1. What Distinguishes Primary, Secondary, Tertiary, And Quaternary Protein Structure?
Primary: Defines The Sequence Of Amino Acids In A Polypeptide Pr Protein Chain; The Conformation A Protein Assumes Is Determined By Its Primary Structure; Any Additional Structures Form To Increase Thermodynamic Stability In Its System.
Secondary: The Spatial Relationships Between Amino Acids Which Are Close To One Another In The Chain; The Entire Key To Secondary Structure Is Maximizing Hydrogen Bonds; We Are After Optimal Hydrogen Bonding; Pleated Sheet And Alpha Helix Structures Permit Optimal Hydrogen Bonding.
Tertiary: The Spatial Relationships Between Amino Acids Which Are Far From One Another In The Linear Sequence; The Distinction Between Secondary And Tertiary Structure Is Not Always Easy To Make; Both Terms Define The Folding Of Protein Chains; Still Intrachain Folding.
Quaternary: The Relationships Between The Individual Protein Chains Forming A More Complex Multisubunit Structure. Many Larger Proteins Contain Two Or More Polypeptide Chains That Are Not Covalently Linked.
2. What Is The Difference Between A Prosthetic Group And A Cosubstrate?
Prosthetic Group: The Non-amino Acid Part Of A Conjugated Protein (lipid=lipoproteins, Sugar, Metal); A Coenzyme Or Metal Ion That Is Covalently Bound To The Enzyme Protein.
Cosubstrate: Enzymatic Reactions In Which There Are Two Substrates (bisubstrate Reactions) Usually Involve Transfer Of An Atom Or A Functional Group From One Substrate To The Other. Such Reactions Proceed By One Of Several Different Pathways. In Some Cases, Both Substrates Are Bound To The Enzyme At The Same Time At Some Point In Thecourse Of The Raction, Forming A Ternary Complex.
3. What Chemical Properties Of The Peptide Bond Are Important In Determining The Structure Of A Protein?
The Characteristics Of The Peptide Bond Which Are Important Include Its Stability, And That The Two Alpha Carbons Of The Bond Are Often Oriented In A Trans Configuration. The C-n Bond Has Some Double-bond Characteristics Due To The Resonance Structure: Difficult To Hydrolyze And Limited Rotation Around The Amide Bond. The Final Orientation Of The Amino Acid Side Chains Ins Strongly Influences By The Trans Orientation Around The Peptide Bond. Also, The Elements Of The Peptide Bond Also Contain A Hydrogen Bond Donor And A Hydrogen Bond Acceptor.
4. What Is The Difference Between A Cis And Trans Peptide Bond?
5. Define Zwitterionic.
6. What Is The Charge Of The Terminal Amino Group At Ph 2?
7. What Three Residues Are Beta Branched?
8. Why Do Proteins (in General) Absorb Ultraviolet Light?
(116) Proteins Absorb Light Strongly At A Wavelength Of 280 Nm, Due To The Absorbance Spectrum Of Phenyl-rings Of Trp, Tyr, And Phe.
9. What Are Amino Acid Exchange Groups?
10. List At Least One Amino Acid Which Has The Following Properties:
A. No Asymmetric Atom--gly
B. Two Asymmetric Atoms--thr, Val, Ile
C. Generally Is Not Found To Be A Part Of Alpha Helical Structure--pro
D. Contains A Thiol--cys
E. Commonly Contributes To Covalent Inter- And Intra-chain Linkages In Globular Proteins--cys
F. Has A Side Chain That Exists Equally In A Protonated And Unprotonated State At Physiological Ph--his
G. Has A Side Chain Which Can Be A Hydrogen Bond Donor Or A Hydrogen Bond Acceptor--trp, Asn, Gln, Tyr, Thr, Ser, Lys, Asp, Glu, Arg
11. How Is Selenocysteine Formed?
12. What Is A Zymogen?
13. What Is A Secretory Signal Sequence?
14. Describe One Membrane Anchor In Proteins.
15. What Does The Mosaic Structure Of The Ldl Receptor Imply?
16. Describe The Types Of Non-covalent Bonding Which Are Important To Maintenance Of The Native Structure Of A Protein.
A. Hydrophobic Bonding: Association Between Two Hydrophobic Resides Is Called A Hydrophobic Interaction Or Hydrophobic Bonding; Purposes To Minimize Exposure To The Aqueous Hydrophilic Environment; Often Times The Most Important Forces Maintaining The Native Conformation.
