Carbon: The Backbone of Life

Transcription

1 Organic Chemistry

2 Carbon: The Backbone of Life Living organisms consist mostly of carbon-based compounds due to 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 2

3 Carbon: Organic Chemistry The study of carbon compounds is called Organic chemistry (main elements = CHONPS) Organic compounds range from simple molecules to colossal ones Most organic compounds contain hydrogen atoms in addition to carbon atoms with O, N and P among others thrown in from time to time. 3

4 Carbon has 4 valence electrons, thus makes 4 bonds With four valence electrons, carbon can form four covalent bonds with a variety of atoms This ability makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape 4

5 Those four bonds can vary 5

6 Carbon Skeletons Vary Carbon chains form the skeletons of most organic molecules and can vary in length and shape

7 Functional Groups A few chemical groups are key to the function of biomolecules Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules 7

8 Functional Groups FGs are the pieces that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties Let s meet the FGs 8

9 Hydroxyl STRUCTURE (may be written HO ) Alcohols (Their specific names usually end in -ol.) NAME OF COMPOUND EXAMPLE Is polar as a result of the electrons spending more time near the electronegative oxygen atom. FUNCTIONAL PROPERTIES Ethanol Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

10 Carbonyl STRUCTURE EXAMPLE Acetone Propanal Ketones if the carbonyl group is within a carbon skeleton Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. 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). NAME OF COMPOUND FUNCTIONAL PROPERTIES

11 Carboxyl STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND EXAMPLE Acts as an acid; can donate an H + because the covalent bond between oxygen and hydrogen is so polar: FUNCTIONAL PROPERTIES Acetic acid Nonionized Ionized Found in cells in the ionized form with a charge of 1 and called a carboxylate ion.

12 Amino STRUCTURE Amines NAME OF COMPOUND EXAMPLE Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms): FUNCTIONAL PROPERTIES Glycine Nonionized Ionized Found in cells in the ionized form with a charge of 1.

13 Sulfhydryl STRUCTURE Thiols NAME OF COMPOUND (may be written HS ) EXAMPLE Two sulfhydryl groups can react, forming a covalent bond. This cross-linking helps stabilize protein structure. FUNCTIONAL PROPERTIES Cysteine 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.

14 Phosphate STRUCTURE Organic phosphates NAME OF COMPOUND EXAMPLE Glycerol phosphate Contributes negative charge to the molecule of which it is a part (2 when at the end of a molecule, as at left; 1 when located internally in a chain of phosphates). Molecules containing phosphate groups have the potential to react with water, releasing energy. FUNCTIONAL PROPERTIES

15 Methyl STRUCTURE Methylated compounds NAME OF COMPOUND EXAMPLE Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. FUNCTIONAL PROPERTIES 5-Methyl cytidine Arrangement of methyl groups in male and female sex hormones affects their shape and function.

16 Example of FG in action- ATP: Chemical Energy for Cells Adenosine triphosphate (ATP), is made of adenosine bonded to three phosphate groups. Adding or removing phosphate groups stores and releases energy. Draw 16

17 Organic Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids

18 The FOUR Classes of Large Biomolecules All living things are made of four classes of biomolecules: Carbohydrates Lipids Protein Nucleic Acids Macromolecules are large molecules composed of thousands of covalently bonded atoms Their structure determines their function!!! 18

19 The FOUR Classes of Large Biomolecules Macromolecules are polymers, built from monomers A polymer is a long molecule made of many similar building blocks called monomers Three of the four classes of life s organic molecules are polymers Carbohydrates Proteins Nucleic acids 19

20 Building polymers A dehydration reaction links monomers together by removing a water molecule (leave space for a drawing!) Hydrolysis is the reverse, and disassembles polymers by adding water Why is water important for food digestion? 20

