Chapter 5 Exam 2
This coupling of energy requiring and energy releasing reactions is made possible through the molecule ___________
ATP (adenosine triphosphate)
What is chemiosmosis?
ATP synthesis using the electron transport chain -This involves oxidative phosphorylation
much of the energy released during oxiidation-reduction reactions is trapped within the cell by the formation of _____... specifically in an ______,(P) , is added to ADP with the input of energy to form ATP
ATP, inorganic phosphate group -ATP is generated by the addition of an inorganic phosphate group to ADP with the input of energy The addition pf P to a chemical compound is called phosphorylation
What are the 6 classes of enzymes (and the reaction they catalyze)?
*refer to table on page 113* - oxidoreductases: involved with oxidation-reduction reactions (in which oxygen or hydrogen are gained or lost) -transferase: transfer of functional groups, such as an amino group, acetyl group or phosphate group -hydrolase: hydrolysis (addition of water) -lyase: removal of groups of atoms without hydrolysis isomerase: rearrangement of atoms within a molecule -ligase: joining of two molecules (using energy usually derived form the breakdown of ATP) within classes there are more specific names... such as in ocidoreductase is dehydrogenases; those that remove hydrogen from a substrate, those that add electrons to molecular oxygen are called oxidases.
Howe does temperature influence enzyme activity?
- As temperature increases, rates of most reactions also increases (lower temperetures: molecules move slowly. Higher temperatures: molecules move faster, which increases their chances of collision)
Organisims release and store energy from organic molecules by...?
- a series of controlled reactions (enzymatically catalyzed chemical reactions) rather than a single burst. (if that were to happen it could not be used to drive chemical reactions properly, it would damage the cell) -to extract energy from organic compounds and store it in chemical form, organisms pass electrons from one compound to another through a series of oxidation reduction reactions, and stores it in chemical form (ATP)
What is metabolism?
- describes the breakdown and build up of nutrients within a cell - term used to describe all chemical reactions within a cell -can be viewed as an energy balancing act -can be divided into two classes of chemical reactions: those that release energy, and those that require energy -these chemical reactions can provide energy and create substances that sustain life -although microbial metabolism can cause disease and food spoilage, many pathways are beneficial rather than pathogenic.
Reaction rate
- is the frequency of collisions containing enough energy to bring about a reaction -depends on the number of reactants molecules at or above activation level
Where does the electron transport chain occur?
- plasma membrane of prokaryotes -inner mitochondria membrane of eukaryotes
Competitive inhibitors:
- they fill the active site of an enzyme and compete with the substrate competitive inhibitors shape and structure are very similar to the substrate -once bound does not form products -inhibitors bind irreversible to active site to amino acids in the active site preventing any further interactions with substrate others bind reversible alternately occupying and leaving the active site these slow the enzymes interactions with the substrate increasing the substrate concentration can overcome reversible competition inhibitors molecules.
What is the yield of ATP during respiration process?
-36 ATP's om bacteria... can produce 38 if it can produce more than Eukaryotic cells
Substrate level phosphorylation
-ATP is usually generated when a high-energy P (PO4-) is directly transferred from a phosphorylated compound (a substrate) to ADP -the substrate is high energy because in an earlier reaction in which the substrate itself was oxidized. -generates ATP
Oxidative Phosphroylation
-Electrons are transferred from organic compounds to one group of electron carriers (usually to NAD+ and FAD). - then the electroons are passed through a series of different electron carriers to molecules of oxygen or other oxidized inorganic and organic molecules (this process occurs in the plasma membrane of prokaryotes and inner mitochondrial membrane of eukaryotes)
Why is glucose such an important molecule for organisms?
