Biochemistry Exam 2 PDF

Biochemistry Exam 2 Chapter 10 - Carbohydrates Enantiomers: mirror images of each other Diastereoisomers: not mirror images of each other Epimers: diastereoisomers differing in configuration at only a single asymmetric center. Anomers: diastereoisomers generated when an additional asymmetric center...

Biochemistry Exam 2 Chapter 10 - Carbohydrates Enantiomers: mirror images of each other Diastereoisomers: not mirror images of each other Epimers: diastereoisomers differing in configuration at only a single asymmetric center. Anomers: diastereoisomers generated when an additional asymmetric center is created when a cyclic hemiacetal is formed. Polysaccharides Are polymers of covalently linked monosaccharides are called polysaccharides Large polymeric oligosaccharides are formed by the linkage of multiple monosaccharides Glycosidic bonds can join one monosaccharide to another - these reactions are catalyzed by specific glycosyltransferases Multiple hydroxyl groups (OH) means that many different glycosidic linkages are possible Disaccharides: two sugars joined by an O-glycosidic bond Biochemistry Exam 2 1 Sucrose can be cleaved into its component monosaccharides by the enzyme sucrase. Get it… Sucrose = Sucrase More Examples: lactose = lactase, maltose = maltase Glycogen: branched homopolymer A polysaccharide where all the subunits (monosaccharides) are the same of glucose residues Monosaccharides Are aldehydes or ketones that have two or more hydroxyl groups Carbon-based molecules that are rich in hydroxyl groups Simple carbohydrates are called monosaccharides Monosaccharides are the subunits of polysaccharides. Naming Saccharides Ketone = Ketose Aldehyde = Aldose Must contain ONE of the sugar designations & count number of carbons. Example: Dihydroxyacetone would be a triose ketose sugar. In the case of D-form sugars… Biochemistry Exam 2 2 𝛼 = hydroxyl group (OH) attached to C-1 is below the plane of the ring. β = hydroxyl group (OH) attached to C-1 is above the plane of the ring. Worth Noting… Fructose forms both pyranose (6 sides) and furanose (5 sides) rings Most of the glucose units in glycogen are linked by 𝛼-1,4-glycosidic bonds. However, the branches are formed by 𝛼-1,6-glycosidic bonds, which are present about 1 in every 12 units. Starch differs in structure to glycogen with 𝛼-1,6-glycosidic bonds, which are present 1 in every 30 units. Cellulose is an unbranched polymer of glucose residues joined by β-1,4 linkages. Three Major Classes of Glycoproteins 1. Glycoprotein: A carbohydrate group covalently attached to a protein 2. Proteoglycans: Protein conjugated to a particular type of polysaccharide called a glycosaminoglycan 3. Mucins: Key component of mucus, N-Acetylgalactosamine (GalNAc) is usually the carbohydrate moiety bound to the protein in mucins. Sugars attach to the amide nitrogen atom of asparagine (via N-linkage) or the hydroxyl oxygen of serine or threonine (via O-linkage). N-linked oligosaccharides have a common pentasaccharide core Three mannoses; a six-carbon sugar; and two N-acetylglucosamines (a glucosamine where nitrogen atom binds an acetyl group). Proteoglycans Are proteins conjugated to a particular type of polysaccharide called a glycosaminoglycan Proteoglycans function as structural components and lubricants Carbohydrates make up a larger percentage of the proteoglycan compared with simple glycoproteins (up to~95% of total weight) Biochemistry Exam 2 3 Glycosaminoglycan: A heteropolysaccharide made of repeating disaccharide units containing amino sugars glucosamine or galactosamine One of the two sugars in the repeating unit has a negatively charged carboxylate or sulfate group What is the point of complex sugar structures and glycoproteins? Glycan-binding proteins exist in all life: Glycan-binding proteins are proteins that bind to specific carbohydrate structures These are typically important in cell-to-cell surface signaling. One subclass of glycan-binding proteins called Lectins binds to specific short carbohydrate