21 (Draw this!) Dehydration Synthesis 21

22 (Draw this!) Hydrolysis 22

23 Biomolecule 1: Carbohydrates Include sugars and sugar polymers called starches. They provide chemical energy and building material. The simplest carbohydrates are monosaccharides, or single sugars with formula ratios of 1C:2H:1O used for quick energy (draw one) Carbohydrate macromolecules are polysaccharides, or chains of sugars; often used to build cell parts or for energy storage (draw one) 23

24 Sugars: Monosaccharides Glucose (C 6 H 12 O 6 ) is the most common monosaccharide Monosaccharides are classified by The location of the carbonyl group The number of carbons in the carbon skeleton 24

25 Sugars: Disaccharides A disaccharide is formed when dehydration reaction joins two monosaccharides 25

26 Synthesizing Maltose & Sucrose 26

27 Types of Polysaccharides Starch is a storage polysaccharide of plants that consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose 27

28 Types of Polysaccharides Glycogen is a storage polysaccharide in animals ( animal starch ) Humans and other vertebrates store glycogen mainly in liver and muscle cells 28

29 Types of Polysaccharides Cellulose is a polysaccharide used to build plant cell walls Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ 29

30 Such Elegance! 30

31 Polysaccharide Random Acts of Biology Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores, from cows to termites, have symbiotic relationships with these microbes Chitin is the structural polysaccharide in animal exoskeletons (crunch!) and fungi cell walls (surprise!) 31

32 Biomolecule 2: Lipids Lipids are a diverse group of hydrophobic molecules Lipids are the one class of large biological molecules that do not form polymers The unifying feature of lipids is having little or no affinity for water (water fearing) Lipids are hydrophobic because they are nonpolar The most biologically important lipids are fats, phospholipids, and steroids 32

33 Fats: Start with a Simple Little Glycerol Molecule Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton 33

34 Dehydration Rxn 1: Add a Fatty Acid Next, add a fatty acid through a dehydration synthesis reaction What makes it an acid? The C double bond O, single bond OH! 34

35 Dehydration Rxn 2!! Next, add a SECOND fatty acid through a dehydration synthesis reaction

36 Dehydration Reaction THREE!!! How many water molecules will it take to disassemble this molecule? 36

37 Saturated or Unsaturated? Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature Most animal fats are saturated (lard) Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds, so they are straight 37

38 Saturated or Unsaturated? Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature Plant fats and fish fats are usually unsaturated Unsaturated fatty acids have one or more double bonds, so they bend 38

39 Fats: Major function is storage! The major function of fats is long-term energy storage! Humans and other mammals store their fat in adipose cells Adipose tissue also cushions and insulates the body 39

40 Phospholipids Phospholipids are the major component of all cell membranes; b/c the phosphate head is hydrophilic and the lipid tail is hydrophobic, they self assemble into a bilayer in water (draw) 40

41 Hydrophobic tails Hydrophilic head A Single Phospholipid Molecule Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol

42 Steroids Steroids are lipids with a carbon skeleton consisting of four fused rings The steroid Cholesterol is a component in animal cell membranes Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease 42

43 Biomolecule 3: Proteins Proteins are very diverse. Cells are mostly made of Proteins, as they account for more than 50% of the dry mass of most cells Protein functions include structural support, storage, transport, cellular communication, movement, and defense (basically everything that keeps you alive ) Let s take a look at a few we ll learn this year! 43

44 Enzymatic Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Enzyme 44

45 Storage Storage proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Ovalbumin Amino acids for embryo 45

46 Hormonal Hormonal proteins Function: Coordination of an organism s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration High blood sugar Insulin secreted Normal blood sugar 46

47 Defensive Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Virus Bacterium 47

48 Transport Transport proteins Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Transport protein Cell membrane 48

49 Receptor Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Signaling molecules Receptor protein 49

50 Structural Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Collagen Connective tissue 60 m

51 Enzymes SPECIAL PROTEIN: Enzymes are protein catalysts that speed up reactions; they are reusable and specific to one function (based on their shape) 51

52 Protein Monomer Amino acids are the monomers of all proteins. Side chain (R group) carbon Amino acids differ in their properties due to differing side chains, called R groups Amino group Carboxyl group 52

