Chapter 1: Introduction to the chemistry of lifeLearning 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 energy2. Know the differences between prokaryotes and eukaryotesProkaryotesBothEukaryotesNucleoidDNANucleusCircular DNAribosomesLinear DNA with histonesSmall (0.1-5μm)cytoplasmLarge (10-100μm)Unicellular onlyflagellaUsually multicellular but canbe unicellularBacteria and archaeaPlasma membraneAnimal, plant, protist, fungiNo membrane boundorganelleschromosomesMembrane bound organellesNaked DNAProtein bound DNA70s ribosomes80s ribosomesReproduction: binary fissionReproduction: mitosis +meiosisSingle chromosomePaired chromosomesComplex cell wallcytoskeleton3. 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 3domains- 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 ancestorthat emerged from a member of bacteria- Growing evidence that eukaryotes may have originated from a subset of archaea4. Know the chemical elements of important biological molecules such as proteins,carbohydrates, nucleic acids, and lipids- 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, P5. Know the different kinds of biological molecules present in cells- Protein: 20 amino acids- DNA and RNA: 4+4 nucleotides- Cellulose and starch: glucose- Fatty acids: synthesized from acetyl CoA- Protein, carbohydrate, fatty acid catabolism: common intermediate is acetyl CoA- Source of energy: ATP, GTP, NAD(P)H6. 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 polysaccharides7. Know the kinds of covalent bonds present in proteins, carbohydrates, and nucleic acids- peptide bonds- Disulfide bonds- Glycosidic bonds- Glucose linked by alpha-1,4 glycosidic bond to form start- Glucose linked by beta-1,4 glycosidic bond to make cellulose- Phosphodiester bonds8. Know the kinds of non-covalent bonds present in proteins, nucleic acids, and lipid bilayers.Understand what are hydrophobic interactions- hydrogen bonds- Ionic bonds- Van der walls interactions- Hydrophobic interaction- Hydrophobes are nonpolar molecules and usually have a long chain of carbonsthat do not interact with water molecules- interaction of hydrophobicmolecules when they are surrounded by hydrophilicenvironment9. Know the structure of ATP and understand how ATP hydrolysis provides energy for processesin life- Adenosine triphosphate: nucleotide containing adenine, ribose, and triphosphate group- ATP diffuses throughout the cell to provide energy for other cellular work, such asbiosynthetic reactions, ion transport, and cell movement- The chemical potential energy of ATP is made available when it transfers one (or two) ofits phosphate groups to another molecule. This process can be represented by the reverseof the preceding reaction, namely, the hydrolysis of ATP to ADP10. 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 chemicalreaction11. 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 chemicalprocess- 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 chemicalreaction 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- The reaction is both enthalpically and entropically opposed so it isnonspontanrous (endergonic) at all temperatures- - H and - S- The reaction is enthalpically favored by entropically opposed- Spontanreous only at temperatures below T = deltaH / deltaS- + H and + S- The reaction is enthalpically opposed (endothermic) but entropically favored- Spontaneous only at temperatures above T = deltaH / deltaS13. Understand the definition of equilibrium constant and the relationship between Keqand DG.(DG = DGo+ RT ln [Products]/ [Reactants])- At equilibrium when deltaS universe= 0 and deltaG system= 0- Q = K- Because ΔH and ΔS determine the magnitude and sign of ΔGo and also because K is ameasure of the ratio of the concentrations of products to the concentrations of reactants,we should be able to express K in terms ofΔG and vice versa14. Understand the definition of the standard state and standard free energy change; be able tocalculate Keqfrom DGousing the equations DGo= -RT ln Keqand Keq= exp (-DGo/RT)- The relationship between the concentration and the free energy of a substance A isGA = 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 ΔG = cGC + dGD − aGA − bGBand ΔG°= cG°C + dG°D − aG°A − bG°B [1-14]- because free energies are additive and the free energy change of a reaction is thesum of the free energies of the products less those of the reactants.- Substituting these relationships into the first equation getsΔG =ΔG°+ RT ln([C]c[D]d /