University of Balamand BioL 205 Principles of Human Biology PDF

University of Balamand Faculty of Health Sciences BIOL 205– Principles of Human Biology CHAPTER 2- THE CHEMISTRY OF LIFE: ORGANIC COMPOUNDS Dr. Espérance Debs  Carbon structure 2  Carbon is the element upon which all organic che...

University of Balamand Faculty of Health Sciences BIOL 205– Principles of Human Biology CHAPTER 2- THE CHEMISTRY OF LIFE: ORGANIC COMPOUNDS Dr. Espérance Debs  Carbon structure 2  Carbon is the element upon which all organic chemistry is based  It generally contains 6 protons and 6 neutrons  4 electrons in the outer energy level of carbon are unpaired forming non-polar covalent bonds  Bound Carbon has a tetrahedral shape  The study of carbon compounds is called Organic Chemistry The chemistry of life: organic compounds  Carbon structure 3 Atomic nucleus (a) Carbon (b) Methane (c) Carbon dioxide The chemistry of life: organic compounds  Importance of carbon 4  Carbon is a very common element having a very high self bonding capacity.  This allows it to form the long chains and rings that make up most of the complex organic molecules  Organic compounds are the molecules of life.  Organic compounds can range from the simple (CO2 or CH4) to complex molecules, like proteins.  Variations in organic molecules can distinguish even between individuals of a single species (e.g. DNA) The chemistry of life: organic compounds  Common carbon compounds 5 The chemistry of life: organic compounds  Isomers 6  Compounds with the same molecular formula but different structure and properties are called Isomers  They differ in the covalent arrangement of their atoms  Geometric isomers are identical in the arrangement of their atoms Geometric isomers but different in the spatial arrangement The chemistry of life: organic compounds  Enantiomers 7  Enantiomers are geometric isomers that are mirror images of each other  Enantiomers cannot be superimposed. Very common with carbon atoms  Cells recognize the difference in shape and usually only one form is active The chemistry of life: organic compounds  Enantiomers 8 The chemistry of life: organic compounds  Carbon-based functional groups 9  The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups.  The number and arrangement of functional groups help give each molecule its distinctive properties  7 functional groups are important to the chemistry of life: 1. Hydroxyl 2. Carbonyl 3. Carboxyl 4. Amino 5. Sulfhydryl 6. Methyl 7. Phosphate groups The chemistry of life: organic compounds  Functional groups 10  The fundamental structure of testosterone (male hormone) and estrogen (female hormone) is indistinguishable  Both are steroids with four fused carbon rings, but they vary in the functional groups attached to the rings The chemistry of life: organic compounds  Hydroxyl group 11  In a hydroxyl group (-OH) , a hydrogen atom forms a polar covalent bond with an oxygen which forms a polar covalent bond to the carbon skeleton The chemistry of life: organic compounds  Carbonyl group 12  A carbonyl group (C=O) is made of an oxygen atom linked to the carbon skeleton by a double bond.  If the carbonyl group is on the end of the skeleton, the compound is an aldehyde.  If not, then the compound is a ketone. The chemistry of life: organic compounds  Carboxyl group 13  A carboxyl group (-COOH) is made of a carbon atom with a double bond with an oxygen atom and a single bond to a hydroxyl group.  Carboxylic acids (weak acids) are compounds with carboxyl groups (essential constituents of amino acids) The chemistry of life: organic compounds  Amino group 14  An amino group (-NH2) weakly basic: a nitrogen atom joined to 2 hydrogen atoms and the carbon skeleton.  Amines are organic compounds with amino groups.  Amino acids, the building blocks of proteins, have amino and carboxyl groups. The chemistry of life: organic compounds  Sulfhydryl group 15  A sulfhydryl group (-SH) consists of a sulfur atom bound to a hydrogen atom and to the backbone.  This group resembles a hydroxyl group in shape.  Organic molecules with sulfhydryl groups are thiols.  Sulfhydryl groups help stabilize the structure of proteins. The chemistry of life: organic compounds  Methyl group 16  A methyl group (-CH3) is made of a Carbon atom bound to 3 Hydrogen atoms. It is derived from methane CH4  Known to be the “Most stable functional group” in a molecular compound.  Methyl groups are added or removed from proteins or nucleic acids and may change the way these molecules act in the body. Methyl Alkyl The chemistry of life: organic compounds  Phosphate group 17  A phosphate group (-OPO32-) consists of phosphorus bound to four oxygen atoms (three with single bonds and one with a double bond).  