-Energy rich compound that is being oxidized in the carb cycle -oxidation of glucose (glycolisis) to pruvic acid produces ATP and NADH
NADH transfers high energy electrons to ________
-FM, the first carrier in the chin -a hydrogen atom wiith two electrons passes to FMN which picks up an additional H+ from the surrounding aqueoius medium. As a result, NADH is oxidized to NAD + and FMN is reduced to FMNH2 -page 124
Noncompetitive or allosteric inhibitors play a role in a type of biochemical control called_________or _____________
-Feedback inhibition or end-product inhibition -this control mechanism stops the cell from making more of a substance than it needs and thereby wasting chemical resources. -in some metabolic reactions, several steps are required for the synthesis of a particular chemical compound called the end-product. (the production of this compound is similar to an assembly line) - in many metabolic pathways, the end product can allosterically inhibit the activity of one of the enzymes earlier in the pathway
What is catabolisim?
-In living cells, the enzyme-regulated chemical reactions that release energy are generally the ones involved in catabolisim -this is the breakdown of complex organic compounds into simpler ones -catabolic reactions are generally hydrolic reactions (reactions which use water and in which chemical bonds are broken) -are exergonic (produce more energy than they consume) -example of this is when cells break down sugars into carbon dioxide and water -These reactions are called catabolic or degradative
Substrate fits like a __________in the 3-D shape (______) of specific amino acids of active site
-Key, Lock -Key and Lock model -Each of the known enzymes have this specificityy becaus e the three dimensional shape of the specific amino acids of the active site fits the substrate somewhat as a lock fits with its key. (the unique configuration of enzymes enables it to find the correct substrate from amongs the diverse molecules in a cell) - the active site and substrate are flexible, and they change shape somewhat as they meet to fit together more tightly. -the same compound can be substrate for many different enzymes
What are the most important products of the kerb cycle?
-NADH -FADH2 -these two coenzymes contain most of the that was stored in the glucose molecule
There are additional pathways to glycolysis, list two of them...
-Pentose phosphate pathway: operates simultaneously with glycolysis and provides a means for the breakdown of 5 carbon sugars (pentoses) as well as glucose. It produces NADPH from NADP+. this yields a net gain of one ATP for every molecule of glucose oxidized. -enter-doudroff pathway: produces 2 NADP+ and one molecule of ATP for use in cellular biosynthetic reactions. -this does not involve either glycolysis or PPP (pentose phosphate pathway)
What is a turnover number?
-The number of substrate molecules an enzyme converts to a product each second -generally between 1-10,000 (can be as high as 15,000) -for example; DNA polymerse has a tunrover number 1-15 ... in opposition...lactate dehydrogenase has a turnover number of 1000 (a process which removes hydrogen atoms form lactic acid) -enzymes exist in both active and inactive forms, the rate at which enzymes switch between these two forms sis determined by the cellular environment
What is the optimum temperature?
-This is the maximum rate of reaction -in the human body it is between 35-40 degrees Celsius. -beyond this, it starts to slow down again
What is the electron transport chain (system)?
-This is the sequence of electron carriers that is used in oxidative phosphorylation -the transfer of electrons from one electron carrier to the next releases energy, some of wich is used to generate ATP from ADP through the process calld chemiosmosis
Many coenzymes are derived from ____________
-Vitamins -Two of the most important coenzymes in cellular metabolisim are: -nicotinamide adenine dinucleotide (NAD+) (involved with catabolic reactions) - nicotinamide adenine dinucleotide phosphate (NADP+) (involved with anabolic reactions (energy requiring) -Both compounds contain derivatives of the B vitamin niacin (nicotinic acid) and both function as electron carriers
What are the two types of respiration?
-aerobic and anarobic
What is a holoenzyme?
-apoenzyme are inactive by themselves, they must be activated by cofactors. -together (apoenzyme and cofactors) form holoenzyme, or whole active enzyme
FMNH2 passes 2H+ to the other side og the mitochondrial membrane and passes two electrons to Q... as a result...
-as a result FMNH2 is oxidized to FMN -Q also picks up an additional 2H+ from the surrounding aqueoud medium and releases it on the other side of the membrane
Respiration is defined as...
