Carbon and the Molecular Diversity of Life

1. Chapter 4 Carbon and the Molecular Diversity of Life

2. Overview: Carbon: The Backbone of Life • living organisms consist mostly of carbon-based compounds • carbon is unparalleled in its ability to form large, complex, and diverse molecules • proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

3. Molecules of Life: • the chemicals used in metabolic reactions or those that are produced by them can be classified into 2 groups:

4. Inorganic Compounds • difficult to define • compounds that are not organic • water • oxygen, carbon dioxide • inorganic salts

5. Organic Compounds • compounds that contain carbon-hydrogen bonds • e.g. hydrocarbons • BUT are derived from biologic sources • most contain carbon, hydrogen, oxygen • addition elements – nitrogen, phosphorus, sulfur

6. Carbon atoms can form diverse molecules by bonding to four other atoms • electron configuration is the key to an atom’s characteristics • electron configuration determines the kinds and number of bonds an atom will form with other atoms • e.g. ionic vs. covalent

7. The Formation of Bonds with Carbon • with four valence electron - carbon can form four covalent bonds with a variety of atoms • this ability makes large, complex organic, biologic molecules possible • all biological molecules are organized around the carbon atom

8. Figure 4.3 Name andComment Structural Formula Space-Filling Model Molecular Formula Ball-and- Stick Model 109.5º (a) Methane CH4 (b) Ethane C2H6 • in molecules with multiple carbons, each carbon bonded to four other atoms with single bonds has a tetrahedral shape • however, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons • C=C double bonds are rigid (c) Ethene (ethylene) C2H4

9. The Formation of Bonds with Carbon • the valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules Oxygen (valence  2) Hydrogen (valence  1) Nitrogen (valence  3) Carbon (valence  4)

10. The Formation of Bonds with Carbon (c) Double bond position (a) Length • Carbon chains form the skeletons of most organic molecules • Carbon chains vary in length and shape Ethane Propane 2-Butene 1-Butene (b) Branching (d) Presence of rings Benzene 2-Methylpropane (isobutane) Butane Cyclohexane

11. (a) Structural isomers Isomers • isomers are compounds with the same molecular formula but different structures and properties • structural isomershave different covalent arrangements of their atoms • cis-trans isomershave the same covalent bonds but differ in spatial arrangements • enantiomers are isomers that are mirror images of each other (b) Cis-trans isomers cis isomer: The two Xsare on the same side. trans isomer: The two Xsare on opposite sides. (c) Enantiomers CO2H CO2H H NH2 H NH2 CH3 CH3 L isomer or S isomer D isomer or R isomer

12. (a) Structural isomers Isomers • when carbon forms bonds with 4 different atoms (i.e. a tetrahedron) – asymmetric carbon atom • produces enantiomers/steroisomers (b) Cis-trans isomers cis isomer: The two Xsare on the same side. trans isomer: The two Xsare on opposite sides. (c) Enantiomers CO2H CO2H H NH2 H NH2 CH3 CH3 L isomer or S isomer D isomer or R isomer

13. Isomers Ineffective Enantiomer Effective Enantiomer Drug Condition • enantiomers/stereoisomers are important in the pharmaceutical industry • two enantiomers of a drug may have different effects • usually only one isomer is biologically active • the differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Pain;inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Albuterol Asthma R-Albuterol S-Albuterol

14. A few functional groups are key to the functioning of biological molecules Estradiol • distinctive properties of organic molecules depend on the carbon skeleton and on the characteristic functional groups attached to it • functional groups can replace the hydrogens attached to skeletons of organic molecules • the number and arrangement of functional groups give each molecule its unique properties Testosterone

15. H H H H H H O O H H C C C C C C C C OH Od- H H H H H H Hydrocarbons & Functional Groups • Hydrocarbons are organic molecules consisting of only carbon and hydrogen • hydrocarbons can undergo reactions that release a large amount of energy • modification of a hydrocarbon with functional groups can turn a non-polar hydrocarbon into a structure with polar characteristics • the functional groups usually contain O, N, P or S de-protonated carboxyl group carboxyl group = hydrophilic

