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Biochem Exam 3
BIochem 1, 2nd half, Candas Exam 1
| Question | Answer | Reasoning |
|---|---|---|
| Monosaccharides | simple sugars, cannot be brokenm down into simplar sugars under mild conditions | |
| Oligosaccharides | "few" sugars, 2-10 simple sugar residues | |
| Polysaccharides | polymers of simple sugars | |
| What sugars contain a aldehyde FG? | Aldoses | |
| What sugars contain a ketone FG? | Ketoses | |
| How are the number of carbons denoted in sugars? | greek number prefix, (tri, tetra, penta, hexa, etc...) | |
| Aldoses with 3C+ and Ketoses with 4C+ are... | Chiral | |
| What are the isomers sugars can be in? | Ketone or Aldehyde | |
| How would you determine wheter a sugar is L or D conformation? | R configuration= D S configuration= L | |
| What is a Diastereomer? | pair of isomers with opposite configuration but are not mirrors | |
| What is an Epimer? | suagrs that differ in configuration ONLY at one chiral center | |
| What configuration are most monosaccharides found in nature in? | D | |
| Why is it rare to find a monosaccharide that contains more than 7 carbons? | 6C sugars are more reactive than 7C | Cyclization |
| What ways can sugars cyclize? | Furanose or Pyranose forms | |
| What can Aldoses like glucose cyclize to form ? | cyclic hemiacetal | |
| What can Ketoses like fructoses cyclize to form? | cyclic hemiketal | |
| Which carbon becomes asymmetric when hemiacetals and hemiketals are formed? | Carbonyl carbon | |
| What are isomers of monosaccharides that differ only in their configuration about the asymmetric carbon? | Anomers | |
| What is the cyclic form of glucose? | Pyranose | |
| What is the cyclic form of fructose? | Furanose | |
| The linear form of what monosaccharide forms a cyclic hemiacetal with an anomeric carbon after an intramolecular rxn | D-glucose | |
| What is the configuration at the anomeric carbon when the hydroxyl group & anomeric carbon are on the same side of a fisher projection? | alpa-D-glucose | |
| In a Hawworth projection, what direction is the OH pointing for D-sugars? | Down | |
| In a Haworth projection, what direction is the OH pointing for L-sugars? | Up | |
| How can a sugar be converted into a sugar-acid? | redox rxn to have free anomeric carbons | the anomeric carbon reduces oxidizing agents like peroxide, ferricyanide, and some metals |
| What sugars dont generate compounds with an aldehyde group? | Non-reducing sugars | ex: sucrose, it doesnt contain a hemiacetal or hemiketal group thus stable in water and a non-reducing sugar |
| What is benedit's sugar and how is it helpful? | mixture of sodium carbonatem sodium citrate, and copper(II) sulfate pentahydrate that is used to detect reducing sugars | |
| If beneditc's reagent is used, what color would the soln change in presence of reducing sugars? | Blue-> Yellow | |
| How does oxidation conditions affect monosaccharide oxidation? | yield different sugar acid(s) | |
| How would mild chemical oxidation affect the oxidation of an aldose? | convert aldehyde FG into carbox acid FG at C1 | |
| What does the mild chemical oxidation of an aldose yield? | aldonic acids | ex: gluconic acids |
| What would oxidation of C6 in an aldose yield? | Alduronic acids | ex: glucuronic acid |
| Oxidation of an aldose at C1 and C6 would yield? | Dibasic Aldaric acids | ex: aldaric- and - glucaric acids |
| What are the most common derivatives of monosaccharides? | Sugar; acids, alcohos, esters Deoxy sugars Amino sugars Acetals Ketals Glycosides | |
| How are sugar alcohols formed? | mild reduction of sugars | |
| Is Myoinositol a sugar alcohol? | no | its an Polyhydroxy cyclohexane |
| How are sugar alchols like xylitol, sorbitol, and mannitol used? | sweeten "sugarless" gums | |
| What are Deoxy sugars? | monosaccharides with 1+ OH FGs replaced with H | |
| What is Fucose a component of? | (come) cell walls | |
| What is Rhamnose a component of? | Ouabain | |
