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biochem 1 exam
biochem covering heme, hb, glycolysis,tca,ox phos
| Question | Answer |
|---|---|
| Homeostasis | the ability of a system to do maintenance (regulation) of stable internal conditions despite fluctuating external conditions such as: energy, pH, water balance, and redox states |
| covalent bonding | bonding where electrons are shared by two molecules. |
| polar covalent bonds | are when the electrons spend a greater amount of time towards the more electronegatively charged molecule creating a charge separation with a negative charge on 1 molecule and a positive charge on another molecule. |
| non polar covalent bonds | equal sharing of electrons where no charge separation takes place |
| ionic bonding | 1 molecule gives up an electron and another molecule takes the electron. |
| hydrophobic | water fearing |
| hydrophilic | water loving |
| amphipathic | contains both hydrophobic and hydrophilic regions |
| a phospholipid bilayers is an aexample of what? | amphipathic thing |
| osmolality | concentration of solutes(including cations, anions, proteins, etc.) in a given solution. it is proportional to the total concentration of all dissolved molecules, including ions, organic metabolites and proteins |
| isotonic | term of osmosis that has both concentrations of water inside and out of a cell in equilibrium |
| hypertonic | concentration of water is greater inside the cell than the external environment which causes the water to migrate out of the cell causing it to shrink. |
| hypotonic | concentration of water is greater outside of the cell than inside the cell which causes the water to move inside the cell. |
| acidosis | acid like conditions |
| alkalosis | basic like conditions |
| catabolism | releasing energy from reactions in which nutrients and cell constituents are broken down |
| anabolism | using energy in reactions to make biomolecules |
| oxidation | loss of an electron |
| oxidizing agent | an electron acceptor. The molecule that gets the electron (the one being reduced) |
| reduction | gain of an electron |
| reducing agent | - an electron donor. The molecule that is giving up an electron (the one that is being oxidized) |
| glycolysis | breakdown of glucose in a 10 step process to pyruvate, 2ATP, and the reduction of 2NAD+ to 2NADH. |
| gluconeogenesis | making of glucose from any non-carbohydrate precursor |
| polar molecules | are “like” water and therefore will dissolve in water due to the charge separation found the polar molecules |
| non polar molecules | are not like water and lack any charge separation and therefore will not dissolve in water |
| the main biological buffer systems used to maintain acid-base balance | Bicarbonate Buffer System,Bicarbonate and Hemoglobin in RBC, Phosphate Buffer System, |
| The Bicarbonate Buffer system takes place | in the extracellular fluid |
| The Phosphate buffer system takes place | in the intracellular fluid |
| Carbonic anhydrase | enzyme that speeds up the making of carbonic acid |
| structure and function of carbohydrates | serve as energy and carbon sources, store energy in the form of glycogen, can be used to modify other molecules |
| stereoisomer | molecules that have the same atom to atom connections but nonsuperimposable shapes |
| epimer | stereoisomer that differs at only 1 asymmetric carbon |
| glucose | monosaccharide found in meats and plants |
| galactose | monosaccharide found in dairy and milk |
| fructose- | monosaccharide found in processed foods and sugar |
| sucrose | disaccharide made of glucose and fructose and found in sugar, honey, fruits and processed foods |
| lactose | disaccharide made of glucose and galactose found in dairy and milk |
| maltose | disaccharide made of 2 glucose, found in complex carb digestion and some grains |
| Reducing sugar test | The aldehyde groups of sugars can be oxidized and the donated electrons go to copper which turns the test blue to promote a positive test. If reducing sugar test is positive than there is sugar present in the blood. |
| glucose oxidase test | specifically looking for just glucose in the blood |
| galactose oxidase test | specifically looking for just galactose in the blood |
| Lipid Properties and Function | nonpolar, insoluble in aqueous media, Functions: energy storage, components of membranes, cell-signaling, hormone synthesis |