-as an ATP generating process i which molecules are oxidized, and the final electron acceptor comes from outside the cell and is an inorganic molecule (oxidation of molecules liberates electrons of molecules liberates electrons) -electron transfer operates effectively -ATP is generated by oxidative phosphorylation
What is the suffix for enzymes?
-ase
Enzymes are ___________
-biological catalyses -catalysts are substances that can speed up a chemical reaction without permanently altering themselves -enzymes typically accelerate chemical reactions (by acting on a substrate) by lowering there activation energy
What are the two processes to produce energy from glucose?
-cellular respiration - fermentation (review page 120)
Definition of fermentation
-defined as the process that releases energy from sugars or other organic molecules, such as amino acids, organic acids, purines, and pyrimidines. -does not require oxygen(but can occur in O2 presence) -does not require the use of the kerbs cycle or an electron transport chain -uses an organic molecule synthesized in the cell as the final electron acceptor -produces only small amounts of ATP because much of the original energy in glucose remains in the chemical bonds of the organic end-products, such as lactic acid or ethanol
The rate of reaction declines beyond the optimal temperature because of the enzymes ___________
-denaturation; the loss of its characteristic three-dimensional structure. -denuturation of protein involves the breakage of hydrogen bonds and other noncovalent bonds -denaturation also changes the arrangement of amino acids in the active site, altering its shape and causing the enzyme to lose its catalytic ability.
Some coenzynes act as _______
-electron carriers -what is meant by electron carriers, is that coenzymes remove electrons from the substrate and donate them to other molecules in subsequent reactions.
Optimum pH:__________________________
-enzyme most active -above and below the optimum pH, there is reduced activity (reaction rate) -extreme changes in pH is called denaturation
What is anabolisim?
-enzyme-regulated energy requiring reactions are mostly involved with anabolisim -anabolisim is the building of complex organic molecules from simpler ones -these reactions are called anabolic or biosynthetic -often involve dehydration synthesis reactions (reactions that release water) -they are endergonic (consume more energy than they produce) -examples of anabolic processes are the formation of proteins from amino acids, nucleic acids from nucleotides, and polysaccharides from simple sugars biosynthetic reactions generate the materials for cell growth
__________(___) and ________(___) contain derivatives of the B vitamin riboflavin and are also electron carriers.
-falvin mononucleotide (FMN) and falvin adenine nicleotide (FAD)
Summary of aerobic respiration
-final electron acceptor in the ETC is molecular oxygen -During ETC, NADH and FADH2 gets oxidized to NAD+ and FAD which can be reused -Each NADH oxidized in the ETC produces 3 molecules of ATP -each FADH2 oxidized produces 2 molecules of ATP
Summarize the process, glycoylisis (two basic stages)
-first, in the preparatory stage, two molecules of ATP are used as a six carbon glucose molecules is phosphorylated, restructured and split into two three carbon compounds: glyceraldehyde 3-phosphate (GP) and dihydrooxyacetone phosphate (DHAP) -second is the endergy conversion stage, where the two three carbon molecule is oxidized in several steps to two molecules of pyruvic acid. In these reactions, two molecules of NAD+ are reduced to NADH, and four molecules of ATP are formed by substrate-level phosphorylation ...4 atp are produced, 2NADH are produced Since we needed two atp molecules to get this process started, there was a net gain of 2 ATP for each molecule that was produced.
What are the three classes of carrier molecules
-flavoproteins: contain flavin, a coenxyme derived from riboflavin (votamin B2) and are capable of performing alternating oxidations and reductions. Eg. flavin mononucleotide (FMN) -CytochromesL are proteins with an iorn containing group (heme) capable of existing alternately as a reduced form of (Fe 2+) and an oxidized form Fe 3_. the cytochromes involved in electron transport chains include cytochrome b (cyt b), c1 (cyt c1), c (cyt c1) t, (cyt a), a3 (cyt a3) -Ubuquinones or coenzyme Q: small nonprotein carriers
the respiration of glucose typically occurs in three stages:
-glycolysis, the kerbs cycle and electran transport chain (system) -both (cellular resperation and fermentation) start with a common step- glycolysis
What are the stages(3) of fermentation?
