Chapter 4 The Chemical Composition of Proteins Homework II(contd): Ch 6 problems 6, 7, 8 (optionally 10)and Ch. 7 problems 3, 6, 7, 9, 10 (optionally 12) ausefulsitewww.cbi.pku.edu.cn Use blast search in data base swissprot PDB is available on this site. rasmol is available for Win98 if you dont want to download Chemscape
Chapter 4 The Chemical Composition of Proteins Homework II (cont’d): Ch. 6 problems 6, 7, 8 (optionally 10) and Ch. 7 problems 3, 6, 7, 9, 10 (optionally 12) a useful site: www.cbi.pku.edu.cn Use blast search in database swissprot PDB is available on this site. Rasmol is available for Win98 if you don’t want to download Chemscape
e in 1. Proteins are macromolecules and variable sIes 1. There is no simple generalization between size and function. Small ones can be less than 10 kD(insulin-6 kD); big ones more than 1000 kD 1.2 Proteins can be monomeric or oligomeric Monomeric proteins contain only one covalent structure (either a single polypeptide chain or more chains connected by covalent bonds. Oligomeric proteins contain more than one covalent structures interacting by noncovalent interactions. Each covalent structure in an oligomeric protein is called a subunit(hence multisubunit proteins)
1. Proteins are macromolecules and variable in sizes 1.1 There is no simple generalization between size and function. Small ones can be less than 10 kD (insulin ~6 kD); big ones more than 1000 kD. 1.2 Proteins can be monomeric or oligomeric. Monomeric proteins contain only one covalent structure (either a single polypeptide chain or more chains connected by covalent bonds). Oligomeric proteins contain more than one covalent structures interacting by noncovalent interactions. Each covalent structure in an oligomeric protein is called a subunit (hence multisubunit proteins)
table 5-2 Molecular Data on Some Proteins Number of Molecular Number of polypeptide eight residues chains Cytochrome c(human) 13000 104 Ribonuclease a(bovine pancreas) 13,700 124 Lysozyme (egg white 13,930 129 Myoglobin(equine heart 16,890 Chymotrypsin(bovine pancreas 21,600 241 3 Chymotrypsinogen(bovine 22,000 245 Hemoglobin(human) 64.500 574 4 Serum albumin(human) 68.500 609 Hexokinase (yeast) 102,000 972 2 RNA polymerase(E coli) 450.000 4,158 Apolipoprotein b(human) 513,000 4,536 Glutamine synthetase(E. coli) 619,000 5,628 12 Titin(human) 2,993,000 26,926
2. Proteins have characteristic amino acid compositions 2.1 Proteins can be hydrolyzed in bases or acids to free a-amino acids. They are usually hydrolyzed in 6 M HCl at 110C for 24 hours 2.2 The resulting characteristic proportion of different amino acids, namely, the amino acid composition was used to distinguish different proteins before the days of protein sequencing Various proteins are currently distinguished by their specific amino acid sequences(by 3-D structures in the future?)
2. Proteins have characteristic amino acid compositions 2.1 Proteins can be hydrolyzed in bases or acids to free a-amino acids. They are usually hydrolyzed in 6 M HCl at 110ºC for 24 hours. 2.2 The resulting characteristic proportion of different amino acids, namely, the amino acid composition was used to distinguish different proteins before the days of protein sequencing. Various proteins are currently distinguished by their specific amino acid sequences (by 3-D structures in the future?)