| saturated fatty acids | have no double bonds and are saturated with H bonds |
| monunsaturated fatty acids | have one double bond |
| polyunsaturated fatty acids | have more than one double bond in chain |
| lipolysis and triglycerides | breakdown of triglycerides/lipids to make fatty acids which can further be broken down via beta oxidation to make acetyl CoA that can lead on down to TCA to Oxidative Phosphorylation to ATP |
| Examples of saturated fatty acids | palmitate, stearate and are found in animal fat |
| Examples of unsaturated fatty acids | found in plant fats-ex. Oleate, linoleate, linolenate, arachindonate, |
| Essential fatty acids | linoleate and linolenate |
| non essential fatty acids | arachidonate |
| sphingolipids backbone type | ceramide |
| sphingolipids help with what in the body | with myelin, lipid rafts, and cell signaling |
| Steroids contain | cholesterol |
| cholesterol is an important component of | memberanes |
| nonpolar aliphatic amino acids | glycine, alanine, proline, valine, leucine, isoleucine |
| Aromatic nonpolar amino acids | phenylalanine, aromatic more polar- tyrosine and tryptophan |
| Polar, uncharged amino acids | asparagine, glutamine, serine, and threonine |
| Sulfur-containing amino acids | methionine and cysteine |
| Charged: negative(acidic) amino acids | aspartate and glutamate |
| Charged: positive (basic) amino acids | histidine, arginine and lysine |
| The carboxylic acid side chains amino acids | aspartic acid and glutamic acid |
| amino acids that are all polar but NOT charged so they can only H bond. | Asparagine, glutamine, and tryptophan |
| Positively charged at neutral pH, participate in H bonding and ionic bonding, can be modified, have significant hydrophobic regions therefore they are frequently hiding in the interior with the positive ends sticking out | lysine and arginine |
| Hydroxyl containing groups that are polar but not charged so they can only H bond | Serine, threonine and tyrosine |
| can both H bond and Ionic bond | histidine |
| amino acid that can be easily oxidized and reduced and can form covalent bonds. Contains S | cysteine |
| The hydrophobic leftovers that are non polar | glycine, alanine, phenylalanine, proline, valine, leucine, isoleucine, and methionine and they stay in hydrophobic region |
| primary structure of protein | order or sequence of amino acids joined by peptide bonds to form a polypeptide chain. This is linear and sets the precedent for how the protein will fold |
| secondary structure of protein | are the common repeating elements (alpha helix and beta sheets) that form in short localized regions of a polypeptide chain. These are based on H bonds. |
| tertiary structure of protein | the overall 3D conformation of a protein that’s determined by H bonds, ionic, disulfide or hydrophobic interaction bonds |
| quaternary structure of protein | - proteins with more than 1 subunit (chains, polypeptide) Subunits can be the same or different. The folding is determined by H bonds, ionic, disulfide bonds, or hydrophobic interactions regarding the amino acid residues |
| alpha helix | H bonds between backbone carbonyl O and H amide on same chain. It gets the helical shape bc each H bonds takes place between amino acid residues further alone the chain (4 residues). Disrupted by proline and large numbers of bulky or charged side chains |
| beta sheets | H bonds between the backbones of 2 separate polypeptide chains. These can be either parallel or antiparallel |
| glutathione | helps prevent formation of unwanted S-S bonds, Neutralizes ROS by acting as an electron donor and allows the disulfide bonds to break, found in cytosol |
| glutathione reductase | enzyme responsible for reducing glutathione so that it can break disulfide bonds |
| Heat Shock Proteins (HSP) | assist in folding proteins (aka chaperones/ chaperonins). These use energy from ATP hydrolysis to overcome the kinetic barriers of folding and vary in size. |
| Isomerases | assist in protein folding. Ex.) include prolyl cis/trans isomerases which convert transpeptide bonds preceding proline into cis conformation which helps with making hairpins. |
