General Chemistry II
General Chemistry II CHEM 1020
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This 20 page Class Notes was uploaded by Rebeka Zemlak MD on Wednesday October 21, 2015. The Class Notes belongs to CHEM 1020 at Tennessee Tech University taught by Barbara Jackson in Fall. Since its upload, it has received 34 views. For similar materials see /class/225691/chem-1020-tennessee-tech-university in Chemistry at Tennessee Tech University.
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Date Created: 10/21/15
Glycolysis Embdem Meyerhof Pathway Glucose enters the cell In the cytoplasm the 6 carbon glucose is broken down to two 3 carbon compounds pyruvate pyruVic acid or lactate lactic acid If there is enough oxygen then pyruvate forms giVing 5 ATPs to the good If there is not enough oxygen lactate forms giVing only 2 ATPs to the good Without oxygen the term anaerobic is used Pyruvate goes into the mitochondria where it is completely oxidized to carbon dioxide and ATP is formed ATP gt ADP ATP gt ADP glucose glucose6phos fructose 6phos fructose 16diphos fructose 16 bisphos NADH NAD 13diphospho lt glyceraldehyde ltgt dihydroxy glyceric acid 3phos acetone phos Pi ADP gt ATP ADP ATP gt gt 3phospho 2phospho phosphoenol pyruVic acid glyceric acid glyceric acid pyruVic acid NADHgt NAD lactic acid OVERVIEW OF WHAT HAPPENS IN THE CYTOPLASM 1 glucose yields 2 pyruVic acids or 5 ATPs 2 ATPs are needed for start up 2 lactic acids 2 ATPs to the good You make 2 ATPs when the diphosphate l3diphospglyceric acid goes to the monophosphate 3phosphoglyceric acid You make 2 ATPs when the monophosphate PEP goes to a nonphosphate compound pyruVic acid Why do you get 2 ATPs Because you get 2 glyceraldehydes from 1 glucose When you get 2 pyruVic acids as the end product you make 2 NADHHs worth 15 ATPs each 3 ATP When you get 2 lactic acids as the end product you use up the the NADHs generated so you do not get the extra ATPs Tally Pyruvic acid Start up 2 ATP 2 l3diphosphoglyceric acid 2 ATP goes to 3 phosphoglyceric acid 2 phosphoenol pyruVic acid 2 ATP goes to pyruVic acid 2 NADHHs formed in cytoplasm 3 ATP 2 ATPs each when the aldehyde goes to the glyceric acid 2 NADHs used up when pyruVic 0 ATP acid goes to lactic acid in the cytoplasm 2 ATPs each Net ATPs 5 ATP Lactic acid 2 ATP 2 ATP 2 ATP 3 ATP 3ATP 2 ATP GLUCOSE OXIDIZED TO 2 PYRUVIC ACIDS 5 This occurs in the cytoplasm The pyruvic acid goes into the mitochondria where it is converted to the acetyl Coenzyme derivative and C02 As the 3 carbon acid with a keto group gets oxidized to a 2 carbon acid and carbon dioxide NAD gets reduced to NADHH Since there are 2 pyruvic acids for each starting glucose 2 NADHHs are formed giving 5 ATP OXIDATION OF PYRUVATE TO ACETYL CO A 5 Occurs in mitochondria 0 0 H3CCCOOH Coenzyme ASH NAD gt H3CCSCoA NADHH CO2 pyruvic acid acetyl CoA 2 NAD gt 2 NADHH 25 ATP 5 ATP OVERVIEW OF KREBS CYCLE per turn 1 mole of glucose yields 2 moles of acetyl CoA giving 2 turns ofthe cycle per mole of glucose Each turn of the cycle gives 3 NADHH 25 75 l FADHH 15 15 l GTP l 10 ATP NADH S ARE GENERATED I When 6 Carbon acid gets oxidized to a 5 Carbon acid and CO isocitrate gt uketoglutarate OH goes to 0 II When 5 Carbon acid gets oxidized to a 4 Carbon acid and CO or ketoglutarate gt succinyl CoA III When an alcohol group gets oxidized to a ketone malate gt oxaloacetate FADH IS GENERATED When two hydrogens are removed from an acid and a double bond occurs GTP IS GENERATED When the Coenzyme A moiety comes off the CoA compound Acetyl CoA NUCLEIC ACID DNA and RNA contain 1 5 carbon sugar ribose or deoxyribose 2 purines and pyrimidines 3 phosphoric acid Purines General Structure Adenine for Purines Pyrimidines General Structure Uracil Cytosine Thymine found in DNA Uracil found in RNA RNA Base sugar nucleoside adenosine guanosine deoxyguanosine uridine cytidine Guanine Thymine DNA deoxyadenosine deoxythymidine deoxycytid If base is adenine adenosine 539 monophosphate MP What is ATP DNA