INTRODUCTION TO ORGANIC COMPOUNDS

Transcription

1 BIOCHEMISTRY

2 INTRODUCTION TO ORGANIC COMPOUNDS

3 ORGANIC COMPOUNDS Diverse molecules found in cells are composed of carbon bonded to other elements Carbon-based molecules are called organic compounds Carbon can covalently bond to four other atoms (remember valence electrons) It can branch in up to four directions Makes large, complex, diverse molecules possible.

4 EXAMPLE Methane (CH 4 ) is one of the simplest organic compounds Four covalent bonds link four hydrogen atoms to the carbon atom (remember the valence electrons) Each of the four lines in the formula for methane represents a pair of shared electrons

5 Methane (molecular formula) CH4 Structural formula Methane The four single bonds of carbon point to the corners of a tetrahedron.

6 HYDROCARBONS Compounds made up of only carbon and hydrogen - hydrocarbons

7 Carbon Skeletons A chain of carbon atoms is called a carbon skeleton Carbon skeletons can be branched or unbranched

8 Ethane Propane Length. Carbon skeletons vary in length.

9 Butane Isobutane Branching. Skeletons may be unbranched or branched.

10 1-Butene Double bonds. 2-Butene Skeletons may have double bonds, which can vary in location.

11 Cyclohexane Benzene Rings. Skeletons may be arranged in rings.

12 ISOMERS Organic compounds that have the same molecular formula BUT different structural formulas are known as ISOMERS Glucose C 6 H 12 O 6 Fructose C 6 H 12 O 6

13 Glucose Main product of photosynthesis. Main sugar used in cellular respiration Fructose Sugar found in fruit, honey, etc

14 CHARACTERISTIC CHEMICAL GROUPS HELP DETERMINE THE PROPERTIES OF ORGANIC COMPOUNDS An organic compound has unique properties that depend upon two things: 1. Size and shape of the molecule 2. Functional groups attached A functional group affects a biological molecule s function in a characteristic way

15 CHARACTERISTIC CHEMICAL GROUPS HELP DETERMINE THE PROPERTIES OF ORGANIC COMPOUNDS Compounds containing functional groups are hydrophilic (water-loving) This means that they are soluble in water, which is a necessary for their roles in water-based life

16 CHARACTERISTIC CHEMICAL GROUPS HELP DETERMINE THE PROPERTIES OF ORGANIC COMPOUNDS The functional groups are Hydroxyl group consists of a hydrogen bonded to an oxygen Carbonyl group a carbon linked by a double bond to an oxygen atom Carboxyl group consists of a carbon double-bonded to both an oxygen and a hydroxyl group Amino group composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton Phosphate group consists of a phosphorus atom bonded to four oxygen atoms Methyl group consists of a carbon atom bonded to four hydrogen atoms

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19 CHARACTERISTIC CHEMICAL GROUPS HELP DETERMINE THE PROPERTIES OF ORGANIC COMPOUNDS An example of similar compounds that differ only in functional groups is sex hormones Male and female sex hormones differ only in functional groups The differences cause varied molecular actions The result is distinguishable features of males and females

20 Estradiol Female lion Testosterone Male lion

21 CLASSES OF MACROMOLECULES There are four classes of biological molecules Carbohydrates Proteins Lipids Nucleic acids

22 MONOMERS AND POLYMERS The four classes of biological molecules contain very large molecules They are called macromolecules because of their large size They are also called polymers because they are made from identical building blocks strung together The building blocks are called monomers

23 MONOMERS AND POLYMERS A cell makes a large number of polymers from a small group of monomers Starch is a polymer constructed from glucose monomers Protein is a polymer constructed from amino acid monomers

24 DEEHYDATION REACTIONS AND HYDROLYSIS Monomers are linked together to form polymers through dehydration reactions Dehydration reactions remove water Polymers are broken apart by hydrolysis Hydrolysis is the addition of water All biological reactions of this sort are mediated by enzymes, Enzymes - speed up chemical reactions in cells

25 Short polymer Unlinked monomer

26 Short polymer Dehydration reaction Unlinked monomer Longer polymer

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28 Hydrolysis

29 CARBOHYDRATES

30 MONOSACCHARIDES ARE THE SIMPLEST CARBOHYDRATES Carbohydrates range from small sugar molecules (monomers) to large polysaccharides Sugar monomers are monosaccharides, such as glucose and fructose These can be hooked together to form the polysaccharides

