Chapter 2

1. Chapter 2 Chemical Principles part B

2. Structure and Function • The chain of carbon atoms in an organic molecule is the carbon skeleton • Saturated hydrocarbons: Carbon-carbon single bond • Ethane – C2H6 • Hexane – C6H14 -Cyclohexane • Unsaturated hydrocarbons:Carbon-carbon double bond, • Ethylene – C2H4 Benzene – C6H6

3. Structure and Function • Replacing one of the H atoms in propane molecule with a functional group: • Propane – C3H8 • With OH- will become an alcohol (Propanol) Propanol - C3H7OH - Isopropanol • Replacing two more H atoms from the same C with Oxygen –will become an acid - Propanoic acid - CH3CH2COOH – C2H5COOH Functional group – hydroxyl group Radical Functional group – carboxyl group - COOH

4. Organic compounds in life organisms

5. Organic Compounds M Glucose C6H12O6 • The small molecules are called monomers. • Monomers join by dehydration synthesis or condensation reactions into large molecules -polymers . • Macromolecules are polymers consisting of many small repeating molecules-monomers. n M M n Cellulose (C6H10O5)n M M M M M M M M M

6. Organic Compounds 1. Monomers join by dehydration synthesis or condensation reactions. 2. Macromolecules degrade to monomers by hydrolysis or decomposition reactions 1 Enzyme 1 R-OH + HO-R R-O-R + H2O Enzyme 2 2 Figure 2.8

7. Organic compounds in life organisms

8. 1. Carbohydrates Glucose – C6H12O6 • Consist of C, H, and O with the formula (CH2O)n • Monomers - Monosaccharides are simple sugars with 3 to 7 carbon atoms. • glucose, fructose, galactose, ribose, deoxyribose • Disaccharides are formed when two monosaccharides are joined in a dehydrationsynthesis. • Sucrose (glucose-fructose), lactose (glucose-galactose) • Disaccharides can be broken down by hydrolysis. Figure 2.8

9. Oligosaccharides consist of 2 to 20 monosaccharides. • Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis. • Starch, glycogen, dextran, and cellulose are polymers of glucose that are covalently bonded differently. • Chitin is a polymer of two sugars repeating many times.

10. Function of Carbohydrates • Cellstructures • Nucleic acids - ribose, deoxyribose • Cell wall – peptidoglycan, cellulose, chitin • Bacterial capsule • Cell energy • Energy sources • Short term energy storage

11. C C C C 2. Lipids • Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), phospholipids, and others. • Consist of C, H, and O. A. Simple lipids - called fats – contain an alcohol glycerol and a group of compounds as fatty acids • Fatty acids - longchains of carbon and hydrogen atoms, with a carboxylic acid group at one end • Saturated • Unsaturated fats have one or more double bonds between carbons in the fatty acids. • Are nonpolar and insoluble in water

12. A molecule of fat is formed when a molecule of glycerol combines with one to three fatty acid molecules by dehydration synthesis • Monoglycerides, diglycerides,triglycerides • Saturated and Unsaturated fatty acids Figure 2.9c

13. B. Complex lipids • Contain C, H, and O + P, N, or S. • Membranes are made of phospholipids

14. C. Steroids • Steroid skeleton consist of four carbon rings • Steroids vary by the functional groups attached to these rings • Sterol - modified steroid with an –OH group attached to the ring A. • Are part of membranes. Figure 2.11

15. Function of Lipids • Plasma membranes • Cell organelles • Some cell walls • Long term energy storage

16. 3. Proteins • Consist of one or more polypeptide molecules typically folded into a globular or fibrous form, facilitating a biological function. • Protein macromolecules monomers - amino acids • Only 20 amino acids

17. Amino acids Table 2.4.1

18. Peptide Bonds • A peptide bond is a covalent bond that is formed between two amino acids when the carboxyl group of one molecule reacts with the amino group of the another molecule. • Peptide bonds between amino acids are formed by dehydration synthesis. • A single linear chain of amino acids bonded together by peptide bonds is called polypeptide • For chains under 40 residues the term peptide is frequently used instead of protein. Figure 2.14

19. The primary structure of a protein is the amino acid sequence of the peptide chains. It is reported starting from the amino-terminal (NH2) end to the carboxyl-terminal (COOH) Proteins structure - Primary structure Met - Cys - Val - Ala - Tyr - Arg Peptide bonds