B. Hydrogen Bonds: Hydrogen Atom Leaves One Covalent Bond To Join With Another, The Acceptor; Formed Between Distant Nh Group And Carbonyl Groups To Account For Prevalence Of Alpha Helix; Each Nitrogen And Oxygen Has Potential To Participate; Strongest When The Three Atoms Involved Lie In A Straight Line With Optimal Spacing Between Hydrogen Atom And The Acceptor.
C. Disulfide: Covalent Bond; Formed By The Oxidation Of Two Molecules Of Cysteine Can Covalently Link Different Regions Of A Protein To One Another. Can Be Intrachain Or Interchain.
D. Ion-ion Interactions: Negatively Charged Carboxylate Ions Are Attracted To Positively Charged Amino, Guanido, Or Imidazole Groups; Salt Bridges In Aqueous Solutions.
E. Van Der Waals Interactions:(88) Force Of Two Dipoles Weakly Attracted To Each Other, Bringing The Two Nuclei Closer Together; Especially In Alpha Helix Structure.
17. How Does A Hydrogen Bond Differ From An Electrostatic Bond?
18. Explain Why Alpha Helical Structure Is A Reoccurring Element In Many Proteins?
166 The Simplest Arrangement The Polypeptide Chain Could Assume With Its Rigid Peptide Bonds Is A Helical Structure; This Owes, In Part, To The Fact That It Makes Optimal Use Of Internal Hydrogen Bonds (n-h-o).
19. What Is A Beta-pleated Sheet?
(169) This Is The More Extended Conformation Of The Polypeptide Chains. The Backbone Of The Polypeptide Chain Is Extended Into A Zigzag Rather Than Helical Structure. The Sheets Can Be Either Anti-parallel, In Which The Amino-terminal To Carboxyl-terminal Orientation Of Adjacent Chains In Inverse, Or Parallel. Hydrogen Bonds Can Be Either Intrachain Or Interchain Between The Peptide Linkages Of Adjacent Polypeptide Chains.
20. What Is The Difference Between D- And L-amino Acids?
The Big Letters D And L Refer To Actual Configuration In Space In Analogy To That Of D-glyceraldehyde Which Has Been Determined By X-ray. They Can Only Be Distinguished By Their Interactions With Other Optically Active Substances, Or By Their Interactions With Plane Polarized Light. They Do Not Refer To The Direction Of Rotation Of Plane Polarized Light. Almost Every Single Amino Acid In Cells Is An L-amino Acid.
21. You Should Be Able To Classify Amino Acids As Hydrophobic, Hydrophilic, Etc., When You Are Provided Their Respective Three Letter Abbreviations.
(115)
Non-polar, Aliphatic R Groups: Gly, Ala, Val, Leu, Ile, Pro
Aromatic R Groups: Phe, Tyr, Trp
Polar, Uncharged R Groups: Ser, Thr, Cys, Met, Asn, Gln
Positively Charged R Groups: Lys, Arg, His
Negatively Charged R Groups: Asp, Glu
Hydrophobic Bonding: Phe, Tyr, Trp, Ile, Leu, Val, Ala, Gly, Pro
Hydrophilic: Arg, Glu, Lys, Asp, His, Ser, Thr, Cys, Met, Gln, Asn
22. What Is A Beta-turn?
(170) This Is Another Repetitive Structure Common Enough To Be Worth Mentioning; It Is Often Found Where A Polypeptide Chain Abruptly Reverses Direction (often The End Of Antiparallel Beta-pleated Sheets). It Is A Tight Turn Involving Four Amino Acids. The Peptide Groups Flanking The First Amino Acid Are Hydrogen Bonded To The Peptide Groups Flanking The Fourth. Gly And Pro Residues Often Occur In Beta Turns, The Former Because It Is Small And Flexible And The Second Because Peptide Bonds Involving The Imino Nitrogen Of Proline Readily Assume The Cis Configuration. Often Found Near The Surface Of A Protein.
