Molecules of Life - Biology Textbook - PDF

The Molecules of Life Chapter 2  In this chapter we will study Elements and atom Chemical bonds and reactions Water, pH and buffers Organic molecules A Glimpse of History Beijerinck isolated nitrogen-fixing microorganisms called rhizobia from the root nodules of legumes What...

The Molecules of Life Chapter 2  In this chapter we will study Elements and atom Chemical bonds and reactions Water, pH and buffers Organic molecules A Glimpse of History Beijerinck isolated nitrogen-fixing microorganisms called rhizobia from the root nodules of legumes What is nitrogen and why is it important? 2.1- Elements and Atoms Describe the general structure of an atom and its isotopes. Describe the importance of valence electrons.  Elements and Atoms – Table 2.1 Elements consist of only one type Atom Symbol Atomic Mass Number Number Number of of atom (Numbe (Proton Covalen Cannot be chemically r of s+ t Bonds separated into simpler parts Protons Neutron Formed Living matter primarily composed ) s) of six elements Hydroge H 1 1 1 n Carbon (C), hydrogen (H), Carbon C 6 12 4 oxygen (O), nitrogen (N), phosphorus (P), sulfur (S) Nitrogen N 7 14 3 Oxygen O 8 16 2 Phosphor P 15 31 3 us Sulfur S 16 32 2 Atom: basic unit of matter Three major components Neutrons: uncharged particles Protons: positively charged particles Electrons: negatively charged particles A “neutral” atom has equal numbers of protons and electrons therefore it has no charge. Atomic Structure – Figure 2.2-a and b Atomic number is number of protons in nucleus Mass number is sum of protons and neutrons (electrons too light) Periodic table  The Role of Electrons – Figure 2.2c Electrons move in a cloud around the nucleus Precise location is impossible to determine Most likely to be in specific regions called shells Shells closer to nucleus fill first Innermost shell can hold up to 2 electrons Biological molecules are most stable with 8 electrons in outer shell (“octet rule”) Electrons farther from nucleus have higher energy level Valence electrons are those in outer shell Isotopes – Figure 2.3 Isotopes of an element have different numbers of neutrons Atomic mass is the average of mass numbers of atoms of an element Energy emitted from radioactive isotopes may be useful in diagnosis A scan of thyroid gland shows location of radioactive iodine 2.2- Chemical Bonds and Reactions Compare and contrast ionic bonds, covalent bonds, and hydrogen bonds. Explain the role of an enzyme in chemical reactions. Chemical Bonds and Reactions Atoms lose, gain, or share valence electrons to achieve a more stable state Basis for chemical bond formation Three main types of chemical bonds: Ionic bonds Covalent bonds Hydrogen bonds Ions and Ionic Bonds – Figure 2.4 Ion: atom that has gained or lost electron(s) Anions gain electron(s) and are negatively charged Cations lose electron(s) and are positively charged Ionic bonds form because of attraction between negative and positive charges Produces salts also called electrolytes because they conduct electricity  Covalent Bonds 1 Covalent bonds form when atoms share electrons One pair of shared electrons equals to a single covalent bond Molecule: two or more atoms joined together by covalent bonds Compound: molecule containing atoms of different elements Carbon forms four covalent bonds Basis for many diverse structures Carbon bonds with hydrogen to form organic compounds Other compounds are inorganic compounds Covalent Bonds 2 Non-polar covalent bond: equal sharing of electrons Polar covalent bond: unequal sharing of electrons One atom more electronegative than the other Covalent Bonds3 Polar covalent bond- Figure 2.6 Polar covalent bond- Polar covalent bonds result in slight separation of charge Important in biological systems May result in formation of hydrogen bonds Molarity A mole is 6.02 X 1023 particles A mole of one substance has the same number of particles as a mole of any other Measured in grams Molarity (M) of a solution is the number of moles dissolved in 1 liter of the solution A 1 Molarity solution of NaCl is 58.44 grams of NaCl dissolved in 1 liter of aqueous solution Chemical Reactions 1 Chemical reactions transfer electrons, often involving making and breaking bonds Reactants are starting components of a reaction that are changed to products Synthesis reaction A + B → AB Decomposition Reaction AB → A + B Exchange AB  CD AC  BD reactions (reactants) (products) Hydrogen Bonds – Figure 2.7 Hydrogen bonds: weak bonds formed when a hydrogen atom in polar molecule is attracted to electronegative atom in same or another polar molecule May be short-lived, but numerous bonds add strength Velcro analogy  Oxidation-Reduction Reactions – Figure 2.8 Reactions in which electrons are transferred from one reactant to the other are called oxidation-reduction (redox) reactions The reactant that loses electrons is oxidized The reactant that gains