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147 Cards in this Set
- Front
- Back
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Ch:6
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Enzymes
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Energy Diagrams
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Show the progression of a reaction
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Transitions State
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High energy and unstable state when the molecule is best able to under go a reaction. It is the state when bonds simuntaneouslybeing broken and formed
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SN2
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single step reaction where atticking nucleophile and the displacement of leaving group occur simuntaneously, only has transition state
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SN1
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2 step reaction where nucleophile is add which forms and intermediate. Then the leaving group leaves forming the final product
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Intermediate
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Occurs in the trough between 2 transition states. It is more stable than the transition states
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Rate determining step
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The formation of the first transition state determines the rate of the reaction
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Proximity Effect
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The proper positioning and configuration of 2 reacting groups in the active site of an enzyme.
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What the Proximity Effect does
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It increases the rate of acceleration in a reaction by reducing their degree of freedom which produces a large loss of entropy. It also enhances the relative concentration of reacting groups, this is called the effective molarity
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Transition State Stabilization
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One of the major factors that lower the activation energy. After a substrate binds to an enzyme, the enzyme distorts the structure of the substrate, forcing it towards the transition state
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Enzyme Active Site
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Region of the enzyme that the substrate binds. It is hydrophobic. When substrates bind to the enzyme they lose entrophy, making propability for a reaction higher
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2 Types of Chemical Modes of Enzyme Catalysis
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Acid-Base Catalysis
Covalent Catalysis |
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Acid-Base Catalysis
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Acceleration of a reaction by transfer of a proton. Bases act as proton acceptors and produce a nucleophilic reactant. Acids act as proton donators and can make covalent bonds easier to break
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Covalent Catalysis
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Part or all of the Substrate forms a covalent bond with the Enzyme forming a reactive intermedatite and then covalently bonds to the second Substrate
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pH Optimun Curve
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The effect of pH on the reaction rate can suggest which ionizable residues are in the active site. At the pH Optimun, the midway between 2 pKa values, the greatest number of enzyme molecules are in the active form.
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Bell Shape Curve
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Results from 2 overlapping titrations. Ascending is deprotonation and decending is protonation of active site Amino Acid residues
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Diffusion Controlled Reactions
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Fastest reactions. Rates approch rate of diffusion. The speed of binding substrates to the enzyme may be rate-determing which is a rapid reaction
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Energy Diagram for TPI Reaction
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Becasue peaks are relativly even the catalyst is at max efficiency
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Thermodynamic Pit
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Caused by excessive ES stabilization, E binding to S too tightly, and gives little to no catalysis. Km values indicate weak binding to enzymes and can not be extreamly low or the binding of ES will be too tight
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Comparsion of Enzymatic Catalysis
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Chemical Modes inc 10-100
Proximity Effect inc 10^4-10^5 TS Stabilization in 10^4-10^5 Enzyme Rate Acc ~ 10^8-10^12 |
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Transititon State Analogs
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Chemical analogs of transititon states are enzyme inhibitors. They are stable compounds whose structure resemble unstable transititon states and they bind tightly to the Enzyme which is why it is an inhibitor
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Lock-and-Key
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Proposed by Emil Fisher. Enzymes (locks) are rigid templates that only accept certain transition states (key). The transition state must be stabilized for the catalysis to occur
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Induced Fit
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Activates an enzyme by substrate-initiated conformation effect. It is a substrate specificity effect. After binding the enzyme undergos a shape alteration. Changes from inactive to active form.
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3 Digestive Serine Proteases
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Trypsin, Chemotrysin and Elastase. These are synthesized and stored in pancrease
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Zymogen
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Which is the inacive enzyme precursors that have to be covalently modified to become active. Are stored this wat to prevent them from damaging cell proteins. Are activate by Selective Proteolysis and regulated by inhibitors
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Each Serine Proteases has a Zymogen
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Trypsinogen --> Trypsin
Chemotrypsinogen --> Chemotrysin Protelastase --> Elastase |
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Zymogen Enzyme Cascade
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Enteropeptidase initates reaction by cleavage of Trypsinogen to Trypsin. Trypsin then cleaves both Chemotrypsinogen and Protelastase and additionl Trypsinogen molecules
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Simulartites of Serine Proteases
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All have dimulare backbone conformation and active-site residues but are substrate specific due to small structural differences
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Chemotrysin
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bind and cleave side chains of aromatic and bulky hydrophobic AA residues.
