the oxidizing agent make ATP using an ETC and PMF as in oxidative phosphorylation |
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How do plants absorb nitrogen?
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in the form of nitrate
urine from animals is broken down by soil bacteria to yield ammonia; nitrifying bacteria derive energy by oxidizing the ammonia; plants then use nitrates that the bacteria excrete as waste |
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nitrosomes oxidize ammonia to nitrite reaction?
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3NH3 + 3O2 --> 2HNO2 + 2H2O
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nitrobacter oxidize nitrite to nitrate in what reaction?
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2HNO2 + 3O2 --> 2HNO3
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what is denitrification?
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a form of anaerobic respiration that uses nitrate and nitrite as the terminal electron acceptor
nitrite and nitrate get reduced to nitrogen or nitrous oxide |
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Nitrification vs Denitrification
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nitrification: uses oxygen, ammonia oxidized, nitrate is produced
denitrification: anaerobic, organic matter is oxidized nitrate is converted to nitrogen |
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what is hydrogen sulfide oxidation?
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use H2S as a reducing agent in chemoheterotrophy energy production
thibacillus, rhodopsuedomonas uses an ETC important in deep sea thermal vent communities bacteria on the lowest rung of food chain |
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Thiobacillus ferroxidans
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lithotrophic bacterium
uses oxygen as the terminal electron acceptor; uses elemental sulfur and ferrous iron ions as the reducing agents thio = sulfur ferro = iron |
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How does rain water become acidic?
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runs off a pile of mine tailings
due to sulfide oxidation by lithotrophic bacteria |
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what do you get from utilizing the proton motive force?
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ATP synthesis
active uptake of nutrients ion pumps flagella rotation |
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what is hydrogen oxidizing bacteria?
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AEROBIC
alcaligenes eutrophus can fix carbon dioxide using rubisco-type enzyme (calvin cycle) if grown on methanol in N-limiting conditions, it produces polyydroxybutyrate (which is a biodegradable plastic) ANAEROBIC paracoccus denitrification |
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what is methanotrophic bacteria
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able to use methane aerobically as a carbon and energy source
methane is oxidized to methanol, which is then oxidized to formaldehyde, which can be oxidized to co2 |
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additional metabolic pathways
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-amino acid synthesis and breakdown
-fatty acid synthesis and breakdown -ethanol metabolism |
