Chapter 1 Introduction to the chemistry of life Learning objectives Important topics are highlighted in red 1 Understand why the earth has the suitable environment to sustain life Water is the solvent for life Oxygen is for respiration Nitrogen is the essential element for proteins and nucleic acids Carbon is the backbone of all biomolecules Temperature is between 40 C to 40 C And the sun is the source of energy 2 Know the differences between prokaryotes and eukaryotes Bacteria and archaea Plasma membrane Animal plant protist fungi chromosomes Membrane bound organelles Prokaryotes Nucleoid Circular DNA Small 0 1 5 m Unicellular only Both DNA ribosomes cytoplasm flagella No membrane bound organelles Naked DNA 70s ribosomes Reproduction binary fission Single chromosome Complex cell wall Eukaryotes Nucleus Linear DNA with histones Large 10 100 m Usually multicellular but can be unicellular Protein bound DNA 80s ribosomes Reproduction mitosis meiosis Paired chromosomes cytoskeleton 3 Know the three domains of organisms and their evolutionary relationship Bacteria prokaryotic Archaea prokaryotic Eukaryota eukaryotes All cells came from LUCA last universal common ancestor and evolved into these 3 domains Some think the diploid of eukaryota came from the fusion of 2 haploid prokaryotes Others think archaea and eukaryota came from a common archael eukaryotic ancestor that emerged from a member of bacteria Growing evidence that eukaryotes may have originated from a subset of archaea 4 Know the chemical elements of important biological molecules such as proteins carbohydrates nucleic acids and lipids 5 Know the different kinds of biological molecules present in cells Protein C H O N S Fe Mg Zn Ni Cu Carbohydrates C H O N HC2O n Nucleic acids C H O P N Lipids C H O N P Protein 20 amino acids DNA and RNA 4 4 nucleotides Cellulose and starch glucose Fatty acids synthesized from acetyl CoA Source of energy ATP GTP NAD P H Protein carbohydrate fatty acid catabolism common intermediate is acetyl CoA 6 Understand the modular structure of biological molecules including proteins carbohydrates and nucleic acids DNA and RNA nucleic acids DNA and RNA polymers of nucleotides DNA forms a double helix RNA single stranded nucleic acid Composed of nitrogenous base linked to a sugar with at least one phosphate group Made of purines adenine guanine and pyrimidines cytosine uracil thymine Proteins made up of 20 amino acids Peptide bonds link amino acids into a polypeptide chain Carbohydrates made from monosaccharides and polysaccharides 7 Know the kinds of covalent bonds present in proteins carbohydrates and nucleic acids peptide bonds Glucose linked by alpha 1 4 glycosidic bond to form start Glucose linked by beta 1 4 glycosidic bond to make cellulose 8 Know the kinds of non covalent bonds present in proteins nucleic acids and lipid bilayers Understand what are hydrophobic interactions Disulfide bonds Glycosidic bonds Phosphodiester bonds hydrogen bonds Ionic bonds Van der walls interactions Hydrophobic interaction Hydrophobes are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules interaction of hydrophobicmolecules when they are surrounded by hydrophilic environment 9 Know the structure of ATP and understand how ATP hydrolysis provides energy for processes in life Adenosine triphosphate nucleotide containing adenine ribose and triphosphate group ATP diffuses throughout the cell to provide energy for other cellular work such as biosynthetic reactions ion transport and cell movement The chemical potential energy of ATP is made available when it transfers one or two of its phosphate groups to another molecule This process can be represented by the reverse of the preceding reaction namely the hydrolysis of ATP to ADP 10 Understand what are the thermodynamic property and kinetic property of a chemical reaction Thermodynamics was applied to determine the energy content and changed of a chemical reaction process 11 Understand the meanings of enthalpy H entropy S and free energy G Enthalpy represents the amount of heat absorbed or released by a reaction or chemical Entropy represents the degree of order or randomness of the system S kBlnW Free energy represents the amount of useful work that can be done by a chemical reaction or process 12 Know how to determine the spontaneity of a process using the free energy equation DG DH TDS If G is less than 0 the reaction will be spontaneous If G is more than 0 the reaction is not spontaneous H and S The reaction is both enthalpically favored exothermic and entropically favored It is spontaneous exergonic at all temperatures H and S H and S H and S The reaction is both enthalpically and entropically opposed so it is nonspontanrous endergonic at all temperatures The reaction is enthalpically favored by entropically opposed Spontanreous only at temperatures below T deltaH deltaS The reaction is enthalpically opposed endothermic but entropically favored Spontaneous only at temperatures above T deltaH deltaS 13 Understand the definition of equilibrium constant and the relationship between Keq and DG DG DGo RT ln Products Reactants At equilibrium when deltaS universe 0 and deltaG system 0 Q K Because H and S determine the magnitude and sign of Go and also because K is a measure of the ratio of the concentrations of products to the concentrations of reactants we should be able to express K in terms of G and vice versa 14 Understand the definition of the standard state and standard free energy change be able to calculate Keq from DGo using the equations DGo RT ln Keq and Keq exp DGo RT The relationship between the concentration and the free energy of a substance A is GA G A RT ln A GA partial molar free energy or chemical potential of A G A partial molar free energy of A in its standard state R gas constant A molar concentration of A the general reaction aA bB cC dD the free energy change is G cGC dGD aGA bGB and G cG C dG D aG A bG B 1 14 because free energies are additive and the free energy change of a reaction is the sum of the free energies of the products less those of the reactants Substituting these relationships into the rst equation gets G G RT ln C c D d A a B b where G is the free energy change of the reaction when all of its reactants and products are in their standard states the expression for the free energy change of a reaction consists of two parts 1 a constant term whose value depends only on the reaction taking