electrons is reduced Reactants that typically lose electrons in a redox reaction are called reducing agents – reactants that typically lose electrons oxidizing agents -reactants that typically gain electrons Enzymes Most biologically important chemical reactions would occur too slowly to be useful to a cell Enzymes are biological catalysts that speed the rate of reactions bind to one or more reactant molecules Position them in such a way that certain bonds are more likely to be broken or to form Reactants in enzyme-catalyzed reactions are referred to as substrates 2.3- Water, pH, and Buffers Describe the properties of water and explain why it is so important in biological systems. Explain the concept of pH, and how the pH of a solution relates to its acidity. Describe the role of buffers and neutralization. Water, pH, and Buffers – Figure 2.9 Water (H2O) is a polar molecule Hydrogen bonding explains properties Liquid: hydrogen bonds continually form and break, allowing molecules to slide over one another Solid: each water molecule forms 4 hydrogen bonds with surrounding water molecules producing a less dense structure called ice  Water – Figure 2.10 Polar nature makes water an excellent solvent in which solutes are dissolved Polar and charged substances are hydrophilic (“water loving”); dissolve in water Non-polar substances are hydrophobic (“water fearing”); do not dissolve in water Water with dissolved substances freezes at lower temperatures  pH of Aqueous Solutions – Figure 2.11 pH is a measure of acidity (H+ concentration) Water (H2O) tends to split into H+ ions and OH− ions Pure water has equal concentrations of H+ and OH- ions at pH = 7, molarity 10-7 Acids increase H+ concentration (pH < 7), bases decrease it (pH > 7) Each pH unit (0 to 14) represents ten-fold change in H+ concentration Buffers Buffer: a chemical that helps to maintain a relatively constant pH of a solution Base added: buffer releases H+ Acid added: buffer combines with H+ Buffers important to action of enzymes that may change shape when pH changes Neutralization of acids and bases When an acid and a base react to form water and a salt and involves the combination of H+ ions and OH- ions to generate water, it is called a neutralization reaction. 2.4- Organic Molecules Describe the characteristics of the different types of carbohydrates. Compare and contrast the structure and function of simple lipids, compound lipids, and steroids. Describe the factors that affect protein structure and function. Compare and contrast the chemical compositions, structures, and major functions of DNA, RNA, and ATP. Organic Molecules 1 Organic molecules contain carbon and hydrogen Each carbon atom forms four covalent bonds, so an incredible assortment of organic molecules exists Covalent bonds joining carbon atoms within an organic molecule may be single, double, or triple Organic molecules are often macromolecules Different classes of macromolecules are made up of different monomers The four major classes of organic molecules are carbohydrates, lipids, proteins, and nucleic acids Organic Molecules – Figure 2.12 Polymers are macromolecules made by joining monomers (subunits) Dehydration synthesis Removes water and joins monomers to build polymers Hydrolysis Requires water and breaks a polymer into monomers Organic Molecules 2 Carbon skeleton: arrangement of carbon atoms in organic molecule Functional groups attached to carbon skeleton contribute to molecule’s properties  Table 2.5 Biologically Important Functional Groups Functional Group Structure Where Found Aldehyde Carbohydrates Amino Amino acids, the subunits of protein Carboxyl Organic acids, including amino acids and fatty acids Hydroxyl Carbohydrates, fatty acids, alcohol, some amino acids Keto Carbohydrates, polypeptides Methyl Some amino acids, attached to DNA Phosphate Nucleotides (subunit of nucleic acids), ATP, signaling molecules Sulfhydryl Part of the amino acid  Major Classes of Organic Molecules – Table 2.4 Chemical Function Chemical Carbohydrat Monosaccharides Structural component of cell es walls; energy source Lipids Varies—subunits are not Important component of cell always similar membranes Proteins Amino acids Enzyme catalysts; structural portion of many cell components Nucleic Nucleotides acids DNA Deoxyribonucleotides Carrier of genetic information RNA Ribonucleotides Various roles in protein Carbohydrates – Figure 2.13 Diverse group includes sugars and starches Energy source Energy storage Carbon source Component of DNA and RNA Structural components of cells Carbon, hydrogen, oxygen in 1:2:1 ratio Building block: CH2O  Monosaccharides – Figure 2.14 Monosaccharide: basic unit of carbohydrates 5-carbon sugars include ribose, deoxyribose 6-carbon sugars include glucose, galactose, mannose, fructose Structural isomers: same atoms, but different arrangement Distinct sugars with different properties Disaccharides – Figure 2.15 