BCHM Exam 4 Week 1 Notes
BCHM Exam 4 Week 1 Notes 3050
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This 13 page Class Notes was uploaded by Luke Holden on Wednesday April 6, 2016. The Class Notes belongs to 3050 at Clemson University taught by Dr. Srikripa Chandrasekaran in Winter 2016. Since its upload, it has received 62 views. For similar materials see Essential Elements of Biochemistry in Biochemistry at Clemson University.
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Date Created: 04/06/16
Exam 4 Week 1 Notes (3/27/16 4/1/16) 3/27/16 “THIS IS A LOT OF MEMORIZATION SO START EARLY” Warning: These Notes may not contain all molecules required for memorization!! Verify with Dr. Sri first! Monosaccharaides Single Sugar Memorize what a ketone and aldehyde looks like Sample Question: What types of molecules are these?? Answer: Glyceraldehyde: Aldotriose Dihydroxyacetone: Ketotriose Aldotriose=> this refers to the type of functional group Aldo triose=> this refers to the number of sugars Some organic review: Stereoisomers: Same chemical formula and molecule but different chirality o Example: Your hands Enantiomers: Mirror images (D ribose and L ribose) Diasteriomers: Basically mirror images but at least one chiral center is held the same ( D ribose and D arabinose) o Anomers: This is the difference around the anomeric carbon and is the only difference between the alpha and beta forms. o Epimers: This is like the anomer except it can happen anywhere on the carbon chain. Again, it is only at one center where it is different; everywhere else is the same o If you are looking at a Ring structure and what to know if it is D or L… D: the oxygen is on the right of the molecule L: the oxygen is on the left of the molecule If you are looking at the fisher projection and want to know if it is D or L D: Find the second to last carbon at the bottom of the chain. If the hydroxyl group points to the right then it is D L: Find the second to last carbon at the bottom of the chain4r5. If the hydroxyl group points to the left then it is L LIKE ORGANIC, SHE WILL GIVE YOU TO STRUCTURES AND THEN ASK WHAT IS THE RELATIONSHIP BETWEEN THE TWO For Example: The answer: Diasteriomers: KNOW HOW TO GO BETWEEN FISHER PROJECTIONS AND CYCLE MODEL VERY WELL!!!!! Now for some cycles: So instead of just linear stuff, these molecues can form rings. For example: Some terms to know: Hemiketals: This is a cyclized ring that is formed from a ketone Hemiacetal: This is a cyclized molecule that is formed from an aldehyde Anomers: Two possible diasteriomers that forma as a result of cyclizaiton Furanose: looks like a pentagon Pyranose: Looks like a hexagon Anomers!!!! So when looking at these type of structures, you can know what type of sugar it is by observing carbons 1,2,3, and 4. Sugar α or β on Carbon 2 Carbon 3 Carbon 4 Picture carbon 1 up or down up or down up or down IF THE OH UP OR UP OR UP OR IS ON THE DOWN DOWN DOWN SAME SIDE AS c6 THEN IN IT IS β If THE OH IS ON DIFFERENT SIDE THAN C6 IT IS DOWN IT IS α Glucose (D β Down Up Down glucose) In this example Fructose α Up Down Up (D In this Fructose) example Galactose β Down Up Up In this example Mannose β Up Up Down In this example When looking at a fisher projection of a molecule, if you want to cyclize it, you must perform the attack by the alcohol and remember this concept: if the substituent is pointing to the right on the fisher projection, then it will point down on the cyclized molecule if the substituent is facing to the left on the fisher projection, then it will point up on the cyclized molecule Some important monosaccarides Glucose: Found in large quantities throughout the world o Fuel for almost all processes in the body o preferred energy source for brain cells erythrocytes (cells without mitochondrion) Fructose: fruit sugar o perm germ cell, it is 2x sweeter than sucrose. Therefore, it is used as a sweeting agent in fruit. o Sperm use it as an energy source Galactose necessary to synthesize a variety of important biomolecules o lactose, glycolipids, phospholipids, proteoglycan, and glycoproteins o Galactosemia is a genetic disorder resulting from a missing enzyme in galactose metabolism Chemical Reactions with Monosaccarides Oxidation Reactions o monosaccarides can readily undergo oxidation reactions when there are ions present or enzymes o A lactone can be produced if the carbonyl groups of aldonic or uronic acids react with an OH group in the same molecule o Vitamin C, a lactone, is a powerful reducing agent that protects cells from reactive oxygen and nitrogen species Reduction Reactions o Reduction—Sugar alcohols (alditols) are produced by the reduction of aldehyde and ketone groups of monosaccharides used in commercial food processing for example, sorbitol can be used to prevent moisture loss. 3/30/16 Glycosidic Bonding o This is CRUCIAL in the linking of monosaccarides together to form disaccharides. o TWO PARTS TO THIS PROBLEM!!!! the bond is named either in the α or the β conformation. and the carbon that it is attached to. (14) (12) The first number corresponds to the first sugar and the second number is for the second sugar. Sample Question: Given a structure, give the nature of the bond or what sugars are present (etc) Disaccharides to Remember (Again May Not Contain All of Them) Sugar