BIOCHEMISTRY SUPPLEMENT C
Amines & Amides 1. You should be able to define and/or identify the following terms: primary amine biological activity secondary amine primary structure tertiary amine secondary structure amide alpha-helix alpha-amino acid beta-structure peptide bond tertiary structure N-terminal quaternary structure C-terminal subunit isoelectric point conjugated peptide denaturation protein enzyme 2. You should be able to differentiate between the structures of primary, secondary and tertiary amines. 3. You should be able to write formulas for amines and amides when given the names and vice-versa. 4. You should be able to describe the general properties of amines in terms of their structure. 5. You should be able to write equations for the preparation of amides from amines. 6. You should be able to a) write equations for the reactions of amines with acids and b) describe the solubility of the product in water. 7. You should be able to determine whether an amino acid is "neutral", "basic" or "acidic" when given the structure. 8. You should be able to explain the unusual physical properties of amino acids in terms of their structure and "dipolar" nature. 9. You should be able to show how a peptide bond forms between amino acids. 10. You should be able to describe the type of bonding responsible for the primary, secondary, and tertiary structure of protein. 11. You should be able to explain how the amino acid sequence is determined for a protein. 12. You should be able to describe the action of an enzyme. AMINES AND AMIDES 1. Classification of Amines: Comparison: C: primary C attached to one other C secondary C attached to two other C's tertiary C attached to three other C's quaternary C attached to four other C's But for amines look at C's attached to N: [CH3NH2] primary amine: N attached to one C [(CH3)2NH] secondary amine: N attached to two C's [(CH3)3N] tertiary amine: N attached to three C's and there is a quaternary N ion, with N attached to four C's; example: N(CH3)4+ (These are called quaternary ammonium ions.) 2. Preparation of Amines: a. Alkyl halides + NH3: CH3CH2Cl + NH3 CH3CH2NH2 + HCl primary amine b. Alkyl halide + amines: 1) CH3CH2Cl + CH3CH2NH2 CH3CH2-N-H + HCl | CH2CH3 secondary amine 2) CH3CH2Cl + CH3CH2-N-H CH3CH2-N-CH2CH3 | | CH2CH3 CH2CH3 + HCl tertiary amine 3. Preparation of Amides: a. Unsubstituted: *RCOOH + NH3, : (review!) O O " " CH3COH + NH3 -----> CH3CNH2 + H2O b. Substituted: *RCOOH + R'NH2, 1) O O " " CH3COH + CH3NH2-----> CH3CNHCH3 + H2O 2) O O " " CH3COH + (CH3)2NH -----> CH3CN(CH3)2 + H2O NOTE: only primary amines and secondary amines form amides O " *RCOOH or RCCl react the same way. 4. Reactions: a. Amines are bases: RNH2 + HCl react. CH3NH2 + HCl CH3NH3+ + Cl- salt (solubility increases) b. Formation of Amides: See #3 above. 5. Names: a. Common names for amines: (CH3)3N trimethylamine b. Substituted amides: O " CH3CN(CH3)2 N,N-dimethylethanamide PRACTICE SET Amines, Amides 1. Draw a structure for each of the following: a. isopropylamine b. isobutylmethylamine c. ethylmethyl-n-propylamine 2. Classify each of the amines in 1. above as primary, secondary or tertiary. 3. Complete the following reactions with the organic product: a. CH3CH2CH2NH2 + HI b. N-CH3 + HCl | CH3 4. Complete the following hydrolysis reactions: a. O " CH3CH2CH2CNH2 + H2O -----> H+ b. O " CH3CH2CH2C-N-CH3 + H2O -----> H+ CH2CH3 PRACTICE SET ANSWERS Amines, Amides 1. a. CH3CHCH3 isopropylamine | NH2 b. CH3 | CH3-N-CH2CHCH3 isobutylmethylamine | H c. CH3-N-CH2CH3 ethylmethyl-n-propylamine | CH2CH2CH3 2. a. primary amine b. secondary amine in 1. above c. tertiary amine 3. a. CH3CH2CH2NH2 + HI CH3CH2CH2NH3+I- b. H+ | CH3-N-CH3 + HCl -----> CH3-N-CH3 + Cl - | | C C / \ / \ H-C C-H H-C C-H |O| |O| H-C C-H H-C C-H \ / \ / C C | | H H H H | | C-C CH3 / \ | H-C O C-N + HCl -----> \ / | C-C CH3 | | H H H H | | C-C CH3 / \ | + - H-C O C-N-H + Cl \ / | C-C CH3 | | H H 4. a. O O O " H+ " " CH3CH2CH2CNH2 + H2O ----> CH3CH2CH2COH + NH3 CH3CH2CH2CO- NH4+ b. O O " H+ " CH3CH2CH2C-N-CH2CH3 + H2 ------> CH3CH2CH2COH + NHCH2CH3 | CH3 CH3 || || || H+ || || \/ H | + H-N-CH2CH3 | CH3 Amino Acids and Proteins O " 1. -Amino acids are the only ones we will focus on. -N-C-C-OH 2. Description of a protein includes PRIMARY - amino acid sequence (amides; covalent bonds) SECONDARY - alpha-helix or ß-pleats (H-bonding; polar forces) TERTIARY - coiling, bending and folding into 3-D shape and QUATERNARY - aggregation of biologically active sub-units. Not all proteins have a tertiary or quaternary structure. Hemoglobin, a globular protein, does. 3. The primary structure is very important to the protein. Any change in amino acid sequence changes the protein. Example: sickle cell anemia 4. Denaturing proteins: irreversible destruction of all but primary structure. Heat; pH; solvents; agitation; heavy metals, etc. 5. Enzymes: wholly or in part proteins, that act as biological catalysts PRACTICE SET Amino Acids and Proteins 12. Define the following terms: a. tripeptide b. isoelectric point c. N-terminal d. C-terminal 13. Identify the peptide (amide) linkages in the following structure: O " H2N-C-C-N | CH3 O C O O NH__CH__C NH__CH__C__OH CH2 CH2 OH C=O OH 14. List and describe the types of forces that determine the tertiary structure of a protein. 15. Distinguish between the 1 , 2 , 3 and 4 structures of a protein. ANSWERS 12. a. tripeptide: a polymer consisting of three amino acids linked as amides. O R R' O R" R O R__CH__C__N__CH__C__N__CH__C__OH NH2 b. isoelectric point: the pH at which an amino acid exists in its dipolar form. O R__CH__C O- NH3+ c. N-terminal end of a peptide: the end with the free amino group. d. C-terminal end of a peptide: the end with the free carboxyl group. 13. O H2N__CH__C__N CH3 alanine O ala C O O NH__CH__C proline NH__CH__C__OH pro CH2 CH2 OH C=O serine ser OH aspartic acid asp ala pro ser asp sequence 14. The tertiary structure of a protein refers to the coiling and bending of the helix. One type of force which is responsible for the coiling and bending is the "salt bridge" linkage, the attraction of two oppositely charged groups such as -NH3 + and O -C-O - Hydroxy side groups will align towards water because of H-bond. S-S linkages form from S-H groups. In general, the protein will coil with non-polar groups to the center and polar groups to the outside. 15. Primary structure of proteins: sequence of amino acids in the peptide. Secondary structure of proteins: the -helix with H-bonding between coils. Tertiary structure of proteins: the twisting, bending and coiling of the -helices due to ionic attractions, H-bonding. Quaternary structure of proteins: large superstructures resulting from the aggregation of subunits made up of the coiled, bent alpha-helices.