table 5-3 Amino Acid Composition of Two Proteins Number of residues per molecule of protein Amino Bovine Bovine acid cytochrome c chymotrypsinogen AAA mpsm 62532394366824 580 G Glu Gly His 3209 Met Phe Pro Thr 4181 Trp Tyr Val 38435 Total 104 2 Note that standard procedures for the acid hydrolysis of proteins convert Asn and GIn to Asp and Glu, respectively In addition, Trp is destroyed. Special procedures must b employed to determine the amounts of these amino acids
3. Some proteins contain chemical groups other han amino acids 3.1 Many proteins contain only amino acids, e. g insulin, ribonuclease A, chymotrypsin. 3.2 Some proteins(conjugated proteins) contain other components 3.2.1 Cytochrome c and myoglobin contain heme groups. Immunoglobulin G contains carbohydrate groups
3. Some proteins contain chemical groups other than amino acids 3.1 Many proteins contain only amino acids, e.g., insulin, ribonuclease A, chymotrypsin. 3.2 Some proteins (conjugated proteins) contain other components. 3.2.1 Cytochrome c and myoglobin contain heme groups. Immunoglobulin G contains carbohydrate groups
3.2.2TI he non-amino acid parts are usuall called prosthetic groups and the protein part alone called apoprotein. (holoenzyme=apoenzyme+substrates+ cofactors+prosth etic groups) 3.2.3 Prosthetic groups usually play important roles for protein functions 3.2.4 The conjugated proteins are usually classified according to the nature of their prosthetic groups。 Lipoproteins: lipids Glycoproteins: carbohydrate groups Metalloproteins: different metals (ions)
3.2.2 The non-amino acid parts are usually called prosthetic groups and the protein part alone called apoprotein. (holoenzyme=apoenzyme+substrates+cofactors+prosth etic groups) 3.2.3 Prosthetic groups usually play important roles for protein functions. 3.2.4 The conjugated proteins are usually classified according to the nature of their prosthetic groups. Lipoproteins: lipids Glycoproteins: carbohydrate groups Metalloproteins: different metals (ions)
4. The amino acid sequence of short polypeptide chains can be determined by y chemical methods 4.1 Amino acid sequence of a peptide chain is the identity and linking order of its amino acid residues. No other properties so clearly distinguish one peptide from another. 4.2 Sanger worked out the first amino acid sequence of a peptide(bovine insulin) in 1953
4. The amino acid sequence of short polypeptide chains can be determined by chemical methods. 4.1 Amino acid sequence of a peptide chain is the identity and linking order of its amino acid residues. No other properties so clearly distinguish one peptide from another. 4.2 Sanger worked out the first amino acid sequence of a peptide (bovine insulin) in 1953
He accomplished this by using l-fluoro-2, 4- dinitrobenzene(1-氟-2,4-硝基苯) to react with the N-terminal residues of cleaved short peptides. 100 g of insulin were consumed over ten years to determine the sequence. The peptide chains were cut into 150 fragments of different lengths. He was awarded the nobel Prize in 1958 in chemistry for this breakthrough nvention
He accomplished this by using 1-fluoro-2,4- dinitrobenzene(1- 氟-2，4-硝基苯）to react with the N-terminal residues of cleaved short peptides. 100 g of insulin were consumed over ten years to determine the sequence. The peptide chains were cut into 150 fragments of different lengths. He was awarded the Nobel Prize in 1958 in chemistry for this breakthrough invention
4.3 The amino acid sequence of a short peptide can be efficiently determined by Edman degradation(埃德曼 降解) 4.3.1 The uncharged terminal amino group is reac ted with phenylisot isocyanate(苯异硫氰酸盐,异 硫氰酸 o form a phenylthiocarbamyl(苯氨基硫代甲 酰基) peptide 4.3.2 The N-terminal amino acid residue is liberated as a cyclic phenylthiohydantoin(PTh) derivative under mildly acid conditions, leaving the rest of the peptide chain intact. 4.3.3 The PTH derivative(thus the amino acid residue) can be identified by chromatographic methods 4.3.4 The newly exposed N-terminal amino acid residue can be identified by repeating the above procedure
4.3 The amino acid sequence of a short peptide can be efficiently determined by Edman degradation(埃德曼 降解）. 4.3.1 The uncharged terminal amino group is reacted with phenylisothiocyanate(苯异硫氰酸盐,异 硫氰酸)to form a phenylthiocarbamyl(苯氨基硫代甲 酰基) peptide. 4.3.2 The N-terminal amino acid residue is liberated as a cyclic phenylthiohydantoin (PTH) derivative under mildly acid conditions, leaving the rest of the peptide chain intact. 4.3.3 The PTH derivative (thus the amino acid residue) can be identified by chromatographic methods 4.3.4 The newly exposed N-terminal amino acid residue can be identified by repeating the above procedure