31 MONOSACCHARIDES ARE THE SIMPLEST CARBOHYDRATES The carbon skeletons of monosaccharides vary in length Glucose and fructose are six carbons long Others have three to seven carbon atoms Monosaccharides are the main fuels for cellular work Monosaccharides are also used as raw materials to manufacture other organic molecules

32 Glucose (an aldose) Fructose (a ketose)

33 Structural formula Abbreviated structure Simplified structure

34 MONOSACCHARIDES OF IMPORTANCE Glucose Galactose

35 MONOSACCHARIDES OF IMPORTANCE Fructose Ribose

36 MONOSACCHARIDES OF IMPORTANCE

37 ALPHA VERSUS BETA GLUCOSE

38 CELLS LINK TWO SINGLE SUGARS TO FORM DISACCHARIDES Two monosaccharides (monomers) can bond to form a disaccharide in a dehydration reaction An example is a glucose monomer bonding to a fructose monomer to form sucrose, a common disaccharide. Sucrose is also known as common Table Sugar

39 Glucose Glucose

40 Glucose Glucose Maltose

41 DISACCHARIDES OF IMPORTANCE Sucrose

42 DISACCHARIDES OF IMPORTANCE Glucose Glucose Maltose

43 DISACCHARIDES OF IMPORTANCE Galactose Glucose Lactose

44 CONNECTION: WHAT IS HIGH-FRUCTOSE CORN SYRUP AND IS IT TO BLAME FOR OBESITY? When you drink a soda, you are probably consuming a sweetener called high-fructose corn syrup (HFCS) Because fructose is sweeter than glucose, glucose atoms produced from starch are rearranged to make the glucose isomer, fructose This is used to sweeten sodas So, if you overconsume sweeteners as well as fat and do not exercise, you may experience weight gain

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46 POLYSACCHARIDES ARE LONG CHAINS OF SUGAR UNITS Polysaccharides are polymers of monosaccharides They can function in the cell as a storage molecule or as a structural compound

47 POLYSACCHARIDES ARE LONG CHAINS OF SUGAR UNITS Starch is a storage polysaccharide composed of glucose monomers and found in plants Glycogen is a storage polysaccharide composed of glucose, which is hydrolyzed by animals when glucose is needed Cellulose is a polymer of glucose that forms plant cell walls Chitin is a polysaccharide used by insects and crustaceans to build an exoskeleton

48 POLYSACCHARIDES ARE LONG CHAINS OF SUGAR UNITS Polysaccharides are hydrophilic (water-loving) Cotton fibers, such as those in bath towels, are water absorbent

49 Starch granules in potato tuber cells STARCH Glucose monomer Glycogen granules in muscle tissue GLYCOGEN Cellulose fibrils in a plant cell wall CELLULOSE Hydrogen bonds Cellulose molecules

50 Two types of starches Amylose Amylopectin

51 Glycogen granules in muscle tissue GLYCOGEN

52 Glycogen

53 Cellulose fibrils in a plant cell wall CELLULOSE Hydrogen bonds Cellulose molecules

54 Chitin Notice the bonding and the functional group

55 Starch granules in potato tuber cells STARCH Glucose monomer

56 Cellulose Notice the bonding arrangement between the glucose molecules

57 CELLULOSE VERSUS STARCH Let us look back at the pictures. What differences did you see? Most mammals, including humans, do not have enzymes necessary to digest cellulose. This is because we do not have enzymes to break the beta bonds. However cows and termites can!

58 LIPIDS

59 FATS ARE LIPIDS THAT ARE MOSTLY ENERGY- STORAGE MOLECULES Lipids are water insoluble (hydrophobic, or water fearing) compounds that are important in energy storage They contain twice as much energy as a polysaccharide Fats are lipids made from glycerol and fatty acids

60 FATS ARE LIPIDS THAT ARE MOSTLY ENERGY- STORAGE MOLECULES Fatty acids link to glycerol by a dehydration reaction A fat contains one glycerol linked to three fatty acids Fats are often called triglycerides because of their structure

61 Glycerol C3H8O3 Dehydration Synthesis Fatty acid CH3(CH2)nCOOH

62 Triglyceride

63 FATS ARE LIPIDS THAT ARE MOSTLY ENERGY- STORAGE MOLECULES Saturated vs. Unsaturated Fatty Acids Fats with the maximum number of hydrogens are called saturated fats Compounds are called unsaturated fats when they have fewer than the maximum number of hydrogens