(Phe, Trp, Tyr) |
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Trypsin
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Binds and cleaves Lys and Arg
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Elastase
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Binds and cleaves proteins with small residues
(Ala, Gly and Val) |
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Catalytic Triad
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In Chemotrypsin
Asp, His, Ser Must know this structure |
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Ch 7:
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Coenzymes and Vitamins
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Cofactors
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Are required by inactive apoenzymes to convert them to active holenzymes. Many minerals are cofactors and therefore are are essential
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Apoenzymes
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Inactive protein without cofactor
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Holenzymes
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Active protein with cofactor
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2 Types of Cofactors
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Essential Ions (mostly metal ions)
Coenzymes (orgainc compounds) |
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Coenzymes
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Act as group-transfer reagents
Hydrogen, electrons or other groups can be transferred |
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2 Types of Coenzymes
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Metabolite Coenzymes
Vitamin-Derived Coenzymes |
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2 Classes of Coenzymes
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Cosubstrates (loosely bound)
Prosthetic Groups (tightly bound) |
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2 Classes of Essential Ions
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Activator Ions (loosely bound)
Metal Ions "Metalloenzymes" (tightly bound) |
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Activator Ions
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Either have and requirment or are stimulated by metal ions.
Ca++ K+ Mg++ Mn++ |
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Metalloenzymes
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Contain firmly bound ions at active site.
Iron, Zinc, Copper and Cobalt |
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Cosubstrates
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Are substrates that are altered during the reaction, released from active site and then regenerated by a different enzyme. This process is recycled repetedly
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Prosthetic Groups
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Remains bound to the enzyme during the reaction, and may be covalently or tightly bound to the enzyme. Returns to original form after catalytic event
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Vitamin Derived Coenzymes
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Vitamins are required for synthesis of some coenzymes, must be obtained from nutrients
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Vitamin C
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Ascorbic Acid
Scurvy Not a Coenzyme |
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Vitamin B3
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Nicotinic Acid
Pellagra NAD, NADH, NADP, NADPH |
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Vitamin B1
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Thiamine
Beriber TPP |
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Vitamin B2
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Riboflavin
Growth Retardation FMN, FMNH2, FAD, FADH2 |
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Vitamin B5
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Pantothenate
Dermititus in Chickens Coenzyme A |
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Vitamin B6
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Perixyaxal
Dermititus in Rats PLP (Pyridoxal-5-Phosphate) |
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Biotin
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Dermititus in Humans
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Folate
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Anemia
Tetrahydofolate |
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Vitamin B12
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Cobalamin
Pernicious Anemia Adenosylcobalamin or Methycobalamin |
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Lipid Soluable Vitamins
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A,D,E, and K
All hydrophobic |
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Carbohydrate
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Most abundant orgainc molecule on earth
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Functions of Carbohydrates
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Energy Storage
Metabolic Intermedatites Part of DNA and RNA Structural Elements Exoskeleton of Arthropods Extracellular Matrix of animals Cell-cell communicating/signalling |
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Monomeric Units
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Monosaccharides (CH20)
Oligosacchrides (2-20 Monosaccharides) Disacchrides (2 Monosaccharides) Polysacchrides ( >20 Monosaccharides) |
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2 Types of Monosaccharides
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Aldoses and Ketoses
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Glycan
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Carbohydrate attached to a polymer
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Glycoconjugate
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Carbohydrate attached to a peptide, protein or lipid
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Glucoconjugate
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Carbohydrate attached to a Glucose
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Steroisomer
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Compounds witht the same molecular formula but different spatial arrangment
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Enantomers
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Differ at only one Chiral center
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Naming Based on # of Carbons
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3 = triose
4 = tetrose 5 = pentose 6 = hexose |
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Aldoses
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Glyceraldehyde
Erythrose Ribose Glucose Mannose Galactose |
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Ketoses
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Dihydroxyacetone
Ribulose Xylulose Fructose |
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Hemiacetal
