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1、1,Biophysical Chemistry,COURSE DESCRIPTION,Biophysical chemistry is the branch of chemistry(specifically,a branch of physical chemistry)that develops principles of the subject,and it is closely linked up the physics,chemistry and biology.Its concepts are used to explain observations on the physical
2、and chemical properties of biological objects.Biophysical chemistry deals with either the structure of biological molecules and their functions,or the metabolic process of biological organisms.This course will particularly focus on the structures and properties of typical biological macromolecules,a
3、nd on the principles of the experimental techniques,as well.,Alan Cooper Professor of Biophysical ChemistryDepartment of Chemistry,University of GlasgowChief Editor of the Biophysical Chemistry,Cooper A.Biophysical Chemistry.RSC,2004,REFERNCE BOOK,Templer R H,et al(Eds).Biophysical Chemistry.RSC,200
4、2.,Richard H.TemplerChair Professor of Biophysical Chemistry Department of Chemistry,Imperial College Sci Tech London,Alan G.Marshall Professor of ChemistryDepartment of Chemistry&Biochemistry,Florida State University,Marshall A G.Biophysical Chemistry.Wiley,1978.,Cooper A.Biophysical Chemistry.RSC,
5、2004.Templer R H,et al(Eds).Biophysical Chemistry.RSC,2002.Bergethon P R,et al.Biophysical Chemistry.Springer,1990.Cantor C R,et al.Biophysical Chemistry(pt.1,2,3).Freeman,1980.Marshall A G.Biophysical Chemistry.Wiley,1978.Marshall A G.Biophysical Chemistry.Wiley,1976.程传煊.生物物理化学.科学技术文献出版社，1998,REFER
6、NCE BOOKS,1.Fundamentals 2.Biological molecules3.Microbial lipopeptides4.Cell membranes5.Biofilm6.Experimental techniques,OUTLINE,A quick review on Physical Chemistry,1.Fundamentals,0-1 Matter/SubstanceA substance is a distinct,pure form of matter.0-2 EnergyThe kinetic energy and the potential energ
7、y.0-3 System and surroundingsAn open-,closed-and isolated system.0-4 The equation of StatesThe state,function of states and equation of states.0-5 PropertiesPressure,p,Pa,1 Pa=1 Nm-2;Temperature,;T/K=/+273.15Volume,V,m3;Amount,n,mole(mol);NA=6.021023 mol-1.,0.Basic concepts,1.1 The properties of gas
8、es,p=f(T,V,n),Boyles Law,At constant T,pV=constant,Charles Law,At constant p,V/T=constant,At constant V,p/T=constant,Avogadros Principle,At constant T,p,V=constantn,The combined gas Law-the perfect gas equation,For real gases:The molecule itself occupies a volume;There are interactions among molecul
9、es;,The van de Waals equation,1.1 The properties of gases,1.2 The First Law of Thermodynamics,Work,heat and the internal energy,Standard reaction enthalpy,Hesss law,Kirchhoff law,The enthalpy,H=U+pV,1.2 The First Law of Thermodynamics,The entropy,S:,1.3 The Second Law of Thermodynamics,(irreversible
10、,=reversible,impossible),dH=TdS+Vdp dA=-pdV-SdT dG=Vdp-SdT,The chemical potential,For an ideal gas:,For real gases:,1.3 The Second Law of Thermodynamics,The p,V,T relations-for a perfect gas,isothermal plane,isotonic plane,isotherm,isobar,1.4 The Phase Diagrams,The p,V,T relations-for real fluids,k,
11、saturated fluid,i,saturated gas,1.4 The Phase Diagrams,The p,V,T relations-for real fluids,1.4 The Phase Diagrams,At equilibrium,the chemical potential of a substance is the same throughout a sample,regardless of how many phases are present.,The thermodynamic criterion of equilibrium:,1.4 The Phase
12、Diagrams,The reaction Gibbs energy,rG,1.5 Chemical equilibrium,Thermodynamic equilibrium constant,Biological standard states,The conventional standard state of hydrogen ions(unity activity pH=0)is not appropriate to normal biological conditions.In biochemistry it is common to adopt the biological st
13、andard state,in which pH=7(an activity of 10-7,neutral solution).,Based on the biological standard state,the corresponding standard thermodynamic functions are labeled as,and;and they are related to the standard thermodynamic functions.,1.5 Chemical equilibrium,For a reaction of the Form A+H+(aq)P:,
14、If all the species other than H+are in their standard states,this expression becomes:,Biological standard states,1.5 Chemical equilibrium,When we set pH=7,it follows that,This equation shows the relation between the thermodynamic and biological standard Gibbs energies of reaction for the reaction of
15、 the form above.,Biological standard states,1.5 Chemical equilibrium,An important biochemical is adenosine triphosphate(ATP).Its function is to store the energy made available when food is metabolized and then to supply it on demand to a wide variety of biological processes.The essence of ATPs actio
16、n is its ability to lose its terminal phosphate group by hydrolysis and to form adenosine diphosphate(ADP):,ATP(aq)+H2O(l)ADP(aq)+Pi-(aq)+H3O+(aq),Pi-denotes an inorganic phosphate group,such as H2PO4-.,Biological standard states,1.5 Chemical equilibrium,The standard values for ATP hydrolysis at 37(
17、blood temperature)are as followings,Biological standard states,1.5 Chemical equilibrium,Anaerobic and aerobic metabolism,Anaerobic metabolism is a form of metabolism in which inhaled oxygen plays no role.The energy source of anaerobic cells is glycolysis,the partial oxidation of glucose to lactic ac