| amyloidosis | a class of disorders whose common feature is deposition of “amyloid fibrils” which have aggregated and accumulated somewhere. The fibrils are composed of aggregates or fibrils that have undergone a conformational change rendering them insoluble |
| holoprotein | protein with its prosthetic group and attached components |
| apoprotein | protein without its prosthetic group and attached components |
| cooperativity | Cooperativity is the affinity of Hb for the last bound oxygen is much higher than affinity for the first. So once the first oxygen binds, it increases the likelihood that another will bind. Unloading of oxygen is also cooperative. |
| allosteric effects | generality saying that the binding of a protein is affected by changes at a different site in the protein. |
| NADH methemoglobin reductase | that it takes the ferric (3+) iron in the heme group of Hb and converts it to the ferrous (2+) iron form via redox reaction so that oxygen can bind to the heme |
| 3 potential causes of methemoglobinemia | drugs, toxins, and mutations. |
| glycoslyation | glucose gets attached to proteins with a low turnover rate (longer half life due to the balance between synthesis and degradation). This is dependent on glucose concentration if enough glucose and time is present,aggregates of it start to form. |
| ubiquination | that ubiquitin is added to proteins’ lysine reside to signal to the proteosome that protein is ready for degradation and be broken down |
| E3 ligases | enzymes that conjugate ubiquitin to specific proteins, proteosome is what does the chopping. |
| Creatine Kinase Isoforms | M, and B respectively. MM is skeletal muscle, BB is brain, and MB is cardiac. CK is small and can leak out of damaged cells, therefore it is a useful marker of tissue damage since it can be detected in the blood |
| HbA | considered normal adult Hb without any variance,composed of 2 alpha and 2 beta chains |
| HbA2 | “normal” variant of HbA the only difference is it is made of alpha and delta sheets |
| HbF | fetal hemoglobin,Composed of 2 alpha and 2 gamma chains |
| HbS | sickle cell hemoglobin, Composed of 2 alpha and 2 mutated beta chains |
| HbC | carriers of sickle cell hemoglobin. Composed of cells with 50% of their beta chains like HbS. |
| accuracy | ability to get close to a known quantity. It is an agreement of a measured value with a “true” or expected value. This can only be determined using known standards and is commonly expressed as percent recovery |
| precision | the amount of agreement between measurements. It is the reproducibility of an experiment and how close repeated measurements are to one another. |
| sensitivity | the limit of detection. The smallest amount of analyte that can be accurately and reproducibly measured. |
| specificity/selectivity | the ability of a method to measure one analyte vs. another |
| clinical use for protein electrophoresis | Proteins are separated based on a mass/charge ratio and move thru medium based on how (-) and mass the protein is. This is used for id purposes and enables detection of specific proteins that might not be visible or distinguishable from other proteins |
| uses for enzyme assays | a. Enzyme assays take advantage of the fact that many molecules of diagnostic interest are substrates for enzymes or are enzymes themselves. |
| Describe mass spec | sample is placed into machine and gets zapped with a beam of electrons to break into charged fragments. fragments are sorted and measured. This tells both the sequence of the protein in question and how much of it you have. Used in combo w other test. |
| Describe immunoassays | are done on antibodies. Antibodies are proteins that bind with high specificity to other molecules. These properties enable the design of many types of assays and they range from simple but have limited sensitivity. Ex. ELISA |
| exergonic reaction | releasing energy. negative delta G, considered favorable and are spontaneous |
| endergonic reaction | requires energy, positive delta G, considered unfavorable and are NOT spontaneous |
| coenzyme | also cofactors and they are helpers to enzymes in the catalysis process |
| apoenzyme | enzyme without its cofactors and thus less active |
| holoenzyme | enzyme with its cofactors and readily active |
| Vitamin of NAD | niacin |
| Vitamin of FAD | Riboflavin |
| Vitamin of TPP | thiamin |
| CoA Vitamin | pantothenate |
| Vitamin of tetrohydrofolate | folic acid |
