Carbon & Biochemistry BIOL-101 Section 802RL Mr. Fusco

1. Carbon & Biochemistry BIOL-101 Section 802RLMr. Fusco Chapter 4: Carbon and the Molecular Diversity of Life Chapter 5: The Structure & Function of Large Biological Molecules

2. Chemistry of Life • Carbon is essential to life • Although cells are 70–95% water, the rest consists mostly of carbon-based compounds • An is any carbon-containing compound • Organic compounds in living organisms: -proteins, amino acids, carbohydrates, fats (lipids), nucleic acids, etc…

3. Carbon Structure • Carbon - - -Enables carbon to form large molecules • Electron configuration is the key to an atom’s characteristics • Electron configuration determines the an atom will form with other atoms

4. Fig. 4-4 Valence Electrons Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) H N O C

5. Carbon Backbones:Hydrocarbons • Hydrocarbons are • Many organic molecules, such as fats, have hydrocarbon components • Hydrocarbons can undergo reactions that release a large amount of energy • With four valence electrons, carbon can form with a variety of atoms

6. Fig. 4-6 Fat droplets (stained red) 100 µm (a) Mammalian adipose cells (b) A fat molecule

7. Hydrocarbon Bonding 1) C – H bonds -only single bonds 2) C – C bonds (different shapes and numbers) a) b)

8. Carbon - CarbonBond Numbers • Single = has a tetrahedral shape • Double = , the molecule has a flat shape • Triple = , the molecule has a linear shape

9. Carbon - CarbonBonding Types Rings Straight Chains Branched Chains

10. Fig. 4-3 Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Name (a) Methane (b) Ethane (c) Ethene (ethylene)

11. Isomers Structural Formula Chemical Formula • Isomers are compounds with the : • Structural isomers have of their atoms • Geometric isomers have the same covalent arrangements but • Enantiomers are isomers that are of each other Hexane:C6H14 CH3CH2CH2CH2CH2CH3 Isohexane:C6H14 CH3 l CH3CH2CHCH2CH3

12. Enantiomers • Enantiomers are important in the industry • Two enantiomers of a drug may have different effects • Differing effects of enantiomers demonstrate that • Example: L-dopa is used to treat symptoms of Parkinson’s disease, while R-dopa (its enantiomer) has no effect

13. Functional Groups • Functional groups are the components of organic molecules that are • The of functional groups give each molecule its unique properties

14. Functional Groups • The seven functional groups that are most important in the chemistry of life: • Hydroxyl group • Carbonyl group • Carboxyl group • Amino group • Sulfhydryl group • Phosphate group • Methyl group

15. Fig. 4-10a CHEMICAL GROUP Hydroxyl Carboxyl Carbonyl STRUCTURE (may be written HO—) The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. When an oxygen atom is double-bonded to a carbon atom that is also bonded to an —OH group, the entire assembly of atoms is called a carboxyl group (—COOH). In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) Alcohols (their specific names usually end in -ol) NAME OF COMPOUND Carboxylic acids, or organic acids Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Acetone, the simplest ketone Ethanol, the alcohol present in alcoholic beverages Acetic acid, which gives vinegar its sour taste Propanal, an aldehyde FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom. A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Has acidic properties because the covalent bond between oxygen and hydrogen is so polar; for example, Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. These two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone). Acetate ion Acetic acid Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

16. Fig. 4-10b CHEMICAL GROUP Amino Sulfhydryl Phosphate Methyl (may be written HS—) STRUCTURE The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges. The phosphate group (—OPO32–, abbreviated ) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). A methyl group consists of a carbon bonded to three hydrogen atoms. The methyl group may be attached to a carbon or to a different atom. P NAME OF COMPOUND Amines Thiols Organic phosphates Methylated compounds EXAMPLE Glycine Glycerol phosphate Cysteine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes. 5-Methyl cytidine Cysteine is an important sulfur-containing amino acid. 5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group. FUNCTIONAL PROPERTIES 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. Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates). Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function. Has the potential to react with water, releasing energy. 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, then breaking and re-forming the cross-linking bonds. (ionized) (nonionized) Ionized, with a charge of 1+, under cellular conditions.

17. Reacts with H2O Energy Adenosine Adenosine P P P P i P P ATP ADP Inorganic phosphate ATP • One phosphate molecule, adenosine triphosphate (ATP), is the • ATP consists of an organic molecule called attached to a string of • Energy is when a phosphate group is from ATP to form ADP (adenosine diphosphate) • Energy is when a phosphate group is to ADP to form ATP

18. Macromolecules • All living things are made up of four classes of large biological molecules: • Within cells, small organic molecules are joined together to form larger molecules • are large molecules composed of thousands of covalently connected atoms • One key concept is that

19. Macromolecules • A monomer is a (building block) • A polymer is a • Macromolecules are polymers, and identified by their specific subunits (monomers) • Monomers are covalently bonded in to make macromolecules

20. The Synthesis and Breakdown of Polymers • A condensation reaction, or more specifically dehydration synthesis, occurs when • Polymers are digested to monomers by hydrolysis, a reaction that

21. Fig. 5-2a HO H HO H 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond H2O H HO 1 4 2 3 Longer polymer (a) Dehydration reaction in the synthesis of a polymer