22. Why Do A Helices Predominate Over 3,10 Helices?
23. Describe The Hydrogen Bonding Arrangements In A Helices Vs. ß Strands.
24. How Are Antiparallel ß Strands Connected?
26. What Is A ß Meander?
27. Describe Four General Features Of Globular Proteins.
28. Are Enzymes Designed For Maximal Stability?
29. What Types Of Motion Are Observed In Proteins?
30. Name Two Prosthetic Groups.
31. Why Is It Important That The Heme Iron In Hemoglobin Be Ferrous?
32. Why Doesn't Myoglobin Show Cooperativity In Oxygen Binding?
33. Why Are Salt Bridges Important In The Hemoglobin Structure?
34. You Should Be Able To Describe The Quaternary Structure Of Hemoglobin.
Normal Adult Hemoglobin (hba) Is A Tetramer Of Two Different Protein Chains (2a-141 And 2á-146). The Association Among Different Chains Of Hb Are Non-covalent And Involve Ionic And Hydrophobic Bonding. Each Alpha And Beta Chain Contains A Heme Group Bound In A Heme Pocket Similar To That Described For Mb. Presence Of Necessary Charged And Hydrophobic Amino Acid Residues On The Surface Of Each Hb Chain That Facilitate Tetramer Structure While Mb Does Not. Quaternary Structure Shifts With Oxygen Binding In A Positive Cooperativity Effect. Roughly Spherical With The Four Polypeptide Chains Fitting Together In A Roughly Tetrahedral Arrangement. Most Of The Contacts Are Between The Alpha And Beta Chains
35. What Are The Salient Features In The Cooperativity Of Oxygen Binding In Hb?
36. What Is The Role Of 2,3-dpg In Oxygen Binding?
37. How Does Hemoglobin Transport Co2 And Protons?
38. What Distinguishes A From ß Thalassemia?
39. Comparing Collagen To A Typical Globular Protein, How Are Glycine Residues Used.
40. What Is The Significance Of Hyp Residues In Collagen?
41. How Does The Collagen Helix Compare To The A Helix In Hydrogen Bonding?
42. Describe One Type Of Crosslink In Tropocollagen.
43. Why Can Elastin Fibers Stretch And Not Collagen Fibers?
44. Define (briefly) Each Of The Following: Substrate, Catalyst, Cosubstrate.
Substrate-(201): The Molecule That Is Bound By The Active Site And Acted Upon By The Enzyme.
Catalyst-(203): Enhance Reaction Rates By Lowering Activation Energies. They Do Not Affect Reaciton Equilibria. Its Only Role Is To Accelarate The Interconversion Of S And P.
Cosubstrate: Enzymatic Reactions In Which There Are Two Substrates (bisubstrate Reactions) Usually Involve Transfer Of An Atom Or A Functional Group From One Substrate To The Other. Such Reactions Proceed By One Of Several Different Pathways. In Some Cases, Both Substrates Are Bound To The Enzyme At The Same Time At Some Point In The Course Of The Raction, Forming A Ternary Complex.
45. Give Four Examples Of Cosubstrates.
(notes) Nad, Nadp, Fad, Biotin. Know All Of Them From Notes.
46. What Does A Hydrolase Enzyme Do?
47. What Is The Active Site Of An Enzyme?
(201) The Distinguishing Feature Of An Enzyme-catalyed Reaction Is That It Occurs Within The Confines Of A Pocket On The Enzyme Called The Active Site. The Molecule That Is Bound By The Active Site And Acted Upon By The Enzyme Is Called The Substrate. (207) It Is Shaped So That A Full Complement Of Weak Bonds Is Reached At The Substrate's Transition State.