18、id,and at Tblood=-218 kJmol-1.The glycolysis is coupled to a reaction in which two ADP molecules are converted into two ATP molecules,The reaction is exergonic,and spontaneous:the metabolism of the food has been used to recharge ATP.,1.5 Chemical equilibrium,In the overall reaction,38 ATP molecules
19、are generated for each glucose molecule consumed.Each mole of ATP extracts 30 kJ from the 2880 kJ supplied by 1 mol C6H12O6.and so 1140 kJ has been stored for later use.,Aerobic metabolism is a series of reactions in which inhaled oxygen plays a role.Metabolism by aerobic respiration is much more ef
20、ficient.The standard Gibbs energy of combustion of glucose is-2880 kJmol-1,and so terminating its oxidation at lactic acid is a poor use of resources.In aerobic respiration the oxidation is carried out to completion.,Anaerobic and aerobic metabolism,1.5 Chemical equilibrium,1.1 The properties of gas
21、es 1.2 The First Law of Thermodynamics1.3 The Second Law of Thermodynamics1.4 The Phase Diagrams1.5 Chemical equilibrium1.6 Statistical thermodynamics1.7 The rates of reactions1.8 Macromolecules1.9 Interfacial Behavior 1.10 Surfactants,1)For energies,Oscillator,V,Translational motion,T,For a unsymme
22、trical linear rotor,R,1.6 Statistical thermodynamics,2)The weight of the configuration,3)The Boltzmann distribution,4)Defination of molecular partition function,1.6 Statistical thermodynamics,7)Two-level system,energies 0,8)Evenly spaced,infinite system,energies 0,2,6).The partition function when T
23、0 and,5).Factorization,1.6 Statistical thermodynamics,10)The total energy,E,9).Translational motion of particle of mass m in volume V,1.6 Statistical thermodynamics,11)The internal energy(independent particles),12)Entropy(independent particles),U=U(0)+E,1.6 Statistical thermodynamics,The mean energy
24、,Rotational(TR),Vibrational(TR),Translational,The overall heat capacity,1.6 Statistical thermodynamics,Reaction rate,Consumption(Formation)Rate,Reaction type,Unimolecular Reactions,Elementary Reactions,Bimolecular Reactions,Trimolecular Reactions,1.7 The rates of reactions,aAbB P,1.7 The rates of re
25、actions,The Michaelis-Menten mechanism,1.7 The rates of reactions,KM,Michaelis constant.when S KM,when S KM,1.7 The rates of reactions,The Arrhenius equation,A,pre-exponential factor;Ea,activation energy.,The primary structure of a macromolecule is the sequence of small molecular residues making up
26、the chain.The secondary structure of macromolecules refers to the spatially well-characterized arrangement of the basic structural units.The secondary structure of an isolated molecule of polyethylene is a random coil,whereas that of a protein is a highly organized arrangement determined largely by
27、hydrogen bonds,and taking the form of helices or sheets in various segments of the molecule.The loss of secondary structure is called denaturation.When the hydrogen bonds in a protein are destroyed the structure denatures into a random coil.,1.8 Macromolecules,The conformation and configuration,The
28、difference between primary and secondary structure is closely related to the difference between the configuration and the conformation of a chain.The term configuration refers to the structural features that can be changed only by breaking chemical bonds and forming new ones.Thus,the chains-A-B-C-an
29、d-A-C-B-have different configurations.The term conformation refers to the spatial arrangement of the different parts of a chain,and one conformation can be changed into another by rotating one part of a chain around a bond.,The conformation and configuration,1.8 Macromolecules,The osmotic virial coe
30、fficient,B,where vp is called the excluded volume due to a single molecule.The excluded volume of spherical molecules of volume v is vp=8v.,The Flory theta temperature,For most solute-solvent system there is a unique temperature at which theses effects cancel and the solution is virtually ideal.This
31、 temperature is called the Flory theta temperature,and at this particular temperature,B=0.A solution at its Flory theta temperature is called solution.,1.8 Macromolecules,Polyelectrolyte Polymers that are strings od acid groups or strings and bases are called polyelectrolytes,and,depending on their
32、state of ionization,polyanions or polycations.A macromolecule with mixed cation and anion character known as a polyampholyte.,1.8 Macromolecules,The surface tension,G=(T,p,),1.9 Interfacial Behavior,(At constant T and p),A bubble:a region in which vapour is trapped by a thin film;A cavity:a vapour-f
33、illed hole in a liquid;A droplet:a small volume of liquid at equilibrium surrounded by its vapour.,The surface excess,J,1.Laplace Equation:The pressure difference across a curved surface,2.Kelvin Equation:-The change in vapor pressure with curvature of a surface,3.Yang-Laplace Equation:-The relation
34、 of the contact angel with interfacial tensions,4.Gibbs IsothermThe L/L&G/L interfaces5.Langmuir IsothermThe S/L&S/G interfaces,1.9 Interfacial Behavior,Critical Micelle Concentration,CMC,43,1.10 Surfactants,Micelle formation and the hydrophobic interaction,1.10 Surfactants,Surface pressure,Type A:i
35、norganic substances such as NaCl,Na2SO4,KOH,NH4Cl,KNO3.,The positive and negative adsorption,Type B:organic substances such as alcohol,aldehyde,carboxyl acid,ester.,Type C:usually surfactants,*,1.10 Surfactants,OUTLINE,1.Fundamentals 2.Biological molecules3.Microbial lipopeptides4.Cell membranes5.Biofilm6.Experimental techniques,
