Department of Chemistry CHEM1020 General Chemistry ***********************************************

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. (L16)-Biochemistry • Today’s Outline …Nucleic acids types of nucleic acids: DNA, RNA monomers of nucleic acids: Nucleotides components of nucleotide monomers formation of DNA and RNA polymers base sequence in DNA and RNA …Comparison between proteins and nucleic acids in terms of polymer chemistry

3. Chapter 15. (L16)-Biochemistry • Nucleic acids …Nucleic acids Present in cell, serving as (genetic) information and control center of the cell …Two kinds of nucleic acids DNA: deoxyribonucleic acid, blueprint for all the proteins of an organism found mainly in cell nucleus RNA: ribonucleic acid, directing protein assembly (help to synthesize proteins) found in all parts of the cell

4. Chapter 15. (L16)-Biochemistry • Nucleic acids …Both DNA and RNA are long chain polymers …Basic monomers for DNA and RNA The basic monomers are various kinds of nucleotides, or each monomer is a nucleotide …Basic chemical components for the nucleotide monomers for DNA and RNA each nucleotide has three basic components: -a pentose sugar (5 C ring, organic hydrocarbon) -a heterocyclic amine base (organic base) -a phosphate unit (inorganic unit) a nucleotide = a phosphate + a pentose + a base

5. Chapter 15. (L16)-Biochemistry • Nucleic acids …Each nucleotide has three basic components: -A pentose sugar (5 C ring, organic hydrocarbon): For DNA: 2-Deoxyribose For RNA: Ribose -A heterocyclic amine base (organic base) For DNA: Guanine (G), Cytosine (C), Adenine (A), Thymine(T) For RNA: Guanine (G), Cytosine (C), Adenine (A), Uracil (U) -A phosphate unit (inorganic unit) For both DNA and RNA: PO43- anion (Pi)

6. Chapter 15. (L16)-Biochemistry • Nucleic acids …Each nucleotide has three basic components: -Pentose sugars, 5 C ring, organic hydrocarbon ..For DNA: 2-Deoxyribose the O from the –OH on 2-C is lost, only –H present (deoxydized, reduced) ..For RNA: Ribose The -OH on 2-C is present How to tell if a nucleic acid is a DNA or an RNA? Check the 2-C to see if only –H is there or –OH is there.

7. Chapter 15. (L16)-Biochemistry • Nucleic acids …Each nucleotide has three basic components: -Heterocyclic amine bases (organic base) For DNA: Guanine, Cytosine, Adenine, Thymine For RNA: Guanine, Cytosine, Adenine, Uracil Adenine and Guanine have two fused rings, classified as pruines Cytosine, thymine, and uracil have only one ring classified as primidines The five bases behave as bases because they all have amine groups, which are basic. -Difference between thymine and uracil: thymine has a -CH3 group in its base ring, but uracil does not.

8. Chapter 15. (L16)-Biochemistry • Nucleic acids …Structure of nucleotides Each nucleotide is composed of a sugar with two side components, a phosphate and an organic base .Linkage between the phosphate and the sugar: …phosphate ester linkage between Pi and C-5 formed by condensation through elimination of –H from phosphate and the –OH group on C-5 of the sugar .Linkage between base and sugar …β-glycosidic bond (glycoside linkage) between the –N of the base and C-1 formed by condensation through elimination of the –H from the N on the base and –OH from the C-1 on the sugar

9. Chapter 15. (L16)-Biochemistry • Nucleic acids …Structure of nucleotides General formula for nucleotide monomers: base | Pi-sugar Example: Adenosine monophosphate (AMP) adenine | Pi-sugar …Nucleotides differ because of their different bases, much as amino acids differ because of their –R groups.

10. Chapter 15. (L16)-Biochemistry • Nucleic acids …Structure of nucleotide polymers, i.e., nucleic acids General formula for nucleotide polymers: base base base base base | | | | | -Pi-sugar-Pi-sugar-Pi-sugar-Pi-sugar-Pi-sugar- Linkage between two nucleotide monomers: phosphate ester linkage formed by condensation between the –OH of the phosphate and the –OH on C-3

11. Chapter 15. (L16)-Biochemistry • Sequence of bases in nucleic acids …The sequence of bases in nucleic acids are highly important, which carries the genetic information. …The four bases for DNA: G, C, A, T, or GCAT, only four letters, but these can form various combinations like various words or sentences in DNA, thus carrying various bioinformation.

12. Chapter 15. (L16)-Biochemistry • Polymer chemistry of proteins and nucleic acids …Comparison between proteins and nucleic acids in their polymer chemistry Item ProteinNucleic Acid monomers amino acids nucleotides sequence component -R in AA base in nucleotide monomer linkage amide phosphate ester 1st level structure AA sequence base sequence 2nd level structure α-helix double-helix (DH) 3rd level structure helix folding DH strand folding 4th level structure complicated complicated

13. Chapter 15. (L16)-Biochemistry Quiz Time Homework: Make up three quiz practice questions with four choices regarding this lecture (L16), due Feb. 28 (M). (a) ; (b) ; (c) ; (d) .