48. Describe The Difference Between Gý And G.
49. What Is Covalent Catalysis?
50. In The Reaction Of Chymotrypsin And P-nitrophenylacetate, What Distinguishes The Burst From The Steady-state Rates?
51. What Is The Biochemical Basis For The Bacteriostatic Action Of The Sulfonilamides?
(notes) Sulfanilamide Has Antibacterial Activity Because Of Its Resemblance To P-aminobenzoic Acid (paba) Which Is An Essential Nutrient For Many Bacteria. Bacteria Require Paba For The Synthesis Of Folic Acid. Mammalian Cells Require Preformed Folic Acid (a Vitamin); So The "sulfa" Drugs Have Limited Effects. Sulfanilamide Binds Competitively To The Enzyme Dihydropteroate Synthetase.
52. Define Vmax And Km (graphically Or With An Equation).
Vmax Is A Point Beyond Which There Are Only Vanishingly Small Increases In Vo (initial Rate) With Increasing [s].
Km Is The Michaelis-menten Constant Which Relates The Initial Velocity Vo, The Maximum Initial Velocity Vmax, And The Initial Substrate Concentration [s]. It Reflects An Enzyme's Affinity For A Substrate. It Is A Constant (under Set Conditions) For An Enzyme-substrate System. Km Will Vary With Ph, Temperature, Etc.
Km Can Be Used To 1) Analyze The Enzymatic Reaction In Terms Of Variables That Change Substrate Affinity; 2) Compare Various Inhibiters; And 3)compare Various Substrates.
53. Given Km Values And Vmax Values, Measured With And Without Inhibitors Present, Be Able To Discern Between Competitive Or Noncompetitive Inhibition.
(220) Competitive Reactions Do Not Affect The Vmax But Do Increase Km. Noncomopetitive Reactions Lower Vmax But Km Remains Constant.
55. List At Lest Three Factors Which Can Govern Enzyme Activity In A Tissue At A Given Time.
Ph, Temperature, [s], Inhibition
Differentiate Between Fibrous, Globular, And Complex (conjugated) Proteins.
Fibrous: Fibrous Proteins Are Mostly Amorphous Structural Components And Insoluble In Water.
Globular: Globular Proteins Are Generally Ellipsoid In Shape With A Relatively High Solubility In Buffer Solutions.
1. Have The Following Properties: L
A. Relatively High Solubility In Buffer Or Salt Solutions Of Low Concentration;
B. Circular To Ellipsoid In Shape.
C. No Measurable Strength;
D. Many Can Be Crystallized, I.e. They Ar Not Amorphous.
2. Hydrophobic Side Chains Tend To Cluster Toward The Center Of The Molecule; In May Proteins, The Numerous Hydrophobic Interactions Are The Most Important Forces Maintaining The Native Conformation; Charged Side Chains Oriented Outward.
Conjugated: (or Complex) Proteins Describes Those Proteins Which Occur In Combination With Non-protein Constituents; These May Be Either Fibrous Or Globular.
Amino Acid Composition
Refers To The Number Of Each Different Amino Acid Which Makes Up A Pure Protein
1. Tells Several Things:
A. Helps Predict Overall Charge On The Molecule As Well As I.p.
B. Most Proteins Contain Each Of Know Aa's.
C. Some Deletions Are Not Uncommon.
D. Can't Say Much About What It Does By Its Comp. Alone.
Denaturation
Process By Which The Tertiary And Secondary Structure Of The Enzyme Can Be Destroyed Leaving The Primary Structure Intact. The Resulting Enzyme Has No Biological Activity. Evidence Shows That Slow Renaturation Will Result In The Nascent Form As It Is The Most Thermodynamically Stable.
Apoprotein
The Protein Part Of A Holoenzyme, Less The Coenzyme And/or Metal Ions (a.k.a. Apoenzyme).
Isoelectric Point
The Fully Ionized Form But With No Net Electric Charge. Pi = 1/2 (pk1 + Pk2).
56. What Is The Significance Of Observations That Some Proteins Can Revert To Their Native Structure After Being Denatured?