-glycosos (oxidation of glucose into pyruvic acid) -pyruvic acid converted into fermentation process, producing alchohol, carious acids and CO2 -NADH oxidized back to NAD+ -no kerbs cycle or electron transport chain -ATP yield much lower than respiration
What are some ways to increase the reaction rate?
-increasing temperature (by causing molecules to move faster, this increases the collision frequency and increases the number of molecules that attain activation energy) -increasing pressure (makes the distance between molecules less, thus making the concentration of molecules increase) -Enzymes (in living organisms, enzymes increase the reaction rate without increasing the temperature)
noncompetetive inhibitors
-interact with another part of the enzyme (allosteric site) rather than the active site -this is called allosteric ("other space") inhibition, in this process the noncompetitive inhibitor binds to the allosteric site, this causes the active site to change its shape, making it nonfunctional, as a result, the enzyme's activity is reduced. -can be either reversible or irreversible depending on whether the active site can be returned to its original shape -in SOME cases, allosteric interactions can activate an enzyme rather than inhibit it.
Activation energy
-is the collision energy required for a chemical reaction to occur -this is the amount of energy needed to distribute the stable electronic configuration of any specific molecule so that the electrons can be rearranged
Ribozymes
-it is an RNA that can cut and slice RNA -also involved with protein synthesis at ribosomes -can function as catalysts, have active sites that bind to substrates, and are not used up in a chemical reaction -before the discovery of ribozynes, it was thought that only proteins had enzymatic activity
ATP (adenosine triphosphate)
-links reactions together -stores energy released from catabolism -releases energy to drive anabolic reactions
A cells _________ are determined by its enzymes (encoded by genes), which are in turn determined by the cells genetic makeup
-metabolic pathways (sequence of chemical reactions) -Metabolic pathways- sequences of enzymatically catalyzed chemical reactions in a cell.
electrical gradient
-more positive charge on the outside compared to the inside -resulting electrochemical gradient has potential energy -the proton-motive force is generated by an electron transport chain which acts as a proton pump, using the Gibbs free energy of redox reactions to pump protons (hydrogen ions) out across the membrane, separating the charge across the membrane. -protons can also diffuse back into the cell only through special protein channels that contain the enzyme ATP synthase (releases energy to synthesize ATP)
What are the two ways that coenzymes may assist enzymes
-nay assist the enzyme by accepting atoms removed from the substrate or... -by donating atoms required by the substrate
Oxidation of each acytal CoA
-producess 3 NADH -produces 1 FADH2 -produces 1 ATP (by substrate level phophorlization) -liberates 2 CO2
As electrons are moving down the chain...
-protons (H+) are pumped out -build up of protons on the outer surface of the plasma membrane -provides the energy to generate ATP by the process of chemiosmosis
Proton gradient
-protons in higher concentration on one side of the membrane -in chemiosmosis the energy re;eased when substance moves along a gradient is used to synthesize ATP -in respiration, chemiosmosis is responsible for the most of the ATP that is generated
What is the primary step in aerobic respiration?
-pyruvic acid is first converted into CoA (prep step since pyruvica acid cannot enter the kerbs cycle directly). In the prep step, it must lose one molecule of CO2 and become a two-carbon compound (this is called decarboxylation)... the resulting two carbon compound (acetyal group) attaches to coenzyme A through a high energy bond; then the resulting complex that is formed is acetyl coenxyme A. -During this reaction, pyruvic acid is also oxidized and NAD+ is reduced to NADH. -Acetyl CoA enters the Kreb's cycle
From Q to cytochromes, each cytochrome in the chain is ______as it picks up electrons and is oxidized as it gives up electrons (oxidized as electrons are passed down the chain)
-reduced -the last cytochrome (cyt a3, passes its electrons to molecular oxygen (O2) which becomes negatively charged and pick up protons from the surrounding medium to form H2O
What is oxidation? What is reduction?