sequences. Binding of lectins to cell-surface glycoproteins facilitates cell-to-cell interactions, and also serves to help viruses bind to surface-glycoproteins for endocytic entry into cells Chapter 14 & 15 - Digestion + Basic Metabolism Basics of Metabolism Catabolism: Conversion of energy from fuels into biologically useful forms such as ATP or ion gradients Anabolism: Aynthesis of more complex molecules from simple precursors - requires energy Amphibolic pathways: Can be catabolic or anabolic depending on energy condition in the cell Conversion of small molecules (from digestion) into only a few different things mostly acetyl COA - small amounts of adenosine triphosphate made (ATP, the molecular unit of energy currency) Oxidation of acetyl COA to produce large amounts of ATP - citric acid cycle, TCA cycle, Krebs cycle - breakdown products from consumed nutrients completely oxidized to CO 2 Biochemistry Exam 2 4 Digestion - what it is… All digestive enzymes are hydrolases - cleave their substrates by addition of a water molecule All digestive enzymes are originally secreted as zymogens or proenzymes (catalytically inactive precursor of an enzyme) which are activated by proteolytic cleavage Protein Digestion Stomach Low pH of stomach (mechanism, Ch 14.2 Clinical Insight) leads to denaturation of protein, allowing for easier enzyme access for degradation Pepsinogen - Self-cleaving into Pepsin - proteolytic enzyme in the stomach nonspecific cleavage of proteins into smaller fragments Pancreas→Small Intestine Low pH of stomach acids activate secretin (stimulates NaHCO 3 release, neutralizing the acid) Peptide digestion products of pepsin stimulate cholecystokinin (CCK), which causes pancreas to secrete host of digestive enzymes Enteropeptidase (enterokinase): Secreted by small intestine - cleaves trypsinogen (proenzyme) into trypsin (active enzyme) that is secreted from the pancreas into the small intestine Trypsin: Serine protease (like chymotrypsin) - cleaves peptides on C-terminus of lysine and arginine residues ((+) amino acids) - cleaves proenzyme forms and activates all small intestine digestive enzymes (trypsin, carboxypeptidase A and B, elastase) By the end of this digestion process, proteins are cleaved to 1, 2, or 3 amino acids in length, allowing for easy absorption into the blood and distribution to tissues Biochemistry Exam 2 5 Carbohydrate Digestion Mouth Saliva contains ⍺-amylase which breaks down polysaccharides (⍺-1, 4 glycosidic bond cleavage) Lipid Digestion Mouth Lipids ingested in the form of triacylglycerols - presents a problem because of hydrophobicity Stomach Triacylglycerols are emulsified (mixed with water) in the stomach Small Intestine Biochemistry Exam 2 6 Lipids also activate cholecystokinin (CCK), which then promotes bile salt secretion from the gall-bladder into the small intestine (bile salts are detergent-like molecules that help solubilize the lipids These solubilized lipids can be enzymatically digested by lipases secreted by the pancreas and just like proteolytic pancreatic enzymes, lipases are also secreted as inactive zymogens Basic Metabilosm - ATP ATP is the molecular unit of energy currency The energy of ATP is found in it’s two phosphoanhydride linkages - large amount of free energy released when these linkages are hydrolyzed Why is ATP such a good energy currency? Electrostatic repulsion of the four negative charges carried by the triphosphate repel one another, meaning much of that repulsion energy is released when the bonds are hydrolyzed The relatively intermediate phosphoryl-transfer potential of ATP (its tendency to give up a phosphate) allow it to be used as carrier for phosphoryl groups This large free energy release can be coupled with thermodynamically UNfavorable reactions in order to make them thermodynamically favorable Catabolism: Conversion of energy from fuels into biologically useful forms such as ATP or ion gradients Primarily consists of strings of redox reactions coupling the reduction of carbon