Structure Double Helix Think of a ladder The sides are the sugars and phosphates and the rungs are the purines and pyrimidines Now twist the ladder A links with T and G links with C Histones Major protein class of DNA 5 histone proteins Hl H2A H3B and H4 Histones DNA and non histone proteins called chromatin DNA Replication Doublestranded A T GC TA RNA Types messenger RNA or mRNA ribosomal or rRNA 80 of all RNA transfer or tRNA 15 of all RNA splicing RNA or sRNA Semiconservative Replication MeselsonStahl Used heavy nitrogen in parent cell Next generation had 2 the heavy nitrogen Replication is bidirectional Each strand makes a copy It is synthesized from the 539 to 3 direction One chain is 5 gt3 and the other is 3 gt5 The 539 gt3 goes quickly This is the leading strand The lagging strand still synthesizes 539 gt339 direction It does it in sections called Okasaki fragments The pieces are pulled together by DNA polymerase Protein Synthesis The blue print of the cell is the DNA In the early experiments the scientists synthesized a poly uracil molecule When they placed the poly uracil in a tube of cell homogenate a poly phenylalanine peptide was isolated So UUU coded for phenylalanine The codon is the mRNA The portion ofthe DNA which codes for the messenger is called the sense Genetic Code Three bases code for 1 amino acid page 482 for full chart u u u phenylalanine g g u glycine g c u alanine uuu uuu gcu ggu gives the tetrapeptide phe phe ala gly Since uuu is the code for phenylalanine is the code on DNA or RNA MUTATIONS Three bases code for one amino acid shesawthebadboyhitthedog she saw the bad boy hit the dog Add one letter she saw the bad tbo yhi tth edo g sense nonsense Substitute one letter she saw the bae boy hit the dog sense nonsense sense Delete one letter she saw the adb oyh itt hed og sense nonsense B HbA normal hemoglobin ValHisLeuThrProGluGlu HbS Sickle Cell Hemoglobin ValHisLauThrProValGlu Glutamic GAA Valine GUA Origins of Mutations l UltraViolet light 2 Oxygen radicals 3 Ionizing radiation 4 Chemicals 5 Viruses Repair of Mutations Thyminethymine dimer or photoadduct are recoginzed by uvrABC ultraVioletlight repair system The dimer is cut out resulting in a gap lled by DNA polymerase and sealed with a ligase A segment of DNA is used to make a complementary copy of mRNA The segment has introns and exons Introns are the spaces of the DNA which are not needed The exons are the sections needed for the protein coding The uncut segment of RNA is called hrRNA heterogeneous nuclear RNA or ptRNA primary transcript RNA or primary transcript and sometimes premRNA premessenger RNA The strand of DNA which is copied is called the sense or coding strand The complementary strand is referred to as the antisense strand The genetic code is on the mRNA 3 bases code for 1 amino acid AUG is the starting base methionine The sequences signalling the end of synthesis are UAA UAG amp UGA mRNA is short lived it s destroyed as soon as its mission is completed Transfer RNA tRNA carries the corresponding amino acid over to the ribosomes on the endoplasmic reticulum Looks like a colverleaf with the amino acid attached at the 3 position The tRNA is specific for the individual amino acids The anticodon in the tRNA is important If an alanine tRNA were changed to have a cysteine in the place of alanine the tRNA would still line up where alanine should be The mRNA lines up on the ribosomes There is a 39p39 site and an a site Methionine sits on the 39p site and a tRNA with glycine goes to the a site The methionine residue moves to the glycine and attaches The methionineglycine then moves to the 39p39 site and a third amino acid sits on the a site How do genes get turned on In E Coli when lactose is present the enzyme Bgalactosidase is made in response to the lactose There is a structural gene which codes for the Bgalactosidase itself This gene is turned off when there is no lactose present There is an operator site where the repressor molecule sits Next to the operator