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Aldehyde + Alcohol
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Hemiketal
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Ketone + Alcohol
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Rings
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Pyran = 6
Furan = 5 |
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Anomeric Carbon
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OH group determines Alpha or Beta
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D-Glucose in Equilibrium
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Favors Beta (64%) over Alpha (36%) because more stable
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Sugar Phosphates
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Replace OH with OPO3(-2)
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Deoxy Sugars
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Replace OH with H
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Amino Sugars
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Replace OH with Amino Group (NH2) or Acetly Amino Group (NH-C=O-CH3)
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Sugar Alcohols
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Break C=O bond and replace with OH
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Sugar Acids
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Carboxylic Acids produced from aldoses
Aldonic Acid (oxidation of C1) Uronic Acid (Oxidation at highest numbered C) |
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Glycoside Bond
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Primary structral linkage in all polymers to form Disaccharides (link at Oxygen of the anormic Carbon)
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Glucosides
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A Glucose provides the anomeric carbon
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Glycoside
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A Carbohydrate provides the anomeric carbon
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Maltose
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Hydrolysis product of amylose (starch)
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Cellobiose
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Degration of the Product Cellulose
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Lactose
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Abundant Disaccharide in milk
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Sucrose
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Table sugar, most abundant disaccharide in nature, only synthesized by plants
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Reducing Sugars
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Carbs with a reactive carbonyl (a free C1 "anomeric carbon")
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Non-Reducing Sugar
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Carbs with no free anomeric carbons
Ex Sucrose |
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2 Types of Polysaccharides
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Homoglycans - contains only one type of Monosaccharide
Heteroglycans- contain more than one type of Monosaccharide |
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Energy Storage
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D-Glucose is stored intracellularly in polymetric forms
Plants as Starch Animals as Glycogen |
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Starch
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Mixture of amylose (unbranched, linear) and amylopectin (branched)
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Comparing amylose and amylopectin
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Both are energy storage forms
Both are Alpha-1,4- linked glucose |
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Action of Alpha and Beta amylase on amylopectin
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Cleave Alpha 1-4-Glucan
Alpha-amylase cleaves interanl Beta-amylase cleaves non-reducing ends, releases dimers |
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Cellulose
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Most abundant org molecule on earth
Made up of linked Glucose, everyother one being flipped |
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Cellulose Chains
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Cellulose chains interact forming Intra and Interchain H-Bonds to give strength. Theses interacting chains form microfibrils and fibers
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Chitin
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Repeting units of GlcNAc (every other one flipped)
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Peptidoglycans
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Heteroglycan chains linked to peptides, found in Bacteria Cell walls
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Heteroglycan Chain of Peptidoglycans
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Composed of alternating GlcNAc and MurNAc (polysaccharide chain)
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Structure of Peptidoglycans
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Polysaccharide chain + Tetrapeptide + Pentaglycine bridge
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Penicillin
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First antibotic discoverd. Inhibits a transpeptidase involved in bacterial cell wall formation. Has simular structure
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Proteoglycans
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Carb-protein conjugate
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GAGs
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unbranched Heteroglycan chain, called hyaluronic acid, of GlcUA and GlcNAc attached to a protein
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Types of GAGs
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Not covalently attached to a protein = hyaluronic acid
Covalently attached to protein (proteoglycan) = heparin sulfate, keratin sulfate, chondroitin sulfate and dermatan sulfate |
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Proteoglycan Strand of GAGs
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Central strand of hyaluronic acid that has link proteins that are attach to it
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Glycoproteins
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Proteins that are covalently bound to oligosaccharides. The oligosaccharides may alter physical properties such as size, shape, solubility, stability, folding and its biological roles
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2 Types of Glycoproteins
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O-Glycosidic and N-Glycosidic linkages
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Blood Transfusions
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A, B, AB, or O type of N-linked and O-linked oligosaccharides on the surface of blood. A and B differ at the ends but O lacks this portions which makes it a good donor.