A phosphate group (weakly acidic) connects to the carbon backbone via one of its oxygen atoms. e.g. ATP The chemistry of life: organic compounds  Macromolecules 18  Compounds are considered organic when they contain carbon and at least 1 hydrogen.  Organic compounds also form biological molecules that are large, known as Macromolecules.  These larger molecules may be made of thousands of atoms and weigh over 100,000 Daltons.  Macromolecules include: carbohydrates, lipids, proteins, and nucleic acids.  Major macromolecules are made from simple sugars, fatty acids, amino acids, and nucleotides The chemistry of life: organic compounds  Polymers 19  Macromolecules are polymers formed from linked monomers  The synthetic process by which monomers are linked covalently called condensation or polymerization  Polymers can be degraded to their component monomers by hydrolysis (break with water). The chemistry of life: organic compounds  Condensation and Hydrolysis 20 Condensation Enzyme A Hydrolysis Monomer Monomer Dimer Enzyme B The chemistry of life: organic compounds  Carbohydrates 21  Carbohydrates are the most numerous molecules in life.  Carbohydrates are also called sugars and they can be simple or complex.  They serve as an energy source for the cells and the organism such as glucose  Other functions include structure: e.g. cellulose, the main structural component of the walls that surround plant cells The chemistry of life: organic compounds  Carbohydrates 22  Carbohydrates contain Carbon, Oxygen, and Hydrogen (CH2O)n  Simple sugars are called monosaccharides  There are also disaccharides that consist of 2 monosaccharides linked together  Polysaccharides consist of many monosaccharides linked together. The chemistry of life: organic compounds  Monosaccharides 23  Monosaccharides follow the molecular formula of (CH2O)n: e.g. Glucose  In a monosaccharide a hydroxyl group is bonded to each carbon except the carbonyl carbon  Carbonyl is at the end in an aldose. Carbonyl is in the middle in a ketose  The large number of polar hydroxyl groups, plus the carbonyl group makes monosaccharides hydrophilic The chemistry of life: organic compounds  Monosaccharides 24  Monosaccharides are classified by the number of carbons in the backbone  Three carbon sugars are called trioses: e.g. glyceraldehyde  Five carbon backbones are known as pentoses: e.g. riboses in nucleic acids  Six carbon sugars are known as hexoses: e.g. glucose the most abundant monosaccharide The chemistry of life: organic compounds  Monosaccharides 25 Numbering begins at the carbonyl end or near it in cases of ketoses The chemistry of life: organic compounds  Monosaccharides 26  Carbon 1 binds to the Oxygen on Carbon 5  β: OH & CH2OH are on the same plane  α: OH & CH2OH are on the opposite plane The chemistry of life: organic compounds  Glucose 27  Glucose is a major source of energy  Glucose is oxidized during cellular respiration and made ready for cellular use  Glucose contributes to formation of other compounds such as Amino Acids and Fatty Acids  Glucose is maintained at a fixed level in blood circulation The chemistry of life: organic compounds  Glucose 28  Glucose and fructose are structural isomers  fructose is a ketone, glucose is an aldehyde  This small difference makes fructose tastes sweeter than glucose  Glucose is preferred in human cellular respiration The chemistry of life: organic compounds  Disaccharides 29  Characterized by the joining of two monosaccharides by a glycosidic linkage between two molecules through a condensation reaction. The chemistry of life: organic compounds  Disaccharides 30 Enzyme Alpha-Glucose Alpha-Glucose Maltose C6H12O6 C6H12O6 C12H22O11 Enzyme Sucrose Glucose Fructose C12H22O11 C6H12O6 C6H12O6 The chemistry of life: organic compounds  Disaccharides 31  Maltose consists of two glycosidically linked alpha- glucose  Lactose, the milk sugar, is composed of one glucose and one galactose  Glycosidic linkage can be broken by adding water through a hydrolysis reaction Maltose + Water 2 Glucoses Sucrose + Water Glucose + Fructose The chemistry of life: organic compounds  Polysaccharides 32  Polysaccharides are the most abundant carbohydrates  Polysaccharides consist of hundreds to thousands of monosaccharides joined by glycosidic linkages  They may be single long chains or branched chains, or isomers, all with variation in their chemical properties  Those that are easy to hydrolyze are used for energy storage  Other well architectured polysaccharides serve as building materials for the cell: cellulose The chemistry of life: organic compounds  Energy polysaccharides 33  Starch is a storage polysaccharide composed entirely of alpha-glucose monomers joined by 1,4 glycosidic bonds  Starch is found in plants and used to store energy  Starch occurs in two forms:  (1) unbranched: Amylose  (2) branched: Amylopectin  Starch in plants is stored in granules known as