64 Saturated Fatty Acid Unsaturated Fatty Acid

65 PHOSPHOLIPIDS AND STEROIDS ARE IMPORTANT LIPIDS WITH A VARIETY OF FUNCTIONS Phospholipids are structurally similar to fats and are an important component of all cells For example, they are a major part of cell membranes, in which they cluster into a bilayer of phospholipids The hydrophilic heads are in contact with the water of the environment and the internal part of the cell The hydrophobic tails band in the center of the bilayer

66 Phospholipid

67 Role of Phospholipids in Cell Membrane

68 PHOSPHOLIPIDS AND STEROIDS ARE IMPORTANT LIPIDS WITH A VARIETY OF FUNCTIONS Steroids are lipids composed of fused ring structures Cholesterol is an example of a steroid that plays a significant role in the structure of the cell membrane Cholesterol is a soft, waxy substance found among the lipids (fats) in the bloodstream and in all your body's cells. It's an important part of a healthy body because it's used to form cell membranes and some hormones. Two types: LDL (bad) and HDL (good)

69 CHOLESTEROL LDL: Low-density lipoprotein is the major cholesterol carrier in the blood. If too much LDL cholesterol circulates in the blood, it can slowly build up in the walls of the arteries feeding the heart and brain. Found in fats that are solid at room temperature HDL: About one-third to one-fourth of blood cholesterol is carried by HDL. HDL tends to carry cholesterol away from the arteries and back to the liver, where it's passed from the body. Found in fats that are liquid at room temperature

70 Cholesterol

71 CONNECTION: MEDICINAL USE OF STEROIDS Corticosteroids, work with the immune system to repair damaged cells and tissues within the body. Their anti-inflammatory effects aid in area circulation and help restore normal tissue function.

72 CONNECTION: MEDICINAL USE OF STEROIDS The muscle building mechanism within anabolic steroids causes cells to retain nitrogen and calcium which are needed materials in muscle formation. Nitrogen and calcium also play a role in the formation of bones and bone marrow production. As such, anabolic steroids have been used to treat the occurrence of osteoporosis.

73 CONNECTION: ADVERSE USE OF ANABOLIC STEROIDS POSE HEALTH RISKS Anabolic steroids are synthetic variants of testosterone that can cause a buildup of muscle They may also be abused with serious consequences. Common side effects are psychological and physiological, some of which include increased aggression, high cholesterol, increased risk for heart attack and stroke and liver problems

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75 NUCLEIC ACIDS

76 NUCLEIC ACIDS ARE INFORMATION-RICH POLYMERS OF NUCLEOTIDES DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are composed of monomers called nucleotides Nucleotides have three parts A five-carbon sugar called ribose in RNA and deoxyribose in DNA A phosphate group A nitrogenous base

77 Phosphate group Nitrogenous base (adenine) Sugar

78 NITROGENOUS BASES Nitrogenous Bases are divided into 2 groups Purines Adenine and Guanine Pyrimidines Thymine, Cytosine and Uracil

79 NITROGENOUS BASE ARRANGEMENT In DNA Adenine pairs with Thymine A-T Guanine pairs with Cytosine G-C In RNA Thymine is replaced by Uracil therefore Adenine pairs with Uracil A-U Guanine pairs with Cytosine G-C

80 NUCLEIC ACIDS ARE INFORMATION-RICH POLYMERS OF NUCLEOTIDES A nucleic acid polymer, a polynucleotide, forms from the nucleotide monomers when the phosphate of one nucleotide bonds to the sugar of the next nucleotide The result is a repeating sugar-phosphate backbone with protruding nitrogenous bases

81 Sugar-phosphate backbone Nucleotide

82 NUCLEIC ACIDS ARE INFORMATION-RICH POLYMERS OF NUCLEOTIDES Two polynucleotide strands wrap around each other to form a DNA double helix The two strands are associated because particular bases always hydrogen bond to one another A pairs with T, and C pairs with G, producing base pairs RNA is usually a single polynucleotide strand

83 Base pair

84 NUCLEIC ACIDS ARE INFORMATION-RICH POLYMERS OF NUCLEOTIDES A particular nucleotide sequence that can instruct the formation of a polypeptide is called a gene Most DNA molecules consist of millions of base pairs and, consequently, many genes These genes, many of which are unique to the species, determine the structure of proteins and, thus, life s structures and functions

85 EVOLUTION CONNECTION: LACTOSE TOLERANCE IS A RECENT EVENT IN HUMAN EVOLUTION Mutations are alterations in bases or the sequence of bases in DNA Lactose tolerance is the result of mutations In many people, the gene that dictates lactose utilization is turned off in adulthood Apparently, mutations occurred over time that prevented the gene from turning off This is an excellent example of human evolution

