Biology Chapter 2 Part 2 Fall 2024-2025 PDF

Chapter 2 Basic Chemistry Part 2 1  Chapter 2 Basic Chemistry Organic molecules: In biology, there are 4 major types of organic molecules (macromolecules): lipids, carbohydrates, proteins, and nucleic acids (RNA & DNA)...

Chapter 2 Basic Chemistry Part 2 1  Chapter 2 Basic Chemistry Organic molecules: In biology, there are 4 major types of organic molecules (macromolecules): lipids, carbohydrates, proteins, and nucleic acids (RNA & DNA) Macromolecules such as proteins and carbohydrates are polymers (chain) that are made of many similar or repeating units called monomers.  The polymers form by adding monomers in what is called the dehydration (loss of a water molecule) reaction. Break down by removing monomers by what is called as hydrolysis (addition of a water molecule) reaction Sugars, proteins and nucleic acids are true polymers while lipids are not true polymers; they are just large molecule 3 Figure 2.13a Dehydration synthesis and hydrolysis of biological molecules. (a) Dehydration synthesis Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation. H2 O Monomers linked by covalent bond Monomer 1 Monomer 2 (b) Hydrolysis Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other. H2 O Monomers linked by covalent bond 4 Carbohydrates 5  Carbohydrates (cont.) Sugars, starch, cellulose, glycogen, chitin: all consist of carbon, hydrogen and oxygen. Carbohydrates means: hydrated carbon (C + H2O) All consist of basic building blocks called simple sugar (monosaccharide) Types of Carbohydrates a. Monosaccharides Monosaccharides generally have molecular formulas that are multiples of nCH2O (n number of carbon atoms) n = 3 (trioses); 4 (tetroses); 5 (pentoses) or 6 (hexoses like C6H12O6 = glucose). 6  Carbohydrates (cont.) Monosaccharides (cont) Structure of Monosaccharides Examples on Pentoses: Ribose and Deoxyribose (nucleic acids) Examples on Hexoses: Glucose, fructose, galactose Monosaccharides are classified either Ketoses or Aldoses. Ketoses: Contain ketone group (Fructose) Aldoses: Contain aldehyde group (glucose, galactose, ribose) 7  Carbohydrates b. Disaccharides: consists of two monosaccharides joined with each others through a dehydration reaction. The bond that is formed is called glycosidic linkage (bond). Dehydration synthesis H2O Hydrolysis Glucose Fructose Sucrose Water (d) Dehydration synthesis and hydrolysis of a molecule of sucrose Glucose + glucose = maltose (malt sugar) Glucose + galactose = lactose (milk sugar) Glucose + fructose = sucrose (table sugar, cane sugar) 8  Carbohydrates. C. Polysaccharides: Polymers of glucose; very large (1000s of linked monomers), insoluble à good for storage, lack sweetness; store high levels of energy 2 types: Starch: storage form of polysaccharide in plants (we consume); consists entirely of glucose monomers Glycogen: storage form of polysaccharide in animals (liver and muscles); also made of glucose monomers; more extensively branched than starch. 9  Carbohydrates Q: Why the body needs carbohydrates? I. Provide easy -ready to use- source of energy -When we eat, most of our food is carbohydrate à digested in small intestineà absorbed as monomers (glucose) in small intestine à goes to blood: (i) Part of it then go to cells à where it is broken down into H2O + CO2 +ATP (energy to power cell/body metabolism). (ii) Another part goes to liver (and muscles) for storage in the form of glycogen - If we do not eat for few hours or if glucose content in food is low à glycogen from liver is degraded into glucose à blood à cells à ATP production II. Small amount of carbohydrates is used for structural/ functional purposes in our cells and tissues; 1-2% of cell mass 10 is sugar.  