site is a promoter site It holds in readiness RNA polymerase which is needed to transcribe the structural gene The repressor is a polypeptide made at the direction of its own gene a regulator gene located just above the promoter site When recptor molecules they bind to the DNA of the operator site This binding of the repressor is what prevents gene transcription and translation When lactose is present a modi cation of the lactose occurs and binds to the repressor which alters the shape of the repressor and the repressor comes off the DNA The system is now on Over 100000 human genes are in 46 chromosomes Scientists are mapping out which section codes what protein introns no information The same sections can be used for different coding depending on the introns sort of like skipping a few bases here and there and you39ve got a new protein Like Amino Acids Building block of proteins General formula NHZ l O R C C OH Types A Simple l Glycine 2 Alanine B Acidic 2 acid groups 1 Aspartic acid 2 Glutamic acid C Basic Lysine D Aromatic l Phenylalanine 2 Tyrosine PROTEINS AMINO ACID ENZYMES L form predominant COOH acid R determins the character of the amino acid gly ala asp glu lys phe tyr 3 Trytophan try E Sulfur Cysteine cys Cystine cyscys Proteins Proteins are made up of amino acids linked together as the acid and amine groups Peptide linkage Peptide means amino acids linked together in a chain Dipeptide 2 amino acids aspartylphyenylanine methyl ester is aspartamen Tripeptide 3 amino acids Glutathione is an antioxidant yglutamylcystylglycine Proteins are made up of peptide chains which are made up of amino acids Sickle cell glutamic acid replaced valeine Structure Primary order of amino acids Secondary Spacial arrangement helix keratin pleated triple helix collagen 30 of total protein Tertiary bonding amp folding of chains Quaternary chains subunits Compounds derived from amino acids Try Serotonin Neurotransmitter Changes in activity of serotonin neurons related to actions of psychedelic drugs Tyr Thyroxin Catechol Epinephrine Norepinephrine Dopamine Epinephrine is adrenalin Dopamine 20 normal level in Parkinson39s Phenylethylamine is a neurotransmitter gives people the feeling of Abeing in love Metabolite phenylacetic acid is excreted in urine Low levels of phyenylacetic acid correlates with depression For the protein to function as a protein it needs to retain its shape A protein may be inactivated or denatured by a heat b oxygen c acids d bases e chemicals Example of heat denaturation cooking an egg the clear albumin goes white Enzymes Enzymes are proteins that make a reaction go act as a catalysts End in ase proteinase methyl transferase DNA polymerase Example In liver we have detoxi cation enzymes which react with drugs or chemicals and then it can be excreted in the urine phenol OH glucuronic gt phenyl glucuronic acid a product of glucose Our whole system is enzymes For sucrose to go to actate and yield energy better than 20 enzymes are needed Some genetic defects are due to a missing enzyme Albinism loss of one of the amino acid metabolising enzymes PKU loss of an enzyme which reacts with phenylalanine Characteristics of Enzyme Activity 1 Dependent of temperature Cooling slows down the activity 2 Dependent on pH Each enzyme has a pH value where it works best 3 Dependent on concentration The more present and if substrate is available the greater the activity Substrate is the compound the enzyme works on and then gives a product S E gt SE gt E P 4 Cofactors some need metals or vitamins to work Proteins Functions Catalysis enzymer 2 Transport lipoproteins hemoglobin 3 Action actin 4 Support collagen 5 Protection antibodies 6 Chemical Messengers hormones throxin 7 8 9 Transmission of nerve impulses Rhodopsin Storage Toxin 10 Gene regulation Peptides Draw TyrGlyGly PheLeu Enkephalin endomorphins tolerance to pain receptor Morphine ties up the sites on brain Body site stops production of endomorphins Withdrawal Painful Separation of Proteins