| Why sugar esters, specifically phosphate esters of glucose, fructose and other monosaccharides important? | metabolic intermediates | |
| Fructose-1,6-biphosphate is important because... | it is an important step in glycolysis/glucogenesis | |
| What is the prominant form of fructose in Honey? | beta-D-fructopyranose | |
| Where is the amino FG in Amino sugars? | C2 | replaces -OH |
| Where are amino sugars found? | Oligosaccharides and polysaccharides | |
| Glucosamine and Galactosamine are examples of... | Amino sugars | |
| What is Muramic acid? | component (along with glucosamine) of bacterial cell walls | |
| What is the structure of Muramic acid? | glycosamine linked at C3 to 3 carbon acid | |
| What is Ouabain? | toxic cardiac glycoside | |
| What are Sialic acids? | N-acetyl and N-glycolyl deravites of Neuraminic acid | |
| What do Sialic acids contribute to? | cell adhesion (and cell signaling?) | |
| What rxns are the basis for oligo- and polysaccharides? | Acetals <=> Hemiacetals Ketals <=> Hemiketals | Dehydration syntheses |
| What react to form Glycosides through dehydration synthesis rxns? | Pyranose & Furanose forms of monosaccharides and alcohols | |
| What new bond is formed when Pyranose & Furanose forms of monosaccharides react with alcohols? | Glycosidic bond | |
| Disaccharides like Lactose, Maltose, Sucrose, Cellobiose, and Isomaltose are .... | mixed acetals, one OH provided intramolecularly and on from other monosaccharide | |
| Which of the mixed acetal disaccharides have anomeric carbons? | Lactose, Maltose, Cellobiose, and Isomaltose | |
| which mixed acetal disaccharides are made up of 2 glucose molecules? | Maltose, Isomaltose, and Cellobiose | |
| Which mixed acetal disaccharide is made up of a galactose and glucose molecule? | Lactose | |
| Which mixed acetal disaccharide is made up of a fructose and glucose molecule? | Sucrose | |
| Which mixed acetal disaccharide is not a reducing sugar? | Sucrose | |
| What is Trehalose? | disacchairde that is a natural component of plants, algae, fungi and bacteria | |
| What disaccharide is made when 2 glucose molecules are linked head-head? | Trehalose | |
| What are the mechanisms that allow trehalose to protect structural and functional integrity of biological molecules? | 1) Greater fexibility in the glycosidic linkage 2) Stable at high temperatures or desiccation 3) Resistant to hydrolysis and generally chemically inert | |
| What is an oligosaccharide that is an antibiotic produced by a strain of streptomyces erytherues? | Erythromycin | |
| What is an oligosaccharide produced by Streptomyces griseus? | Streptomycin | |
| Which basic polysaccharides f(x) as storage? | Starch in plants and Glycogen in animals | |
| Which basic polysaccharide f(x) as structure? | Chitin and Cellulose | |
| Which basic polysaccharides f(x) as recognition? | Glycans on cell surface | |
| What are the two forms polysaccharides can exist in? | Homopolysaccharides or Heteropolysaccharides | |
| What is Starch? | energy storage polysaccharide in plants | |
| What two forms does starch exist in? | Amylose and Amylopectin | |
| When do branches in amylopectin of starch occur ? | ~12-30 residues | |
| What is the strucuture of Amylose? | alpha(1,4) links with a reducing end | |
| When do the branches in amylopectin occur? | alpha (1-->6) | |
| What is poorly soluble in water and forms micellar suspensions? | Amylose | |
| Amylose is _____ in micellar suspensins? | Helical | |
| How does iodine give starch its characteristic blue color? | Iodine slips/fit in middle of amylose helicase | |
| What is glycogen? | glucose storage from in animals | |
| What percent of the liver is made up of glycogen? | ~10 or less | |
| what percent of muscle mass is made up of glycogen? | 1-2 | |
| What is the difference between glycogen and amylopectin? | frequency of brancing, glcogen brances more | |
| Where and when does glycogen branch | alpha(1,6) every 8-12 residues | |