16. Functional Groups • The seven functional groups that are most important in the chemistry of life: • Hydroxyl group =negative charge • Carbonyl group • Carboxyl group = negative charge • Amino group = positive charge • Sulfhydryl • Sulfate group = negative charge • Phosphate group = negative charge • Methyl group

17. Hydrophilic Hydrophilic CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO—) Alcohols (Their specific namesusually end in -ol.) NAME OF COMPOUND Ketones if the carbonyl group iswithin a carbon skeleton Carboxylic acids, or organic acids Aldehydes if the carbonyl groupis at the end of the carbon skeleton EXAMPLE Acetic acid Ethanol Acetone Propanal FUNCTIONAL PROPERTIES • Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar: • A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. • Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). Nonionized Ionized • Found in cells in the ionized form with a charge of 1 and called a carboxylate ion.

18. Hydrophilic Hydrophilic Hydrophilic Amino Sulfhydryl Phosphate Methyl (may bewritten HS—) Organic phosphates Amines Thiols Methylated compounds Glycerol phosphate Cysteine Glycine 5-Methyl cytidine • Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as above; 1– when located internally in a chain of phosphates). • Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): • Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. • Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. • Arrangement of methyl groups in male and female sex hormones affects their shape and function. • Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. • Molecules containing phosphate groups have the potential to react with water, releasing energy. Nonionized Ionized • Found in cells in the ionized form with a charge of 1+. -the H+ of a carboxyl group is often picked up by the NH2  NH3+ -creates a zwitterion

19. Organic macromolecules: 1. carbohydrates 2. lipids 3. proteins 4. nucleic acids

20. (a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removesa water molecule,forming a new bond. 1 4 2 3 Longer polymer (b) Hydrolysis: breaking down a polymer 4 2 3 1 Hydrolysis addsa water molecule,breaking a bond. 2 3 1

21. 1. Carbohydrates: • provide energy to cells • can be stored as reserve energy supply (humans = glycogen) • supply “building materials” to build certain cell structures • e.g. cell wall of plants • water soluble = hydrophilic • characterized H - C - OH (ratio C:H is ~1:2) e.g. glucose C6H12O6 sucrose C12H22O11

22. 1. Carbohydrates: • carbohydrates are classified many ways: • 1. the location of the carbonyl group (as aldose or ketose) • -aldose = carbonyl group (C=O) is at the end of the carbon skeleton • -ketose – carbonyl is within the carbon skeleton • 2. the number of carbons in the carbon skeleton • -e.g. five carbon sugars = pentose (ribose and deoxyribose) • -e.g. six carbon = hexose (glucose, fructose and galactose) • 3. also by the number of subunits – simple saccharides (sugars) and complex polysaccharides

23. A. Simple carbohydrates – monosaccharides • monosaccharides = single saccharide subunit in which the # of carbon atoms is low (from 3 to 7 carbons) • formula: C:2H:O • basic unit of a carbohydrate • cannot be hydrolyzed into smaller subunits • the carbons that support the hydroxyl groups are chiral – can have more than one isomeric form • can be found in linear and ring forms – depending on the environment

24. A. Simple carbohydrates – monosaccharides Ketose (Ketone Sugar) Aldose (Aldehyde Sugar) • linear forms can be classified according to the position of the carbonyl group • glucose and galactose with their carbonyls at the end are aldose sugars • Note that glucose and galactose only differ with respect to their arrangements of H and OH groups at one carbon!! (see purple boxes) • fructose is a ketosesugar Hexoses: 6-carbon sugars (C6H12O6) Galactose Fructose Glucose

25. A. Simple carbohydrates – monosaccharides - in aqueous solutions – the monosaccharides are not linear -they form rings -three ways to represent the ring structure of a monosaccharide 3. Simplest form 2. Abbreviated ring structure • Molecular • ring form

26. Glucose, Fructose and Galactose beta-glucose (OH above the ring plane) beta-galactose (isomer of glucose at the 4 carbon) alpha-glucose (OH below the ring plane)

27. A. Simple carbohydrates – disaccharides • disaccharide= two monosaccharides bound together • -form by a dehydration synthesisreaction to form a • glycosidic linkage • -broken up by a hydrolysis reaction • e.g. glucose + glucose = maltose • e.g. glucose + fructose = sucrose • e.g. glucose + galactose = lactose