14. Chapter 15. (L16)-Biochemistry Quiz Time The two general kinds of nucleic acids are (a) DAN and RAN; (b) DDT and PCB; (c) DNA and RNA; (d) none of above.

15. Chapter 15. (L16)-Biochemistry Quiz Time DNA and RNA are shout-cuts in biochemistry respectively for (a) deoxyribonucleic alcohol and ribonucleic alcohol; (b) deoxyribonucleic acid and ribonucleic acid; (c) definitely not applicable and relatively not applicable; (d) none of above.

16. Chapter 15. (L16)-Biochemistry Quiz Time In a cell, DNA and RNA are present, respectively (a) in all parts of the cell for DNA and mainly in cell nucleus for RNA; (b) mainly in cell nucleus for both DNA and RNA; (c) all parts of cell for both DNA and RNA; (d) mainly in cell nucleus for DNA and found in all parts of the cell for RNA.

17. Chapter 15. (L16)-Biochemistry Quiz Time The major biological functions of DNA are (a) having fun in the cell; (b) directing and facilitating synthesizing proteins; (c) carrying the genetic information and serving as the blueprint for all the proteins of an organism; (d) controlling the temperature of the living thing.

18. Chapter 15. (L16)-Biochemistry Quiz Time The major biological functions of RNA are (a) having fun in the cell; (b) directing and facilitating synthesizing proteins; (c) carrying the genetic information and serving as the blueprint for all the proteins of an organism; (d) controlling the temperature of the living thing.

19. Chapter 15. (L16)-Biochemistry Quiz Time Both DNA and RNA are (a) large inorganic molecules; (b) small biochemical molecules; (c) biochemical monomers; (d) biochemical polymers.

20. Chapter 15. (L16)-Biochemistry Quiz Time The monomers for DNA and RNA are (a) monosaccharides; (b) nuclear particles; (c) nucleic acids; (d) nucleotides.

21. Chapter 15. (L16)-Biochemistry Quiz Time A nucleotide has three basic chemical components, which are (a) a 5 carbon ring sugar, an organic base, and an inorganic sulfate; (b) a 5 carbon ring sugar, an organic base, and an inorganic phosphate; (c) a 5 carbon ring alkane, an organic base, and an inorganic phosphate; (d) a 5 carbon ring sugar, an inorganic base, and an inorganic phosphate.

22. Chapter 15. (L16)-Biochemistry Quiz Time The 5 carbon ring sugar for DNA is (a) fructose; (b) glucose; (c) ribose ; (d) 2-deoxyribose.

23. Chapter 15. (L16)-Biochemistry Quiz Time The 5 carbon ring sugar for RNA is (a) fructose; (b) glucose; (c) ribose; (d) 2-deoxyribose.

24. Chapter 15. (L16)-Biochemistry Quiz Time The difference between ribose and deoxyribose is that (a) the deoxyribose does not have the –COOH group on its C-2 carbon while ribose has; (b) the deoxyribose has the –OH group on its C-2 carbon, while the ribose does not; (c) the deoxyribose does not have the –OH group on its C-2 carbon, while the ribose has; (d) none of above.

25. Chapter 15. (L16)-Biochemistry Quiz Time The four organic bases for DNA nucleotides are (a) guanine, adenine, thymine, and uracil or G, A, T, U; (b) guanine, cytosine, adenine, and thymine, or G, C, A, T; (c) guanine, cytosine, adenine, and uracil or G, C, A, U; (d) none of above.

26. Chapter 15. (L16)-Biochemistry Quiz Time The four organic bases for RNA nucleotides are (a) guanine, adenine, thymine, and uracil or G, A, T, U; (b) guanine, cytosine, adenine, and thymine, or G, C, A, T; (c) guanine, cytosine, adenine, and uracil or G, C, A, U; (d) none of above.

27. Chapter 15. (L16)-Biochemistry Quiz Time A DNA nucleotide or an RNA nucleotide is formed by the three units of sugar, base, and phosphate in the way of (a) the sugar connects to the base and the base connects to the phosphate, i.e. sugar-base-Pi; (b) the sugar connects to the phosphate and the phosphate connects to the base, i.e. sugar-Pi-base; (c) the sugar connects to the phosphate on one position of the sugar ring and to the base on another position of the sugar ring, i.e. Pi–sugar-base; (d) none of above.

28. Chapter 15. (L16)-Biochemistry Quiz Time DNA nucleotides or RNA nucleotides differ by (a) the sugars in the nucleotides; (b) the bases in the nucleotides; (c) the phosphate in the nucleotides; (d) none of above.

29. Chapter 15. (L16)-Biochemistry Quiz Time A DNA or an RNA is formed by which polymerization reaction? (a) addition polymerization; (b) condensation polymerization; (c) hydrogen bonding polymerization; (d) ionic bonding polymerization.

30. Chapter 15. (L16)-Biochemistry Quiz Time The general schematic formula for a DNA or an RNA is (a) –base-sugar-Pi-base-sugar-Pi-base-sugar-Pi-; (b) Pi Pi Pi | | | -base-sugar-base-sugar-base-sugar-; (c) base base base base | | | | -Pi-sugar-Pi-sugar-Pi-sugar-Pi-sugar-; (d) none of above.