| What does the branching of pollysaccharides allow? | more sites for phosphorylase to attack and release glucose from chain | |
| What does the Phosphorylase rxn release? | glucose for metabolic energy | |
| What polysaccharides primarily consist of alpha(1,4) linkages? | Starch and Glycogen | |
| What strucutural polysaccharide consist mostly of beta(1,4) linkages? | Cellulose | |
| What is Cellulose? | polysaccharide that provides physical struture and strength to plants | |
| What is the most abundant polymer in the world? | Cellulose | |
| Where is cellulose mostly found? | cell walls of most plants | |
| Why are the wood and bark of trees insoluble? | highly organized structures of cellulose and lignin | |
| What strengthens the structure of cellulose? | H-bonds | |
| What fabric/material is mostly made of cellulose? | cotton | |
| What is Cellulase? | cellulose hydrolyzing enzyme | |
| What produces cellulase? | fungi, bacteria, and protozoans | |
| What is the most familiar cellulase activity? | breakdown of cellulose to beta-glucose by cellulase | |
| Which animals can digest cellulose? | Giraffes, cattle, deer, and camels | |
| Why are animals such as giraffes able to digest cellulose? | rumen harbors symbiotic bacteria that secret cellulase | |
| Aside from Ruminant animals (those with rumens), how do most animals digest cellulose? | partly digest through fermentation | |
| What is Dextran? | polysaccharide similar to amylopectin, oral bacterial product that adhered to teeth (plaque) | |
| How does dextran differ from amlylopectin? | alpha(1-6) glycosidic linkages and branches attached by alpa(1-2,3 or 4) linakges | |
| How are dextrans formed? | by bacteria | |
| What do dextrans in plaque provide for oral bacteria? | protection | |
| How are dextrans used commercially? | polishing materials, food additaives, and plasma volume expanders | |
| How is dextran used in column chromatography? | cross-linked "sephadex" gels used to seperate biomolecules based on size | |
| What is Chitin? | found in exoskeletons of crustaceans, insects and spiders, also makes up cell walls of fungi | |
| How does Chitin differ from Cellulose? | C2s are N-acetyl, and strands can be parallel or antiparallel | |
| How is chitin linked to allergic reactions? | neither synthesized or digested in human body which leads to allregic reaction | |
| What are Glycoaminoglycans? | linear chains of repeating disaccharides that are components of proteoglycans | |
| What make up a Glycoaminoglycan? | disaccharide with atleast one amino sugar and atleast one negative charge | |
| What are bacterial cell walls composed of ? | 1 (G+) or 2 (G-) bilayers with a petidoglycan shell between (G-) or coat (G+) | |
| How do Gram(+) and Gram(-) bacterial cell walls differ? | Gram(+): pentaglycine bridge connects tetrapeptides Gram(-): direct amide bond between tetrapeptides | |
| What are Lipopolysaccharides? | coat outermembrane of Gram(-) bacteria | |
| What is PAMP? | Pathogen associated molecular pattern | |
| What is the structure of a lipopolysaccharide? | lipid group anchored to outer membrane joined to a polysaccharide | |
| What is Sugar code? | ID information related to (bacterial?) cells | still dont mostly understand |
| How do surface polysaccharides affect animal cells? | surface polysaccharides can 1)alter phys and chem properties 2)stabilize conformatins 3)protect against proteolysis 4) cushion cells 5) regulate cell to cell recognition 6) modulate cell growth cycle 7) | |
| What are O-linked saccharides? | carbohydrates moieties of glycoproteins linked to the protein via serin or theronine | |
| What are N-linked saccharides? | carbohydrate moieties of glycoproteins are linked to the protein via asparagine | |
| What are the biological f(x)s of Glycoconjugates? | Cell-adhesion, signaling, migration Extracellular matrix formation inflammatory responses Leukocyte trafficking Immunity (innate and adaptive) Transcription control Organelle biosyntehsis Lysosomal enzyme targeting QC of glycoprotein biosyn | |