28. B. Complex carbohydrates • also known as polysaccharides or oligosaccharides • built of monosaccharides to form macromolecules • a type of polymer = macromolecule made of multiple, repeating monomers or “building blocks” • two types: • 1. Storage - hydrolyzed into individual monosaccharides • 2. Structural – serve as building materials

29. Storage Polysaccharides Starch granules Chloroplast • Starch & Glycogen • stored by plants and animals as a future sugar supply • Starch = storage form of glucose found in plants • hydrolyzed into glucose by enzymes – found in both plants and animals • simplest ones are joined by 1-4 glycosidic linkages (e.g. amylose) • are helical and unbranched in conformation • stored within plastids – e.g. chloroplast • some are more complex & have branch points - 1-6 glycosidic linkages (e.g. amylopectin) Amylopectin Amylose (a) Starch: a plant polysaccharide 1 m

30. Storage Polysaccharides • Glycogen= storage form of glucose found in animals • glucose is joined through 1-4 glycosidic linkages • very highly branched • hydrolyzed into glucose by an enzyme – glycogen phosphorylase Glycogen granules Mitochondria Glycogen (b) Glycogen: an animal polysaccharide 0.5 m

31. Structural Polysaccharides • cellulose & chitin • cellulose – main component of the cell wall of plants • also found in algae • secreted by some bacteria • (C6H10O5)n • chitin – main component of the fungal cell wall • also found in animals - invertebrates

32. Structural Polysaccharides: Cellulose • remember that there are two forms of D-glucose: alpha () and beta () • OH group at carbon 1 is above the plane – beta form • below – alpha form • starch – all alpha forms; joined by 1-4 glycosidic linkages (alpha 1-4 linkages) • cellulose – all beta forms; joined by 1-4 glycosidic linkages (beta 1-4 linkages) • BUT every other glucose is “upside down” (a)  and  glucose ring structures  Glucose  Glucose (c) Cellulose: 1–4 linkage of  glucose monomers (b) Starch: 1–4 linkage of  glucose monomers

33. Structural Polysaccharides: Cellulose • unlike starch – cellulose is not helical or branched • some OH groups on the glucose monomers of cellulose can hydrogen bond with OHs from neighboring cellulose molecules = cross-linking • this results in cellulose molecules grouped parallel to one another - called microfibrils • the microfibrils are then “woven” together to form the basis of the plant cell wall

34. Cellulosemicrofibrils in aplant cell wall Structural Polysaccharides: Cellulose Cell wall Microfibril • enzymes that digest starch are unable to break the beta 1-4 glycosidic linkages of cellulose because of their different shapes • prokaryotes possess cellulase • humans unable to hydrolyze cellulose – “insoluble fiber” • cellulose “scrapes” the lining of the GI tract and causes the production of mucus (aids in smooth passage of other food through the GI tract) 10 m 0.5 m Cellulosemolecules  Glucosemonomer

35. Lipids • 1. triglycerides = fats and oils • 2. phospholipids • 3. steroids • cholesterol – animal cell membranes, basis for steroid hormones • bile salts - digestion • vitamin D – calcium regulation • 4. Eicanosoids • prostaglandins • leukotrienes • 5. Others • fatty acids • carotenes – synthesis of vitamin A • vitamin E – wound healing • vitamin K – blood clotting • lipoproteins – HDL and LDL • waxes and pigments

36. 2. Lipids fatty acid fatty acid fatty acid • A. Fats • energy supply • most plentiful lipids in your body • composed of C, H and O • “building blocks” = 3 fatty acid chains (hydrocarbons usually from 16 to 18 carbons) PLUS 1 glycerol molecule fatty acid portion glycerol portion

37. A. Fats Ester linkage • formed through dehydration synthesis reactions to form an ester linkage • the three fatty acids joined to glycerol creates a triacylglycerol, or triglyceride • fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats Fatty acid(in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat (b) Fat molecule (triacylglycerol)

38. fatty acids -differ in chain length with each fat • also differ in the location and number of double bonds within the hydrocarbon chains 1. single C bonds - saturated • Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds • Unsaturated fatty acids have one or more double bonds 2. double C bonds - unsaturated monounsaturated: 1 double bond polyunsaturated: 2 or more double bonds