| Vitamin of Pyridoxal phosphate | pyridoxine |
| km | the affinity of a substrate to bind to an enzyme. It is also the concentration needed to reach ½ Vmax |
| rule of km | The rule is the lower the km= the greater the affinity for the substrate to an enzyme. |
| Vmax | the maximum velocity that can be reached (by velocity we mean the amount of substrate that disappears or the amount of Product that appears in a specific time frame. This involves the catalytic rate of the reaction. |
| km and kd are related | iv. Km and kd are related bc binding is required before a reaction can occur. Kd is used to describe the “binding” affinity of ligands for receptors. |
| kd | i. Kd measures the binding affinity of a ligand for receptors. Km=kd bc binding is required before a reaction can occur. Like km, the lower the kd the better the binding of the ligand to a receptor. |
| kd vs km | Km is concentration of substrate needed for ½ vmax. measures affinity of substrate for an enzyme (how well the substrate binds in active site), kd is ½ max bound and is specifically looking at binding affinity while km is looking at concentration. |
| receptor agonist | will activate the signaling cascade when bound |
| receptor antagonist | will not activate signaling upon binding |
| Vmax and km on competitive inhibitors | km is altered while Vmax stays the same |
| Vmax and km on noncompetitive inhibitors | km is same while Vmax is altered |
| Vmax and km on uncompetitive inhibitors | very rare, both km and Vmax are altered |
| competitive inhibitor | compete with substrate for active site |
| noncompetitive inhibitor | bind to an allosteric site in the presence or absence of substrate |
| uncompetitive inhibitor | inhibitor only binds when substrate is bound |
| reversible inhibitors | that can leave the active site and substrate can bind to active site also (compete with it) |
| irreversible inhibitors | when the inhibitors either change the conformation of an enzyme to an inactive form by messing with the active site, or binding to the active site itself and not allowing the enzyme to release it. |
| allosteric inhibitors | inhibit enzymes from performing catalysis when they bind to sites other than the active site |
| feedback inhibition | the product in a certain pathway can be the inhibitor of an enzyme further up the reaction and when it binds it tells that reaction change to stop making product for the time being |
| feed forward regulation(activation) | the accumulation of certain substrates will drive the reaction forward so that more product is produced |
| rate determining step | slowest step in the pathway,where the most energy is used to make a product that will be a substrate in the next and once enough of it is made some sort of feedback can turn the pathway off or on. |
| heme synthesis | Located: reticulocytes, hepatocytes, other cells synthesizing heme Fe proteins Starting materials: Succinyl CoA cycle, Glycine, Fe 2+ Regulation and cofactors: Aminolevulinic acid (ALA) synthase- first enzyme in pathway. Requires B6 cofactor. |
| Heme synthesis is feedback inhibited by | heme |
| transferrin | enzyme that moves Fe in body via the bloodstream |
| hemosiderin | enzyme that promotes the long term storage of iron |
| ferritin | enzyme that promotes the short term storage of iron |
| bilirubin | yellow breakdown product of heme degradation |
| bilirubin production and excretion | spleen to the bloodstream albumin bound and enter the liver. Bili and UDP- glucuronate converted to bili diglucuronide via hepatic conjugation with help from glucuronyl transferase. helps make it soluble.Bil diglucuronide is excreted by gall bladder |
| conjugated bilirubin | direct bilirubin NOT bound to albumin |
| unconjugated bilirubin | indirect bilirubin and bound to albumin |
| elevated levels of unconjugated bilirubin indicate what | Pre-hepaticpathology, Pre-conjugation pathology in the heme catabolism pathway |
| Presence of conjugated bilirubin indicate what | Hepatic post conjugation-in liver after processing or in bile ducts transfer Post hepatic pathology in heme catabolism pathway. |
| Presence of direct bilirubin indicate what | Hepatic post conjugation-in liver after processing or in bile ducts transfer Post hepatic pathology in heme catabolism pathway. |