Column Chromatography l size 2 charge Electrophoresis charge isoelectric point Coenzymes Niacin Nicotinamide adenine dinucleotide NAD Ribo avin Flavin adenine dinudeotide FAD Pantothenic Acid Co enzyme A Thiamine Pyridoxine Biotin Folic Acid B12 Metals Copper Zinc iron Zymogens inactive form of enzyme Chymotrypsinogen cleaves off a small secction to make the active form of the enzyme chymotrypsin Makes the protein active Inhibitors 1 Competitive Inhibition looks a lot like the subtrate to interact with the enzyme ties up EZ E s gt ES gt E 1 E 1 gt E1 gt paminobenzoic acid sulfanilamide 2 Noncompetitive destroys a site breaks an 88 bond Metals will precipitate proteins 3 Feedback also called allosteric enzymes A gt gt gt gt gt gt choleterol Diagnostic Use of Enzymes Heart attack CPK creatine phosphokinase Liver damage SGOT serum glutamicoxaloacetic transaminase LDH Lactate Dehydrogenase Damaged heart muscles pours enzymes into the blood Nitrogen Balance BUN Blood urea nitrogen O nitrogen of amino acids generally appears as urea HzNCNHz positive nitrogen balance BUN low negative nitrogen balance BUN high breakdown of Protein LIPIDS DEF Compounds soluble in organic solvent Folch Extract Chloroformmethanol 21 Classi cation Phospholipids Triacylglycerides Fatty Acids Sphingolipids glycolipids Sterols Function Structure membranes Activation of enzymes Energy Storage Fatty Acids O R C OH Palmitic 160 Stearic 180 Oleic 181 Where is the double bond If you count from carboxyl group is at carbon 9 it is delta A9 If you count from the methyl group is also at 9 omega m 9 A 9 organic chemistry 03 9 biochemistry Polyunsaturated Fatty Acids linoleic 182 0369 linolenic 183 m369 Arachidonic 204 m691215 All three used to be called essential fatty acids Now 182 and 183 Needed for growth Linoleic gt arachidonic Draw 182 0369 Omega 3 Fatty Acids Monkeys fed high cholesterol diets developed atherosclerosis giving rise to a correlation between high fat diets and heart disease Eskimo diets were very high in fat yet they had a low incidence heart attacks Eskimo diets had a ve fold excess of omega 3 fatty acids compared to the diets of the Danes This prompted research into the omega 3 fatty acids SFA fully Saturated Fatty Acids MUFAMonoUnsaturated Fatty Acids PUFA PolyUnsaturated Fatty Acids EPA EicosaPentanoic Acid 205 Very high concentrations in sh anchovies DHA DocosaHexanoic Acid 226 herring sardines fresh tuna whitefish Diets high in omega 3 fatty acids Normalized blood pressure Reduced triglycerides Slower progression of atherosclerosis Enhanced defenses against cancer Diets too high in omega 3 fatty acids Increased susceptibility to strokes to the same extent it reduces heart attacks Can precipitate vitamin E deficiency Trans Fatty Acids Trans refers to the spacial arrangement of the carbon atoms A trans configuration gives a kink in the molecule The trans formation is found in ruminant fat made by microorganisms in thr rumen The major source is due to an artifact in the hydrogenation of unsaturated fatty acids Trans fatty acids are metabolized like the saturated fatty acids It is though that the trans may antagonize the metabolism of the essential fattya cids and make the deficiency worse Trans raises the LDL cholesterol levels and lowers the HDL cholesterol levels has an increase in cancer On autopsy 15 of the fatty acids were found to be trans Prostanglandins C20 comes from arachidonic acid Put in where the double bonds would be if the prostaglandins come from arachidonic acid Prostanoic Acid Function as hormones raising or lowering blood pressure constricting or dilating vessels or muscle contraction Nomenclature PG PGA PGEGz PGFz OH s on compound Metabolism not stored made in response aspirin inhibits synthesis of PG from arachidonic arachidonic gt PG Triacylglycerides glycerol stearic acid triacylglyceride tristearin Old literature and commercial press call them triglycerides Diglycerides have 2 FA Phospholipids Phosphatic Acid Phosphatidyl choline Lecithin