39. A. Fats (a) Saturated fat • at room temperature – the molecules of a saturated fat are packed closely together • the fatty acid tails are more flexible • forms a solid at room temperature – have a higher melting temperature vs. unsaturated • common types – palmitic acid and stearic acid (animal fats) Structuralformula of asaturated fatmolecule Space-fillingmodel of stearicacid, a saturatedfatty acid

40. A. Fats (b) Unsaturated fat Structuralformula of anunsaturated fatmolecule Space-filling modelof oleic acid, anunsaturated fattyacid Cis double bondcauses bending. • the C=C bonds of an unsaturated FA produce a “kink” in the chain • the fat molecules cannot pack closely together enough to solidify – liquid at room temperature • if the fat contains one fatty acid that is unsaturated – then the fat is considered unsaturated • hydrogenated oils – the unsaturated fats have been chemically converted to saturated by adding hydrogens • keeping them solid

41. B. Phospholipids • similar to triglycerides – glycerol backbone and fatty acid “tails” • BUT glycerol + 2 fatty acids • modified through the replacement of one FA with a polarhead group (negative electrical charge) • phosphate gp hydrophilic “head” • fatty acid gps hydrophobic “tails”

42. B. Phospholipids • when added to water – phospholipids self-assemble and form a phospholipid bilayer – major component of the plasma membrane

43. C. Steroids • backbone is called cholesterol = 4 fused carbon rings • animals - synthesized in the liver • steroid diversity is obtained through attached functional groups • e.g. testosterone, estrogen, aldosterone, ACTH, cortisol

45. 3. Proteins • nearly every dynamic function of a living organism depends on proteins • Greek – proteios= “first place” • more than 50% of the dry mass of most cells • numerous cellular functions

46. 3. Proteins & their Functions Figure 5.15-a Enzymatic reactions Immunity Example: Digestive enzymes catalyze the hydrolysisof bonds in food molecules. Example: Antibodies inactivate and help destroyviruses and bacteria. Antibodies Enzyme Virus Bacterium Storage of amino acids Transport Examples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes. Examples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo. Transportprotein Amino acidsfor embryo Ovalbumin Cell membrane

47. 3. Proteins & their Functions Signaling: Hormonal proteins Signaling: Receptor proteins Example: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells. Example: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration Receptorprotein Signalingmolecules Insulinsecreted Highblood sugar Normalblood sugar Support: Structural proteins Movement: Contractile and motor proteins Examples: Motor proteins are responsible for theundulations of cilia and flagella. Actin and myosinproteins are responsible for the contraction ofmuscles. Examples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue Connectivetissue 100 m 60 m

48. 3. Proteins • building blocks = amino acids Side chain (R group) a.a. = amino group at 1 end, carboxyl at the other - between is a single C called the alpha carbon -the alpha carbon is assymetrical and is bound to: 1. H atom 2. R group  carbon • 22 amino acids available for human protein synthesis • 20 of them are coded for by our DNA • the R group give the amino acid its unique physical and chemical characteristic • divided into three groups: • polar amino acids • non-polar amino acids • electrically charged amino acids –basic or acidic Aminogroup Carboxylgroup

49. the 20 amino acids coded by DNA: • non-polar: • Methionine – Met or M • Phenylalanine – Phe or F • Tryptophan – Trp or W • Proline – Pro or P • Glycine – Gly or G • Alanine – Ala or A • Valine – Val or V • Leucine – Leu or L • Isoleucine – Iso or I • polar: • Serine – Ser or S • Threonine – Thr or T • Cysteine – Cys or C • Tyrosine – Tyr or Y • Asparagine – Asp or N • Glutamine – Glu or Q • charged acidic • Aspartic acid – Asp or D (acidic) • Glutamic acid – Glut or E (acidic) • Lysine – Lys or K (basic) • Arginine – Arg or R (basic) • Histidine – His or H (basic)

50. 3. Proteins • amino acids joined together by a dehydration synthesis reaction forming a peptide bond • between the NH2 of 1 amino acid and the COOH of the next amino acid Peptide bond New peptidebond forming Side chains 2 a.a.  dipeptide Back-bone 3 a.a.  tripeptide 4 or more a.a.  polypeptide Peptidebond Carboxyl end(C-terminus) Amino end(N-terminus)