| What are some implications of Glycoconjugates? | Cancer Autoimmune diseases imflammatory diseases Diabetes Cogenital Muscular Dystrophies Multiple Hereditary Exostoses Glomerulonephropathies Congentital disorders of glycosylation | |
| When would feedback inhibition occur during enzyme regulation pathways? | when end product fo rxn interferes with rxns "upstream" | |
| What is the engine that sails the ship? | metabolism | |
| What are Zymogens? | inactive precursors of enzymes | |
| What rxn/process usually produces an active enzyme? | Proteolytic cleavage | |
| What is the origin of Zymogens like Trypsinogen, Chymotrypsinogen, Procarboxypeptidase, and Proelastase? | Pancreas | |
| What is the origin of Pepsinogen? | stomach | |
| What are Trypsinogen, Chymotrypsinogen, Procarboxypeptidase, Proelastase, Pepsinogen? | Zymogens | |
| What is the active protease for Trypsinogen? | Trypsin | |
| What is the active protease for Chymotrypsinogen? | Chymotrypsin | |
| What is the active protease for Procarboxypeptidase? | Carboxypeptidase | |
| What is the active protease for Proelastase? | Elastase | |
| Waht is the active protease for Pepsinogen? | Pepsin | |
| How are zymogens activated? | after portion of zymogen peptide is removed | |
| Why dont zymogens digest the cells and tissues they are produced in? | b/c they are inactive | |
| What is Chymotrypsin? | digestive enzyme used for proteolysis | |
| What is proteolysis? | breakdown of proteins or peptides into amino acids by the action of enzymes | |
| Where is Chymotrypsin synthesized? | pancrease | |
| What is the precursor to Chymotrypsin? | Chymotrypsinogen | |
| How could 2 chymotrypsinogen molecues activate each other? | removing two small peptides in a trans-proteolysis rxn | |
| How are chymotrypsinogen molecules connected after cleavage? | disulfide bond S-S | |
| What are Isozymes? | aka isoenzymes, proteins with different stucture that can catalyze the same rxn | |
| Why would isozymes have differeing mechanisms and/or kinetics? | differeing polypetide chains (length and/or residues) | |
| What could alternative spilicing of a single gene produce? | isozymes (multiple related proteins) | |
| What is LDH? | Lactate Dehydrogenase | |
| Why is LDH important? | 5 isomers with differeing units all target different and specific organs | |
| Where is LDH alpa-4 mostly active? | Liver and some in muscle | |
| Where is LDH alpha-3 beta somewhat active? | small in liver and muscels and even less elsehwere | |
| Where is LDH alpha-2 beta-2 mostly active? | WBC and Brain | |
| Where is LDH alpha beta-3 mostly active? | Brain, RBC, Kidney and Heart | |
| Where is LDH beta-4 mostly active? | Kideny and Heart | |
| What does LDH-B gene transribe and encode? | LDH-H | |
| How is LDH-A inducible? | Hypoxia | |
| What does LDH-A gene transcribe ane encode? | LDH-M | |
| Which LDH preferentially catalyze the oxidation of lactate into pyruvate? | LDH1 and LDH-4H | |
| Which LDH have intermediate enzymatic activites in the oxidation of lactate into pyruvate? | LDH2, LDH3, and LDH4 | |
| Compared to LDH-H, which LDH has a higher Km and Vmax for pyruvate reduction? | LDH-M | |
| Which LDH preferentially catalyze the reduction of pyruvate into lactate? | LDH5/LDH-4M | |
| What is LDH a serum marker for? | diagnosis of a heart attack (myocardial infartion) | |
| When is LDH released? | after tissue damage that was caused by MI, Hepatitis, or actue renal failure | |
| What is the normal relationship of LDH-2 and LDH-1? | LDH-2 levels > LDH-1 | |
| What is the flipped LDH pattern? | LDH-1 levels are higher than LDH-2 after MI | |
| When do LDH levels rise after MI? | within 24-72 hours | |
| When do LDH levels peak after MI? | 3-4 days | |
| When do LDH levels return to normal after MI? | ~14 days | |
| What enzymes increase in level after a heart attack? | LDH, Troponin, CK | |
