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Week 7 Notes

by: Jordana Baraad
Jordana Baraad
GPA 3.9
Fundamentals of Biochemistry
Dr. Ramonell

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About this Document

Notes corresponding to Dr. Ramonell's Wednesday 10/6 Carbohydrates powerpoint slides and Dr. Wang's Friday 10/8 Nucleic Acids slides
Fundamentals of Biochemistry
Dr. Ramonell
Class Notes
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This 9 page Class Notes was uploaded by Jordana Baraad on Friday October 9, 2015. The Class Notes belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 69 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.

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Date Created: 10/09/15
106 Chapter 7 Carbohydrates Ramonell Carbohydrates Most abundant biomolecule EXAM Q Most abundant carb cellulose Glucose important for our energy metabolism Plants make sucrose not glucose Central role in energyyielding pathways Structural role in DNA RNA Structural element of cell walls Cellulose structural polysaccharide Durable polymer of glucose like starch and glycogen Diversity of sugars Glucose and fructose nutritional polysaccharides Different shapes in polysaccharides Lots of hydroxyl OH groups 9 linkages Important any many processes Cell signaling cell identification Addition to cell always pointing outward Carbohydrates 2 Formula Cn H20n Cn carbo H20n hydrate From C02 amp H20 9 6C sugar for Calvin Cycle Use G3P for molecular synthesis and making fructose diphosphate Fructose diphosphate used to make glucose sucrose starch and other carbs range in size covalent linkage 9 proteins extracellular matrix and cell signals Monosaccharides Aldehydes or ketones Names osequot 3C triose 4C tetrose 5C pentose 6C hexose 7C heptose etc multiple OH groups from SC on must consider stereochemistry chiral carbons multiple chiral centers etc 3 C aldoses have a single chiral center H O C H I OH hiral center H stereochemistry important for all biomolecules enzymes recognize only 1 isomer stereospecificity is key Fischer Projections are used to symbolize stereochemistry Flattened structure Look at Where are OH groups located L or D right or left Dglyc 9 R 9 Rglyc Aldehyde ketone always on top Aldehyde C1 position ketone C2 Aldoses that have 4C have 2 chiral centers In book everything explained in terms of D OH on right or L OH on left 99 of biomolecules we cover are D consider chiral C farthest from aldehyde ketone Dthreose is epimer to Derythrose Only difference position of C2 OH group 5C sugars are often found in biological symptoms know structures on this slide glucose for test Dribose key in genetic molecules DNA like RNA but with one less OH Chemical Structure of Aldohexoses Dglucose know structure OH on left opposite rest of structures have OH on right alternate between cyclical and linear form cyclical favored interactions between aldehyde ketone and alcohol 9 cyclizing rxn Hemiacetal and Hemiketals Intermolecular cyclization rxns The Open Chain Form of DGlucose Can Cyclize See Fig 76 H o C l C2 O 39l 39I I C5 6 H nucleophilic attack 9 alpha and beta forms see fig Alpha and beta forms are anomers Only difference possible C6 carbon Freely reversible rxns How to determine alpha v beta Alpha OH group and C6 carbon on opp sides Beta OH group and C6 carbon on same side Bottom right pic new chiral center anomeric Carbon 5C and 6C aldoses can cyclize to form furanose and pyranose rings 0 O O D furanose 9 furan r1ng 5C betadfructofuranose 1 amp 6 C outside ring V betaDglucopyranose just 6 C outside ring pyranose 9 pyran ring 6C Ketose 3C and 4C Structures 6 C Ketose sugars can also cyclize to furanose and pyranose rings H H H 020 H Cs H 6C OH H i H 5C ring ring 0 394 Ce Ca I I OH OH H CSOH furanose CI39lon pyranose Cs C3 2 C 06 OH 4 C5 C2 C4C OR 3 CHZOH Sugars Chem Nucleophilic Rxns amp Sugars can also act as electrophiles main pt 1 Anomeric carbon key for rxns a Nucleophile and electrophile 2 ALL OH groups can act as electrophiles a Multiple centers of reactivity in any sugar b All groups very reactive c Frequent modifications in biological systems particularly for transport i EX sucrose synthesized in cytoplasm Calvin cycle in leaves must transport 9 rest of plant ii Ex sugar in liver 9 rest of body transport to cells without reacting along the way Organisms can have many hexose derivatives Sugars in dark blue central box important to joints Acid sugars Negative charges 9 interactions w water Form complex polymers Hydrate Gellike protective layer cushion and important in signaling Important long chains polymers Reaction of the Hemiacetal w Alcohol 9 Glycsoside Bond glycosidic Condensation rxn Bottom maltose Anomeric carbon C4 Sugar polymers have polarity Reducing end w hemiacetal Reactive end add to chains on this end Nonreducing end no hemiacetal