86 PROTEINS

87 PROTEINS ARE ESSENTIAL TO THE STRUCTURES AND FUNCTIONS OF LIFE A protein is a polymer built from various combinations of 20 amino acid monomers Proteins have unique structures that are directly related to their functions Enzymes, proteins that serve as metabolic catalysts, regulate the chemical reactions within cells Catalyst: a substance that initiates or accelerates a chemical reaction without itself being affected

88 PROTEINS ARE ESSENTIAL TO THE STRUCTURES AND FUNCTIONS OF LIFE Structural proteins provide associations between body parts Contractile proteins are found within muscle Defensive proteins include antibodies of the immune system Signal proteins are best exemplified by the hormones Receptor proteins serve as antenna for outside signals Transport proteins carry oxygen

89 PROTEINS ARE MADE FROM AMINO ACIDS LINKED BY PEPTIDE BONDS Amino acids, the building blocks of proteins, have an amino group and a carboxyl group Both of these are covalently bonded to a central carbon atom Also bonded to the central carbon is a hydrogen atom and some other chemical group symbolized by the letter R All proteins are made from just 20 amino acids

90 Amino Acid Amino group Carboxyl group

91 PROTEINS ARE MADE FROM AMINO ACIDS LINKED BY PEPTIDE BONDS Amino acids are classified as hydrophobic or hydrophilic Some amino acids have a nonpolar R group and are hydrophobic Others have a polar R group and are hydrophilic, which means they easily dissolve in aqueous solutions

92 Leucine (Leu) Hydrophobic Serine (Ser) Aspartic acid (Asp) Hydrophilic

93 PROTEINS ARE MADE FROM AMINO ACIDS LINKED BY PEPTIDE BONDS Amino acid monomers are linked together to form polymeric proteins This is accomplished by an enzyme-mediated dehydration reaction This links the carboxyl group of one amino acid to the amino group of the next amino acid The covalent linkage resulting is called a peptide bond

94 Carboxyl group Amino group Amino acid Amino acid

95 Carboxyl group Amino group Dehydration reaction Peptide bond Amino acid Amino acid Dipeptide

96 A PROTEIN S SPECIFIC SHAPE DETERMINES ITS FUNCTION A polypeptide chain contains hundreds or thousands of amino acids linked by peptide bonds The amino acid sequence causes the polypeptide to assume a particular shape The shape of a protein determines its specific function

97 A PROTEIN S SPECIFIC SHAPE DETERMINES ITS FUNCTION If for some reason a protein s shape is altered, it can no longer function Denaturation will cause polypeptide chains to unravel and lose their shape and, thus, their function Proteins can be denatured by changes in temperature, ph or salt concentrations

98 A PROTEIN S SHAPE DEPENDS ON FOUR LEVELS OF STRUCTURE A protein can have four levels of structure Primary structure Secondary structure Tertiary structure Quaternary structure

99 PRIMARY STRUCTURE (LINEAR) The primary structure of a protein is its unique amino acid sequence The correct amino acid sequence is determined by the cell s genetic information The slightest change in this sequence affects the protein s ability to function Held together by peptide bonds Examples: DNA

100 Primary structure Amino acids

101 SECONDARY STRUCTURE Protein secondary structure results from coiling or folding of the polypeptide Coiling results in a helical structure called an alpha helix Folding may lead to a structure called a beta pleated sheet Coiling and folding result from hydrogen bonding between certain areas of the polypeptide chain Examples: Silk

102 Amino acids Hydrogen bond Alpha helix Pleated sheet Secondary structure

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104 A PROTEIN S SHAPE DEPENDS ON FOUR LEVELS OF STRUCTURE The overall three-dimensional shape of a protein is called its tertiary structure Tertiary structure generally results from interactions between the R groups of the various amino acids Disulfide bonds (bridges) are covalent bonds that further strengthen the protein s shape Disulfide bonds create permanent loops or coils in a polypeptide bond Examples: hair and nails

105 Polypeptide (single subunit of transthyretin) Tertiary structure

106 Tertiary Structure the folding pattern of the tertiary structure resulting in three-dimensional conformation

107 QUATERNARY STRUCTURE Two or more polypeptide chains (subunits) associate providing quaternary structure Results from interaction between individual polypeptide chains A major force stabilizing the quaternary structure is the hydrophobic interaction among nonpolar side chains at the contact regions of the subunits. Additional stabilizing forces include interactions between side chains of the subunits, including electrostatic interactions between ionic groups of opposite charge:

