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Biochemistry Exam 2 Notes

by: Courtney Poulos

Biochemistry Exam 2 Notes BSC 450

Courtney Poulos

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About this Document

Notes work taken and translated onto a powerpoint created by Dr. Yu Wang. These will be the focus for Exam 2 in Spring 2016.
Fundamentals of Biochemistry
Yu Wang
biochemistry, protein functions, Enzymes
75 ?




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This 76 page Bundle was uploaded by Courtney Poulos on Monday February 29, 2016. The Bundle belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Yu Wang in Fall 2016. Since its upload, it has received 50 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.

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Date Created: 02/29/16
Protein Functions Globular Proteins Could myoglobin transport O ? 2 • pO i2 lungs is about 13 kPa: it sure binds oxygen well • pO i2 tissues is about 4 kPa: it will not release it! • Would lowering the affinity (P ) of myoglobin to oxygen help? 50 Hemoglobin Subunits have similar structure to myoglobin • Hemoglobin (Hb) is a tetramer of two subunits(α2β2) • Each subunit is similar to myoglobin (contains a heme) K: Lys Y: Tyr R: Arg H: His Subunit Interactions in Hemoglobin α β and α β 1 1 2 2 Hydrophobic interactions; But H-bonds and salt bridges (electrostatic interactions) impact the function α 1 2nd α β 2 1 Subunit Interactions: Details (showing salt bridges) Subunit Interactions: Details Hemoglobin undergoes major structural changes upon O binding: R 2nd T States • T = Tensestate, – Moreinteractions between subunits, morestable – Lower affinity for 2 • R = Relaxed state, – Fewer Interactions, more flexible – Higher affinity for O 2 • Conformational change from the T state to the R state involves breaking ion pairs between the α1-β2 interface – α1Lys… COO β - 2 R and T States of Hemoglobin Conformational change is triggered by oxygen binding For effective transport, affinity must vary with pO between tissue and lung 2 How can Hb change affinity to oxygen? Part I: Cooperativity • Must be a protein with multiple binding sites – If a single site, the affinity cannot be adjusted to the sigmoid curve • Binding sites must be able to interact with each other (not directly) • cooperativity – positive cooperativity • first binding event increases binding affinity of remaining sites • recognized by sigmoidal binding curves – negative cooperativity • first binding event reduces binding affinity of remaining sites • O binding to the first binding site triggersa T  R conformational 2 change – Do you expect a larger or smaller Kdfor the first 2 binding site comparing to other sites after the first2O binding? Cooperativity Cooperativity: Quantitative Description [PL n] K = a [P][L] n n [L] θ = [L] + K d The Hill Plot of Cooperativity Two Models of Cooperativity: Concerted vs. Sequential Cooperativity is a special case of allosteric regulation • Allosteric protein – Binding of a ligand to one site affects the binding properties of a different site, on the same protein – Can be positive or negative – Homotropic • Normal ligand of the protein is the allosteric regulator – Heterotropic • Different ligand affects binding of the normal ligand • Cooperativity = positive homotropic regulation CO binds to heme in hemoglobin tighter , but why so toxic? Using cooperativity to explain How can Hb change affinity to oxygen? Part II: pH Effect on O Binding to He2oglobin + • Actively metabolizing tissues generate H and CO 2 • CO 2 H O 2 H + HCO by carbo3ic anhydrase • Increased [H ] of the blood near the tissues relative to the lungs • [H ] affects Hb affinity for O 2 – H protonatesHis146 which then forms a salt bridge with Asp94 • Favoring the conformational transition to T state • Lower affinity for O = release of O (in the tissues) 2 2 + – In T state, the protonated His HC won’t lose the H – In R state, it is very easy to lose the H + • Also where O is 2icked up (in the lung) • High pO wi2l push Hb to R state,H is released, previous reaction moves to the left, CO is released 2 • The pH difference between lungs and metabolic tissues increases efficiency of the O 2transport • This is known as the Bohr effect How can Hb change affinity to oxygen? Part III: 2,3-BPG regulates O binding 2 • 2,3-Bisphosphoglycerate • Small negatively chargedmolecule • binds to the positively chargedcentral cavity of Hb – Only one 2,3-BPG per Hb – Stabilizes the T states – Promote O 2elease • Negative heterotropic regulator of Hb function • Present at mM concentrations in erythrocytes 2,3-BPG binds to the central cavity of hemeglobin Between β subunits in the T state 2,3-BPG allows for O release in the tissues 2 and adaptation to changes in altitude Fetus Hb is α γ 2 2 • Lower affinity for 2,3-BPG • So fetus can extract O from its mother’s 2 blood • What if the fetus and its mother move from sea level to high altitude (4500 meters)? • Hint: low affinity for 2,3-BPG means less efficient in 2 release to tissue Sickle-cell anemia is due to a mutation in hemoglobin • Glu6  Val in the β chain of Hb • Formation of hydrophobic surface • The new Val side chain can bind to a differentHb molecule to form a strand • This sickles the red blood cells • Untreated homozygous individuals generally die in childhood • Heterozygous individuals exhibit a resistance to malaria Formation of Hb Strands in Sickle-Cell Anemia Two Types of Immune Systems • Cellular immune system - targetsown cells that have been infected - also clears up virus particles and infecting bacteria - key players: Macrophages, killer T cells (T), c and inflammatory T cells (TH 1 • Humoral “fluid” immune system - targetsextracellular pathogens - can also recognize foreign proteins - makes soluble antibodies - keeps “memory” of past infections - key players: B-lymphocytes and helper T-cells (TH2) Cellular Immune System • Antibodies bind to fragments displayed on the surface of invading cells • Phagocytes: specialized cells that eat invaders • Macrophages: large phagocytes that ingest bacteria that are tagged by antibodies Humoral Immune System • Vertebrates also fight infections with solubleantibodies that specifically bind antigens – Antigens are substances that stimulate production of antibodies • Typically macromolecular in nature • Recognized as foreign by the immune system • Coat proteins of bacteria and viruses • Surface carbohydrates of cells or viruses – Antibodies are proteins that are produced by B cells and specifically bind to antigens • Binding will mark the antigen for destruction or interfere with its function • A given antibody will bind to a small region (epitope) of the antigen • One antigen can have several epitopes Antibodies: example as Immunoglobulin G • Composed of two heavy chains and two light chains • Composed of constant domains and variable domains • Light chains: one constant and one variable domain • Heavy chains: three constant and one variable domain • Variable domains of each chain make up antigen- binding site (two/antibody) • Variable domains contain regions that are hypervariable (specifically the antigen-binding site) • Confers high antigen specificity Antibodies: Immunoglobulin G Antibodies: Immunoglobulin G Antigens bind via induced fit Antigen binding causes significant structural changes to the antibody Antibody specificity is an important analytical reagent Antibody detection can be colormetric or luminescent


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