181 This Observation Evidences The Fact That The Native Structure Is The Most Thermodynamically Stable Conformation The Protein Chain Can Assume In Its Environment, And All Less Stable Conformations Eventually Convert To This. The Most Important Proof That The Tertiary Structure Of A Globular Protein Is Determined By Its Primary Structure, That The Amino Acid Sequence Of The Polypeptide Chain Contains All The Information Required To Fold The Chain Into Its Native, Three-dimensional Structure.
57. What Is A Lipoprotein?
( 137) A Group Of Conjugated Proteins With Lipids As The Prosthetic Group.
58. What Is "post-translational Modification"? Give A Specific Example Of This.
(925) Some Newly Made Proteins Do Not Attain Their Final Biologically Active Conformations Until They Have Been Altered By One Or More Processing Reactions.
A. Amino-terminal And Carboxy-terminal Modifications.
B. Loss Of Signal Sequences.
C. Modification Of Individual Amino Acids.
D. Attachment Of Carbohydrate Side Chains.
E. Addition Of Isoprenyl Groups.
F. Addition Of Prosthetic Groups.
G. Proteolytic Processing
H. Formation Of Disulfide Cross-links
59. Explain, In General Terms, How The Amino Acid Composition Of A Protein Is Determined.
(137-141) Hydrolysis Of Proteins With Acid Or Base Yields A Mixture Of Free Alpha-amino Acids. When Completely Hydrolyzed, Each Type Of Protein Yields A Characteristic Proportion Or Mixture Of The Different Amino Acids. Then, Through A Series Of Chromatography Steps (ion-exchange, Size Exclusion, Affinity) The Proteins Are Isolated. Am Alternative Step Is Electrophoresis.
60. What Structural Characteristic Of The Amino Acid Gly Makes It An Important Part Of Protein Structure?
Glycine, With Its Small And Flexible Structure, Is Ideal For Turns In The Secondary + Structure (170). It Has Minimal Stearic Hindrance In Its Side Chain Which Allows The Structural Flexibility Not Possible In The Other Amino Acids (115).
61. What Are Some Different Types Of Lipids Found In Cell Membranes?
(247) Three Gneral Types Of Membrane Lipids: Glycerophospholikds (phosphoglycerides), In Which The Hydrophobic Regions Are Composed Of Two Fatty Acids Joined To Glycerol; Sphingolipids (include Glycolipids), In Which A Single Fatty Acid Is Joined To A Fatty Amine, Sphingosine; And Sterols, Compounds Characterized By A Rigid System Of Four Fused Hydrocarbon Rings (cholesterol).
62. Where Are Carbohydrates Localized In An Asymmetric Cell Plasma Membrane?
(269) The Small Amount Of Carbohydrate Present Is Generally Part Of Glycoproteins Or Glycolipids. (271) Plasma Membranes Contain Many Glycopriteins, But Intracellular Membranes Such As Those Of Mitochondria And Chloroplasts Rarely Contain Covalently Bound Carbohydrates. The Sugar Moieties Of Surface Glyucoproteins Influence The Protein Folding, Transport To The Cell Surface, And Receptor Functions Of These Glycoproteins. They Are Almost All In The Extracellualr Matrix. (276) Glycoproteins Of The Poasma Membrane Are Invariably Situated With Their Sugar Residues On The Outer Surface Of The Cell.
63. Represent The "fluid Mosaic" Model Of A Membrane And Label Each Of The Structural Components.
64. List At Least Two Functions Carried Out By Intrinsic Membrane Proteins?
(274) Some Proteins Conduct Solutes Or Signals Across The Membrane. (286) They Are Involved In Transport (symport, Antiport, Uniport).
65. What Are Some Functions Of Membranes In Eukaryotic Cells?
(268) Membranes Define Th Eexternal Boundary Of Cells And Ruglate The Molecular Traffic Across That Boundary; They Divide The Internal Space Into Discrete Compartments To Sgregate Processes And Components; They Organize Complex Reaction Sequences; And They Are Central To Both Biological Energy Conservation And Cell-to-cell Communication. They Are Not Passive Barriers. (270) The Membranes With Different Functions Each Have Different Compositions.