| elevated levels of indirect bilirubin indicate what? | Pre-hepaticpathology, Pre-conjugation pathology in the heme catabolism pathway |
| hemostasis | The process of blood clotting and then the subsequent dissolution of the clot, following repair of the injured tissue |
| thrombus | A bloodclot that is formed from thrombosis (the process of forming a bloodclot) |
| function of platelets in thrombus | major role is to form mechanical plugs at the site of vessel injury and to secrete regulators of the blotting process and vascular repair. They arise through budding of megakaryocytes |
| structure of platelets | non-nucleated, heavily granulated disc-like cells in blood |
| What do platelets form? | primary plug |
| How do platelets form primary plug? | Platelets become activated in response to endothelial injury, They release of ADP, serotonin, TXA2, and vWf. Then comes adhesion and aggregation to form primary plug |
| How are platelets activated? | in response to endothelial injury casuses change in architecture of the membrane. Long pseudopodia are made. As this is done, there is a release of ADP, serotonin, TXA2, and vWf that activate other platelets. |
| Describe adhesion in platelets | once a BV injury happens, the BV exposes collagen, vWf & other matrix components.platelets bind collagen by GPIa and GPIb & cause shape change vWf binds GPIb to anchor platelets. GPIIa/b are exposed to bind vWf and factor I to start to aggregate. |
| Describe aggregation in platelets | After adherence some platelets release ADP,fibrinogen bc it promotes platelet/platelet contact. TXA2 allows more aggregation of platelets 2 strengthen clot. Cleaved fibrinogen by thrombin makes fibrin that polymerize with the platelets= “primary plug”. |
| thromboxane A2(TXA2) | TXA2 goes to the site of membrane stimulus and aids in the vasoconstriction of it and in allowing platelet aggregation to take place there bc helps reduce the blood flow to the damaged area. |
| How is TXA2 synthesized? | A stimulus on the phospholipid membrane heads that sends signals for phospholipases A and C to react with them to make arachadonic acid. Arachadonic acid is reduced by cyclooxygenase to PGH2 and PGH2 is reacted with thromboxane synthetase to make TXA2 |
| von Willebrand disease | increased/easy bruising, acute hemorrhage nose,heavy menstrual blood,post-op bleeding, fam history, bleeding wounds, gingival beeding, postpartum bleeding. Ppl w it dont have enough vWf or its damaged.clot may take longer to form or may not form properly |
| Bernard-Soulier syndrome | glycoprotein disorder: : caused by a deficiency in the GPIb protein which disrupts platelet adhesion to the subendothelial collagen |
| Glanzmann’s throbasthenia | a bleeding disorder caused by a decrease in the functional platelet membrane protein GPIIb (which is responsible for platelet aggregation) |
| Name 2 glycoprotein disorders | Bernard-Soulier syndrome and Glanzmann's throbasthenia |
| Thrombocytopenia | any disorder in which there are not enough platelets and can sometimes be associated with abnormal bleeding |
| cyclooxygenase inhibitors and coagulation | Without cyclooxygenase the arachidonic acid would be unable to form PGH2 a precursor of TXA2 and thus vasoconstriction of the membrane would be unable to take place |
| example of cyclooxygenase inhibitor | aspirin |
| extrinsic pathway | caused by some external stimuli. This causes Circulating Factor VII bind to tissue factor which catalyzes its own activation to Factor VIIa which activates Factor X (to Xa) in the extrinsic pathway and Factor IX (to IXa) in the intrinsic pathway |
| intrinsic pathway | caused by XII, HMWP & kalicrin activates XI becomes XIa and interacts w IX to make IXa which then reacts with PL and Ca to make the Xa. The intrinsic pathway is thought to sustain the coagulation response intitiated by the extrinsic pathway |
| the common pathway | Xa, PL, Ca and prothrombin react to make thrombin (IIa). Thrombin then reacts with Fibrinogen (I) to make Fibrin aggregate (Ia) and w XIII make cross-linked clot which is a hard clot. Factor XIII comes from Prothrombin being readily converted to XIII |
| What factors from the extrinsic pathway help with the intrinsic pathway? | Factor VII |
| What factors are considered cofactors of the intrinsic pathway? | Factor VIII |
| What factors are considered cofactors for the common pathway? | Factor V |