-removal one or more electrons, this is a reaction that often produces energy -is where an atom or molecule gains one or more electrons -these reactions are always coupled, each time one substance is oxidized, another is simultaneous reduced -the pairing of these reactions is called oxidation-reduction or a redox reaction
The breakdown of pyruvic acid, involved in two processes.... which ones?
-respiration -fermentation
Collision theory
-states that chemical reactions ( when bonds are either created or destroyed) occur when atoms, ions, and molecules collide - the energy transferred by the particles in the collision can disrupt their electron structures enough to break chemical bonds or form new ones -the higher the particles velocity, the more probable that their collision will cause a reaction.
Organisms use three mechanisms of phosphorylation t generate ATP from ADP ... what are the three?
-substrate level phosphorylation -oxidative phosphorylation -proton phosphorylation
What are factors that influence enzyme activity?
-temperature -pH -substrate concentration -inhibitors
After the acetal CoA detaches from the acetyl group, what happens?
-the acetyl group combines with oxaloacetic acid to form citric acid
Why does FADH2 produce less energy
-the electron transport chain produces about one-third less energy for ATP generation when FADH2 donates electrons than when NADH is involved -skips FMN and transfers electrons to Q
What is ananarobic respiration?
-the final electron acceptor is an inorganic molecule other than O2 or, rarely an organic molecule
What is Glycolysis?
-the oxidation of glucose to pryivic acid, is usually the first stage in carbohydrate catabolisim. (occurs in most living things) -this is also called Embden-Meyerhof pathway (glysis means splitting of sugar and this is exactly what happens) -the enzymes of glucose -this is the preparatory stage
What are nutrient molecules?
-they have energy associated with electrons, that form bonds between their atoms. when it is spread throughout the molecule, this energy is difficult for the cell to use, and this is usually the case :/... -reactions in catabolic pathwaays, concentrate the energy into the bonds of ATP which serves as a convenient energy carrier. ATP is referred to as having "high energy" bonds, or "unstable" bonds... -although the amount of energy on these "high energy" binds are not large, it can be released quickly and easily, providing the cell with readily available energy for anabolic reactions.
Photophosphorylation
-this occurs only in photosynthetic cells, which contain light-trapping pigments such as chlorohylls -in photosynthesis, organic molecules (such as sugars) are synthesized using energy of sunlight from the energy poor building blocks, CO2, and water -Photophosphorylation stats this process by converting light energy to the chemical energy of ATP and NADPH, which, in turn, are used to synthesize organic molecules. -Light energy excites chlorophyll -electrons from chlorophyll pas through an electron transport chain (just as in oxidative phosphoroylation) -ATP and NADPH are generated -light energy to chemical energy
What is aerobic respiration?
-uses O2 -final electron acceptor is O2
What are the general sequence of events in enzyme action?
1) the surface of the substrate contacts a specific region of the surface of the enzyme molecule (this is called active site) 2) a temporary intermediate compound forms called an enzyme-substrate complex. The enzyme orients the substrate into position that INCREASES the probability of reaction which enables the collisions to be MORE effective. 3) the substrate molecule is transformed by the rearrangement of existing atoms, the breakdown of the substrate molecule, or in combination with another substrate molecule. 4) the transformed substrate molecules- the products of the reaction-are released from the enzyme molecule because they no longer fit in the active site of the enzyme (this is where the substrate is transformed and rearranged into products, which are released from the enzyme) 5) the transformed substrate molecule- the products of the reaction- are released from the enzyme molecule because they no longer fit in the active site of the enzyme 5) the unchanged enzyme is now free to react with other substrate molecules Page of image is 112
For every molecule of glucose, ______acytal CoA and ______ NADH are formed
2,2
This is another important coenzyme, ________(CoA) contains derivatives of pantothenic acid, another B vitamin.