compounds (carbohydrates and fats) with reactions that create high phosphoryltransfer potential compounds (and thus ATP) or ion gradients. Biochemistry Exam 2 7 This is why fats are a more efficient fuel source than carbohydrates such as glucose because the carbon in fats is more reduced The energy of oxidation is initially trapped as a high phosphoryl-transfer potential compound and then used to form ATP Generation of ATP is one of the primary roles of catabolism Coenzyme A is an activated carrier of 2-carbon fragments (acetyl groups) Metabolism of carbon-based fuels (carbohydrates and lipids particularly) is done 2 carbons at a time, and Coenzyme A serves as the carrier molecule for each 2 carbon molecule that comes off said fuel. Similarly for catabolism, organic molecules are constructed 2 carbons at a time (carbohydrates and lipids particularly) and Coenzyme A serves as the carrier there as well - Acetyl CoA Activated Carriers ATP is an activated carrier of phosphoryl groups Other activated carriers function Fuel Oxidation NAD + - Oxidized form (electron acceptor) NADH - Reduced form (electron donor) FAD - Oxidized form FADH 2 - Reduced form Biochemistry Exam 2 8 Three Major Regulation Paths of Metabolism 1. Enzyme concentration - At the gene/protein expression level 2. Enzyme function - Allosteric regulation/feedback inhibition (already learned about) at a tissue specific level these are often achieved by hormonal regulation (more later as we go) 3. Access to substrates - Cellular and tissue specific compartmentalization (one example is the need for insulin to allow glucose into cells for metabolism) Chapters 16 & 17 - Glycolysis and Gluconeogenesis Glycolysis - What it is… Glycolysis is the sequence of reactions that converts one molecule of glucose into two molecules of pyruvate while generating ATP First and foremost, the primary function of glycolysis is generation of ATP However, the byproducts of glycolysis are also important for providing simple building blocks for biosynthesis Stage 1 - Conversion of glucose into Glyceraldehyde 3-phosphate and/or Dihydroxyacetone phosphate. Stage 2 - Progressive oxidation of Glyceraldehyde 3-phosphate to pyruvate Biochemistry Exam 2 9 Glycolysis - Stage 1 Phosphorylation traps glucose inside cells (no longer a substrate for glucose transporters) Requires ATP→ADP Kinases add phosphate groups Irreversible reaction - key regulatory point for glycolysis Requires ATP→ADP Glycolysis - Stage 2 Series of enzyme catalyzed reactions which generate ATP (usable energy) and NADH (electron transporter to electron transport chain) through subsequent oxidation reactions to pyruvate Net ATP: -2 x ATP used in stage 1 of glycolysis +2 x (+2 x ATP generated per oxidation to pyruvate) +2 ATPs generated per glucose molecule Also 2 NADH molecules NAD + is a finite resource needed for the oxidation of glyceraldehyde 3-phosphate into pyruvate This is regenerated through conversion of pyruvate to either ethanol (alcoholic fermentation) or lactic acid (lactic acid fermentation) This allows for regeneration of NAD+ to continue the glycolytic cycle Conversion of pyruvate into Acetyl CoA leads to further leads to further extraction of energy through combustion to CO 2 and H 2 (in the citric acid cycle) Glycolysis - Regulation (Muscle) Hexokinase Function is inhibited by its product, glucose 6-phosphate Biochemistry Exam 2 10 Inhibition of PFK leads to build up of glucose 6-phosphate which then inhibits hexokinase Phosphofructokinase (PFK) ↑ ATP allosterically inhibits AMP binds to the same allosteric site as ATP, but does not inhibit ↓ ATP/AMP ratio increases enzyme activity Low pH also inhibits PFK activity (prevents damage from too much lactic acid fermentation in anaerobic conditions) Pyruvate kinase ↑ ATP allosterically inhibits Fructose 1, 6-bisphosphate activates Recurring theme in regulation of metabolic processes - the end-product of the pathway often has a feedback inhibition effect on the system - and for irreversible steps, often the