| What is another name for Factor III? | tissue factor |
| Name all the factors that are serine proteases | II, VII, IX, X, XI |
| Name Factor II for its function and active form | prothrombin-thrombin |
| Name factor I for its function and active form | Fibrinogen-fibrin |
| What is Factor IV? | calcium |
| What is Protein C? | it is activated by thrombomodulin-bound thrombin on adjacent endothelial cells, it is a serine protease with Protein S as a cofactor, it degrades VIII and V to stop common pathway, helps in anticoagulation |
| What is protein S? | a cofactor for protein c |
| thrombomodulin | endothelial cell receptor that binds to thrombin |
| antithrombin (aka antithrombin III) | irreversibly inactivates thrombin and is enhanced by heparin |
| Inhibitors of platelet activation | cyclooxygenase inhibitor, thromboxane synthase inhibitors, thromboxan receptor blockers, GPIIb-IIa antagonists, ADP inhibitors, ADP receptor inhibitors, Adjacent endothelial cells |
| Inhibitors of coagulation | thrombin, serine protease inhibitors, antithrombin III, neighboring endothelial cells |
| Thromboxane Synthase Inhibitor | blocks conversion of PGH2 to thromboxane which means no TXA2 and therefore no activation of platelets |
| Thromboxane receptor blockers | inhibits activation of GPIIb-IIa and GPIb-Ia so no aggregation of platelets can occur |
| GPIIb-IIa antagonists | blocks platelet aggregation in acute coronary thrombosis |
| ADP inhibitors | reduces availability of ADP |
| ADP receptor inhibitors | ex. plavix, blocks receptors so no platelet activation can take place |
| Endothelial cell as an inhibitor of coagulation | bc it is negatively charged and so are platelets, they can synthesize protsacyclin (vasodilator) and produce heparin |
| thrombin | factor II, acts as both an activator and a inhibitor of coagulation |
| serine protease inhibitors | serpins and plasma proteins that block serine proteases from going to active form |
| Hemophilia A | deficiency in VIII, x linked, suffer joint, muscle hemorrhage, easy bruising, and prolonged bleeding, most common type |
| Hemophilia B | deficiency in IX, prolonged coagulation time, and decrease in factor IX clotting, intrinsic with crosstalk from extrinsic |
| Factor XIII deficiency | auto recessive, a decrease in activity of XIII resulting in prolonged clotting and possibility of secondary plug not being mesh like and easy to come off |
| antithrombin III deficiency | deep vein thrombosis and pulmonary embolism unable to degrade clot |
| Activated partial thromboplastin time (aPTT or PTT) | intrinsic and common pathway, and prolonged time in this signals a possible deficiency in the following XII, XI, IX, VIII, II, V, X, and I |
| prothrombin time | extrinsic and common pathway and prolonged could indicate a deficency in III, VII, II, V, X and I |
| D-dimer test | Looking for fibrinolysis products. positive dimer test means there is clots forming that are not breaking down |
| if aPTT (PTT) is prolonged and prothrombin time is normal | intrinsic pathway problem |
| if aPTT (PTT) is normal and prothrombin time is prolonged | extrinsic pathway problem |
| if both aPTT (PTT) and prothrombin time are prolonged | common pathway problem |
| fibrinolysis | break down of fibrin into degraded products using plasmin, a form of anticoagulation |
| plasmin | from plasminogen, enzyme that helps degrade fibrin into product and is activated by t-PA which is stimulated by an activated Protein C |
| Role of Vitamin K for clotting | Responsible for the gamma carboxylation of coagulation factors X, IX, VII, II, Carboxylation of these is required to bind ca2+ which are required for the activation of coagulation factors. W/o these clots wouldnt form & blood flow wouldnt stop easily |
| Role of Vitamin K for anticoagulation | Required for Proteins C and S. Without Vitamin K, these proteins cannot be activated and help with stopping the coagulation pathway by degrading VIII and V. |
| TCA, Ox phos, beta oxidation | take place in mitochondria |
| glycolysis, gluconeogenesis, fatty acid synthesis take place | cytosol |
| insulin | fed state-activates metabolic processes for fed state and inactivates processes for fasted state |
| glucagon | fasted state- activates metabolic processes for fasted state and inactivates processes for fed state |