66. What Is A Phospholipid?
A Glycerol Molecule With Two Fatty Acid Chains And A Third Chain With A Polar Phosphate Chain. (248) Diacyglycerols Linked To Head-group Alcohols Through A Phosphodiester Bond. Each Derivative Is Named For The Head-group Alcohol (x), With The Prefix "phosphatidyl".
67. What Is A Glycolipid?
Neutral Glycolipids Have One Or More Sugars In Their Head Groupu, Connected Directly To The -oh At C-1 Of The Ceramide Moiety; They Do Not Contain Phosphate.
68. How Does Cholesterol Influence A Membrane's Fluidity?
69. How Does An Increased Percentage Of Unsaturated Fatty Acids Influence A Membrane?
(273) Saturated Fatty Acids Pack Well Into A Paracrystalline Array, But The Kinks In Unsaturated Fatty Acids Interfere With This Packing, Preventing The Formation Of A Paracrystalline Solid State. The Higher The Proportion Of Saturated Fatty Acids, The Higher Is The Solid-to-fluid Transition Temperature Of The Membrane.
70. What Is The Difference Between An Intrinsic And Extrinsic Membrane Protein?
(277) Membrane Proteins May Be Divided Operationally Into Two Groups: Integral (intrinsic) Proteins, Which Are Very Firmly Bound To The Membrane, And Peripheral (extrinsic) Proteins, Which Are Bound More Loosely, Or Reversibly. Peripheral Membrane Protinwsw Can Be Rel3ased From Membranes By Relativel Ymild Tratments, And Once Relaeased Form The Membrane They Are Generally Water Soluble. In Contrast, The Release Of Integral Proteins From Membranes Requires The Action Of Agents That Interfree With Hydrophobic Interactions. Integral Membrane Proteins Generally Have Domains Rich In Hydorphobic Amino Acids, Long Enough To Span The Membrane (about 20 Residues With High Hydropathy Index Long).
71. Where Is Adenylate Cyclase Located? What Controls The Activity Of This Enzyme System?
Figure 22-25 And (764) It Is An Integral Protein Of The Plasma Memnbrane, With Its Acitve Site On The Cytosolic Face. Binding Of Epinephrine To A Hormone Receptor, Or Other Signal, Activates A Receptor To Catalyze The Displacement Of The Gdp Bound To Inactive Gs By Gtp. This Converts Gs To Its Active Form. The Association Of Active Gsa With Adenylate Cyclase Converts The Cyclase To Its Catalytically Active Form. Activation Of Adenylate Cyclase By Gsa, Gsa Has A Weak Gtpase Activity And Turns Itself Off By Converting Its Bound Gtp To Gdp.
72. Describe The Protein Glycophorin.
(276) Glycophorin Molecule Spans Theerythrocyte Membrane. Its Amino-terminal Domain (bearing The Carbohydrate) Is On The Outer Surface Of The Erythrocyte, And Its Carboxyl Terminus Protrudes On The Inside Of The Cell. The Amino-terminal And Carboxyl-terminal Domains Contain Many Polar Or Charged Amino Acid Residues, And Are Therefore Quite Hydrophilic. However, A Long Segment In The Center Of The Protein Contains Mainly Hydrophobic Amino Acid Residues. It Does Not Move From One Face Of The Bilayer To The Other; Its Disposition In The Membrane Is Asymmetric.
73. How Can The Transmembrane Spanning Portion Of A Protein Be Predicted?
(278) To Estimate The Overall Hydrophobicity Of A Sequence Of Amino Acids, One Sums The Fee Energies Of Tranfer For Those Residues, Obtaining A Hydropathy Index For That Region. A Region Of About 20 Residues Of High Hydropathy Index Is Presumed To Be A Transmembrane Segment.
74. How Can You Separate The Proteins From Lipids In A Membrane?
See "30". (277) Peripheral Proteins Can Be Separated By Relatively Mild Tratments (changes In Ph Or Ionic Strength, Etc.); Integral Proteins Require Agents Such As Detergents, Organic Solvents, Or Denaturants That Interfre With Hydrophobic Interactions.
75. Describe What Is Meant By A Reconstitution Experiment?
(notes) An Experiment In Which Phospholipid Vesicles Can Be "reconstitued" With Isolated Membrane Proteins To Form A Structure Where The Properties Of The Membrane Protein Are Retained.