product of that step directly inhibits the enzyme that catalyzes it. Glycolysis - Regulation (Liver) Glucokinase (rather than Hexokinase) Liver uses this enzyme primarily to phosphorylate glucose in the liver KM of glucokinase >> than KM of hexokinase - glucose must be much more abundant Brain and muscle have dibs on glucose before liver cells Phosphofructokinase (PFK) Same regulatory mechanisms true in liver as in muscle - not usually need for rapid ATP production in the liver (compared to muscle) Inhibited by citrate (intermediate of citric acid cycle) Second PFK2 enzyme in liver converts some F-6P into F-2,6-BP - a potent activator of PFK1 Pyruvate kinase (isozyme in liver, L form vs M form in muscles) Biochemistry Exam 2 11 ↑ ATP allosterically inhibits Fructose 1, 6-bisphosphate activates Allosterically hindered by alanine (simple conversion product of pyruvate) Gluconeogenesis - What it is… Gluconeogenesis - Synthesis of glucose from noncarbohydrate precursors Major site of gluconeogenesis is the liver Conversion of pyruvate to glucose THE IRREVERSIBLE STEP How is gluconeogenesis powered in the cell? Addition of a phosphoryl group to pyruvate is highly endergonic (+31 kJ/mol) Formation of phosphoenolpyruvate from pyruvate is much less endergonic (+0.8 kJ/mol) Decarboxylations often drive reactions that are otherwise highly endergonic (learn more in Citric Acid Cycle and Fatty Acid Synthesis) Just like in glycolysis, in gluconeogenesis energetically unfavorable reactions are coupled with energetically favorable ones to drive spontaneity of the process. Gluconeogenesis - Reciprocal regulation with glycolysis Gluconeogenesis and glycolysis are coordinated so that, within a cell, one pathway is relatively inactive while the other one is highly active Biochemistry Exam 2 12 The basic premise of the reciprocal regulation is that when glucose is abundant, glycolysis will predominate. When glucose is scarce, gluconeogenesis will take over In contracting skeletal muscle, the formation and release of lactate lets the muscle generate ATP in the absence of oxygen and shifts the burden of metabolizing lactate from muscle to other organs, such as the liver Liver restores the level of glucose necessary for active muscle cells, which derive ATP from the glycolytic conversion of glucose into lactate Biochemistry Exam 2 13 Chapters 18 & 19 - Citric Acid Cycle Citric Acid Cycle Most pyruvate is processed aerobically by first being converted into acetyl CoA Pyruvate is processed aerobically because oxygen is readily available Pyruvate dehydrogenase is a three enzyme complex that is regulated by ↑ acetyl CoA and ↑ NADH High concentrations of NADH and acetyl CoA inform the enzyme that the energy needs of the cell have been met or that enough acetyl CoA and NADH have been produced from fatty acid degradation. Essentially - products of the pyruvate dehydrogenase complex inhibit its activity Steps of Cycle Two-carbon acetyl unit condenses with a four-carbon component of the citric acid cycle oxaloacetate to yield the six-carbon tricarboxylic acid citrate Citrate releases CO 2 twice, which yields high-energy electrons A four-carbon compound remains and this four-carbon compound is further oxidized to regenerate oxaloacetate, which can initiate another round of the cycle Two carbon atoms enter the cycle as an acetyl unit, and two carbon atoms leave the cycle in the form of two molecules of CO 2 This cycle generates very little ATP Biochemistry Exam 2 14 TCA cycle will produce 2 GTP, 6 NADH, 2 FADH₂, and 4 CO₂ for every glucose molecule Biochemistry Exam 2 15 💡 Can I Keep Selling Seashells For Money, Officer Chapters 20 & 21 - Electron Transport Chain (Oxidative Phosphorylation) Electron Transport Chain - Overview Glycolysis and the Citric Acid Cycle generates high energy electron carriers (NADH and FADH 2) which transfer those electrons to oxygen through a series of embedded inner mitochondrial membrane proteins (the electron transport chain). Exergonic energy released from these redox