Lipids Represent a unique group of hydrophobic molecules with diverse structures and functions both in plants and animals. Consist mostly of hydrocarbons (hydrogen & carbon atoms; few oxygen atoms = i.e., less oxidized than sugars, therefore, have lots of chemical energy. Example: tristearin C57H110O6. Most lipids are insoluble in water (hydrophobic); dissolve in organic solvents like alcohol and acetone. Types of lipids: 1. Triglycerides (most abundant in the body) 2. Phospholipids 3. Steroid 11 Table 2.5 Representative Lipids Found in the Body (1 of 2). 12 Table 2.5 Representative Lipids Found in the Body (2 of 2). 13 Triglycerides Phospholipids Steroid 14  Lipids (cont.) Triglycerides (neutral fats) Includes fat (in animals) and oil (in plants). Large molecules (not polymers) constructed from two kinds of molecules 1 glycerol (3 carbon alcohol with 3 OH groups) + 3 fatty acid (long hydrocarbon chain with carboxyl group) O ester bonds CH 2 OH HO C (CH 2)14CH3 O O CH2 O C (CH 2)14CH 3 + H 2O CH OH + HO C (CH 2)14CH3 O O CH2 OH HO C (CH2)14CH3 CH O C (CH 2)14CH 3 + H 2O glycerol palmitic acid (a fatty acid) O CH 2 O C (CH 2)14CH 3 + H 2O 15  Lipids (cont.) Fatty Acids Fatty acids are long hydrocarbon chain molecules that contain a polar carboxyl head group attached to a nonpolar hydrocarbon Tail (Head – hydrophilic; Tail – hydrophobic) Saturated: no double bonds between carbons, solid at room temperature, in animal fat. Unsaturated: contain one or more double bonds within chain, liquid at room temperature, in plants. 16  Lipids (cont.) Functions of triglycerides Compact energy storage Insulation (subcutaneous fat) Cushions internal organs Trans Fat: are oils that have been solidified by addition of hydrogen atom at the sites of double bonds (margarines). Omega-3 fatty acids: found in cold-water fish, decrease risk of heart disease. 17 Figure 2.15b Lipids. Lipids (cont.) Phospholipids Polar “head” Nonpolar “tail” (schematic phospholipid) Phosphorus-containing Glycerol 2 fatty acid chains group (polar head) backbone (nonpolar tail) (b) Typical structure of a phospholipid molecule (phosphatidylcholine). Two fatty acid chains and a phosphorous-containing group are attached to a glycerol backbone. Important structural component of cell membrane 18  Lipids (cont.) Phospholipids in water spontaneously assemble into micelles and phospholipid bilayers (and liposomes). In these structures, the nonpolar, hydrophobic tails are tucked away from contact with water, and the polar, hydrophilic heads of the phospholipids are facing the aqueous environment. Cell membranes are made of phospholipids and are also bilayers 19  Lipids (cont.) Steroids Characterized by the presence of a carbon skeleton consisting of 4 interconnected rings Cholesterol is a precursor of all steroid hormones (e.g. sex hormones). Also present in cell membranes, where they regulate membrane fluidity. Different steroids differ in functional groups attached Examples: Cholesterol Estradiol Progesterone Progesterone 20  Proteins (cont.) Proteins are polymers formed by monomers called amino acids. Amino acids consist of an asymmetric carbon bonded to 4 different covalent partners: Amino group: basic part Carboxyl group: Acidic part Hydrogen atom R (side chain group) All amino acids are identical except for the R group. Accordingly, there are 20 amino acids in proteins 21 22  Amino Acids Amine Acid group group (a) Generalized (b) Glycine is (c) Aspartic acid (d) Lysine (a (e) Cysteine (a structure of the simplest (an acidic basic amino basic amino all amino amino acid. amino acid) acid) has an acid) has a acids. has an acid amine group sulfhydryl group (—COOH) (—NH2) in the (—SH) group in in the R group. R group. the R group, which suggests that this amino acid is likely to participate in intramolecular bonding. Figure 2.17 Amino acid structures. 23  Structural levels of proteins – Primary structure – Secondary structure Alpha helix Beta-pleated sheet – Tertiary structure – Quaternary structure 24 Figure 2.18a The four levels of protein structure. Primary structure Ala Ala Glu Leu Ala Cys Ala Met Lys Aps Arg His Gly Leu Amino acids (a) Primary structure. A protein’s primary structure is the unique sequence of amino acids in the polypeptide chain. Amino acids are linked with each other by covalent bond known as Peptide Bond. 25  Hydrogen bonds Secondary structure 𝛃-pleated sheet Alpha-helix Secondary structure (b) Secondary structure. Two types of secondary structure are the alpha-helix and beta-pleated sheet. Secondary structure is reinforced by hydrogen bonds, represented by dashed lines in the figure. 