22. Fig. 5-2b HO H 4 1 2 3 Hydrolysis adds a water molecule, breaking a bond H2O HO H H HO 2 1 3 (b) Hydrolysis of a polymer

23. The four types of macromolecules include: Carbohydrates Lipids (fats) Proteins Nucleic Acids Macromolecules Types

24. Carbohydrates • Carbohydrates include sugars and the polymers of sugars • Sugar polymers made of • The simplest carbohydrates are , or single sugars • Simple to complex: Monosaccharides  Disaccharides  Polysaccharides

25. Carbs may be as much as 70% of an Endurance Athlete’s Diet! Michael Phelps 8400 Kcal/day Lance Armstrong 6500Kcal/day

26. Our Primary Energy Source • from monosaccharides - glucose, fructose, galactose • from polysaccharides -glycogen (in animals) -starch (in plants) -structural components of cells (ex. cellulose in plant cell walls) -Fiber in our diets

27. Monosaccharidesmono- “” saccharide- “” • Monosaccharides have molecular formulas that are usually multiples of CH2O • (C6H12O6) is the most common monosaccharide (right) and our • Another is (C6H12O6) • Monosaccharides serve as a

28. Hexoses (C6H12O6) Glucose Galactose Glucose and Fructose • Monosaccharides • Isomers • C6H12O6 • Glucose is the form of sugar carried in our blood • Fructose is the sweet sugar found in most fruits and sweets

29. Disaccharidesdi- “” -saccharide “” • Disaccharides are • This covalent bond is called a • Molecular formula of • Examples include: • Sucrose (glucose + fructose) • This is table sugar • Lactose (glucose + galactose) • This is a milk sugar • Maltose (glucose + glucose) • This is a grain sugar

30. Fig. 5-5 1–4 glycosidic linkage Glucose Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 1–2 glycosidic linkage Glucose Fructose Sucrose (b) Dehydration reaction in the synthesis of sucrose

31. Polysaccharidespoly-: “” -saccharides: “” • Polysaccharides are long sugar chains • Often not water soluble due to great size • Used primarily for • (Plants store surplus starch as granules within chloroplasts and other plastids) • (Humans and other vertebrates store glycogen mainly in liver and muscle cells)

32. Polysaccharides: Glycogen and Starch

33. Cellulose • The polysaccharide cellulose is a major • Like starch, cellulose is a , but the glycosidic linkages differ • Cellulose in human food passes through the digestive tract as • What evidence do we have of this? • Many herbivores, from cows to termites, have symbiotic relationships with microbes that use enzymes to digest cellulose

34. Cellulose

35. Chitin • Chitin, another structural polysaccharide, is found in the • Chitin also provides

36. Lipids • Lipids are the one class of large biological molecules that • The unifying feature of lipids is having • Lipids are becausethey consist mostly of hydrocarbons, which form • The most biologically important lipids are fats, phospholipids, and steroids 4.5 Kcal/g in carbs VS. 9 Kcal/g in fats

37. Lipids • The major function of fats is • Humans and other mammals store their fat in • Adipose tissue also • Energy storage -Stored mostly as • Other functions -Steroid hormones -Plasma membrane structural stability

38. Fats • Fats are constructed from • is a three-carbon alcohol with a hydroxyl group attached to each carbon • A consists of a carboxyl group attached to a long carbon skeleton • Many C-H bonds • Structure is a fatty acid chain bonded to a carboxyl group • 2 Types: 1) saturated 2) unsaturated Most common form of a fat is a

39. Triglycerides • Joined by an • Our primary lipid storage molecule • Form through • Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats

40. Fig. 5-11b Ester linkage Fat molecule (triacylglycerol)

41. as possible, so “saturated” with hydrogen chain Generally at room temperature Example: fats; butter , so less hydrogen chain (b/c of C=C bonds) Generally at room temperature Example fats; vegetable oil FatsSaturated vs. Unsaturated

44. Fats

45. Triglycerides & Trans Fats • A diet rich in saturated fats may contribute to through plaque deposits • is the process of converting unsaturated fats to saturated fats by adding hydrogen • Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds (trans fats) • Trans fats levels “bad” cholesterol and levels of “good” cholesterol • These trans fats may contribute more than saturated fats to cardiovascular disease

46. Phospholipids • Make up of a cell • In a phospholipid, • The two fatty acid tails are , but the phosphate group and its attachments form a head • Hydrophobic (“water fearing”) tail -nonpolar • Hydrophilic (“water loving”) head -polar • The nucleus, mitochondria and endomembrane system all are surrounded by their own phospholipid bilayers

47. Fig. 5-13 Choline Phosphate Hydrophilic head Glycerol Fatty acids Hydrophobic tails Hydrophilic head Hydrophobic tails Space-filling model Phospholipid symbol (a) (b) (c) Structural formula Phospholipid

48. TEM Image: Plasma Membrane

49. Phospholipids • When phospholipids are added to water, they self-assemble into a bilayer, with the • The structure of phospholipids results in a • Phospholipids are the major component of all cell membranes

50. Fig. 5-14 Hydrophilic head WATER Hydrophobic tail WATER