Disaccharides composed of two monosaccharides Common disaccharides Sucrose (glucose + fructose) Lactose (glucose + galactose) Maltose (glucose + glucose) Dehydration synthesis forms covalent bond between hydroxyl groups of monosaccharides Hydrolysis breaks bond and yields two monosaccharides Polysaccharides – Figure 2.16 Polysaccharides are chains of monosaccharides Structural diversity from branching, linkages Important polymers of glucose: Cellulose Starch Glycogen Dextran Chitin, agar also important Lipids Lipids are non-polar, hydrophobic molecules Diverse group defined by slight solubility in water Important in structure of membranes Not all lipids are composed of similar subunits  Simple Lipids - Figure 2.17 Fatty acids are linear carbon skeletons with a carboxyl group (—COOH) at one end Saturated fatty acids No double bonds Tails pack tightly so solid at room temperature Example- butter, lard Unsaturated fatty acids Double bonds between carbon atoms Kinks prevent tight packing so liquid at room temperature (oils)  Simple Lipids – Figure 2.18 Triglycerides: most common simple lipids Fats or oils composed of three fatty acids linked to glycerol Fatty acids: linear chains of bonded C, H atoms with carboxyl group at one end  Simple Lipids Most natural fatty acids are cis: hydrogens attached to same side of double bond Trans: hydrogens on opposite sides of double bond (linked to certain health problems) Proteins Composed of one or more Functions and examples chains subunits called amino Catalysis- Enzymes acids. Transport- Hemoglobin The chains vary in length Signal reception- receptors among different proteins Regulation, communication- Folded into complex three- hormones dimensional Motility- actin, myosin Proper folding is crucial to a protein’s function Support- collagen Proteins have the most Energy storage- albumen, casein number of functions Buffer- albumin  Amino Acids – Figure 2.21 Proteins composed of amino acid subunits Amino acids share common structure Central carbon, carboxyl group, amino group Side chain (R group) differs Infinite possible combinations of 20 amino acids Protein characteristics depend mainly on shape Shape determined by amino acid sequence Amino Acids All amino acids except glycine exist as optical isomers Mirror images, but may have different properties Most proteins are composed only of L-amino acids Bacteria also utilize D- amino acids 20 Amino Acids Figure 2.22 Peptide Bonds – Figure 2.23 Protein Structure – Figure 2.24 Protein Structure Primary structure: sequence and number of amino acids Secondary structure: localized coiling (helix) or folding (pleated sheet) largely due to hydrogen bonding Tertiary structure: overall 3–dimensional shape of folded polypeptide largely due to interactions between R groups Chaperone may be needed to help with correct folding Quaternary structure: association between multiple polypeptide chains Protein domain: stable substructure associated with a specific function Protein Domains – Figure 2.25 Protein Denaturation – Figure 2.26 When a protein loses its characteristic shape, it is denatured Can be caused by high temperature, extreme pH, certain solvents Protein may become nonfunctional Enzymes function best within narrow range of conditions Nucleic Acids – Figure 2.27 Nucleic acids carry genetic information in sequence of nucleotides Nucleotides are composed of Pentose sugar Phosphate group Nucleobase Nucleic Acids – Figure 2.28 Nucleobases include Purines: adenine (A), guanine (G) Two fused rings Pyrimidines: cytosine (C), thymine (T), uracil (U) Single ring structure Uracil (U) found only in RNA Nucleic Acids Figure 2.29 Deoxyribonucleic Acid (DNA) DNA is the genetic information needed to build and maintain a cell Typically, double-stranded, (composed of two nucleotide chains) The sequence of the nucleotides encodes the amino acid sequences of proteins A change in the DNA sequence that results in changing even a single amino acid in a protein can affect the protein function The pentose sugar in the nucleotides of DNA is DNA – Figure 2.30 RNA Ribonucleic acid (RNA) Several forms of RNA involved in protein synthesis Similar to DNA except: RNA is mostly single-stranded The sugar is ribose instead of deoxyribose Uracil is the nucleobase instead of thymine The Role of ATP – Figure 2.31 Adenosine triphosphate (ATP) Energy currency of cell Three negatively charged phosphate groups repel one another making bonds unstable High-energy phosphate bonds break and release energy to drive cellular processes  In this chapter we covered 2.1- Elements and atom Atom structure Atomic number, mass number, neutral atom Periodic table Isotopes 2.2- Chemical bonds and reactions Ionic bond Covalent bond- polar and non-polar Hydrogen bond Chemical reactions 2.3- Water, pH and buffers 2.4- Organic molecules Monomer vs polymer, dehydration synthesis, hydrolysis Carbohydrates, lipids, proteins, nucleic acids