Molecules of Cells: Structure, Function & Synthesis

1. 0 Chapter 3 The Molecules of Cells

2. Standards By the end of the unit you should be able to: • Model synthesis and hydrolysis reactions and relate the reactions to the human body • Recognize carbs, lipids, proteins and nucleic acids in formula & skeleton form, chemical structure and describe their function in the human body • Recognize monosaccharides, disaccharides and polysaccharides and relate the molecules to how they function in the body • Recognize, describe the location of, and explain the importance of the following in the human body: neutral fats, steroids and phospholipids • I can list the major functions of nucleic acids (RNA & DNA), describe their structure with accurate detail and compare these 2 molecules • I can compare the following pairs: saturated and unsaturated fats, DNA & RNA • I can differentiate among the primary, secondary, tertiary and quaternary structure of proteins and explain how these levels of structure relate to protein functions • I can relate protein structure to protein specific examples from the human body • I ca draw the general structure of the ATP molecule in its role as the “energy currency” of cells

3. Biological Molecules • 3.1 Life’s molecular diversity is based on the properties of carbon • A carbon atom can form four covalent bonds allowing it to build large and diverse organic compounds • Organic Molecules – contain carbon atom and a hydrogen atom • C can bond with up to 4 other atoms

4. H H H H H 0 1 2 3 4. C C C C C H H H H H H H H H Ethane Propane Carbon skeletons vary in length. H C H H H H H H H • Carbon chains vary in many ways • Hydrocarbons are composed of only hydrogen and carbon • Some carbon compounds are isomers: molecules with the same molecular formula but different structures H C C C C C C C H H H H H H H H H H H Butane Isobutane Skeletons may be unbranched or branched. H H H H H H H H C C C H H C H H C C C C H H H H 1-Butene 2-Butene Skeletons may have double bonds, which can vary in location. H H H C C H H H H C C C C H H H C C H C C H H C H H C H H H Benzene Cyclohexane Figure 3.1A Skeletons may be arranged in rings.

5. 0 • 3.2 Functional groups help determine the properties of organic compounds • Some examples of functional groups: Table 3.2

6. 0 • Functional groups are particular groupings of atoms that give organic molecules particular properties OH Estradiol HO Female lion OH O Figure 3.2 Testosterone Male lion

7. Monomer –is a small molecule that may become chemically bonded to other monomers to form a polymer. Polymer – a large molecule that is made of several monomers bonded to each other Basic Vocab.

8. Reactions that form polymers & monomers • Hydrolysis and Synthesis Reactions • Reactions we will see for all biological molecules

9. H OH H OH OH H Short polymer Short polymer Unlinked monomer Unlinked monomer H2O Dehydration reaction Dehydration reaction OH H OH H Longer polymer 0 • Cells make most of their large molecules by joining smaller organic molecules into chains called polymers • Cells link monomers to form polymers by a dehydration reaction Figure 3.3A

10. H2O H OH Hydrolysis H OH H OH 0 • Polymers are broken down to monomers by the reverse process, hydrolysis Figure 3.3B

11. 0 • 3.3 Cells make a huge number of large molecules from a small set of small molecules • The four main classes of biological molecules are carbohydrates, lipids, proteins, and nucleic acids • Many of the molecules are gigantic and are called macromolecules

12. 0 CARBOHYDRATES • 3.4 Monosaccharides are the simplest carbohydrates • The carbohydrate monomers are monosaccharides • A monosaccharide has a formula that is a multiple of CH2O and contains hydroxyl groups and a carbonyl group Figure 3.4A

13. Carb Info: • Function of carbs for humans– source of energy for the cell (cellular respiration) • CARBS contains carbon, hydrogen, and oxygen in the ratio of 1:2:1. (empirical formula)

14. H O H H C C OH OH H C C O HO H C HO H C OH C H C H OH H OH C C OH H C OH H C H OH H H Glucose Fructose 0 • The monosaccharides glucose and fructose are isomers that contain the same atoms but in different arrangements Figure 3.4B

