Biochem Protein Function Ch5

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LIGAND

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ANY MOLECULE RERVERSIBLY BINDING IN A SPECIFIC MANNER TO A PROTEIN

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BINDING SITE

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SPECIFIC REGION OF THE PROTEIN INVOLVED IN THE REVERSE BINDING TO LIGAND

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BINDING SITE COMPLEMENT

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BINDING SITE IS COMPLEMENTARY TO LIGAND IN SIZE, SHAPE, CHARGE, & HYDRO- PHILIC/ PHOBIC CHARACTERISTICS

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INDUCED FIT

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PROTEIN-LIGAND BINDING IS OFTEN COUPLED TO A CONFORMATIONAL CHANGE IN PROTEIN THAT MAKES BINDING SITE MORE COMPLEM. TO LIGAND... TIGHTER BINDING OF FLEX PROTEIN TO LIGAND

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COOPERATIVITY

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DESCRIBES SITUATIONS WHERE BINDING AT ONE SITE EITHER INC. OR DECREASES BINDING @ ANOTHER SITE (eg. on another subunit) BY CHANGING CONFORMATION

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MYOGLOBIN

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Protein consisting of a single polypeptide chain with a heme prosthetic group that binds oxygen reversibly

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FUNCTION OF MYOGLOBIN DDEPENDS ON PROTEIN'S ABILITY TO ??

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PROTEIN'S ABILITY TO BIND OXYGEN AND TO RELEASE IT WHEN AND WHERE ITS NEEDED.

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THE REVERSIBLE BINDING OF A PROTEIN (P) TO A LIGAND (L) CAN BE DESCRIBED BY ??

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A SIMPLE EQUILIBRIUM EQUATION
P+L == PL

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P+L== PL RXN IS CHARACTERRIZED BY ??

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Ka = ASSOCIATION CONSTANT

HIGHER Ka = HIGHER AFFINITY OF THE L FOR THE P

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RATIO OF BOUND TO FREE PROTEIN IS DIRECTLY PROPORTIONAL TO ??

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CONCENTRATIOON OF A FREE LIGAND

Ka[L]= [PL]/[P]

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BINDING EQUILIB. FROM STANDPOINT OF THE FRACTION @, OF WHAT??

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OF LIGAND- BINDING SITES ON THE PROTEIN THAT OCCUPIED THE LIGAND

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WHAAT DOES THE FRACTION (theta) @= ?? (3 forms)

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@= binding sites occupied/ total binding sites

@= [PL]/ [PL]+[P]

@= [L]/[L]+(1/Ka)

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[@] IS A ? FUNCTION OF ??

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HYPEROBLIC FUNCTION x=y/(y+z)of [L]

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DISSOCIATION CONSTANT [Kd]

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EQUILIB CONSTANT FOORR RELEASED LIGAND

[L] AT WHICH HALF OF THE AVAIL. LIGAND BIND SISTES ARE OCCUPIED...AT @=0.5

Kd=1/Ka

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3 EQUATIONS WITH Kd

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Kd= [P][L]/[PL]

[PL]=[P][L]/Kd

@=[L]/[L]+Kd

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EQ. FOR BINDING OF OXYGEN TO MYOGLOBIN

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@=[O2]/[O2]+Kd

substitute concentraation of dissolved o2 for[l] b/c itss a gas
Kd= to [O2]0.5 so,
@=[o2]/[o2]+[o2]0.5

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[VOTILE SUBSSTANCE] IN SOL'N IS PROPORTIONAL TO /??

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LOCAL PAARTIAL PRESSURE OF THE GAS

@=pO2/pO2+P50

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HEMOGLOBIN TRANSPORTS

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Hb TRANSPORTS O2 IN RED BLOOD CELLS IN BLOOD

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Hb MUST AQUIRE O2?? AND THEN???

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AQUIRE O2 IN LUNGS ANAD RELEASE IT IN TISSUE

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Hb TRANSPORT OF O2 IN RBC REQUIRES HIGH ENOUGH AND LOW ENOUGH AFFINITY IN???

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HIGH ENOUGH AFFINITY IN LUNGS, BUT LOW ENOUGH AFFINITY IN TISSSUE TO RESPOND TO SMALL CHANGES IN [O2]

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Hb TRANSPORT OF O2 IS ACCOMPLISHED BY????

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COOPERATIVE EFFECTS FROM O2 BINDING TO DIFF. Hb SUBUNITS

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RELATIONSHIP B/W Hb SUBUNITS AND MYOGLOBIN

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STRUCT. RERLATED BUT SUBUNITS AFFECT O2 BINDING

BOTH BIND heme SAME WAY AND USE CONSERVED His ON BOTH SIDES OF heme TO PROTECT AND STABILIZE Fe2+ & o2 binding

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HEMOGLOBIN'S STRUCTURE

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Mr 64,500 roughly spherical diameter= 5.5nm
TETERAMERIC PROTEIN WITH 4 heme GROUPS (1 ON EACH POLYPEPTIDE CHAIN)

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ADULT Hb STRUCTURE

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2 TYPES OF GLOBIN:
2 ALPHA CHAINS (141 residues each)
2 BETA CHAINS (146 residues each)

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R-STATE CONFORMATION OF Hb

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HAS HIGH AFFINITY FOR O2

STABILIZED BY O2 BINDING

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WHAT IS SHAPE OF HEME GRROUP?

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COMPLEX ORGANIC RING STRUCTURE= PROTOPORPHYRIN =
AND IS BOUND TO A Fe2+ atom

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WHERE IS HEME GROUP IN MYOGLOBIN?

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HEME IS BOUND IN A POCKET MADE UP LARGELY OF THE E&F HELICES, although amino acid residues from other seg.s of protein alsso participate.

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AMINO ACID RESIDUE DESIGNATION IN MYOGLOBIN MOLECULE?

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INDIV A.A. RESIDUE IS DESIGNATED BY EITHER:
ITS POSITION IN A.A. SEQ OR ITTS LOCATION W/IN THE SEQ. OF A PARTICULAR ALPHA-HELICAL SEGMENT.

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IN OXY-BINDING CURVES FOR Mb, WHY pO2 AND NOT [O2]?

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IN EXPERIMENTS USING OXY AS A LIGAND, BINDING TO Mb, IT IS THE PARTIAL PRESSURE OF OXY IN GAS PHASE ABOVE THE SOL'N, pO2, THAT IS VARIED

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LOCAL PARTIAL PRESSSURE OF THE SOL'N GAS IS PROPORTIONAL TO/????

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CONCENTRATION OF VOLITILE SUBSTANCE

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WHAT DOES TERM [PL] MEAN IN TERMS OF SPECIFIC MOLECULES????

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[PL]= P(PROTEINS) L(LIGANDS)

LIGAND-BINDING SITES ON THE PROTEIN THAT ARE OCCUPIED

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HEME BINDS TO CO2 20,000X MORE BETTER THAN TO O2; WHY WE DONT GETT CO2 POISONING?

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IT ONLY BINDS ABOUT 200X BETTER WHEN HEME IS BOUND IN MYOGLOBIN- STERIC HENDERANCE

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WHY IMPORTANT THAT ERYTHROCYTES ARE SMALL CELLS?

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RED BLOOD CELLS- OXYGEN IS BOUND ANAD TRANSPORTED BY Hb IN RBC AND HUMAN ERYTH. ARE SMALL (6-9 um) BICONCAVE DISKS