Coenzyme A
____________may help catalyze a reaction by forming a bridge between an enzyme and its substrate
Cofactors
______ is another source of electrons from Kerb's cycle
FADH2 -however, FADH2 adds its electrons to the electron transport chain at a lower level than NADH, because of this, the electron transport chain produces about one-third less energy for ATP generation when FADH2 donates electrons than when NADH is involved -skips FMN and transfers electrons to Q
What is the most common carbohydrate energy source used by cells?
Glucose
What does the molecule ATP consist of?
Phosphate group, a ribose, and adenine
What are the stages(3) of respiration?
This is defined as an ATP generating process in which molecules are oxidized and ATP generating process in which molecules are oxidized and the final electron acceptor comes from outside of the cell and is an inorganic molecule. -Glycosis (oxidation of glucose (broken down ) to pyruvic acid) and this produces some ATP and energy containing NADH -the kerbs cycle is the oxidation of acetyl Co A (a derivitive of pyruvic acid) to carbon dioxide, with the production of some ATP, energy containing NADH and another reduced electron carrier FADH2 -in the electron transport chain (system) NADH and FADH2 are oxidized, contributing the electrons they have carried from the substrates to a "cascade" of oxiadation-reduction reactions involving a series (energy from these reactions is used to generate a considerable amount of ATP) most ATP is generated in this step
Most microorganisims oxidize carbohydrates as te=heir primary source of cellular energy... the breakdown of carbohydrate molecules to produce energy is called _________
carbohydrate catabolisim
ATP stores energy derived from _______ and releases it later to drive __________and preform other cellular work
catabolic reaction, anabolic reaction
___________ reactions provide building blocks for __________and furnish the energy needed to drive ____________
catabolic reactions, anabolic reactions, anabolic reactions
Electron chains achieve the same basic goal: to release energy while electrons are transferred from higher energy compounds to lower energy compounds... energy released is used to produce ATP by ___________
chemiosmosis
As CoA enters the Kerbs cyc;e, CoA detaches from mthe acetyl group. The acetyl group combines with oxaliacetic acid to form _________
citric acid
In biological systems ________and ___________ are removed at the same time; equivalent to hydrogen atoms
electron and protons -in cellular oxidation, electrons and protons are removed at the same time (hydrogen ions, H+) the is equivalent to the removal of hydrogen atoms because a hydrogen atom is made of one proton and one electron. -biological ocisations are called dehydrogenation reactions (because most biological oxidations involve the loss of hydrogen atoms) -NAD+ assists enzymes from the substrate, by accepting two electrons and one photon, in an oxidation reaction this coenzyme produces NADH and a proton is released...(NADH now contains more energy tgab BAD+)
During the next phase of respiration a series of reductions indirectly transfers the energy stored int hose coenxymes to ATP. These reductions indirectly transfers the energy stored in those coenxymes to ATP, these reactions are collectivly called __________
electron transport chain
The principal properties of a group of proteins involved in almost all biologically important chemical reactions are ________
enzymes
What is the first step of the Kerbs cycle?
formation of citric acid
Some enzymes are entirely made of _________, most enzymes have a ________ portion called __________, and a _________ component called cofactor
proteins, protein portion, called apoenzyme, and a non protein component, called cofactor -example of non-protein component is iron, zinc, magnesium, ect. -if the cofactor is an organic molecule, it is called a coenzyme.
In conditions of high substrate concentration. an enzyme is said to be ________
saturated: that is, its its active site always occupied by substrate (or products) catalyzing at its max rate -further increase ins substrate does not affect rate -enzymes are not saturated at normal conditions
Enzymes have ________ for particular __________
specificity, substrates -a specific enzyme can only react on a particular substrate -examples: a specific enzyme may be able to hydrolyze a peptide bond only between two specific amino acids. -examples: there enzymes can hydrolyze starch but not cellulose; even though both starch and cellulose are both polysachrides composed of glucose sub units.
What are intermidiates in the Krebs cycle uses for?
they are useful for many biosynthetic pathways (amino acids, fatty acids etc.)