General Biology Bio 110 - Chapter 3 PDF

General Biology Bio 110 Chapter 3 CONTENTS Part 1 Life on Earth: An Overview Chapter 1 PART II Chemistry of Life a. Basic Chemistry Chapter 2 b. Chemistry of Organic Molecules Chapter 3 PART III The C...

General Biology Bio 110 Chapter 3 CONTENTS Part 1 Life on Earth: An Overview Chapter 1 PART II Chemistry of Life a. Basic Chemistry Chapter 2 b. Chemistry of Organic Molecules Chapter 3 PART III The Cell a. Cell Structure and Function Chapter 4 b. Membrane Structure and Function Chapter 5  Part II CHEMISTRY OF LIFE b. Chemistry of Organic Molecules 3.1 Organic Molecules Chemistry is divided into organic chemistry, the chemistry of organisms and inorganic chemistry, the chemistry of the non- living world. Organic molecules should contain both carbon and hydrogen atoms (Table 3.1). Classes of organic compound(biomolecules): Carbohydrates. Proteins Lipids Nucleic acids A bacterial cell contains 5,000 different organic molecules and a plant or animal cell has twice that number.  3.1 Organic Molecules a. The Carbon Atom:  Carbon has a total of six electrons: two electrons in the first shell and four electrons in the outer shell.  In order to acquire four electrons to complete its outer shell, a carbon atom almost always shares electrons with CHNOPS, the elements that make up most of the weight of living things.  Methane ( CH4) is one of the simplest organic compounds.  Four covalent bonds link four hydrogen atoms to the carbon atom.  Each of the four lines in the formula for Methane represents a pair of shared electrons  3.1 Organic Molecules  Carbon can share electrons with another carbon atom. The C-C bond is quite stable, and the result is carbon chains that can be quite long.  Branching at any carbon atom is possible and hydrocarbon can turn back on itself to form a ring compound.  Carbon can form double bonds with itself and other atoms. In acetylene, H-C≡C-H, carbon is also capable of forming a triple bond with itself.  Organic molecules containing carboxyl (acidic) groups (‒COOH) are highly polar. 3.1 Organic Molecules: b. The Biomolecules of Cells: Certain foods are rich in biomolecules. Ex., bread is rich in carbohydrate and meat is rich in protein. When you digest food, it gets broken down into smaller molecules; digestion of bread releases glucose AND digestion of meat releases amino acids. Your body then takes these subunits and make up your cells. Table 3.2 Biomolecules Category Example Subunit Carbohydrate Polysaccharide Monosaccharide Lipids Fat Glycerol and fatty acid Proteins Polypeptide Amino acid Nucleic Acids DNA, RNA Nucleotide 3.1 Organic Molecules: c. Synthesis and Degradation:  Synthesis: A cell uses a condensation (or dehydration) reaction to synthesize (build up) any type of biomolecule, where a water molecule; OH (hydroxyl group) and H (hydrogen atom), is removed as subunits are joined (Figure 3.1a).  Degradation :To break down biomolecules, a cell uses an opposite type of reaction; namely hydrolysis, where OH group from water attaches to one subunit and H from water attaches to the other subunit (Figure 3.1b). Figure 3.1 Synthesis and dehydration of  Enzymes are required for cells to biomolecules. carry out dehydration and hydrolysis reactions.  3.1 Organic Molecules: c. Synthesis and Degradation (continued): An enzyme is a molecule that speeds a reaction by bringing reactants together. Enzymes participate in the reaction, but it is unchanged by it. Polymers are the largest of the biomolecules constructed by linking together a large number of the same type of subunit; called monomer. Ex., Polysaccharide, protein and nucleic acid are polymers that contain many monomers, Figure 3.1 Synthesis and dehydration of i.e., monosaccharides, amino biomolecules. acids and nucleotides, respectively.  Part IIb 3.2 Carbohydrates  3.2 Carbohydrates The term carbohydrate includes single or a chain of sugars. Carbohydrates are immediate energy source in living things and play structural roles in a variety of organisms. The majority of carbohydrates have a carbon to hydrogen to oxygen ratio of 1:2:1. a. Monosaccharides: Ready Energy Monosaccharide is a single sugar molecule with a carbon backbone of three to seven carbons. The molecular formula for a simple sugar is a multiple of CH2O. As sugars have many hydroxyl groups, their polar functional group makes them soluble in water. Glucose (Figure 3.2), with six carbon atoms, is a hexose with a molecular formula of C6H12O6. Figure 3.2 Glucose. 