Basic Chemistry of Life Part 2 PDF

Basic Chemistry of Life Part 2  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 (ch...

Basic Chemistry of Life Part 2  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 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 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. H2O 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. H2O Monomers linked by covalent bond  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).  Carbohydrates (cont.) Structure of Monosaccharides Monosaccharides (cont) 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)  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)  Carbohydrates. C. Polysaccharides: Polymers of glucose; very large (1000s of linked monomers), insoluble → 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.  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 → digested in small intestine→ absorbed as monomers (glucose) in small intestine → goes to blood: - (i) part of it then go to cells → 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 → glycogen from liver is degraded into glucose → blood → cells → ATP production II. Small amount of carbohydrates is used for structural/functional purposes in our cells and tissues; 1-2% of cell mass 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: the 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  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) 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. 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. 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  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  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  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)  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 Figure 2.17 Amino acid structures. 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.  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 heme structural protein groups. (Globin is a globular or functional protein.) Table 2.6 Representative Classes of Functional Proteins. 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 Are highly specific Are 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 → hydrolysis reaction polymerase → polymerization reactions phosphatase → removes a phosphate group ……………. etc. Enzymes in our bodies stay inactive except when needed → can be activated or inactivated by complex mechanisms Figure 2.20 A simplified view of enzyme action. Enzyme-Substrate Reactions Product (P) Energy is e.g., dipeptide Substrates (S) Water is absorbed; Peptide e.g., amino acids released. bond is bond formed. H2O 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.  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.  Structure of nucleic acids The building block of nucleic acid, whether DNA or RNA, 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) Figure 2.21a Structure of DNA. Nucleotide Structure Deoxyribose Phosphate sugar Adenine (A) (a) Adenine nucleotide (Chemical 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  Base-pairing and the double-stranded helix In DNA, a purine can only bases pairs with a pyrimidine → 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. Adenosine Triphosphate (ATP) We consume glucose Glucose metabolism (C6H12O6) (cellular respiration) 6 CO2 (g) + 6 H2O + ATP Figure 2.23 Three examples of how ATP drives cellular work. P Pi ADP ATP 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.