| how does glucagon activate and inactivate metabolic processes? | Regulates by signaling for phosphorylation of key enzymes via signal transduction Enzymes regulating processes needed in fast are active when phosphorylated Enzymes regulating processes needed in fed are deactivated when phosphorylated. |
| lactate is produced by | anaerobic metabolism and needs to be utilized to avoid pathologies due to lactate acidosis |
| in the fed state lactate | Can be further catabolized in aerobic cells, especially heart, kidney and liver In excess of ATP need is converted to fatty acids in the liver for storage |
| in the fasted state lactate | Provides carbons for hepatic glucose synthesis |
| how are ketone bodies and lactate alike? | Produced in one organ (fasted liver) and used in another. |
| how are ketone bodies and lactate different | keton bodies Only produced in fasted state and CANNOT be converted to glucose |
| hexokinase and glucokinase | Catalyzes 1st activating reaction of glycolysis Requires ATP Produces G6P Use first and store later The Km values of these enzymes assure that glucose is used for glycolysis 1st. excess fed state glucose converted to glycogen or fatty acid by liver |
| phosphofructokinase(PFK 1) | Uses ATP to phosphorylate F6P to fructose 1,6-biphosphate Is the rate-limiting enzyme Allosterically activated by substrate (feed forward regulation) allosterically feed-back activated by AMP allosterically feed-back inhibited by high ATP |
| pyruvate dehyrodgenase (PDH) | in mitochondria oxidize pyruvate to acetyl CoA (irreversible) NO other enzyme/process to reverse PDH reaction, NAD+ is reduced PDH is also a carboxylase (CO2) High energy S CoA bond is formed Regulated by substrates and/or products |
| How is PDH regulated? | All PDH substrates activate PDH, ex. ADP levels All PDH products inhibit PDH (sans CO2) ex. Acetyl CoA Regulation uses phosphorylation/dephosphorylation process that is sensitive to small changes in regulator metabolites. Not signaled hormonally |
| How is G3P dehydrogenase in glycolysis reoxidized aerobically? | Via electron shuttles (malatee-aspartate, and Glycerol 3 phosphate)from oxidative phosphorylation |
| How is G3P dehydrogenase in glycolysis reoxidized anaerobically? | lactate dehyrogenase recycles nucleotides for reuse in glycolysis so that pyruvate can be made anaerobically |
| pyruvate can be converted into: | acetyl CoA by PDH for TCA, lactate by LDH, oxaloacetate by pyruvate carboxylase for TCA, alanine via transamination, Pyruvate C can be used to produce citrate for fatty acid synthesis |
| pyruvate carboxylase | mitochondrial enzyme that captures CO2 via biotin cofactor, adds C from CO2 to pyruvate to produce oxaloacetate, requires ATP, irreversible |
| isocitrate dehydrogenase | main regulatory enzyme of TCA, allosterically activated by its substrate (feed forward reg) allosterically feed back activated by ADP, allosterically feed back inhibited by NADH |
| citrate synthase | enzyme that makes citrate from oxaloacetate and produces CoASh form acetyl CoA |
| Name the NAD+ to NADH producing dehydrogenases of TCA | isocitrate dehydrogenase, alpha ketoglutarate dehydrogenase, malate dehydrogenase |
| Name the FAD to FADH2 producing dehydrogenase | succinate dehydrogenase |
| co-enzyme A (coA-SH) | made from dietary component of panthothenic acid and used to transfer and activate acyl gorups in TCA cycle, the large negative delta G for the cleavage of the thio-ester bond provides energy to drive reactions |
| Why is succinate dehydrogenase a component of oxidative phosphorylation and TCA? | FAD is reduced to FADH2 by 2 one electron transfers which make an intermediate thats highly reactive making the cofactor pair tightly bound to enzyme |
| transamination | reversibly converts amino acids into keto acids and is catalyzed by readily reversible transaminases |
| Where can amino acid and fatty acid carbon enter TCA? | propionyl CoA can be converted to Succinyl CoA which is in TCA |
| Name the main components of the ETC | Complexes I, II, III, IV, V (ATP synthase) |
| Define proton motive force | generated by the pumping of protons across the inner mitochondrial membrane. The hydrogen proton gradient and charge gradient is referred to as this and used to drive complex V |