amyloplasts The chemistry of life: organic compounds  Energy polysaccharides 34  Animals store glucose in the form of a polysaccharide known as glycogen in their liver and muscle cells  Glycogen is similar to plant starch but more branched and more water soluble The chemistry of life: organic compounds  Structural polysaccharides - Cellulose 35  Cellulose is the most abundant carbohydrate accounts for about 50% of all carbon in plants  Wood is about half cellulose and cotton is about 90% cellulose  Cellulose is the basis for plant cell walls  Cellulose is insoluble, made of Beta-glucose monomers joined by beta 1-4 glycosidic linkages The chemistry of life: organic compounds  Structural polysaccharides - Cellulose 36  Humans do not possess the enzyme necessary to break Beta-glycosidic linkage, hence cannot digest cellulose. Cellulose fibers are important for normal GI (Gastro-Intestinal) functioning The chemistry of life: organic compounds  Cellulose 37 The chemistry of life: organic compounds  Structural polysaccharides 38 Beta-glucose subunits are joined in a way to allow for high hydrogen bonding leading to aggregation and formation of fiber bundles The chemistry of life: organic compounds  Other carbohydrates 39  Carbohydrates may combine with proteins to form glycoproteins (adhere to one another, protection such as mucus)  Carbohydrates may combine with lipids to form glycolipids important in cell-cell communication  Galactosamine present in cartilage of skeletal systems  Other derivatives of carbohydrates exist such as glucosamine involved in external skeletons of insects, and arthropods making chitin The chemistry of life: organic compounds  Lipids 40  Lipids are heterogeneous compounds soluble in non-polar organic solvents and insoluble in polar and aqueous solutions  They consist mainly of a lot of Carbon (C), Hydrogen (H), and few Oxygen (O), which makes them hydrophobic  Lipids are important for energy storage, structure and signaling  Biologically important groups of lipids include the following: 1. Triglycerides 2. Phospholipids 3. Carotenoids 4. Steroids The chemistry of life: organic compounds  1- Triglycerides 41  Most abundant lipids in living organisms with 2 X more energy yield than carbohydrates  Triglycerides have 3 fatty acids attached to a glycerol molecule.  A glycerol molecule is a 3-Carbon backbone with 3 hydroxyl groups Glycerol  A Fatty acid is a long unbranched chain of carbon and a carboxyl group at one end Fatty acid The chemistry of life: organic compounds  Saturated fatty acids 42  More than 30 different fatty acids are commonly found in lipids with an even number of carbons  E.g. Butyric acid (4-carbons), Oleic acid (18-Carbons)  There are saturated and unsaturated fats  Saturated fatty acids have no double bond, leaving them with the maximum number of Hydrogen atoms while unsaturated do have one or more double bonds  Saturated fats tend to solidify at room temperature (e.g. Margarine) whereas unsaturated triglycerides remain liquid because of the presence of double bonds  There is no dietary requirement for saturated FA The chemistry of life: organic compounds  Unsaturated fatty acids 43  Unsaturated fatty acids have one or more double bond(s); they are not fully saturated with hydrogen  FA with one double bond are known as monounsaturated fatty acids  FA with more than one double bond are known as polyunsaturated fatty acids  These tend to be liquid at room temperature because the double bond bends the chain which prevents it from interacting with other chains  At least 2 unsaturated fatty acids are essential dietary requirements (Linoleic acid “omega 6” & Alpha-Linolenic acid “omega 3”) since your body cannot synthesize them The chemistry of life: organic compounds  Fatty acids 44 Palmitic acid Oleic acid Linoleic acid The chemistry of life: organic compounds  Triglycerides 45  When glycerol combines with one FA a monoglyceride is formed  Glycerol with 2 FA, a diglyceride is formed  Glycerol with 3 FA, a triglyceride is formed  The reaction is a condensation reaction where one or more water molecules are produced and a bond known as Ester linkage is formed  Triglycerides are the most common lipids in the body and its best energy source The chemistry of life: organic compounds  Ester linkage 46 Carboxyl Glycerol Fatty acid The chemistry of life: organic compounds  Triglyceride molecule 47 Ester linkage The chemistry of life: organic compounds  2- Phospholipids 48  Phospholipids have 2 fatty acid tails and a polar head. They make up cell membranes  At one end phospholipids are made of a glycerol molecule attached to 2 FA  At the other end the glycerol is attached to a phosphate group linked to an organic molecule such as choline  The first end is hydrophobic whereas the other end is hydrophilic; the molecule is called