One fatty acid of TG has been replaced by a phosphate group Where choline is we can have different compounds ethanolamine serine or inositol Sphingomyelin is both a phospholipid and a sphingolipid Blood Lipids Triacylglycerides are acted up by pancreatic lipase which gives glycerol fatty acids mono and diglycerides The glycerol and short chained 10C amp less fatty acids are absorbed through the intestine wall Chylomicra are synthesized in the intestine and transport mainly triacylglycerides The other blood transport proteins are Very Low Density Lipoproteins VLDL Low Density Lipoproteins LDL and High Density Lipoproteins HDL Human Plasma Lipoproteins Property Density mg plasma protein phospholipids cholesterolfree cholesterolester triglycerides fatty acids Steroids Bile Acids HDL Chylomicra VLDL LDL lt 095 0951006 l006l063 30500 3075 2025 1015 2 9 21 33 7 18 22 29 2 7 8 7 6 15 38 23 83 50 10 8 0 l l 0 Cholesterol ring Dchain has 8 carbons ring D has 5 carbons cholic acid Adrenal Hormones Cortisone Progesterone ring D has 2 carbons ring D has 2 carbons produce by corpus luteum and placenta l063l210 SeX Hormones No C39s also missing methyl group between A amp B rings Estradiol No C39s does have the methyl group between A amp B rings Testosterone Recap Cholesterol has carbons on the side chain Bile acids have carbons on the side chain Adrenal hormones have carbons on the side chain Progesterone has carbons on the side chain SeX hormones have carbons on the side chain The Pill Enovid rst approved birth control pill in 1960 Injection of progesterone worked but needed an oral administered hormone If ingested progesterone would be metabolized They replaced the group on the D ring CH3 with C C l l CO l D ring OH D ring The pill mimics pregnancy quotOral contraceptives may be rendered less effective and increased incidence of breakthrough bleeding may occur by virtue of drug interaction with rifampin isoniazid ampicillin neomycin penicillin V tetracycline chloramphenicol sulfonamides nitrofurantoin griseofulvin barbituates phenytoin primidone phenylbutazone analgesics tranquilizers diazepam and anti migrane preparationsquot Check with your pharmacist for possible interactions DES diethylstilbestrol was used to prevent miscarriages in 1950 1960 s High incidence of vaginal cancers in daughters of mother s given DES RU486 Mifepristone Progesterone is needed to maintain the viability of a fetus Mifepristone blocks the 5 action of progesterone Has other uses slows growth of some cancers treatment for Cushing syndrome too much cortisone Metabolism FATTY ACID OXIDATION Fatty acids serve as an energy reserve The fatty acids are broken down to acetyl CoA units A 16 carbon fatty acid would yield 8 Acetyl CoA s Each acetyl CoA unit would yield 10 ATP39s via the Krebs Cycle The fatty acid must be first activated This requires 2 ATP s In reality 1 ATP breaks down to AMP not ADP Two high energy bonds are used The breakdown of fatty acids beta oxidation occurs in the mitochondria The carbon 2 away from the COOH group gets oxidized This has 2 oxidation steps So we get 2 reductions FAD gt FADHH NAD gt NADHH For a 16 carbon we will have 7 FADHH s 7 NADHH s and 8 acetyl CoA39s Energy Tally O O CH3CH214COH gt 8 CH3COSCoA 7 NADH 7 FADH 7NADH 25 175 7FAD H 15 105 8 TCA CYCLE 10 1080 i 106 ATP s How many ATP39s from stearic acid CHOLESTEROL SYNTHESIS Acetyl CoA units combine to form cholesterol There is a step in the synthesis whereby an early enzyme is turned off by high cholesterol concentrations This is called Feed Back Inhibition The cholesterol molecule then serves to make the other steroids bile acids hormones etc The bile acids are reabsorbed from the gut and go to the liver Some cholesterol lowering drugs work by excreting the bile acids The bile acids then can t be recyled New cholesterol molecules would have to be converted to bile acids Why do you think dieting is also a part of lowering chlolesterol levels 6
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