Chapter 2 - Chemical Principles PDF

Chapter 2 Chemical Principles Learning Objectives  Chapter 2- Vocabulary atom molecules electrons neutrons atomic number; atomic weight element Isotopes electron shell energy levels valence Why is chemistry so important in studying microbiolog...

Chapter 2 Chemical Principles Learning Objectives  Chapter 2- Vocabulary atom molecules electrons neutrons atomic number; atomic weight element Isotopes electron shell energy levels valence Why is chemistry so important in studying microbiology? essential to understand cellular structure and function of microorganisms: many of the pathogenic effects of infectious diseases occur at the molecular level. to understand the infection process, you need to understand basic chemistry. Life on earth is based on chemical reactions: You need to understand how cells and tissues are constructed and how they function. The construction and function of cells and tissues play a role in infection. Biological level of organization: Atoms Molecules Cells Tissues ?.....organs.... ?........organ systems. ?.........organism  The structure of atoms element consists of only one type of particles:  atom: smallest unit of an element  same properties of that element  subatomic particles: – Electron – Proton – Neutron  Atom (cont.) atomic nucleus – center - protons and neutrons electrons move in orbitals (3-D space) - energy: electron energy neutral atom – number of electrons equals number of protons  Atom (cont.) Atoms of elements of living organisms Electron configuration: shells occupied by electrons first shell can hold 2 electrons second shell can hold 8 electrons valence shell:  valence electron(s) - outermost ring - the most energetic  chemical properties of an atom is largely determined by valence electrons  Atoms (cont.) Atomic number - fixed number of protons in the atomic nucleus examples: 1 H or 8O  Atoms (cont.) Atomic weight (mass): mostly mass of protons + neutrons unit: atomic mass unit (AMU) or dalton Particle Charge ~Mass Location Proton Positive 1 amu Nucleus Neutron Neutral 1 amu Nucleus Electron Negative ~1/1800 amu Outside nuc.  Chemical Element - all atoms with the same number of protons behave the same way chemically. - pure substance - one type of particles (atoms)  chemical symbol Some of the chemical elements found in living things  Chemical Element (cont.) Most elements have several isotopes: Isotopes of the same element – atoms of the same element same number of protons 1H; 2H ; 3H (all with1proton) different number of neutrons atomic masses are different  Elements (cont.) Carbon Isotopes same number of protons (all with 6 protons) different number of neutrons atomic masses are different  Elements (cont.) radioisotope unstable isotope breaks down or decays into a more stable isotope radiation is emitted example: 14 C decays to 14N applications: medicine (diagnosis, treatment) biological research Atoms form molecules: chemical bonds https://www.youtube.com/watch?v=lIgLgMnl-1I  Chemical Bonds Forces of attraction hold atoms together: objective: obtain full valence shell; acquire stable electronic configuration. chemical bond - chemical energy; bond energy = energy required to break a chemical bond ways atoms form bonds: gaining, losing or sharing outer electrons  Types of Chemical Bonds 1. Covalent bonds (stronger than ionic bonds) - electrons (pairs) are shared between atoms a molecule is formed: hydrogen gas (H2)  Chemical Bonds (cont.) Types of covalent bonds: Share one single pair of electrons Share two pairs of electrons Share three pairs of electrons  Chemical Bonds (cont.) 2. Ionic bonds atom gains or looses 1 or more electrons becomes an ion ion: electric charge  Ionic bond (cont.) 1) cation loses electrons - becomes positively charged - examples: K+, Na+, Ca2+ 2) anion gains electrons - becomes negatively charged - examples: Cl-, I-  How is an ionic bond formed? attraction - 11 protons and 11 electrons - 17 protons and 17 electrons - one electron in the outer shell - seven electron in the outer shell - electron donor: looses 1 - electron acceptor: gains 1 electron electron - overall positive charge (Na+) - overall negative charge (Cl-)  Chemical Bonds (cont.) 3. Hydrogen bond  relatively weak bonds  easily formed and broken - water molecule attraction: atom with a partial negative charge and a hydrogen atom that is covalently bonded to oxygen or nitrogen  Hydrogen bond (cont.)  very important in living organisms: - DNA and protein (besides of water) Nitrogenous bases  Chemical Reactions making or breaking of chemical bonds: - same total number of atoms - rearranged into new molecules with different properties example: two oxygen atoms combine chemically to form a stable molecule of oxygen  Chemical Reactions Example: oxygen and hydrogen atoms combine chemically to form a stable molecule of water  Chemical Reactions  energy is required to break or form bond  chemical equations  chemical Reactions - activation energy endergonic reaction: absorbs energy exergonic reaction: releases energy Chemical reactions common to living organisms: Synthesis Reactions atoms, ions, or molecules combine to form new, larger molecules a new bond is formed anabolism is the synthesis of molecules in a cell Chemical reactions common to living organisms: Synthesis Reactions aminoacids combining to form proteins nucleotides combining to