amphipathic The chemistry of life: organic compounds  Phospholipid bilayer 49 Water The chemistry of life: organic compounds  3- Carotenoids 50  Orange and yellow pigments of plants  Classified with lipids since they are insoluble in water and oil  They play a role in photosynthesis  Carotenoid molecules such as β-carotene are made of 5-carbon monomers  Most animals can convert β-carotene into Vitamin A converted to the visual pigment Retinal The chemistry of life: organic compounds  4- Steroids 51  Carbon atoms arranged in 4 attached rings: 3 hexagons and 1 pentagon  Steroids are also made of isoprene units  Side chains distinguish one steroid from another  Steroids include cholesterol (cell membrane component), bile salts (fat emulsification), reproductive and other hormones, chemical mediators (prostaglandins) The chemistry of life: organic compounds  PROTEINS 52  Proteins are the most structurally complex molecules known.  Proteins are influential in all cellular activities.  They are extremely versatile and are assembled in a variety of shapes  Functions include storage, structural support, transport of substances, intercellular signaling, movement, growth, repair, and defense against foreign substances  Proteins are the overwhelming enzymes in a cell and regulate metabolism by selectively accelerating chemical reactions The chemistry of life: organic compounds 53 The chemistry of life: organic compounds  Function of proteins 54  Function depends on shape.  Some proteins are globular, others form fibers.  In almost every case, the function depends on its capacity to recognize and bind to some other molecule:  Antibodies bind to particular foreign substances that fit their binding sites.  Neurotransmitters pass signals from one cell to another by binding to receptor sites The chemistry of life: organic compounds  Proteins 55  Humans have tens of thousands of various proteins, each with its own structure and function.  In contrast to carbohydrates and lipids, most proteins are species-specific  They are made of polypeptides which are polymers of amino acids.  There are 20 amino acids that exist in 3 classes:  Polar  Non-polar  Electrically charged The chemistry of life: organic compounds  Amino acids 56  Building blocks of proteins  They have an amino group and a carboxyl group bonded to the same asymmetric α-Carbon  Each uniquely identified by the variable group R  These molecules are able to donate a proton; so they are acids  At cellular pH, amino acids are dipolar: COO- & NH3+ AA Chemical Structure The chemistry of life: organic compounds  1 – Polar amino acids 57 Back bone R group Asparagine Glutamine Tyrosine Serine Threonine Asn Gin Tyr Ser Thr The side chains of polar amino acids make them hydrophilic, meaning they are water-soluble. The chemistry of life: organic compounds  2 – Non-polar amino acids 58 The side chains of these amino acids are long Glycine Alanine Valine Leucine Isoleucine carbon chains Gly Ala Val Leu lle or carbon rings, making them bulky. They are hydrophobic, meaning they repel water. Tryptophan Proline Cysteine Methionine Phenylalanine Trp Pro Cys Met Phe The chemistry of life: organic compounds  3- Electrically charged amino acids 59 Aspartic acid Glutamic acid Arginine Lysine Histidine Asp Glu Arg Lys His Acidic amino acids are negatively Basic amino acids are positively charged, hydrophilic amino acids charged, hydrophilic amino acids The chemistry of life: organic compounds  Electrically charged AA 60  At cellular pH, in acidic chains the carboxyl group releases an H+ leaving R with a negative charge  At cellular pH, the amino group accepts a H+ leaving R with a positive charge  Both types are hydrophilic and ionic at cellular pH The chemistry of life: organic compounds  Essential amino acids 61  Essential Amino Acids constitute the ones that cannot be synthesized (at all or in sufficient amounts) by organisms and must be obtained from the diet.  These are the 20 most common amino acids  With some exceptions, prokaryotes and plants synthesize their needed amino acids from simpler substances.  Animals differ in their biosynthetic capacities. What is an essential AA for one species may not be for another.  