15. CH2OH 6 CH2OH C O 5 H O O H H H H H C C 1 4 OH H OH H OH HO OH OH C C 2 3 H OH H OH Simplified structure Structural formula Abbreviated structure 0 • Monosaccharides can also occur as ring structures Figure 3.4C

16. CH2OH CH2OH O O H H H H H H OH H OH H O OH H HO OH H OH H OH Glucose Glucose H2O CH2OH CH2OH O O H H H H H H OH OH H H O OH HO H OH H OH Maltose 0 • 3.5 Cells link two single sugars to form disaccharides • Monosaccharides can join to form disaccharides such as sucrose (table sugar) and maltose (brewing sugar) Figure 3.5

17. 0 CONNECTION • 3.6 How sweet is sweet? • Various types of molecules, including nonsugars taste sweet because they bind to “sweet” receptors on the tongue Table 3.6

18. 0 Figure 3.7 Glucose monomer STARCH Starch granules in potato tuber cells O O O O O O O O O O O Glycogen granules in muscle tissue GLYCOGEN O O O O O O O O O O O O O Cellulose fibrils in a plant cell wall CELLULOSE O O OH Cellulose molecules O O O O O OH O O O O O O O O O O O O O O O O • 3.7 Polysaccharides are long chains of sugar units • Polysaccharides are polymers of monosaccharides linked together by dehydration reactions • Starch and glycogen are polysaccharides that store sugar for later use • Cellulose is a polysaccharide found in plant cell walls

19. 0 LIPIDS • 3.8 Fats are lipids that are mostly energy-storage molecules • Lipids are diverse compounds that consist mainly of carbon and hydrogen atoms linked by nonpolar covalent bonds • Lipids are grouped together because they are hydrophobic Figure 3.8A

20. H H H H H H H H C C H C H H C C C O O O OH OH OH C C C O O O Glycerol HO CH2 CH2 CH2 C O H2O CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 Fatty acid CH2 CH2 CH CH2 CH2 CH2 CH2 CH CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH3 CH3 CH3 0 • Fats, also called triglycerides (neutral fats) are lipids whose main function is energy storage • Consist of glycerol linked to three fatty acids Figure 3.8B Figure 3.8C

21. CH3 H3C CH3 CH3 CH3 HO 0 • 3.9 Phospholipids, waxes, and steroids are lipids with a variety of functions • Phospholipids are a major component of cell membranes • Waxes form waterproof coatings • Steroids are often hormones Figure 3.9

22. 0 CONNECTION • 3.10 Anabolic steroids pose health risks • Anabolic steroids are synthetic variants of testosterone that can cause serious health problems

23. 3rd group of Bio Cules - Proteins 2 types Functional Structural Enzymes – hydrolytic- (lysosomes, digestive) Found in ligaments, bones, tendons, skin Ex – keratin, collagen

24. 0 PROTEINS • 3.11 Proteins are essential to the structures and activities of life • A protein is a polymer constructed from amino acid monomers • Proteins are involved in almost all of a cell’s activities • As enzymes they regulate chemical reactions. Figure 3.11

25. H O H C N C H OH R Amino group Carboxyl (acid) group 0 • 3.12 Proteins are made from amino acids linked by peptide bonds • Protein diversity is based on different arrangements of a common set of 20 amino acid monomers • Each amino acid contains • An amino group • A carboxyl group • An R group, which distinguishes each of the 20 different amino acids Figure 3.12A

26. H H H H H H O O O N C C N C C N C C OH OH H H H OH CH2 CH2 CH2 CH OH C CH3 CH3 OH O Leucine (Leu) Serine (Ser) Aspartic acid (Asp) Hydrophobic Hydrophilic 0 • Each amino acid has specific properties based on its structure Figure 3.12B

27. Peptide bond Carboxyl group Amino group H H Dehydration reaction H O H H H O O O H N C C + N C C N C C N C C H OH OH H OH H H R R R R H2O Amino acid Amino acid Dipeptide 0 • Cells link amino acids together by dehydration synthesis • The bonds between amino acid monomers are called peptide bonds Figure 3.12C