form acid nucleics sugars combining to form carbohydrates (starch, cellulose) Chemical reactions common to living organisms: Decomposition Reactions Occur when a molecule is split into smaller molecules, ions, or atoms Catabolism are decomposition reactions in a cell Chemical reactions common to living organisms: Decomposition Reactions breakdown of sucrose (table sugar) into glucose and fructose (simple sugars) bioremediation: breakdown of pollutants  Chemical reactions common to living organisms: Exchange Reactions Are part synthesis and part decomposition 1) AB + CD------------AD + BC reactants products - bonds of AB and CD are broken by decomposition - bonds between A,D and B,C are formed (synthesis)  The Reversibility of Chemical Reactions can readily go in either direction the end product can revert to the original molecules product or reactant may not be stable direction may be determined by special conditions  Important Biological Molecules Organic compounds always contain carbon and hydrogen; structurally complex Inorganic compounds typically lack carbon; usually small and structurally simple Important elements constituents of living systems  Important inorganic molecules : water https://www.youtube.com/watch?v=njWsfApthXc large mass of most organisms (65 to 75% of every cell) ~60% of our total body weight (average) ~75% of the Earth’s surface covered by liquid water photosynthesis; oxygen in air hydrogen atoms as part of many organic compounds  Properties of Water Molecules Inorganic molecule It’s unique properties are essential to life polar molecule: – unequal distribution of positive and negative charges – useful medium for living cells  Properties of Water Molecules Polarity:  One molecule of water links to 4 other water molecules through hydrogen bonds  Properties of Water Molecules (cont.) Polarity:  strong attraction between water molecules makes it a good temperature buffer  good solvent (dissolving medium) - polar substances undergo dissociation (separation) in water, forming solutes Figure 2.5 How water acts as a solvent for sodium chloride (NaCl).  Properties of Water Molecules (cont.) Polarity: reactant or product in many chemical reactions - splitting and rejoining of hydrogen ions and hydroxide ions  Inorganic molecules: Acids, Bases, and Salts (cont.) Acid: substance that dissociates into one or more H+ (protons) and one or more negative ions (anions) Or proton donor - HCl H+ + Cl− Hydrogen ion: H+  Inorganic molecules: Acids, Bases, and Salts Base: Substance that dissociates into one or more OH− (hydroxide) ions NaOH Na+ + OH− Hydroxide ion: OH− Hydroxide ions can accept or combine with protons and one or more positive ions (cations)  Inorganic molecules: Acids, Bases, and Salts (cont.) Salts: Substances that dissociate into cations and anions, neither of which is H+ or OH− NaCl Na+ + Cl−  Acid-Base Balance: The Concept of pH What is pH? - the concentration of H+ in a solution - pH = –log10[H+] – increasing [H+] increases acidity – increasing [OH−] increases alkalinity Organisms: pH must be maintained close to constant - too low or too high acid or base negatively affects enzyme activity most grow best between pH 6.5 and 8.5  pH scale 0 Figure 2.7 The pH scale. 1 Stomach acid H+ 2 Lemon juice Increasingly ACIDIC OH– 3 Grapefruit juice Wine Acidic solution 4 Tomato juice 5 6 Urine Milk NEUTRAL Pure water 7 [H+] = [OH–] Human blood 8 Seawater Neutral solution Increasingly BASIC 9 10 11 Milk of magnesia Household ammonia 12 Household bleach 13 Oven cleaner Basic solution 14 Limewater Watch Videos - Basic Chemistry Concepts Part I: https://www.youtube.com/watch?v=iLn1KaFMJj8 https://www.youtube.com/watch?v=MYuh5yErdfA https://www.youtube.com/watch?v=Juw7HBg0zZs NOTE: This is your last slide for chapter 2-part1  Important Biological Molecules Chapter 2-part 2 (begins here) Specific learning objectives: Define and distinguish organic from inorganic compounds Briefly explain the chemistry behind carbon’s affinity for covalently bonding in organic compounds Identify types of organic molecules essential to human functioning Define functional group Discuss the structure of carbohydrates, lipids, proteins, nucleic acids and ATP and their importance in human functioning Important Biological Molecules  Important Biological Molecules Organic compounds:  always contain carbon and hydrogen; structurally complex - form molecules with many different shapes.  Organic compounds: structure and chemistry  Chain of carbon atoms - carbon skeleton  most bonded to hydrogen atoms hydrocarbon  Structure and Chemistry C can bind to hydrogen and other elements such as oxygen and form Functional groups Determine “chemical and physical properties of a particular organic compound  Structure and Chemistry Different functional groups confer different properties” of a particular organic compound Functional group of alcohols : hydroxyl group Is hydrophilic Alcohols In general  functional groups in an amino acid Amino Carboxyl group group  Structure and Chemistry Macromolecules: carbohydrates, lipids, proteins and nucleic acids small organic molecules together (units-monomers) large molecules - polymers - many repeating small units bond by covalent bonds - dehydration synthesis or condensation reaction :  1. Carbohydrates cell structures and cellular energy sources sugars and starches C, H, and O with the formula (CH2O)n many are isomers – same chemical formula, but different structures: (C4H10)  Monosaccharides simple sugars with 3-7 carbons examples:  Disaccharides 2 monosaccharides joined in a dehydration synthesis or condensation reaction  Disaccharides Can be broken down into two units by hydrolysis  Polysaccharides tens or hundreds of monosaccharides joined through dehydration synthesis – polymers of glucose Monomers of  2. Lipids cell membranes – structure and functions energy storage (other cells) C, H, and O nonpolar insoluble in water; dissolve in non polar solvents Polar Nonpolar covalent bonds, with equal sharing of the bond electrons, arise when the electronegativity of the two atoms are equal.  