76. What Is The General Definition Of The Term "lipid?"
(68) Greasy Or Oily Hydrocarbon Derivatives, Sere As Structural Components Of Membranes, As A Storage Form Of Energy-rich Fuel, And In Other Roles.
77. What Are Two Common Saturated Fatty Acids Found In Membrane Phospholipids?
(273) Myristic (14:0) And Palmitic (16:0)
78. What Is The Structure Of A Common Unsaturated Fatty Acid Found In Membrane Phospholipids?
(241) Myristic: Ch3(ch2)12cooh
79. Draw The General Structure Of A Phospholipid. What Type Of Bond Is Formed To Fatty Acids?
(248) Structure. (247) The Two Fatty Acids Are Ester-linked To Glcerol At C-1 And C-2, And A Highly Polar Or Charged (hydrophillic) Head Grop Is Attached To C-3.
80. What Is The Relationship(s) Between Vitamins And Cosubstrates?
(199) Many Vitamins, Organic Nutrients Required In Small Amounts In The Diet, Are Precursors Of Coenzymes. (notes) Vitamins Are Essential Nutritional Factors As They Cannot Be Synthesized By Mammals.
81. What Are Isozymes?
(432) Differetn Proteins That Catalyze The Same Reaction Are Called Isozymes. The Predominant Hexokinase Isozyme In Liver Is Hexokinase D, Also Called Glucokinase, Which Differs In Two Important Respcets From The Hexokinase Isozymes In Muscle.
82. In Enzyme-catalyzed Reactions, Contrast The Meaning Of "absolute Specificity" With "group Or Class Specificiey."
Absolute: If A Single Enzyme Is Missing From An Organism, No Other Enzyme Can Take Its Place. One Example Is The Hereditary Lack Of Phenylalanine Hydroxylase In Humans, Resulting In Phenylketonuria (pka).
Group Or Class: The Enzyme Specificity Depends Mostly On The Structure (conformation) Of The "active Site." Here The Active Site Is Not So Restrictive.
83. What Is Allosteric Activation?
(229) Allosteric Enzymes Function Through Reversible, Noncovalent Binding Of A Regulatory Metabolite Called A Modulator. They Have Other Shapes Or Conformations Induced By The Binding Of Modulators. An Example Is Feedback Inhibition.
84. Know The Principles Of General Acid And General Base Catalysis, And The Importance These Have To Enzyme Catalysis.
(208) These Are Distinct From Mechanisms Based On Binding Energy Because They Generally Involve Covaletn Interaction With A Substrate, Or Group Transfer To Or From A Substrate. (209) Charged Intermediates Can Often Be Stabilized By Transferring Protons To Or From The Substrate Or Intermediate To Form A Species That Breaks Down To Products More Readily Than To Reactants. The Proton Transfers Can Involve The Constituents Of Water Alone Or May Involve Other Weak Proton Donors Or Acceptors. The Term General Acid-base Catalysis Refers To Proton Transfers Mediated By Classes Of Molecules Other Than Water.
85. How Does Diisopropylphosphofluoridate Inhibit Many Enzymes?
(notes) The Site On Chymotrypsis Which Becomes Acetylated Is An Unusually Reactive Serine Residue (serine 195). This Residue Can Be Labeled With Diisopropylfluorophosphate (dipf), A Reagent Which Reacts Specifically With This Residue, But Not With Any Of The Other 27 Serine Residues In Chymotrypsin. A Number Of Other Proteases And Esterases Which Have A Mechanism Similar To That Of Chymotrypsin Also React Specifically With Dipf. Because Dipf Inactivates Acetyl-cholinesterase, An Enzyme Which Is Essential For Nerve Transmission, It Is Also A Poten Nervous Systempoison. (g&g 135) It Works On Esterases By Alkyphosphorylation.