26 Figure 2.18b The four levels of protein structure.  Tertiary structure Polypeptide (single subunit) (c) Tertiary structure. The overall three-dimensional shape of the polypeptide or protein is called tertiary structure. It is reinforced by chemical bonds between the R-groups of amino acids in different regions of the polypeptide chain. Figure 2.18c The four levels of protein structure. 27  Quaternary structure Complete protein, with four polypeptide subunits (d) Quaternary structure. Some proteins consist of two or more polypeptide chains. For example, four polypeptides construct hemoglobin, the blood protein. Such proteins have quaternary structure. Figure 2.18d The four levels of protein structure. 28 29 A tertiary structure of protein showing alpha-helix and Beta sheet segments. 30  Types of proteins based on shape / function Fibrous proteins: mostly known as structural proteins appearing in different body tissues. Could be secondary, tertiary or quaternary. Examples include collagen (in bone, tendons), keratin (skin, hair and nails). Globular proteins (Functional Proteins): compact spherical molecules, water soluble, carry out different functions (enzymes, hemoglobin, antibodies, hormones, signaling receptors etc.) The protein conformation is stabilized by hydrogen bonds, covalent bonds, ionic bonds, etc. However, changes in temp, pH, and salt concentration may lead to lose of three- dimensional structure. In this case the protein is said to be denatured (denaturation : unfolding of protein with resultant loss of function). Examples: Hemoglobin loses function when pH is acidic Pepsin become inactivated when the pH become alkaline. 31  Types of proteins based on shape / function Heme group Globin protein Fibrous proteins Globular proteins Triple helix of Hemoglobin molecule composed of collagen (a fibrous or the protein globin and attached structural protein heme groups. (Globin is a globular or functional protein.) 32  Proteins Types and Functions of proteins Structural proteins (support: e.g. silk, collagen, keratin... etc.) storage proteins (ovalbumin in eggs, zeins in corn seeds, casein in milk, etc...) transport proteins (O2 by hemoglobin, ion transporters in cell membrane) hormonal proteins (coordination of organism's activities: e.g. insulin, glucagon, etc...) receptor proteins (response of cell to chemical stimuli: e.g. neurotransmitter receptors, hormone receptors, etc...) contractile proteins (involved in movement, e.g. actin and myosin.) defense proteins (protection against disease, e.g. antibodies) Enzymatic proteins (most crucial of functions; selective acceleration of chemical reactions) 33 Table 2.6 Representative Classes of Functional Proteins. 34  Enzymes Enzymes are globular protein that function as biological catalysts in biochemical reactions. A catalyst is a substance that increase the rate of reaction without being affected by reactants or product and are: Highly specific Highly efficient Not consumed in the reaction The catalytic activity is based on presence of active site to which a substrate (that needs to react or be changed) binds. Enzymes are named according to the type of reaction they catalyze: hydrolase à hydrolysis reaction polymerase à polymerization reactions phosphatase à removes a phosphate group ……………. etc. – Enzymes in our bodies stay inactive except when needed à can be activated or inactivated by complex mechanisms 35  Enzyme-Substrate Reactions Product (P) Energy is e.g., dipeptide Substrates (S) Water is e.g., amino acids absorbed; Peptide released. bond is bond formed. H2 O Active site Enzyme-substrate complex (E-S) Enzyme (E) 1 Substrates bind at active 2 The E-S complex Enzyme (E) site, temporarily forming an undergoes internal 3 The enzyme enzyme-substrate complex. rearrangements that releases the product form the product. of the reaction. Figure 2.20 A simplified view of enzyme action. 