Department of Chemistry CHEM1020 General Chemistry *********************************************** Instructor: Dr. Hong

1. Department of Chemistry CHEM1020 General Chemistry *********************************************** Instructor: Dr. Hong Zhang Foster Hall, Room 221 Tel: 931-6325 Email: hzhang@tntech.edu

2. CHEM1020/General Chemistry_________________________________________Chapter 15. (L15)-Biochemistry • Today’s Outline ..Peptide bond for peptides and proteins peptides peptide bond ..Protein structures primary structure secondary structure tertiary structure quaternary structure four ways to link proteins …Enzymes

3. Chapter 15. (L15)-Biochemistry • Peptide bond …Two amino acids can join together by the peptide bond: O O O O || || || || H2N-CH-C-OH + HNH-CH-C-OH H2N-CH-C-NH-CH-C-OH | | | | R R’ R R’ + H2O …A peptide bond is an amide linkage as learned before. Amino acids join together by means of condensation through removal of a H2O molecule.

4. Chapter 15. (L15)-Biochemistry • Peptides …Peptides are small units of amino acids (AA) joined together by amide linkage through condensation. So, peptides are small segments of proteins. dipeptide: Gly-Ala tripeptide: Gly-Ala-Cys polypeptide: peptide with more than 10 AAs …A great number of amino acids (102 or 103 or more) joined together form proteins (MW > 10000). Naming peptides: see book on pp.444-445. Proteins are also called polyamides.

5. Chapter 15. (L15)-Biochemistry • Sequence of proteins or peptides …The sequence of a protein starts from the amino end called N-terminal to the carboxylic end called C-terminal. …The amino acids sequence in a protein is very important. The 20 or more basic amino acids are just like the 26 letters in English, which can form various words and sentences and paragraphs and pages and pages, and so on and on.

6. Chapter 15. (L15)-Biochemistry • Structures of proteins …Proteins can have four levels of structures -Primary structure: the amino acid sequence or chain formulized by the peptide bonds or amide linkage. -Secondary structure: Arrangement of the protein polymer chain to form a higher level of structure held by hydrogen bonding between protein chains -pleated sheet structure, held by hydrogen bond between chains and sheets, like in silk, etc. -spiral right-handed called α-helix held by hydrogen bond inside the chain between N-terminals and C-terminals, like in wool, hair, muscle

7. Chapter 15. (L15)-Biochemistry • Structures of proteins …Proteins can have four levels of structures -Tertiary structure: The folding of the helix in space a 3-D structure, example: globular protein in a spherical shape Example: myoglobin -Quaternary structure: Different peptide units are arranged in an aggregate or assembly Example: hemoglobin (each unit is like a myoglobin)

8. Chapter 15. (L15)-Biochemistry • Structures of proteins Analogy by means of telephone cable cord (see pp. 447) …Four types of interactions or “forces” or “bonding” to form the tertiary structure: -hydrogen bond between the H from N-H and O from C=O and between the H from –OH and O from C=O intramolecular, intermolecular -ionic bond between “+” and “-” groups, also called salt bridges -disulfide bond between two Sulfur atoms, covalent bond, strong to hold chains together -dispersion force, inner non-polar portion, outer polar portion

9. Chapter 15. (L15)-Biochemistry • Enzymes Enzymes are highly specialized class of proteins with special structures and functions. biological catalysts speeding up or facilitating specific bioreactions at cell temperature Some terminology: -substrate: reacting substances -active site: particular place in an enzyme where the substrate and the enzyme form an enzyme-substrate complex to lower the energy required for the reaction

10. Chapter 15. (L15)-Biochemistry • Enzymes Some terminology: -cofactor: a chemical component necessary for the proper function of the enzyme ..inorganic cofactors: metal ions, Zn2+, Mg2+, Mn2+, Fe2+, Cu2+ ..organic cofactors: also called coenzymes coenzymes are not proteins, just some organic molecules many coenzymes are vitamins or derivatives of vitamins

11. Chapter 15. (L15)-Biochemistry Quiz Time Which of the following is a peptide bond (a) CH2R-CONH-CHR’COO-; (b) NH3+-CHR-CONH-CHR’COO-; (c) NH3+-CHR-CONH-CH2R’; (d) NH3+-CHR-COO-CH2-CHR’COO-.