53 Polypeptides Polypeptide chains are made chained arrangements of the 20 available amino acids and then folded into proteins. A protein consists of one or more polypeptides 53

54 Hydrophobic Amino Acids Nonpolar side chains; hydrophobic Side chain Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

55 Hydrophilic Amino Acids 55

56 Electrically charged Amino Acids 56

57 Peptide Bonds Amino acids are linked by peptide bonds (through dehydration synthesis) A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers (Yikes!) Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) 57

58 Peptide Bonds 58

59 Peptide Bonds 59

60 Protein Structure & Function At first, all we have is a string of AA s bound with peptide bonds. Once the string of AA s interacts with itself and its environment (often aqueous), then we have a functional protein that consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein s three-dimensional structure A protein s structure determines its function 60

61 Protein Structure: 4 Levels Primary structure is the amino acid chain pipe cleaner Secondary structure consists of alpha helices (coils) or beta pleats (folds) coiled/folded pipe cleaner Tertiary structure is determined by interactions among side chains (IMFs and bonds) within the helix/pleat pipe cleaner connected to itself with paper clip Quaternary structure consists of multiple polypeptide chains multiple pipe cleaners 61

62 Primary Structure Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information

63 Secondary Structure The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet 63

64 Tertiary Structure Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include actual ionic bonds and strong covalent bonds called disulfide bridges which may reinforce the protein s structure. IMFs such as London dispersion forces (LDFs a.k.a. and van der Waals interactions), hydrogen bonds (IMFs), and hydrophobic interactions (IMFs) may affect the protein s structure 64

65 Tertiary Structure 65

66 Quaternary Structure Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope 66

67 Four Levels of Protein Structure Revisited 67

68 Sickle-Cell Disease: A change in Primary Structure A slight change in primary structure can affect a protein s structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin 68

69 Sickle-Cell Disease: A change in Primary Structure 69

70 Changing Protein Structure Proteins are fragile. The environment can affect protein structure and therefore function. Alterations in ph, salt, temperature, etc can cause a protein to unravel; this is denaturing and the protein doesn t function anymore A denatured protein is biologically inactive 70

71 Biomolecule 4: Nucleic Acids Nucleic acids store, transmit, and help express hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid made of monomers called nucleotides 71

72 Two Types of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mrna) and, through mrna, controls protein synthesis Protein synthesis occurs on ribosomes 72

73 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM

74 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM 2 Movement of mrna into cytoplasm mrna

75 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM 2 3 Movement of mrna into cytoplasm Synthesis of protein mrna Ribosome Polypeptide Amino acids

76 The Components of Nucleic Acids Nucleic Acids are made of monomers called nucleotides, which consist of a nitrogenous base, a pentose sugar, and a phosphate group (draw) 76

77 Figure 5.26ab 5 end 5 C Sugar-phosphate backbone 3 C Nucleoside Nitrogenous base 5 C 5 C 3 C 3 end (a) Polynucleotide, or nucleic acid Phosphate group (b) Nucleotide 3 C Sugar (pentose) 1 C

78 The Devil is in the Details Types of nitrogenous bases Pyrimidines (cytosine, thymine, and uracil) have a single ring, that has six-members Purines (adenine and guanine) have two rings; a six-membered ring fused to a five-membered ring DNA vs. RNA nucleotides: In DNA, T is used and the sugar is deoxyribose; in RNA, U is used and the sugar is ribose 78

79 The Devil is in the Details The backbone of both NAs are made of phosphate-sugar covalent bonds. VERY STRONG! 79

80 The Devil is in the Details When NAs link sides it is with hydrogen bonds between complementary base pairs (A w/ T, C w/ G). WEAK BOND! Complementary pairing can also occur between two RNA molecules or DNA to RNA Note: In RNA, thymine is replaced by uracil (U) so A and U pair 80

81 5 3 Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 (a) DNA 5 Base pair joined by hydrogen bonding (b) Transfer RNA