108 QUATERNARY STRUCTURES Examples: Collagen: found in connective tissue, bone, tendons, and ligaments Hemoglobin: found in blood and carries oxygen DNA polymerase: enzyme used to construct DNA Ion channels: proteins that allow various ions to pass through the cell membrane

109 Quaternary Structure of Collagen

110 Quaternary structure of Hemoglobin

111 ENZYMES

112 CHEMICAL REACTIONS

113 CHEMICAL REACTIONS There are two types Release energy (exergonic) Requires an input of energy and store energy (endergonic)

114 EXERGONIC REACTIONS A chemical reaction that releases energy This reaction releases the energy in covalent bonds of the reactants Energy is released to the surroundings Burning wood releases the energy in glucose, producing heat, light, carbon dioxide, and water Cellular respiration also releases energy and heat and produces products but is able to use the released energy to perform work

115 Potential energy of molecules Reactants Energy released Amount of energy released Products

116 ENDERGONIC REACTIONS Requires an input of energy and yields products rich in potential energy The reactants contain little energy in the beginning, but energy is absorbed from the surroundings and stored in covalent bonds of the products Photosynthesis makes energy-rich sugar molecules using energy in sunlight Used in the process of building macromolecules that form the structure and perform the functions of the cell

117 Potential energy of molecules Products Energy required Amount of energy required Reactants

118 ENZYMES

119 ENZYMES Although there is a lot of potential energy in biological molecules it is not released spontaneously Energy must be available to break bonds and form new ones This energy is called energy of activation (E A )

120 The cell uses catalysis to drive (speed up) biological reactions Catalysis is accomplished by enzymes Enzymes are proteins that function as biological catalysts Enzymes speed up the rate of the reaction by lowering the E A Enzymes are not used up and can be used over and over Each enzyme is specific! It has a particular target molecule called the substrate

121 Reaction without enzyme Reactants Reaction with enzyme E A without enzyme E A with enzyme Net change in energy (the same) Progress of the reaction Products

122 ENZYMES ARE SPECIFIC Enzymes have unique three-dimensional shapes (Remember they are proteins!!!) The shape determines their role As a result of its shape, the enzyme has an active site where the enzyme interacts with the enzyme s substrate The enzyme helps with converting the substrate into products through induced fit (a squeeze)

123 1 Enzyme available with empty active site Active site Enzyme (sucrase)

124 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase)

125 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase) 3 Substrate is converted to products

126 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Glucose Enzyme (sucrase) Fructose 4 Products are released 3 Substrate is converted to products

127 RATE OF REACTIONS Enzymes help increase the rate of reaction This is the speed as to how fast an enzyme can help change the substrate in to a product.

128 OPTIMAL CONDITIONS Enzymes require certain environmental conditions Temperature Ph Enzymes work best at different temperatures Human enzymes function best at 37ºC (body temperature) A little increase in temp can help increase the rate of reactions Too high temperature will denature human enzymes Enzymes also require a ph around neutrality for best results Not stomach enzymes though! Too much of a change can cause denaturation.

129 COFACTORS AND COENZYMES Some enzymes require helpers Cofactors are inorganic, such as zinc, iron, or copper Coenzymes are organic molecules and are often vitamins Help with the substrate binding to the active site

130 INHIBITORS Inhibitors are chemicals that inhibit an enzyme s activity If an inhibitor binds with covalent bonds it is irreversible If the inhibitor binds with weak bonds it is reversible Competive versus Noncompetive

131 COMPETITIVE INHIBITION Inhibitor competes for the enzyme s active site This blocks substrates from entering the active site Overcome by adding more substrate

132 NONCOMPETITIVE (ALLOSTERIC) INHIBITION Inhibitor binds somewhere else other than the active site (allosteric site) This causes the enzyme to change shape so that the substrate will no longer fit the active site

133 Substrate Active site Enzyme Normal binding of substrate Competitive inhibitor Noncompetitive inhibitor Enzyme inhibition

134 FEEDBACK INHIBITION A type of inhibition where a metabolic reaction is blocked by its products This helps to regulate metabolism. The more product formed, the greater the inhibition!

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136 SUMMARY OF KEY TRAITS OF ENZYMES Specific Can be denatured Catalytic protein Lower activation energy Reusable Increase the rate of reaction Usually end in -ase