| What is Allostery? | process by which proteins transmit effect of binding at one site to another functional site | |
| What does allostery allow? | regulation | |
| what is allosteric regulation? | process of modulating activity of a protein by binding of an effector to site other than active site | |
| How could alloteric regulation modulate protein activity? | 1) reversibile alteration of protein conformation after effector binds | |
| What are effectors taht increase activity? | Activators | |
| What are effectors that decrease activity? | Inhibitors | |
| T/F: Allosteric effectors can be activators or inhibitors? | T | |
| What accounts for the responsiveness of cells to external signals and for the regulation of metabolic pathways? | Allostery | |
| How many subunits do most allosteric enzymes have? | 2+ | |
| How do allosteric subunits behave? | oscillate between active and inactive forms | |
| Enzymes that are part of key steps in metabolic pathways are modulated by.... | allosteric effectors | |
| Where are allosteric effectors produced? | earlier in metabolic pathways | |
| How does the distance from active site to regulatory trigger vary ? | few angstroms to 10s of angstroms | |
| What kinetics curve do multisubunit enzymes that exhibit allosteric regulation show? | Sigmoidal (s-shaped) | |
| What type of kinetics dont apply to allosteric modulators? | Michaelis-Menten | |
| T/F: Allostery and Cooperativity are the same concept? | F | cooperativity involves affinity, effect is allosteric in nature but it is not allostery |
| What is the Hill coefficeint? | degree of cooperativeness of logand binding to the enzyme or receptor | |
| What is the relationship between cooperativity and affinity? | equal affinity=> no coop. increased affinity=> positive coop decreased affinity=> negative coop | |
| What does a Hill coefficient greater than 1 suggest? | more than one binding site exist | |
| What are the models for allosteric regulation? | Concerted/Symmetry and Sequential | |
| What is the Concerted/Symmetrical model of allosteric regulation? | allosteric proteins can exist in two states, Relaxed or Tight | |
| What is the sequential model of allosteric regulation? | allosteric proteins sequentially undergo state change | |
| In the concerted modle of allosteric regulation, where do effector molecules bind? | either state (tight or relaxed) | |
| Which state does the substrate bind to better in the concerted model of allosteric regulation? | relaxed>>tight | R has higher affinity than T |
| What state is more abindant in absence of substrate in the concerted modle of allosteric regulation? | tight | |
| What will binding of ligand increase Eq in favor of T or R in the concerted allosteric regulation model? | R | |
| Protein subunits are in _______ between T and R states | equilibrium | |
| T/F: all subunits must be in the same state in the concerted model of binding | T | |
| T/F: In the concerted model of binding, substrate binding stabilizes R state | T | |
| T/F: In the concerted model of binding, excess substrate binding does not increses stability for R state? | F | inscreases stability because concerted model based on affinity, substrate has greater affinity for R state and excess binding increses stability |
| In the concerted model of binding how does the allosteric transition between R and T states ocurr? | naturally occurs as regulators shift Eq in either direction | |
| In the concerted model of binding, what would an agonist, inhibitor, and substrate cause to the R and T states? | stabilization | |
| In absence of _____ regulated proteins exist in interconvertible states? | regulator(s) | |
| How is cooperativity achieved in the concerted model of binding? | Substrate binding increases [R] which increases # of binding sites | s exerts positive homotropic effect |
| What are homotropic effectors? | molecules that influence the binding of something other than themselves |
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