1. The molecular logic of life(1) 2 Cells(2) 3. Biomolecules(2) 4. Water(2) 5 Amino acids. etc(2) 6. Protein structure(4); Protein action(2) 7. Protein function(4); Experimental techniques(2) 8. Enzymes: catalysis and regulation(6) midterm: review and Q&a(2); exam(2)
1. The molecular logic of life (1) 2. Cells (2) 3. Biomolecules (2) 4. Water (2) 5. Amino acids…etc (2) 6. Protein structure (4); Protein action (2) 7. Protein function (4); Experimental techniques (2) 8. Enzymes: catalysis and regulation (6) midterm: review and Q&A (2); exam (2)
Chapter 2 Molecular Logic of Life Some Important Chemical Concepts and Principles for Studying Biochemistry
Chapter 2 Molecular Logic of Life Some Important Chemical Concepts and Principles for Studying Biochemistry
1. Living matter is composed mostly of the lighter elements 1.1 The composition of living matter is striking different from that of its physical environment (1810s 1. 2 The elements found in living organisms also exist in nature(especially in seawater and atmosphere). 1.2.1 99 of the mass of living organisms are made ofh. o.n. and c 1.2.2 H, O, N, and c are the lightest elements capable of forming one, two, three, and four bonds (in general, lightest elements form the strongest bonds) 1.2.3 The trace elements, although represent a miniscule fraction in living organisms, all are absolutely essential to life(Fe, Cu, Mn, Zn, L, Mg)
1. Living matter is composed mostly of the lighter elements 1.1 The composition of living matter is strikingly different from that of its physical environment (1810s) 1.2 The elements found in living organisms also exist in nature (especially in seawater and atmosphere). 1.2.1 99% of the mass of living organisms are made of H, O, N, and C. 1.2.2 H, O, N, and C are the lightest elements capable of forming one, two, three, and four bonds (in general, lightest elements form the strongest bonds). 1.2.3 The trace elements, although represent a miniscule fraction in living organisms, all are absolutely essential to life (Fe, Cu, Mn, Zn, I, Mg)
Jellyfish and the sea water
Jellyfish and the sea water
H He Bulk elements Li Be Trace elements BCNOFNe 15161718 Na Mg Al Si P S CIAr K Ca Se Ti V Cr Mn Fe Co Ni Cu Zn GaGeAsSeBrKr 4241444546474849 Rb Sr Y Zr Nb Mo Te Ru Rh PdAgCdIn 757677787980818289 Cs Ba Hf Ta W Re Os Ir Pt Au Hg TI Pb Bi AtRn Lanthanides Fr R Actinides
2. Carbon was selected as the key element for life due to its versatile bonding capacity 2.1 Carbon accounts for more than one-half the cell dry weight 2.2 Each carbon atom can form very stable single bonds with one, two, three, or four other carbon atoms, and double or triple bonds can also be formed between two carbon atoms 2.3 Covalently linked carbon atoms can form linear chains, branched chains, and cyclic and cagelike (E 的) structures 2.4 To these carbon skeletons are added functional groups conferring specific activities to the molecules
2. Carbon was selected as the key element for life due to its versatile bonding capacity 2.1 Carbon accounts for more than one-half the cell dry weight. 2.2 Each carbon atom can form very stable single bonds with one, two, three, or four other carbon atoms, and double or triple bonds can also be formed between two carbon atoms. 2.3 Covalently linked carbon atoms can form linear chains, branched chains, and cyclic and cagelike（笼形 的）structures. 2.4 To these carbon skeletons are added functional groups conferring specific activities to the molecules
2. 4 Molecules containing covalently bonding carbon backbones are called organic compounds(including mainly alcohols, amines, aldehydes and ketones, carboxylic acids, sulfhydryls,.. etc. Most biomolecules are organic compounds 2.5 Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. Carbon-carbon single bonds have freedom of rotation, but not double nor triple bonds 2.6 No other chemical element has the capacity to form molecules of such widely different sizes and shapes or with such a variety of functional groups
2.4 Molecules containing covalently bonding carbon backbones are called organic compounds (including mainly alcohols, amines, aldehydes and ketones, carboxylic acids, sulfhydryls, … etc. Most biomolecules are organic compounds. 2.5 Carbon atoms have a characteristic tetrahedral arrangement of their four single bonds. Carbon-carbon single bonds have freedom of rotation, but not double nor triple bonds. 2.6 No other chemical element has the capacity to form molecules of such widely different sizes and shapes or with such a variety of functional groups
H·+H H: H H-H Filled outer electron shells are Dihydrogen more stable: covalent bonds by :0·+2H :0: H sharing unpaired electrons between H H Water wo atoms H Number of Number of :N·+3H N: H H unpaired electrons in H electrons complete H tor (in red) outer shell Ammonia 2 H H H: C: H H-C-H 2 8 H H Methane 8 :S·+2H H H H ydrogen sulfide H : 0: OH 3H+:P+4·0::O:P:O:H=O=P-O :O: OH
Filled outer electron shells are more stable: covalent bonds by sharing unpaired electrons between two atoms
Versatility of carbon in forming covalent bonds +9:→c:0x0 →C::N .C: C C:::C
Versatility of carbon in forming covalent bonds
10959 109.5 (b) 120° B (c)