reactions powers the movement of protons to the space between the inner and outer mitochondrial membrane. This proton gradient is then used to power ATP synthesis by oxidative phosphorylation. Biochemistry Exam 2 16 What is the primary catabolic function of the citric acid cycle? Harvesting of high-energy electrons from carbon fuels (in the form of NADH and FADH 2) Electrons from NADH and FADH 2 are used to reduce molecular oxygen to water through a series of electron carrier A strong reducing agent (such as NADH) is poised to donate electrons and has a negative reduction potential, whereas a strong oxidizing agent (such as O 2 ) is ready to accept electrons and has a positive reduction potential Electron flow through the electron-transport chain creates a proton gradient If NADH pumps 10 H+ and is equal to 2.5 ATP equivalents, how many protons does it take to catalyze production of a single ATP? 4 H+ makes 1 ATP FADH2 pumps 6 electrons total, how many ATP does it make? FADH2 is worth 1.5 ATP equivalents REMEMBER - 32 Electron flow within three of these transmembrane complexes leads to the transport of protons across the inner mitochondrial membrane Electrons of NADH enter the chain at NADH-Q oxidoreductase (also called Complex I) Biochemistry Exam 2 17 Flow of two electrons from NADH to coenzyme Q through NADH-Q oxidoreductase leads to the pumping of four hydrogen ions out of the matrix of the mitochondrion Electrons of FADH 2 enter the chain at Ubiquinone (Coenzyme Q, or Q) (also called Complex II) Q also serves as the electron transporter between Complex I and Complex III, as well as Complex II and Complex III Second of the three proton pumps in the respiratory chain is Q-cytochrome c oxidoreductase (also known as Complex III) Q-cytochrome c oxidoreductase is to catalyzes the transfer of electrons from produced by Complex I and Complex II to oxidized cytochrome c (Cyt c), a watersoluble protein, and concomitantly pump protons out of the mitochondrial matrix Last of the three proton-pumping assemblies of the respiratory chain is cytochrome c oxidase (Complex IV) Catalyzes the transfer of electrons from the reduced form of cytochrome c to molecular oxygen to form water Proton Motive Force (Chemiosmosis) Proton Motive Force Transfer of electrons through the electron-transport chain leads to the pumping of protons from the matrix to the cytoplasmic side of the inner mitochondrial membrane H+ concentration becomes lower in the matrix, and an electric field with the matrix side negative is generated Protons then flow back into the matrix to equalize the distribution which drives the synthesis of ATP by ATP synthase Chapters 24 & 25 - Glycogen Degradation and Synthesis Glycogenolysis (Glycogen Breakdown) - overview Biochemistry Exam 2 18 Glycogen phosphorylase - cleaves non-reducing (OH terminal) ends of glycogen chain, through addition of a phosphate, making glucose 1-phosphate Transferase - shifts a block of three glucosyl residues from one branch to another ⍺-1,6-glucosidase cleaves off the glucose at the ⍺-1,6-glycosidic linkage Phosphoglucomutase converts glucose 1-phosphate into glucose 6-phosphate through exchange of a phosphate group on a phosphorylated serine at the enzyme active site Regulation Liver contains an hydrolytic enzyme (glucose 6-phosphatase) that dephosphorylates glucose 6-phosphate, allowing for glucose release into the blood for transport to other parts of the body. Liver maintains glucose homeostasis of the entire organism, whereas muscle uses glucose to produce energy just for itself Glycogen phosphorylase in the liver is allosterically regulated by binding of glucose to the active site In contrast, glycogen phosphorylase in the muscle is positively regulated by AMP build-up and negatively regulated by ATP build-up Low blood glucose or stress induce release of glucagon (from the pancreas) and epinephrine (from the adrenal gland) stimulate glycogenolysis and gluconeogenesis in the liver, as well as glycolysis in muscle cells. Biochemistry Exam 2 19