Carbon and the Molecular Diversity of Life

1. CHAPTER 4 Carbon and the Molecular Diversity of Life

2. ESLRS: Core Learning, Critical Thinking, Communication, Community STANDARDS: Chemistry: 1 a,d,e atom structure; 2 a-h bonding; 5 a-d acid/base; more… Cell Biology: 1 h macromolecules

3. organic chemistry (o-chem) • branch of chemistry that specializes in the study of carbon containing compounds. • originated in attempts to purify and improve the yield of organic substances: • ex. food, medicines, cloth, paper • 1st based on VITALISM-the belief in a life force outside the jurisdiction of physical and chemical laws. • organic compounds seemingly could only arise within living organisms and inorganic compounds were found in the nonliving world. • Cumulative nature of Science… Experiments to disprove VITALISM and replace it w/ MECHANISM: • 1) 1800’s Wholler had synthesized Urea from ammonium & cyanate • 2) Kolbe (his student) made citric acid from inorganic compounds.

4. UREAcellular waste product found in mamalian and amphibian urine CO(NH2)2 It was the first organic compound to be artificially synthesized from inorganic starting materials, thus dispelling the concept of vitalism. Made from by the reaction of potassium cyanate with ammonium sulfate.

5. Figure 4.x1 Urea Check the valences…

6. Stanley Miller (1953)University of Chicago Helped pioneer the field of organic chemistry, and replace “Vitalism” with “Mechanism”.Was able to synthesize organic molecules from the inorganic compounds: H20, NH3, H2, CH4 and high voltage. (made hydrocarbons & amino acids)Simulated conditions of primitive Earth to demonstrate the abiotic synthesis of organic compounds in a repeatable experiment.Brought the abiotic synthesis of organic compounds into the context of evolution, to support Oparin-Haldane biochemical evolution. The gasses simulate primitive Earth’s atmosphere. Shows how the molecules necessary for life evolved.

7. Stanley Miller Resulted in a paradigm shift from Vitalism to Mechanism.Mechanism is the belief thatall natural phenomena, including the processes of life are governed by physical and chemical laws.How did Stanley Miller’s work provide evidence to support the theory of Evolution?

8. Big Idea 1: The process of evolution drives the diversity and unity of life. 1.D: The origin of living systems is explained by natural processes. • 1.D.2: Scientific evidence from many different disciplines supports models of the origin of life. • A. Geological evidence provides support for models of the origin of life on Earth. • Evidence of student learning is a demonstrated understanding of each of the following: • 2. Chemical experiments have shown that it is possible to form complex organic molecules from inorganic molecules in the absence of life. • B. Molecular and genetic evidence from extant and extinct organisms indicates that all organisms on Earth share a common ancestral origin of life. • Evidence of student learning is a demonstrated understanding of each of the following: • 1. Scientific evidence includes molecular building blocks that are common to all life forms. • 2. Scientific evidence includes a common genetic code.

9. WHY CARBON? • Carbon atoms are the most versatile building blocks of molecules. • Electron Configuration: • 4 valence e- = 4 bonds to share covalently • giving/taking not practical, does not ionize • Can form chains of differing length, branching shapes, rings… and double bonds. • Carbon is used in storage compounds and cell formation in all organisms.

10. The FOUR MAJOR COMPONENTS OF ORGANIC COMPOUNDS: Carbon provides the “backbone” or “carbon skeleton” that other elements are bonded to.

11. hydrocarbons branches chains rings Are these molecules polar or nopolar? How do you know?

12. Hydrocarbons • Organic molecules consisting only of carbon and hydrogen. • Major components of petroleum. • Hydrophobic (repels water) because bonds are nonpolar. • Store a large amount of energy. • Ex. Lipids (triglyceride) in animals.

13. Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. • 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization. • A. Molecules and atoms from the environment are necessary to build new molecules. • Evidence of student learning is a demonstrated understanding of each of the following: • 1. Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms. • 2. Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.

14. Isomers Compounds that have the same molecular formula but different structures… results in different properties. covalent partners double bond 3 types-differ: 1)Structural-covalent partners 2)Geometric-double bond 3)Enantiomers-asymmetric C asymmetric carbon

15. WHAT TYPE OF ISOMER?

16. STRUCTURAL ISOMER Structural isomers differ in covalent arrangements of atoms, and In the location of double bonds.

17. GEOMETRIC ISOMER Geometric isomers differ in spatial arrangements due to the Inflexibility of double bonds.

18. ENANTIOMERS Enantiomers are molecules containing an assymetric carbon, which are mirror images of each other.

19. What type of isomer?

20. ENANTIOMER

21. Structure FUNCTION

22. Ex. Thalidomide Drug prescribed in the 50’s And early 60’s to prevent Morning sickness for thousands Of women. One enantiomer caused severe Birth defects.

23. II. FUNCTIONAL GROUPS • Structures involved in reactions and in defining the molecule’s properties. • Picture a hydrocarbon… replace a hydrogen with one of these “clusters” of atoms. • Can have different “properties”. • Most important in chemistry of life: Hydroxyl, carbonyl, carboxyl, amino, sulfhydral, and phosphate… All are polar (hydrophilic).

24. Figure 4.8 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

25. Figure 4.8x1 Estrone and testosterone

26. Figure 4.8x2 Male and female mallards

27. Figure 4.8x3 Male and female peacocks

28. FUNCTIONAL GROUPS • HYDROXYL (alcohol) • names end in “ol” (C-OHHO-C) • polar • molecules can dissolve in water • CARBONYL carbon double bonded to oxygen… • 1. Aldehyde - terminal carbon bond H-C=O • 2. Ketone - inner carbon bond -C=O • polar

29. FUNCTIONAL GROUPS • SULFHYDRYL = sulfur and hydrogen • stabilize protein structure • disulfide bridges -SH • ex. # & position in hair proteins determine if curly or straight • polar • PHOSPHATE = OPO3 2- • transfer of energy between organic • molecules • polar

30. FUNCTIONAL GROUPS • AMINO nitrogen & 2 hydrogen, called “amine” • tends to pick up protons in solution, • making it a base • -NH2 +H+ --> -NH3+ • Polar • CARBOXYL (-COOH) organic acids HO-C=O • tends to dissociate in water, gives H+ (makes it an acid) • Polar • Hint: Carbonyl + Hydroxyl = Carboxyl 

31. FUNCTIONAL GROUPS • METHYL 1 CARBON bonded to 3 HYDROGENS • Addition of a METHYL GROUP to DNA, or to molecules bound to DNA, effects the expression of genes. • Epigenetics means “Beyond the Genome” and studies how an organism’s environment • Effects methlyation of the • DNA

32. Big Idea 4: Biological systems interact, and these systems and their interactions possess complex properties. • At the molecular level, the subcomponents of a biological polymer determine the properties of that polymer. • 4.A: Interactions within biological systems lead to complex properties. 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule. • a. Structure and function of polymers are derived from the way their monomers are assembled.