| quinone | Co-Q- lipid soluble, not protein bound and is free to diffuse in lipid membrane. transports electrons from Complex I to III and is an intrinsic part of the proton pump for each of these complexes. 2 forms for passing electrons |
| name the 2 forms of quinone and and how many electrons they can carry | semiquinone can take 1 electron (this is a free radical and number one source for ROS if it reacts with oxygen) or it can take 2 electrons and be fully reduced to quinol. |
| basic components of Complex V | Innermembrane portion made up of C subunits that form a rotor and is connected to headpiece via a shaft made of gamma and epsilon subunits. Headpiece is composed of 3 alpha/beta subunit pairs where beta contains catalytic site for ATP synthesis. |
| How does complex V work? | influx of protons through the proton channel turns the rotor (c subunits) which in turn changes the conformation of the alpha/beta subunits to actively bind ADP and P to make ATP. |
| How many protons are needed to make 1 ATP? | 3 protons |
| How many protons does FADH2 produce? | 6 protons |
| how many protons does NADH produce? | 10 protons |
| Why is there a difference in NADH and FADH2 proton production in Ox phos? | NADH starts in complex I while FADH2 starts in complex II. Complex one gives 4 protons, complex III gives 2 protons and complex IV gives 4 protons. |
| Explain how inhibitors reduce ATP production in Ox phos | block a specific Complex in the ETC. When that happens everything down stream of the complex will shut down bc electron will not be flowing down the gradient which means no protons will make Complex V work to make ATP. |
| Explain the mechanism by which uncouplers reduce ATP production in Ox phos. | act as lipophilic weak acids, disrupt the proton gradient by allowing the protons to leak out of membrane which respiratory rate but produces no ATP since protons don't return to interior through ATP synthase. Instead heat is produced. |
| Explain the production of radicals within mitochondria | they come from many compounds and ox phos is a major site specifically with coenzyme Q. |
| List the 3 enzymes used to eliminate free radicals | superoxide dismutases, glutathione peroxidase, and catalase |
| 3 reasons that mitochondrial DNA is mutated at higher rate than nuclear DNA | mitochondrial DNA lack histones, and lack the proper DNA repair enzymes. Lastly coenzyme Q can produce ROS |
| aldoase b | required to cleave fructose-1-phosphate and will creat DHAP and in the end triglycerides |
| galactose vs lactose malabsorption | in galactose kinase deficiency: u see cataracts, liver damage and intestinal issues, whereas lactose is just stomach problems |
| nonclassical galactosemia | problem with galactokinase which builds up glactose and aldose reductase cause an increase in galactitol. this causes water to rush in so swelling occurs, failure to thrive, emesis, jaundice, liver failure, cataracts, sepsis, hepatomegaly |
| classical galactosemia | GALT deficiency- build up of galactose 1 p, symptoms: blood in urine, cataracts, treat by eliminating galactose from diet |
| essential fructosuria | fructokinase deficiency- no clinical manifestations |
| hereditary fructuse intolerance | deficiency in aldolase b- symptoms vomiting, intestinal discomfort, hypoglycemia, failure to thrive, hepatomegaly, feeding problems |
| fructose malabsorption | bloating IBS after eating something with fructose is due to this, |
| importance of PPP | occurs in cytosol of all cells, makes NADPH and ribose5 phosphate, involved with hematological disorders |
| Name the rate limiting step of the oxidative phase of PPP | G6P dehydrogenase- regulated by NADPH production (feedback inhibition) upregulated by insulin to ensure that fed state when you need NADPH for fatty acid synthesis plenty is available. |
| trasketolase requires? | TPP (thiamine) |
| Explain Favism | G6P dehydrogenase deficiency that is an x linked condition. RBC are most affected bc ppp is only way that NADPH can get made. RBCS are anaerobic and can only undergo glycolysis and need NADPH to produce energy |
| name 3 factors that precipitate symptoms of G6P dehydrogenase deficiency | oxidative stress, some drugs (good oxidizing agents) and fava beans |
| Role of methemoglobin reductase and in RBC | metHb reductase returns FE3+ to FE2+ |
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