12. Chapter 15. (L15)-Biochemistry Quiz Time Proteins are polymers made of the monomers of (a) monosaccharides; (b) ethylene; (c) various amino acids; (d) alkyl groups.

13. Chapter 15. (L15)-Biochemistry Quiz Time The N-terminal in a protein or peptide refers to (a) the amide linkage; (b) the carboxylic group; (c) the amino group; (d) none of above.

14. Chapter 15. (L15)-Biochemistry Quiz Time The C-terminal in a protein or peptide refers to (a) the amide linkage; (b) the carboxylic group; (c) the amino group; (d) none of above.

15. Chapter 15. (L15)-Biochemistry Quiz Time Proteins are polymers made by which bonding or linkage between two monomers? (a) triple bond; (b) double bond; (c) ester bond; (d) peptide bond.

16. Chapter 15. (L15)-Biochemistry Quiz Time A peptide bond is (a) triple bond; (b) double bond; (c) an amide linkage; (d) an ester bond.

17. Chapter 15. (L15)-Biochemistry Quiz Time A peptide bond is formed by (a) addition of chlorine into the double bonds of the amino acids to form single bonds; (b) elimination of a water molecule from the alcohol group and the carboxylic group to form an ester linkage; (c) elimination of a water molecule from the amino group and the carboxylic group to form an amide linkage; (d) none of above.

18. Chapter 15. (L15)-Biochemistry Quiz Time Proteins are polymers formed by connecting the monomers through (a) dispersion force; (b) elimination of double bonds; (c) addition polymerization; (d) condensation polymerization.

19. Chapter 15. (L15)-Biochemistry Quiz Time A peptide is (a) a segment of cellulose; (b) a segment of starch; (c) a segment of Teflon; (d) a chain of a small number of more than ten amino acids joined together, or a segment of a protein.

20. Chapter 15. (L15)-Biochemistry Quiz Time Proteins are amino acid polymers with their molecular mass generally (a) < 5000; (b) > 5000; (c) < 10000; (d) > 10000.

21. Chapter 15. (L15)-Biochemistry Quiz Time Proteins are amino acid polymers with the number of amino acids generally (a) no more than three; (b) a few; (c) less than tens; (d) more than hundreds or even thousands.

22. Chapter 15. (L15)-Biochemistry Quiz Time Proteins generally can have (a) three levels of structures; (b) four levels of structures; (c) two levels of structures; (d) one level of structure.

23. Chapter 15. (L15)-Biochemistry Quiz Time The primary structure of a protein is determined by (a) the position of the N-terminal; (b) the position of the C-terminal; (c) its sequence of amino acid in the polymer chain; (d) the number of amino acids.

24. Chapter 15. (L15)-Biochemistry Quiz Time The secondary structure of a protein refers to (a) the arrangement of the protein chains in the form of cones; (b) the arrangement of the protein chains in the form of pleated sheets or helixes; (c) the arrangement of the protein chains in the form of closed rings; (d) the arrangement of the protein chains in the random forms.

25. Chapter 15. (L15)-Biochemistry Quiz Time The secondary structure of a protein in the form of pleated sheets can be found in (a) bone; (b) silk; (c) wool, muscle, hair; (d) none of above.

26. Chapter 15. (L15)-Biochemistry Quiz Time The secondary structure of a protein in the form of helix can be found in (a) bone; (b) silk; (c) wool, muscle, hair; (d) none of above.

27. Chapter 15. (L15)-Biochemistry Quiz Time The helix structure of a protein is formed by (a) hydrogen bonding between the N on the amino group and the H on the carboxylic group inside the spiral protein chain; (b) hydrogen bonding between the N on the amino group and the O on the carboxylic group inside the spiral protein chain; (c) hydrogen bonding between the H on the amino group and the O on the carboxylic group inside the spiral protein chain; (d) hydrogen bonding between the O on the amino group and the H on the carboxylic group inside the spiral protein chain.