20. Proteins structure - Primary structure R R R R R R

21. Peptide bonds Figure 2.15 Protein structure. Hydrogen bond (a) Primary structure: polypeptide strand (b) Secondary structure: helix and pleated sheets (with three polypeptide strands) Helix Pleated sheet Hydrophobic interaction Insert Fig 2.15a Insert Fig 2.15 Disulfide bridge Polypeptide strand Hydrogen bond (c) Tertiary structure: folded helix and pleated sheet Disulfide bridge (between cysteine molecules) Functionally active Ionic bond (d) Quaternary structure: two or more polypeptides in their folded states Details of bonds associated with tertiary structure Functionally active

22. Conjugated proteins consist of polypeptide chain bound to other organic molecules: • Glycoproteins • Nucleoproteins • Lipoproteins

23. Function of Proteins • Are essential in cell structure and function. • Enzymes are proteins that speed chemical reactions. • Transporter proteins move chemicals across membranes. • Structural or mechanical functions, that maintain cell shape ( actin, cell wall). • Cell signaling - complex system of communication that coordinates cell actions. • Flagella are made of proteins. • Some bacterial toxins are proteins. • Immune responses – antibodies, cytokines are proteins.

24. 4. Nucleic Acids • Macromolecules - DNA and RNA • Monomers are nucleotides. • Nucleotides consist of a: • Sugar pentose (with 5 carbons) • ribose • deoxyribose • Nitrogen-containing base (purine or pyrimidine) • Phosphate group Purines – Adenine and Guanine Pyrimidines – Cytosine, Thymine and Uracil

25. DNA • Monomers are deoxyribonucleotides • sugar-deoxyribose • Purines - Adenine and Guanine; Pyrimidines - Cytosine and Thymine • Primary structure – nucleotide sequence • The primary structure of DNA or RNA molecule is reported from the 5' end to the 3' end • 5’ end – PO4 (phosphate group) • 3’ end – OH (hydroxyl group) • The sugar-phosphate backbone of one strand is upside down, or antiparallel, relative to the backbone of the other strand. PO4 OH PO4 OH Figure 2.16

26. DNA – secondary structure – double helix • Two molecules form the double helix • A hydrogen bonds with T (2 hydrogen bonds) • C hydrogen bonds with G (3 hydrogen bonds) Phosphate Sugar Adenine (A) - Thymine (T) Sugar Phosphate Hydrogen bonds Adenine nucleotide Thymine nucleotide Individual DNA nucleotides are composed of a deoxyribose sugar molecule covalently bonded to a phosphate group at the 5’ carbon,and to a nitrogen-containing base at the 3’ carbon. The two nucleotides shown here are held together by hydrogen bonds. Insert Fig 2.16 Sugars Sugar-phosphate backbone Phosphates

27. RNA • Monomers are ribonucleotides • sugar ribose • Primary structure – nucleotide sequence • Single-stranded • Can form secondary structure • A hydrogen bonds with U (2 hydrogen bonds) • C hydrogen bonds with G (3 hydrogen bonds) tRNA siRNA Figure 2.17

28. Function of Nucleic acids • DNA contains all the information - coding which is used to control functions, behavior and development of an organism. • Long term storage device to store the genetic instructions. • The code from which all proteins in the cell are synthesized • Code for the way proteins turn genes on or off. • RNA carries out the instructions encoded in DNA • Protein synthesis • In some organisms it is also responsible for carrying the genetic code. • Some RNA are involved in the regulation of the gene expression

29. ATP – Adenosine triphosphate • Is made by dehydration synthesis. • Is broken by hydrolysis to liberate useful energy for the cell. ATP ADP

30. Function of ATP • ATP is the main energy source for the majority of cellular functions. • Important player in cell respiration. • Synthesis of macromolecules in the cell - DNA and RNA, proteins, lipids and carbohydrates. • Supply energy for the transport of macromolecules across cell membranes. • ATP is critically involved in maintaining the locomotion of the cell .

31. Learning objectives • Identify the structure and function of carbohydrates. • Identify the structure and function of lipids. • Identify the structure and function of proteins. • Identify the structure and function of nucleic acids • Describe the role of ATP in cellular activities.