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BCHM Exam 4 Week 1 Notes

by: Luke Holden

BCHM Exam 4 Week 1 Notes 3050

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These notes are compiled using Dr. Sri's powerpoint lectures. These notes contain the lecture on sugars as well as all the steps of glycolysis and sample questions that she said in class. Great stu...
Essential Elements of Biochemistry
Dr. Srikripa Chandrasekaran
Class Notes
Biochemistry 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!!!!  NADNADH (low potential energyHigh 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!!!


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