Chapter 26 and Chapter 28 Proteins Amides from Amino Acids Amino acids contain a basic amino group and an acidic carboxyl group Joined as amides between the ¾NH 2 of one amino acid and the ¾CO 2 H to the next amino acid Chains with fewer than 50 units are called peptides Protein: large chains that have structural or catalytic functions in biology 2 1
Proteins Amides from Amino Acids 3 Why this Chapter? Amino acids are the fundamental building blocks of proteins To see how amino acids are incorporated into proteins and the structures of proteins 4 2
26.1 Structures of Amino Acids In neutral solution, the COOH is ionized and the NH 2 is protonated The resulting structures have + and - charges (a dipolar ion, or zwitterion) They are like ionic salts in solution 5 Chirality of Amino Acids Glycine, 2-amino-acetic acid, is achiral In all the others, the a carbons of the amino acids are centers of chirality The stereochemical reference for amino acids is the Fischer projection of L-serine Proteins are derived exclusively from L-amino acids 6 3
Types of side chains Neutral: Fifteen of the twenty have neutral side chains Asp and Glu have a second COOH and are acidic Lys, Arg, His have additional basic amino groups side chains (the N in tryptophan is a very weak base) Cys, Ser, Tyr (OH and SH) are weak acids that are good nucleophiles 7 Histidine Contains an imidazole ring that is partially protonated in neutral solution Only the pyridine-like, doubly bonded nitrogen in histidine is basic. The pyrrole-like singly bonded nitrogen is nonbasic because its lone pair of electrons is part of the 6 p electron aromatic imidazole ring. 8 4
Histidine 9 Essential Amino Acids All 20 of the amino acids are necessary for protein synthesis Humans can synthesize only 10 of the 20 The other 10 must be obtained from food 10 5
26.2 Amino Acids, the Henderson Hasselbalch Equation, and Isoelectric Points In acidic solution, the carboxylate and amine are in their conjugate acid forms, an overall cation In basic solution, the groups are in their base forms, an overall anion In neutral solution cation and anion forms are present This ph where the overall charge is 0 is the isoelectric point, pi 11 26.2 Amino Acids, the Henderson Hasselbalch Equation, and Isoelectric Points 12 6
Titration Curves of Amino Acids If pka values for an amino acid are known the fractions of each protonation state can be calculated (Henderson-Hasselbach Equation) ph = pka + log [A-]/[HA] This permits a titration curve to be calculated or pka to be determined from a titration curve 13 Titration Curves of Amino Acids 14 7
26.4 Peptides and Proteins Proteins and peptides are amino acid polymers in which the individual amino acid units, called residues, are linked together by amide bonds, or peptide bonds An amino group from one residue forms an amide bond with the carboxyl of a second residue 15 26.4 Peptides and Proteins 16 8
Peptide Linkages Two dipeptides can result from reaction between A and S, depending on which COOH reacts with which NH 2 we get AS or SA The long, repetitive sequence of ¾N¾CH¾CO¾ atoms that make up a continuous chain is called the protein s backbone Peptides are always written with the N-terminal amino acid (the one with the free ¾NH 2 group) on the left and the C-terminal amino acid (the one with the free ¾CO 2 H group) on the right Alanylserine is abbreviated Ala-Ser (or A-S), and serylalanine is abbreviated Ser-Ala (or S-A) 17 Peptide Linkages 18 9
26.7 Peptide Synthesis Peptide synthesis requires that different amide bonds must be formed in a desired sequence The growing chain is protected at the carboxyl terminal and added amino acids are N- protected After peptide bond formation, N-protection is removed 19 26.7 Peptide Synthesis 20 10
Carboxyl Protecting Groups Usually converted into methyl or benzyl esters Removed by mild hydrolysis with aqueous NaOH Benzyl esters are cleaved by catalytic hydrogenolysis of the weak benzylic C O bond 21 Carboxyl Protecting Groups 22 11
Amino Group Protection An amide that is less stable than the protein amide is formed and then removed The tert-butoxycarbonyl amide (BOC) protecting group is introduced with di-tertbutyl dicarbonate Removed by brief treatment with trifluoroacetic acid 23 Amino Group Protection 24 12
Peptide Coupling 25 26.9 Protein Structure The primary structure of a protein is simply the amino acid sequence. The secondary structure of a protein describes how segments of the peptide backbone orient into a regular pattern. The tertiary structure describes how the entire protein molecule coils into an overall threedimensional shape. The quaternary structure describes how different protein molecules come together to yield large aggregate structures 26 13
a-helix a-helix stabilized by H-bonds between amide N H groups and C=O groups four residues away a-helical segments in their chains 27 b-pleated Sheet b-pleated sheet secondary structure is exhibited by polypeptide chains lined up in a parallel arrangement, and held together by hydrogen bonds between chains 28 14
Denaturation of Proteins The tertiary structure of a globular protein is the result of many intramolecular attractions that can be disrupted by a change of the environment, causing the protein to become denatured Solubility is drastically decreased as in heating egg white, where the albumins unfold and coagulate Enzymes also lose all catalytic activity when denatured 29 Denaturation of Proteins 30 15
Summary We covered amino acids and their structure at different ph s based on the Henderson-Hasselbalch Equation (26.1-26.2). Not responsible for synthesis of amino acids (26.3). We discussed the structure of peptides and their linkages (26.4). Not responsible for amino acid analysis of peptides (26.5) or peptide sequencing (26.6). We learned about peptide synthesis (26.7). Not responsible for automated peptide synthesis (26.8). We discussed protein structure (26.9). Not responsible for enzymes and coenzymes (26.10). For the final exam practice problems from textbook: 1-4, 8, 9, 16, 17 28.1 Nucleic acids Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are chemical carriers of a cell s genetic information Coded in a cell s DNA is the information that determines the nature of the cell, controls cell growth, and division Nucleic acid derivatives are involved as phosphorylating agents in biochemical pathways 16
Nucleotides and Nucleic acids Nucleic acids are biopolymers made of nucleotides, which are made of nucleosides Nucleosides are made of aldopentoses linked to a purine or pyrimidine base Heterocycles in DNA and RNA Adenine, guanine, cytosine, and thymine are the four amines present in DNA RNA contains uracil rather than thymine 17
Figure 28.1 - Structures of the Four deoxyribonucleotides and the Four Ribonucleotides Phosphodiester bonds They link nucleotides together Found between the 5 -hydroxyl group (5 end) on one nucleoside and the 3 -hydroxyl group (3 end) on the other side Nucleotides in a chain are sequenced beginning at the 5 end Bases are identified in their order of occurrence Abbreviations used are G,C,A,T (or U for RNA) DNA sequence generally looks like TAGGCT 18
Phosphodiester bonds Base pairing in DNA In 1953 Watson and Crick noted that DNA consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix Strands are held together by hydrogen bonds between specific pairs of bases Whenever a G base occurs in one strand, a C base occurs opposite it in the other strand When an A base occurs in one strand, a T base occurs in the other strand 19
Hydrogen bonding between base pairs in the DNA double helix Summary Only covered 28.1 and 28.1. For the final exam practice problems from textbook: 1-3 20