28. Peptide Bonds • The N of one a.a. bonds to C of carboxyl of another a.a. • Dipeptide – has 1 peptide bond & 2 a.a. • Tripeptide – has 2 bonds & 3 a.a • Polypeptides – many amino acids

29. Groove Groove 0 • 3.13 A protein’s specific shape determines its function • A protein consists of one or more polypeptide chains folded into a unique shape that determines the protein’s function Figure 3.13A Figure 3.13B

30. Levels of Protein Structure Leu Met Asn Val Pro Ala Val Ile Arg Cys Val Lys Phe Ala Glu His Gly Val Ser Lys Primary structure Thr Val Gly Pro Ala Val Asp Arg Leu Gly Ser Amino acids 0 • 3.14 A protein’s shape (and therefore its function!) depends on four levels of structure • Primary Structure • A protein’s primary structure is the sequence of amino acids forming its polypeptide chains Figure 3.14A

31. Hydrogen bond O H H O C C C N N H C O C C C R N C C N H H H O N C C O C C C N O H H C N C N O H C H C H C N N C N O C O N H N C H O O C R C C O C O H H H C C O C N H O N C C C N C H Secondary structure C C O O H N C C O N H C C H H N H N O O N C C N C O C H N H N C C H O C O C C N H C C C N O H C O Alpha helix Pleated sheet Amino acids Figure 3.14B 0 • Secondary structure • A protein’s secondary structure is the coiling or folding of the chain, stabilized by hydrogen bonding between a.a. on different parts of the strand

32. Tertiary structure Polypeptide (single subunit of transthyretin) 0 • Tertiary Structure • A protein’s tertiary structure is the overall three-dimensional shape of a polypeptide • This 3D shape is the result of interactions between the R groups of the a.a.s Figure 3.14C

33. Polypeptide chain Quaternary structure Transthyretin, with four identical polypeptide subunits Collagen 0 • Quaternary Structure • A protein’s quaternary structure results from the association of two or more polypeptide chains • EX: hemoglobin Figure 3.14D

34. 0 TALKING ABOUT SCIENCE • 3.19 Linus Pauling contributed to our understanding of the chemistry of life • Linus Pauling made important contributions to our understanding of protein structure and function • Discovered the alpha helical structure in proteins (secondary level) and also the difference in the structure of hemoglobin in regular blood vs sickle cell anemia blood Figure 3.15

36. 0 NUCLEIC ACIDS • 3.20 Nucleic acids are information-rich or energy carrying polymers of nucleotides • There are 3 ex: DNA, RNA, ATP • Nucleic acids such as DNA and RNA serve as the blueprints for proteins and thus control the life of a cell • ATP serves as the energy currency of the cell

37. H H N N N H OH N H N O P O CH2 Nitrogenous base (A) O O H H Phosphate group H H H OH Sugar 0 • The monomers of nucleic acids are nucleotides • Composed of a 5 carbon sugar, phosphate, and nitrogenous base (ATCGU) Figure 3.16A

38. Different Nucleotides: Note same basic shape!

39. Nucleotide A T C G T Sugar-phosphate backbone 0 • The sugar and phosphate form the backbone for the nucleic acid or polynucleotide Figure 3.16B

40. C A T C G C G A T C G A T A T Base pair G C T A A T A T 0 • DNA consists of two polynucleotides twisted around each other in a double helix, the two strands run antiparallel to each other • Stretches of a DNA molecule called genes program the amino acid sequences of proteins Figure 3.16C

41. 0 • RNA, by contrast is a single-stranded polynucleotide • RNA, when compared to DNA, is: • Shorter • Single stranded • Has a U base (uracil) instead of a T base (thymine) • Has MANY more types/jobs, ex: messenger, transfer, ribosomal etc

42. Produced by cellular respiration Glucose + oxygen - Carbon dioxide + water + ATP ATP – needed for active transport Notice – 2 high energy bonds Synthesis of – ADP + Pi → ATP + H2O ATP – Adenosine Triphosphate

43. Nucleic Acids Comparison