Definition What is it What Characteristic Structure bonded type of s too bond Lactose Disaccaride Galactose β (1,4) Common to (milk found in bonded glycosidic have a sugar) milk to bond deficiency in gluclose breaking down this sugar Reducing sugar Maltose Is an Gluclose α (1,4) (malt intermediate bonded linkage sugar) of starch to hydrolysis gluclose Cellobiose Degradation Gluclose β (1,4) Don’t exist product of bonded freely in cellulose to nature gluclose Sucrose Table sugar Glucose α (1,2) NON produced in bonded REDUCING the leaves to and stems fructose of plants Polysaccarides Polysaccharid Definition Type of Special Notes Structure es (use) Bondin g Starch Used for α (1,4) Two parts: energy storage Amylose: This in plant cells. is the linear (Potatoes) part of starch Amylopectin: This is the branched part of starch (just another linear molecule attached to a linear molecule) (Note it is an α (1,6)) Glycogen Used for α (1,4) HIGHLY energy storage BRANCHED! in animals !! (liver and muscles) (storage form of glucose) Cellulose Used for β (1,4) Humans can structural digest support in cell cellulose walls of plants and algae More structured and organized Chitin Used for β (1,4) This is two structural modified support of cell glucoses walls in fungi bonded and the together exoskeletons of insects Modificaiton: NHCOCH 3 Peptidoglycan Used for β (1,4) Has an amino structural acid chan that support in links with bacterial cell another amino walls acid chanin making it a strong structural componet A word about lectins: Lectins are proteins that bind to carbohydrates on cell surfaces however, they can cause some serious problems Lectin poisoning: o Anemia o Gi Distress o Allergic reactions o Nausua, vomiting, bloating, dirrehea How to prevent? o Cook seeds and grain at high heat for an hour. (Boiling water for an hour) o Soaking the seeds and discarding the water gets rid of lectins too (Not all of course) Destroys the glycosidic bond between sugar and nitrogen base in rRNA Prevents eukaryotic translation !!! = Certain Death 4/1/16 Glycolysis: THIS LECTURE IS QUITE MASSIVE AND CONTAINS A LOT OF INFORMATION! SHE COULD ASK BASICALLY ANTHING ON THESE STEPS SO START EARLY!!!!! The big picture: So, everything needs energy, all day every day. The energy currency in our body is ATP. Therefore, we need to get it somewhere. Lots of molecules produce ATP because that is the general reason for other substrates being in the body. However, glucose is the best at it! Why glucose? o Glucose does not modify with proteins! This is excellent because that way, glucose cannot be inactivated o THEREFORE WE NEED A PROCESS TO CONVERT THIS CRAP TON OF GLUCOSE TO ATP => GLYCOLYSIS THE PRODUCTS AT THE END OF GLYCOLYSIS 4 ATP and 2 NADH Important to understanding glycolysis: AFTER STEP 5, ASSUME EVERYTHING IS MULTIPLIED BY 2!!!!!!!!! THIS IS WHY YOU WILL GET 4 ATP WITH ONLY 2 ATP HARVEST STEPS Steps of glycolysis (10 Step) Energy investment Phase (15) o Step 1 ATP + Glucose(Hexokinase) Glucose6PPhosphate Traps glucose inside the cell The addition of a phosphate causes a negative charge to be on the molecule which restricts it from leaving the cell Irreversiable Regulation possible= The product inhibits Hexokinase Inhibition= glucose 6Phosphate Glucose 6 Phosphate is a huge compound Glycogen synthesis Glycolysis Pentose Phosphate o Step 2 Glucose 6 Phosphate (Phosphoglucose) Fructose 6 Phosphate Reversible o Step 3 (Most Heavily Regulated) fructose6phosphate (phosphofructokinase 1) fructose 1,6 bisphosphate Irreversible Activators: o AMP o ADP o fructose 2,6 bisphosphate Inhibitor o ATP o Citrate o glucagon ATP Generally inhibits glycolysis while AMP + ADP to activate it ATP is allosterically inhibited o Step 4 (Super important) fructose 1, 6 bisphosphate (Aldolase) dihydroxyacetone phosphate+ glyceraldehyde 3 phosphate o Step 5 dihydroxyacetone phosphate (triose phosphate) Glyceraldehyde 3 Phosphate Energy Harvest Phase o Step 6 Glyceraldehyde 3 phosphate+ NAD + P(Glyceraldehyde 3Phosphate dehydrogenase) 1,3 bisphsophoglycerate Generation of a reduction agent NADH o 2 molecules of NADH generated Oxidative phosphorylation step!!!! NADNADH (low potential energyHigh potential energy) o Step 7 (Important Enzyme) 1,3 bisphosphoglycerate (Phosphoglycerate Kinase) 3 phosphoglycerate First ATP generated in glycolysis via substrate level phosphorylation All kinases transferase reversible Standard Free Energy of Hydrolysis 1,3 Bisphosphoglycerate 43.4 kJ/mol ATP 30.5 kJ/mol When these are broken down the extra 15 kJ are lost as heat o Step 8 3phosphoglycerate(phosphoglycerate) 2 Phosphoglycerate o Step 9 Phosphoglycerate (Enolase)Phosphopheolpyruvate Inhibitor: Flouride (toothpaste) o Step 10 phosphoenolopyruvate +ADP (pyruvate) pyruvate +ATP Activators Fructose 1,6 bisphosphate Irreversiable Inhibitor o ATP o acetyl CoA o Alanine Second ATP generation in glycolysis via substrate level phosphorylation IMPORTANT THINGS TO REMEMBER: 1. THIS IS A LOT OF MEMORIZAITON SO START EARLY 2. KNOW HOW TO GO BETWEEN FISHER AND CYCLIZED MOLECUES WELL!!!! 3. KNOW GLYCOLYSIS LIKE THE BACK OF YOUR HAND a. KNOW WHERE ATP IS INVESTED b. WHERE ATP IS HARVESTED c. WHERE NADH IS HARVESTED d. KNOW ALL THE ENZYMES, SUBSTRATES, AND PRODUCTS e. KNOW THE ORDER THAT THEY COME IN f. DON’T PROCRATSTINATE!!!