28. Chapter 15. (L15)-Biochemistry Quiz Time The helix structure of a protein is (a) a γ-helix; (b) a β-helix; (c) an α-corn; (d) an α-helix.

29. Chapter 15. (L15)-Biochemistry Quiz Time An α-helix of a protein is (a) left-handed; (b) right-handed; (c) either left- or right-handed; (d) none of above.

30. Chapter 15. (L15)-Biochemistry Quiz Time The tertiary structure of a protein refers to (a) left-handed helix structure of a protein; (b) the variation of the sequence of the amino acids; (c) the folding of the protein helix in a certain way in the space; (d) none of above.

31. Chapter 15. (L15)-Biochemistry Quiz Time The quaternary structure of proteins refers to (a) the aggregate of several peptides in a certain way in the space; (b) the aggregate of several amino acids in a certain way in the space; (c) the aggregate of several protein helix subunits in a certain way in the space; (d) none of above.

32. Chapter 15. (L15)-Biochemistry Quiz Time The forces holding the various levels of the structures of proteins include (a) gravitation, dipole force, ester-linkage, and magnetic attraction; (b) H-bond, salt-bridge, dipole force, and gravitation; (c) hydrogen bond, ionic attraction, disulfide covalent bond, and dispersion force; (d) none of above.

33. Chapter 15. (L15)-Biochemistry Quiz Time The ionic attraction or salt-bridge in a protein occurs between (a) the negative N-terminal of a side chain and the positive C-terminal of a side chain; (b) the positive N-terminal of a side chain and the negative C-terminal of a side chain; (c) the zero-charged N-terminal of a side chain and the negative C-terminal of a side chain; (d) the positive N-terminal of a side chain and the zero-charged C-terminal of a side chain.

34. Chapter 15. (L15)-Biochemistry Quiz Time Enzymes are (a) a highly specialized class of amines; (b) a highly specialized class of amino acids; (c) a highly specialized class of peptides; (d) a highly specialized class of proteins.

35. Chapter 15. (L15)-Biochemistry Quiz Time Enzymes function as (a) biosolvents; (b) biological catalysts to speed up specific bioreactions at the temperatures of biosystems; (c) bio-matrixes for animals; (d) biological catalysts to increase the temperatures at which bioreactions occur in biosystems.

36. Chapter 15. (L15)-Biochemistry Quiz Time In biochemistry, substrates refer to (a) the reaction media; (b) the solvents; (c) the products; (d) the reactants or reacting substances.

37. Chapter 15. (L15)-Biochemistry Quiz Time In biochemistry, the active site of an enzyme refers to (a) the site where the enzyme becomes excited; (b) the site where an enzyme-substrate complex forms to catalyze the specific bioreaction; (c) the site where the enzyme cannot function well; (d) the site where the enzyme decomposes.

38. Chapter 15. (L15)-Biochemistry Quiz Time In biochemistry, the cofactor refers to (a) another important type of enzymes; (b) a special matrix for bioreactions; (c) a special solvent for bioreactions; (d) a chemical component necessary for the proper function of the enzyme.

39. Chapter 15. (L15)-Biochemistry Quiz Time In biochemistry, the common inorganic cofactors are (a) water molecules; (b) inorganic anions such as SO42-, NO3-, and Cl-; (c) metal cations such as Zn2+, Mg2+, Mn2+, Fe2+, and Cu2+; (d) non-polar water molecules.

40. Chapter 15. (L15)-Biochemistry Quiz Time In biochemistry, the organic cofactors are called (a) comolecules; (b) comonomers; (c) coenzymes; (d) copeptides.

41. Chapter 15. (L15)-Biochemistry Quiz Time In biochemistry, many organic cofactors or coenzymes are (a) water molecules; (b) vitamins and derivatives of vitamins; (c) metal ions; (d) salts.