3.2 Carbohydrates a. Monosaccharides: Ready Energy (continued) Glucose functions: major source of cellular fuel for all living things. transports in the blood of animals. broken down in nearly all types of organisms during cellular respiration, with the resulting buildup of ATP molecules. Ribose and deoxyribose are pentoses, with five carbon atoms, that are found in the nucleic acids RNA and DNA, respectively. Figure 3.2 Glucose.  3.2 Carbohydrates b. Disaccharides: Varied Uses They contain two monosaccharides joined during a dehydration reaction. Figure 3.3 shows how disaccharide maltose (an ingredient used in brewing) arises. Sucrose, a disaccharide used at home to sweeten food, is glucose combined with fructose. We acquire sucrose from sugarcane and sugar beets. Lactose, a disaccharide found in milk, is glucose combined with galactose. Individuals that are lactose intolerant cannot break this disaccharide down and have subsequent medical problems. Figure 3.3 Synthesis and degradation of maltose; a disaccharide. 3.2 Carbohydrates c. Polysaccharides- Energy Storage Molecules: Polysaccharides is polymers of monosaccharides. When an organism requires energy, the polysaccharide is broken down to release sugar molecules. Plants store glucose as starch (non-branched or branched, Figure 3.4a), while animals store glucose as glycogen (highly branched, Figure 3.4b). Figure 3.4a Starch structure. 3.2 Carbohydrates c. Polysaccharides- Energy Storage Molecules (cont.): After we eat, the release of the hormone insulin from the pancreas promotes the storage of glucose as glycogen. Polysaccharides serve as storage molecules because they are larger than a sugar and not as soluble in water, therefore, cannot easily pass through the plasma membrane. Figure 3.4b Glycogen structure.  3.2 Carbohydrates d. Polysaccharides- Structural Molecules: Structural polysaccharides include cellulose in plants, chitin in animals and fungi and peptidoglycan in bacteria. In all three, monomers are joined by the type of bond shown for cellulose in Figure 3.5. Figure 3.5 Cellulose Fibers.  3.2 Carbohydrates d. Polysaccharides: Structural Molecules (cont.) The cellulose monomer is simply glucose, but in chitin, the monomer has an attached amino group. The structure of peptidoglycan is even more complex because each monomer also has an amino acid chain. Cellulose is the most abundant organic molecule on Earth. Wood, a cellulose plant product, is used for construction and cotton is used for cloth. Chitin, like cellulose, cannot be digested by animals. Seeds are coated with chitin, and this protects them from attack by soil fungi. Because chitin also has antibacterial and antiviral properties, it is processed and used in medicine as a wound dressing material and is useful in cosmetics. Part Iib 3.3 Lipids  3.3 Lipids Lipids are insoluble in water due to their hydrocarbon chains (Table 3.3), where hydrogen bonded only to carbon has no tendency to form a bond with water molecules. Fat is used for both insulation and long-term energy storage by animals, while plants use oil, instead. Phospholipids and steroids serve as major components of the plasma membrane in cells. a. Triglycerides: Long-Term Energy Storage Fats and oils contain two types of subunit molecules; fatty acids and glycerol. Fatty acid consists of a long (16-18 atoms) hydrocarbon chain with a ‒COOH (carboxyl) group at one end. 3.3 LIPIDS: a. Triglycerides: Long-Term Energy Storage (continued):  Fatty acids are either saturated or unsaturated. Saturated fatty acids have no double bonds between the carbon atoms, while unsaturated fatty acids have (C=C).  Glycerol is a compound with three polar ‒OH groups, therefore, it is soluble in water.  