Monosaccharides are joined by a glycosidic bond to form disaccharides Common Disaccharides 1 of Carbons linked together a ALWAYS start w anomeric C b Lactose beta form has 14 linkage 2 Was the anomeric C in the alpha or beta position a Fig 711 top pic beta194 linkage b Fig 711 bottom pic alpha191 linkage c trehalose unusual don t worry about this for test too complex 3 3 Carbon polymers are catalyzed by enzymes a regulated at with respect to both formation and breakdown Looking at the most biologically relevant polysaccharides Polysaccharides are described by several parameters Not defined by molecular weight Contrast to proteins Nutritional polysaccharides starch and glycogen Structural polysaccharides cellulose and chitin Macroscopic View of Polysacharides Homopolysaccharides all monomers the same Heteropolysaccharides different monomers Branch points almost always for 196 likages Structure durable resistant to degratdation steel cablequot cellulose has partly crystallized structure unbranched chains bound together Hbonding between multiple fibers Starch and Glycogen starch spiral when packed association amylose and amylopectin Hbond pattern forces spiral Macroscopic View of Starch Reducing amp nonreducing ends Fewer reducing ends mainly nonreducing ends All enzymes work on nonreducing side 108 Nucleotides and Nucleic Acids Wang Nucleotides and Nucleosides 1 C anomeric beta OH on same side as anomeric C Phosphate Groups 5 attachment lots of energy Pentose in Nucleotides DNA removal of 2 OH 9 tight packing RNA can t pack as tightly w 2 OH no double helix formed Chair conformation possible Nucleobases heteroaromatic N amp C on ring double and single bonds function like resonance structure electron cloud evenly distributed resonance 9 UV absorbance 250270 nm Nomenclature Deoxyribonucletodies 2 letter d base type A G C T 4 letter d base type phosphates MPDP TP MP monophosphate 1 DP diphosphate 2 TP triphosphate 3 Nomenclature Ribonucleotides 1 letter and 3 letter same idea wo the quotdquot U instead of T for base type BetaNGlycosidic Bonds N to link base and sugar 1 anomeric C of sugar for linage CN connection Stable bond Cell conditions enzymes cleave bond Lab conditions acid cleaves bond UV Absorption of Nucleobases photoprotection doesn t uoresce Lot 245 nm max absorption for singlestranded 260 nm max absorption for doublestranded Polynucleotides Linkage pentose sugar and phosphate Pentose neutral phosphate negative overall neg charge DNA backbone stable and packed RNA bad packing bc of 2 OH Linear polymers no chains Direction 5 9 3 1St phosphate group attached to pentose at 3 HBonding Neighbors limit polynucleotide pairing DNA 2 possibilities AT 2 Hbonds or GC 3 Hbonds Discovery of DNA Structure Collaboration of 4 individuals Watson and Crick Wilkins and Franklin Franklin had greatest contribution w raw materials Died preventing Nobel award WC Model of BDNA Natural conformation in cell most important Righthanded Complimentary Pairing Fixed pairing bc of Hbond Complimentary bottom 9 top Replication of Genetic Code semiconservative model each strand serves as template for new strand synthesis new helix has 1 new strand 1 old strand mRNA reads from DNA transcription mRNA V DNA mRNA ribose amp Uracil mRNA codes for more than 1 type of protein Palindrome sequence Hbonding w n palindrome problem Hbonding between beginning and end hairpin Especially bad if gt 4 bases Disables PCR primer DNA Denaturation Different from protein denaturation breaking of disulfide bonds Temperature and heat used more than pH for denaturation Reverse process annealing Use cold temps Thermal DNA Denaturation Annealing spontaneous reaction foundation of PCR Figure 8 2 7a TM temp at which 50 primer denatured Sequence determines denaturation temperature If richer in GC bonds higher temp required More heat energy required bc more Hbonds to be broken Too much GC nonspecific association Ionic strength varied more than pH 2 NearComplimentary Pairs not 100 complimentary still OK uorescent probe anneal w target protein sitedirected mutagen purposeful mismatch long primer can still match Mutations in DNA Ch 25 DNA relatively stable Types Spontaneous Deamination everyday process very slow Repaired by cell efficiently Hydrolysis depurination pyrimidines more stable Repaired by cell efficiently Reactive chemicals Radiation UV repaired by cells but inefficiently Xray worst kind of radiation Molecular Mechanisms of Spontaneous Mutagenesis Oxidation easily repaired Others fixable less efficient Molecular Mechanisms of Radiation Ionizing worst kind Breaks covalent bonds DNA Repair for Mutagens DNA polymerase 12 errors mBP E coli methylation to differentiate old and new strands Other Functions of Nucleotides cAMP 2ndary messenger sometimes mediates cell signaling pathway


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