Cell and Molecular Biology (3000719): academic year 2013 Content & Objective :Cell Chemistry and Biosynthesis 3 rd Edition, 1994, pp. 41-88. 4 th Edition, 2002, pp. 47-127. 5 th Edition, 2008, pp. 45-124. Exam: 10 marks/2 h lecture MEQ: 4-6 questions Professor Dr. Jerapan Krungkrai (jerapan.k@chula.ac.th) http://biochem.md.chula.ac.th
1994, 2002, 2008 2000 1995 Gerald Karp: Cell & Mol Biol; 4 th edition, 2005-5 th edition 2008
Cytoplasm of cell is crowded. Proteins=Red, Ribosome=Green, RNAs=Blue Size= 100 nm (1 ribosome has a molecular mass of 2,700 kda; 1 bacterial cell contains ~ 20,000 ribosomes 1 human cell =??) Human cell: Types: ~ 220; number: ~ 10 14-10 16 cells
In an atom, electron = proton = atomic number, (H atom has no neuton), If neutron + proton = atomic weight
hydrophobic
I. Chemical components of a cell In In human body: chemical elements (number of atoms in % of total) (number of atoms in % of total atoms) H= 64%, C= 8%, O= 25%, N= 2%, Ca+Mg+Na+K= 1%, others=1-2%. H = 64%, C= 8%, O = 25%, N= 2%, Ca+Mg+Na+K= 1%, others =1-2%. (Ref: Alberts et al, 2008) In human body: chemical elements (% of total dry weight) H = 10%, C= 50%, O = 20%, N= 8.5%, Ca+Mg+Na+K= 7%, others = 4.5%. (Ref: Biochemistry Textbook)
1.1Water and acid-base Lattice
1.2 Nearly all of the molecules in cell are carbon compounds.
1.3.1 Sugars 1.3 Cells use four basic types of small molecules.
1.3.2 Fatty acids
1.3.3 Amino acids
1.3.4 Nucleotides
coenzyme
Noncovalent bonds specify both the precise shape of a macromolecule and its binding to other molecules.
2. Biological order and energy 2.1 Biological order is made possible by the release of energy from cells Entropy, S disorder energy order Laws of Thermodynamics: 1. Energy conservation 2. Universe constantly changes so as to become more disordered (increase entropy, S) Gibbs free energy, G,
2.2 Photosynthetic organisms use sunlight to synthesize organic compounds
2.3 Chemical energy passes from plants to animals, as carbon cycle Respiration by microorganisms
2.4 Cells obtain energy by the oxidation of biological molecules Reduced Oxidized atom Reduced atom energy Oxidized Each of these steps is energetically favorable inside a cell.
2.5 The breakdown of an organic molecule takes place in a sequence of enzyme-catalyzed reactions Principle of activation energy Enzyme catalysis; a) jiggling-box model b) energy distribution of the identical molecules
Enzyme catalysis
Coupling reactions
2.6 Parts of energy released in oxidation reactions is coupled to the ATP formation. Catabolism Anabolism 2.7 ATP hydrolysis generates order in cells.
3. Food and the derivation of cellular energy 3.1 Food molecules are broken down in three stages to give ATP. Catabolism from food ATP waste products (CO 2, H 2 O, NH 3 )
3.2 Glycolysis
3.3 NADH is a central intermediate NADH=Nicotinamide adenine dinucleotide Pyruvate dehydrogenase Acetyl CoA
3.4 Krebs cycle (tricarboxylic acid, TCA cycle or citric acid cycle) 3.5 Electron transport chain forms a proton gradient and generate ATP 1 Glucose 36-38 ATP ATP
4. Biosynthesis and the creation of order 4.1 Free-energy change for a reaction determines whether it can occur. delta G. 4.2 Biosynthetic reactions are often directly coupled to ATP hydrolysis. ATP hydrolysis e.g. high-energy intermediates driven by ATP hydrolysis
High-energy intermediates driven by ATP hydrolysis and generate polymer from its monomer 4.3 The structure of some coenzymes, involving in transfer of specific chemical groups, suggests that they may have originated in an RNA world, e.g., ATP, NADH, acetyl CoA (contains adenine and ribose moiety)
4.4 Biological polymers are synthesized by repetition of elementary dehydration reactions Monomers or subunits Polymers
5. The coordination of catabolism and biosynthesis (anabolism) Metabolism
Coordination of catabolism and anabolism Metabolism Metabolism is organized and regulated, through the change of enzyme activity, Metabolic maps of 500 reactions e.g.,1) allosteric control 2) covalent modification 3) multienzyme complex 4) compartmentation Cholesterol metabolic pathway
Feedback inhibition Glycolysis and Gluconeogenesis (enzymes 1,3, 9 for glucose pyruvate) Phosphofructokinase Example, bacterial amino acids pathway energy
Multienzyme complex Increase enzyme efficiency
Compartmentation: 1) Within cells 2) Within organisms Cori s cycle: Nobel 1947
Cell and Molecular Biology (3000719) Content & Objective Cell Chemistry and Biosynthesis 3 rd Edition, 1994, pp. 41-88. 4 th Edition, 2002, pp. 47-127. 5 th Edition, 2008, pp. 45-124. Exam: 10 marks/ 2h lecture MEQ: 4-6questions