During dehydration reaction to form a fat molecule, the acid portions of three fatty acids react with the ‒OH groups of glycerol and three molecules of water result (Figure 3.6). Figure 3.6 Formation of a fat..  3.3 LIPIDS a. Triglycerides: Long-Term Energy Storage (cont.): During hydrolysis reaction, fats are degraded. Because there are three fatty acids attached to each glycerol molecule, fats and oils are sometimes called triglycerides. As triglycerides have many C‒H bonds, they do not mix with water. Notice that unsaturated bond (C=C) melts at lower temperature than those containing only saturated fatty acids. Fats are mostly of animal origin and oils are of plant origin. Diets high in animal fat are associated with circulatory disorders because fatty material accumulates inside the blood vessels and blocks blood flow. Figure 3.6 Formation of a fat.  3.3 LIPIDS: a. Triglycerides: Long-Term Energy Storage (cont.) Butter, a fat that is solid at room temperature, contains primarily saturated fatty acids, while corn oil, a liquid even when placed in the refrigerator, contains primarily unsaturated fatty acids (Figure 3.7). Figure 3.7 Types of fatty acids and fats. 3.3 LIPIDS: a. Triglycerides- Long-Term Energy Storage (cont.): This difference is useful to living things, ex., the feet of penguins contain unsaturated triglycerides to help them protect exposed parts from freezing. 3.3 LIPIDS : b. Phospholipids- Membrane Components: A phospholipid is constructed like a fat, except that in place of the third fatty acid attached to glycerol, there is a polar phosphate group usually bonded to another organic group, indicated by R (Figure 3.8). This portion of the molecule becomes the polar head (hydrophilic), while the hydrocarbon chains of the fatty acids become the non-polar tails (hydrophobic). A kink causes fluidity of plasma membrane Figure 3.8 Phospholipid structure. 3.3 LIPIDS :- b. Phospholipids: Membrane Components (continued): Therefore, when surrounded by water, phospholipids become a bilayer (double layer) in which the hydrophilic heads project outward and the hydrophobic tails project inward as in plasma membrane (Figure 3.9). A plasma membrane is essential to the structure and function of a cell. Figure 3.9 Plasma membrane of a cell.  3.3 LIPIDS c. Steroids: Four Fused Rings: Each type of steroid differs primarily by the types of functional groups attached to the carbon skeleton. Cholesterol (Figure 3.10) is essential component of an animal cell’s plasma membrane and the precursor of several other steroids, such as the hormones testosterone and estrogen. Cholesterol can also contribute to circulatory disorders. The presence of cholesterol encourages the accumulation of fatty material inside the lining of blood vessels and, therefore, high blood pressure. Figure 3.10 Cholesterol.  Part II b 3.4 Proteins 3.4 Protein: Proteins are large biomolecules and macromolecules that are comprise of one or more amino acid residues.  As much as 50% of the dry weight of most cells are proteins.  Presently, over 100,000 proteins have been identified. 3.4 Proteins Functions in animals: Metabolism: Enzymes bring reactants together and thereby speed chemical reactions in cells. Support: Some proteins have a structural function; keratin makes up hair and nails, while collagen lends support to tendons and skin. Transport: Carrier proteins in the plasma membrane allow substances to enter and exit cells. Also, hemoglobin transport oxygen in the blood. Defense: Antibodies combine with foreign substances, called antigens to prevent them from destroying cells. Regulation: Hormones serve as intercellular messengers that influence the metabolism of cells; insulin regulates the content of glucose in the blood. Motion: Actin and myosin allow parts of cells to move and cause muscles to contract.  3.4 Proteins a. Amino Acids: Amino acid is the monomer of protein. The amino acid has three groups: ‒NH2 (amino group) ‒COOH (acid group R group for an amino acid Besides, the central carbon atom in an amino acid bonds to a hydrogen atom (‒H). The 20 amino acids differ according to their R group, shaded in blue in Figure 3.12. Some of which are shown in figure 13.12 b. Amino Acids: Figure 3.12 Amino acids.  a. Amino Acids: (cont.) The R group Range in complexity from a single hydrogen atom to a complicated ring compound. Some are polar and some are non-polar. The amino acid cysteine has an R group that ends with an ‒SH group, which serves to connect one chain of amino acids to another by a disulfide bond, ‒S‒S‒. Figure 3.12 Amino acids. 