86. Know The Reactions Catalyzed By Trypsin, Chymotrypsin, An Endopeptidase, And And Exopeptidase.
Chymotrypsin: (notes) Employs Transition-state Binding, Acid-base Catalysis, And Covalent Catalysis To Bring About The Hydrolysis Of Peptide Bonds On The C-terminal Side Of Bulky Hydrophobic Side Chains Such As Those Of Phenylalanine, Tyrosine, Tryptophan And Methionine. It Will Also Catalyze The Hydrolysis Of Esters.
Trypsin: Hydrolyzes Peptide Bonds But Is Specific For The Peptide Bond On The C-terminal Side Of Lysine, And Arginine Residues.
Pepsin: Phe, Trp, Tyr (n-terminal)
Endopeptidases Can Cut In The Middle, While Exonucleases Are Limited To The End Peptide Bonds.
87. What Is Meant By "substrate Saturation," Zero-order Kinetics?"
(212) The Maximum Initial Rate Of The Catalyzed Raction (vmax) Is Observed When Virtually All Of The Enzyme Is Present As The Es Complex And The Concentration Of E Is Vanishingly Small. Under These Conditions, The Enxyme Is "saturated" With Its Substrate, So That Further Increases In [s] Have No Effect On Rate. This Will Put Us At Zero-order Kinetics As There Is No Variable, It Is Maxed Out.
88. What Effect Does Cholesterol Have On A Membrane?
(254) Sterols Are Structural Lipids Present In The Membranes Of Most Eukaryotic Cells--phospolipids And Sterols Compose About Half Of The Mass Of Biological Membranes. (273)the Sterol Content Of A Membrane Has Two Effects: Below The Temperatue Of The Solid-to-fluid Transition, Sterol Insertion Prevents The Highly Ordered Packing Of Fatty Acyl Chains, And Thus Fluidizes The Membrane; Above The Thermal Transition Pint, The Rigid Ring System Of The Sterol Reduces The Freedom Of Neighboring Fatty Acyl Chains To Move By Rotation About Carbon-carbon Bonds, And Thus Reduces The Fluidity In The Core Of Trhe Bilayer. They Mnoderate The Extremes Of Solidity And Fluidity.
89. If You Are Provided The Structure Of An Oligopeptide, Be Able To Determine The Net Charge On The Molecule At Different Ph's (e.g. Arg-lys-glu-ala-cys, At Ph = 7.5)
I Would Make The Rule That The Isoelectric Point For All Of The Uncharged Amino Acids Is @ 5.5 As The Average Pk1 Is About 2.0+ And The Average Pk2 Is About 9.0+. The Side Groups Determine Any Differences; The Positive Side Groups (r,k,h) Are About 9.0 (h @ 7.6) While The Negative Side Groups (e,d) Are About 3.0. At Any Point Above The I.p., The Amino Acid Carries A Net Negative Charge.
90. Provide Specific Examples For Each Of The Following:
A. A Prosthetic Group: Ni2+, Fe2+
B. A Fibrous Protein: Collagen
C. A Globular Protein: Serum Albumin.
D. A Protein Which Exists In A "pro" Form:
E. A Lipoprotein: (675)vldl-vhdl Blood Transport Proteins For Phospholipids, Cholesterol, Cholesteryl Esters, And Triacylglycerols.
NOT: Sitedeki dosyalar üye olmak için öğrencilerin, öğretmenlerin,
Akademisyenlerin gönderdiği dosyalardan oluşmaktadır. Tümü Eğitim ve öğretim
amaçlıdır. Bu dosyaların tümünün editörden kontrol edilerek geçirilmesi yoğun
bir emek gerektiğinden, gözden kaçmış olanlar olabilir. Ayrıca bir üyemiz
tarafından gönderilen bir dosyanın telif hakkına tabi olup olmadığını her
durumda tespit edemeyebiliriz. Böyle bir durumu fark etmeniz halinde dosyanın
siteden kaldırılması için dosya adını bize mail atmanız halinde İlgili dosya 1 saat içerisinde ivedilikle
siteden kaldırılır ve kaldırıldığına dair bilgilendirme size mail yolu ile bilgi
verilir.
Telif haklarına gösterilen özen konusunda bize yardımcı olduğunuz için teşekkür ederiz..