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Ch: 9
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Lipids
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Lipids
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Water insoluble org compounds in living organisms
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Types of Lipids
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Hydrophobic or amphipathic
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Classes of Lipids
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Phospolipids
Glycolipids Cholesterol |
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Glycerophospholipid
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Main lipid in most biologial membranes
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Sphingolipids
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Second most abundant
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Unsaturated vs Saturated
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Unsturated has double bonds
Saturated doesnt |
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Triacylglycerol
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The neutral storage of fatty acids, most abundant Lipid based on mass
Glycerol back bone (3-carbon sugar) 3 Fatty acid chins |
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Phospholipids
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Most abundant class of lipids
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Phosphoglycerides
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Glycerol back bone
2 Fatty acid chins Phosphorlated alcohol |
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Fatty Acid Chains
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Long aliphatic tails containg even # of carbons
Can be sat. or unsat. Usually ionized |
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Lipases
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Enzymes that Catalyze hydrolysis of triacylglycerols
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Phospholipases
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Catalyze hydrolysis of Glycerophospholipids
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Cholesterol
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Modulates the fluidity of mammalian cell membranes. Also a precursor of the steroid hormones and bile salts
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Waxes
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Esters of long chained alcohols and long chained fatty acids (nonpolar)
Are water insoluable and have high melting point |
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Eicosanoids
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Prostaglandid
Teromboxane Leukotrine |
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Biological Membranes
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Highly selective permeability barrier
Consists of Lipids and Proteins Lipids are amphiathic, driving force to form bilayers is the hydrophobic tails |
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2 Forms of Membranes
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Micelles and Lipid Bilayers
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Micells
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Circular configuration
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Lipid Bilayer
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Favored structure, self assembled due to hydrophobic tails, water and hydrophobic molecules readly transverse membrane
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Dynamic Structure
(Fluid Mosaic Model) |
Lateral Diffusion - happens readly, rapid
Transverse Diffusion - rare, slow |
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Proteins
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Embedded in bilayer and on surface
Function as pumps, gates, receptors, energy transducers and enzymes Held together by nocovalent interactions Fluid Mosaic Model |
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Freeze Fracture Electron Microscopy
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Shows the distrubution of membrane proteins
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Fluid Properties
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Depend of flexibility of fatty acid chains
Ordered state - rigid with trans conformation Fluid State - disordered state with gauche conformation |
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What effects phase transitions
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Transition occurs at the Tm = melting temperature
Tm depends on length and deg of unsat. Rigid state favors saturated chains Double bonds lower Tm, becomes fluid easier |
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Effect of Cholesterol on Phase Trasition
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prevents tight packing of fatty acids. Loweres the Tm and makes it where it cant change phases a quick. Pure lipid bilayer has sharp phase transition
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3 Types of Membrane Proteins
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Peripheral Membrane
Intergral Membrane Lipid Anchored Membrane |
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Peripheral Membrane
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Loosely bound to membrane, released by contact with high salt of pH. Usually bound to Intergral Membrane
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Intergral Membrane
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Firmly bound to membrane by hydrophobic interactions, have membrane spanning domains
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Lipid Anchored Membrane
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Covalently linked to lipid membrane.
3 types: Direct Prenylation GPI |
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Direct
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Direct amide or ester bond between AA and fatty acid
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Prenylation
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Link to an isoprenoid chain via S of a Cys near the C terminus
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GPI
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C terminal Alpha-carboxyl of protein-phosphoethanolamine-glycan-phosphatidylinositol
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Uniport
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One thing in one direction
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Symport
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2 things in one direction
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Antiport
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2 things in opposite directions
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Active
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Requires energy to move molecules aginst concentration gradient
primary uses primary energy sources (ATP or sunlight) secondary uses ion gradient |
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Passive
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Dont require energy
Both undergo conformational change to drive transprot |
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Lipid Vesicles
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Transport molecules that are too large for protein transport.
Exocytosis - out of cell Endocytosis - into cell |
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G Protein
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Activated by binding to a receptor ligand complex.
They are inactivated slowly by their own GTPase activity |
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Insulin Receptors
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Bind to extracellular Alpha chain. Beta chains autophosphorylate. Tyrosine kinase domains phosphorylate IRS
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