3.4 Proteins: a. Peptides: Proteins are polymers with amino acid monomers joined together by a covalent bond called a peptide bond through dehydration reaction between the carboxyl group of one and the amino group of another (Figure 3.11). A peptide is two or more amino acids bonded together and a polypeptide is a chain of many amino acids joined by peptide bonds. A protein may contain more than one polypeptide chain, each has its own sequence that influences the three-dimensional shape of the protein. Figure 3.11 Synthesis and degradation of a peptide.  3.4 Proteins:- c. Shape of Proteins: Protein has four levels of structure. The primary structure is the particular sequence of amino acids. The secondary structure occurs when the polypeptide coils or folds (Figure 3.13) resulting in an α (alpha) helix or a pleated sheet called a β (beta) sheet. Hydrogen bonding holds the secondary structure. Figure 3.13 Levels of protein organization.  3.4 Proteins c. Shape of Proteins: Hydrogen bonding between every fourth amino acid accounts for the spiral shape of the α helix. In β sheet, the polypeptide turns back upon itself. A tertiary structure is the folding that results in a three-dimensional shape called globular protein. Bonds contribute to the tertiary structure are: Hydrogen bonds Ionic bonds Covalent bonds Figure 3.13 Levels of protein organization. 3.4 Proteins c. Shape of Proteins: Strong disulfide linkages in particular help maintain the tertiary shape. When a protein loses its natural shape, it is said to be denatured. Some globular proteins representing quaternary structure consist of more than one polypeptide; hemoglobin consist of four polypeptides. Each polypeptide in hemoglobin has a primary, secondary and tertiary structure. Figure 3.13 Levels of protein organization.  Part IIb 3.5 Nucleic Acids 3.5 Nucleic Acids Nucleic acids are polymers of nucleotides: DNA (deoxyribonucleic acid) is the genetic material that stores information regarding the order in which amino acids are to be joined to make a protein. RNA (ribonucleic acid), three major types: Messenger RNA or mRNA Ribosome RNA or rRNA Transfer RNA or tRNA mRNA is an intermediary in the process of protein synthesis, conveying information from DNA to a protein. Some nucleotides have independent metabolic functions in cells; coenzymes, to facilitate enzymatic reactions, e.g., ATP (adenosine triphosphate) supplies energy for energy-requiring reactions. 3.5 Nucleic Acids a. Structure of DNA and RNA Nucleotide; a complex of three types of molecules (Figure 3.14a) contains: phosphorous (phosphoric acid) pentose sugar; deoxyribose for DNA and ribose for RNA (Figure 3.14b) nitrogenous base; pyrimidine or purine; single or double ring (Fig. 3.14c) Figure 3.14 Nucleotides.  3.5 Nucleic Acids: a. Structure of DNA and RNA (cont.): In DNA, the pyrimidine base can be cytosine (C) and thymine (T). In RNA, the pyrimidine bases are cytosine (C) and uracil (U). In both DNA and RNA, the purine bases are adenine (A) or guanine (G). The polynucleotide is a linear molecule called a strand in which the backbone is made up of a series of sugar-phosphate- sugar-phosphate molecules. RNA is single-stranded, while DNA is double-stranded, with the two strands usually twisted about each other in the form of a double helix (Figure 3.15a & b). Figure 3.15 DNA structure.. 3.5 Nucleic Acids: a. Structure of DNA and RNA (cont.) The two strands are held together by hydrogen bonds between pyrimidine and purine bases; thymine (T) is always paired with adenine (A) and guanine (G) is always paired with cytosine (C). This is called complementary base pairing. Therefore, the number of purine bases (A+G) always equals the number of pyrimidine bases (T+C) (Figure 3.15c). Figure 3.15 DNA structure.  3.5 Nucleic Acids : a. Structure of DNA and RNA (continued): Table 3.3summarizes the differences between DNA and RNA.  3.5 Nucleic Acids b. ATP (Adenosine Triphosphate): ATP is composed of adenine and ribose and triphosphate stands for the three phosphate groups attached together and to ribose (Figure 3.16). ATP is a high-energy molecule. In cells, the terminal phosphate bond is usually hydrolyzed to give the molecule ADP (adenosine diphosphate) and a phosphate molecule. The energy that is released by ATP breakdown is coupled to energy- requiring processes in cells, like muscle contraction and nerve impulse conduction. Figure 3.16 ATP and ADP. Thank you