36  Nucleic acids (genetic material) Nucleic acids encode the genetic information (i.e. primary structure of proteins). Information flow proceeds from DNA to RNA to protein. This is called "central dogma". 2 types of nucleic acids 1. Deoxyribonucleic acid (DNA) - deoxyribose sugar - double stranded (helix) - have thymine rather than uracil 2. Ribonucleic acid (RNA) - ribose sugar - single stranded - uracil instead of thymine - three varieties: mRNA, rRNA, tRNA. 37  Structure of nucleic acids The building blocks of nucleic acid, whether DNA or RNA, are called nucleotides A nucleotide consists of: (1) pentose sugar (2) nitrogen base (3) phosphate group (PO4-) 1. The sugar (ribose or deoxyribose) 2. The nitrogen base: Come in two types either a: purine (2 ring structure) or pyrimidine (1 ring structure) 38 Figure 2.21a Structure of DNA. Nucleotide Structure Deoxyribose Phosphate sugar Adenine (A) (a) Adenine nucleotide (Chemical structure) 39 21.1 DNA and RNA structure and function DNA structure The phosphate-sugar backbones are oriented in different directions. The strands are antiparallel: the carbons are numbered as 3’-5’ and 5’-3’ directions Base-pairing and the double- stranded helix: In DNA, a purine can only bases pairs with a pyrimidine à T base pairs with A (Complementary bases) => A=T note the 2 hydrogen bonds between the 2 bases C base pairs with G (Complementary bases) => C≡G note the 3 hydrogen bonds between the 2 bases Note A base sequence of ATGA on one chain is bonded to a complementary base sequence TACT on the other strand. 41 Figure 2.21d Structure of DNA. Hydrogen bond Deoxyribose sugar Phosphate KEY: Thymine (T) Adenine (A) Cytosine (C) Guanine (G) (d) Diagram of a DNA molecule 42 21.1 DNA and RNA structure and function RNA structure and function Single-stranded Composed of repeating nucleotides Sugar-phosphate backbone (Ribose-phosphate) Bases are A, C, G and uracil (U) Three types of RNA – Ribosomal (rRNA): Produced in nucleolus by DNA, joins with proteins to form ribosomes – Messenger (mRNA): Produced from DNA in nucleus, carries genetic information from DNA to the ribosomes in cytosol – Transfer (tRNA): Produced in nucleus, transfers amino acids to a ribosome where they are added to a forming protein. – Each tRNA binds with one amino acid (at least 20 different types of tRNA) 21.1 DNA and RNA structure and function RNA structure  DNA vs. RNA structural differences Functional differences: DNA is the genetic material, genes consist of DNA RNA mainly serves as an intermediate language during the translating of DNA (genetic) language into protein 45 21.1 DNA and RNA structure and function Comparing DNA and RNA Similarities: Differences: – Are nucleic acids – DNA is double stranded while – Are made of nucleotides RNA is single stranded – Have sugar-phosphate – DNA has T while RNA has U backbones – RNA is also found in the – Are found in the nucleus cytoplasm as well as the nucleus while DNA is not – Deoxyribose in DNA and Ribose in RNA Adenosine Triphosphate (ATP) We consume glucose Glucose metabolism (C6H12O6) (cellular respiration) 6 CO2 (g) + 6 H2O + ATP 47 ATP: structure and hydrolysis 48 Figure 2.23 Three examples of how ATP drives cellular work. P Pi A ADP ATP B A B Pi (a) Chemical work. ATP provides the energy needed to drive energy-absorbing chemical reactions. Solute Three examples of ADP ATP how ATP drives Pi cellular work Membrane P Pi protein (b) Transport work. ATP drives the transport of certain solutes (amino acids, for example) across cell membranes. ADP ATP Relaxed smooth Contracted smooth Pi muscle cell muscle cell (c) Mechanical work. ATP activates contractile proteins in muscle cells so that the cells can shorten and perform mechanical work. 49