These are 10 AA in humans: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, histidine, and in children arginine. The chemistry of life: organic compounds  Peptides 62  Peptide bond is formed by a condensation reaction  The carboxyl carbon of one molecule bonds to the amino nitrogen of another  When 2 AA combine it is called a dipeptide  When a longer chain is formed it is Formation of a peptide bond called a polypeptide Polypeptide backbone  Proteins have a free amino group on one end and a carboxyl group on the other N-C-C-N-C-C-N-C-C The chemistry of life: organic compounds  Formation of a dipeptide 63 Carboxyl Amino R group R group Peptide bond group group Glycine Alanine Glycylalanine (a dipeptide) - - N-C-C N-C-C N-C-C N-C-C N-C-C - - The chemistry of life: organic compounds  Protein organization – Primary structure 64  Four main protein organization levels: primary, secondary, tertiary, quaternary  Primary: Amino acid sequence joined by the peptide bond Glucagon 1ry structure: 29 amino acids The chemistry of life: organic compounds  Secondary structure 65 -Helix:  Hydrogen bonding between the AA backbones of a polypeptide  Basic structure of fibrous proteins such as hair, skin, nail  High elasticity due to shape and H-bonding -pleated sheet:  Hydrogen bonding between different polypeptide chains or different regions of a polypeptide chain turned on itself  Basic structure of fibroin the protein of silk  Strong and flexible but not elastic since distances are fixed Single polypeptides may include both types The chemistry of life: organic compounds  Secondary structure 66 -Helix  Hydrogen bonding between the AA backbones of the same polypeptide leading into a spiral shape  3.6 AA acids are included in each complete turn  Each AA is H-bonded in this way The chemistry of life: organic compounds  Secondary structure 67 Hydrogen bonds hold neighboring strands of sheet together -Pleated sheets  Hydrogen bonding between different polypeptide chains or different regions of a polypeptide chain turned on itself  Due to zigzag shape a pleated conformation is realized The chemistry of life: organic compounds  Tertiary structure 68  It is the overall shape of Hydrogen each polypeptide chain. bond Ionic bond It is determined by interactions among R groups 1. H-bonding 2. Ionic attraction of charged R-groups 3. Hydrophobic interaction of non-polar R groups Disulfide Hydrophobic bond interaction 4. Disulfide covalent bonds between 2 cysteines of the same chain The chemistry of life: organic compounds  Tertiary structure 69 Alpha Helix Beta -pleated sheet Tertiary structure illustration The chemistry of life: organic compounds  Quaternary structure 70  For proteins made from more than 1 polypetide, it is a 3-D architecture of the protein resulting from a number of interactions between all the polypeptides  The interactions between the different polypeptides also include H-bonding, ionic, covalent, hydrophobic and disulfide bridges  The final conformation of a protein is dictated by the Amino Acid sequence  The folding is thought to be mediated by special proteins known as Chaperones The chemistry of life: organic compounds  Quaternary structure 71  Hemoglobin and Collagen Beta chain (a) Hemoglobin (-globin) Alpha chain (b) Collagen Heme (α -globin) Alpha chain Beta chain (α-globin) ( -globin) The chemistry of life: organic compounds  Protein organization 72  Factors influencing protein structure 73  Proteins may have more than one distinct structure region known as domain that determines more than one functions  Changes in pH, salt concentration, temperature, or other factors can unravel or denature a protein  One amino acid difference can cause a huge change:  E.g. Sickle Cell Anemia (substitution of a Valine for Glutamic acid in a hemoglobin chain) The chemistry of life: organic compounds  NUCLEIC ACIDS 74  Proteins which control or make the majority of our body are coded by genes  DNA includes the genes and all the hereditary information of the cell  Nucleic acids transmit hereditary information  There are two types of nucleic acids:  Ribonucleic acid (RNA)  Deoxyribonucleic acid (DNA) The chemistry of life: organic compounds  Nucleic acids 75  DNA also directs RNA synthesis and controls protein synthesis  Some forms of RNA can act as enzymes: Ribozymes  When a cell reproduces itself by mitosis or division, its DNA is copied and passed to the next generation of cells The chemistry of life: organic compounds  Nucleotides 76  Nucleic acids are made of nucleotides joined together  Each nucleotide consists of three parts: 1. A nitrogenous base 2. A pentose sugar 3. A phosphate group The chemistry of life: organic compounds  Nucleotides 77  The nitrogen base may be a double-ring purine or a single-ring pyrimidine  The three different pyrimidines, cytosine (C), thymine (T), and uracil (U) – part of RNA  The two purines are adenine (A) and guanine (G)  DNA commonly contains A, T, C, G and a deoxyribose sugar and a phosphate  RNA commonly contains A,U,C,G, a ribose sugar and a phosphate The chemistry of life: organic compounds  Nucleotides 78 Pyrimidines Cytosine (C) Thymine (T) Uracil (U) Purines Adenine (A) Guanine (G) The chemistry of life: organic compounds  Nucleotides are Nucleotide joined with a phosphodiester bond A phosphate group covalently bind to the sugar of adjacent Phosphodiester nucleotides linkage DNA forms a Double-strand 79 The chemistry of life: organic compounds