Lipids (cont.) Glycerol (alcohol) 1 or more fatty acids; formed by dehydration synthesis Glycerol Carboxyl- COOH group Fatty acid Hydrocarbon (C15H31COOH) Chain (C and H only)  2. Lipids mono, di (glyceride (s)) Determined by number of fatty acids  2. Lipids fats or triglycerides - glycerol and 3 fatty acids; by dehydration synthesis Structural formulas of simple lipids. Ester linkage Glycerol Palmitic acid (saturated) Oleic acid (C15H31COOH) (unsaturated) (C17H33COOH) + H2O + H2O Stearic acid (saturated) (C17H35COOH) + H2O cis configuration Molecule of fat (triglyceride)  Simple Lipids saturated fat: no double bonds in the fatty acids unsaturated fat: one or more double bonds in the fatty acids  Complex Lipids Phospholipids contain C, H, and O + P, N, and/or S cell membranes glycerol, two fatty acids, and a phosphate group polar as well as nonpolar regions Phospholipid structure: Cell membrane  Steroids four carbon rings with an –OH group attached to one ring Part of cell membranes (plasma membrane and organelle membranes) - keep the membranes fluid (maintain structure and functionality) Cholesterol, a steroid.  3. Proteins made of C, H, O, N, and sometimes S subunits are amino acids cell structure and function: – enzymes – antibodies – transporter proteins – flagella – some bacterial toxins and cell structures  Amino Acids alpha-carbon, attached: – carboxyl group (–COOH) – amino group (–NH2) – side group  Peptide Bonds amino acids joined by peptide bonds (dehydration synthesis) carboxyl amino  Protein structure Peptide bonds Primary structure: polypeptide strand (amino acid sequence) Hydrogen bond Hydrogen bond Secondary structure: helix and pleated sheet (with three polypeptide strands) Helix Pleated sheet Tertiary structure: helix and pleated Disulfide sheets fold into a 3D shape bridge Quaternary structure: the relationship of several folded polypeptide chains, forming a protein  Levels of Protein Structure conjugated proteins consist of amino acids and other organic molecules (non polypeptide or non-pro­tein ) – glycoproteins – nucleoproteins – lipoproteins  5. Nucleic Acids Units are nucleotides – five-carbon (pentose) sugar – phosphate group – nitrogen - containing (purine or pyrimidine) base  DNA deoxyribonucleic acid – deoxyribose (sugar) – double helix: two chains – base pairing:  adenine – thymine (2H-bonds)  cytosine – guanine (3H-bonds) genetic instructions of organisms The Structure of DNA.  RNA ribonucleic acid – ribose (sugar) – single-stranded – base pairing: Adenine (A) – Uracil (U) (no thymine; replaced by Uracil) Cytosine (C) – Guanine (G) several kinds of RNA play a specific role in protein synthesis  RNA. Uracil (U) Phosphate Ribose  6. Adenosine Triphosphate (ATP) adenosine triphosphate stores the chemical energy released by some chemical reactions releases phosphate groups by hydrolysis to liberate useful energy for cell work. ribose, adenine, and three phosphate groups Check Your Understanding: Distinguish organic and inorganic compound. Define functional group, be able to identify some of the functional groups. Know the two functional groups in all amino acids. Identify the building blocks of carbohydrates. Understand the difference and give an example of a monosaccharide, a disaccharide, and a polysaccharide. Check Your Understanding: Differentiate simple lipids, complex lipids, and steroids. Identify the building blocks and structure of proteins. Identify the building blocks of nucleic acids. Differences between DNA and RNA. Understand the role of ATP in cellular activities. Case Study: A Fussy Baby The alarm clock was set to go off at 6:00 am. Staring at it, Harold saw it change from 5:58 to 5:59 am. He reached over and turned it off, gently shook Naomi awake, then grabbed the video monitor to check on Amica. He was relieved to see his daughter was still asleep. Amica had passed a rough night, waking up on multiple occasions. Two weeks earlier, Naomi had noticed small, irregular, white patches inside of Amica’s mouth. She had become increasingly irritable, only breastfeeding or taking the bottle for short periods. Naomi experienced discomfort while nursing Amica, so she purchased some over-the-counter ointment. Five days ago, the patches in Amica’s mouth returned and both Naomi and Amica were more irritable. Amica kept on spitting out the pacifier that Harold gave her. At his wits’ end, Harold searched the Internet for answers after he returned Amica to her crib for the fifth time that night. He came across pictures of similar-looking patches in the mouths of babies. Case Study: A Fussy Baby Harold also mentioned the increased discomfort that Naomi had experienced during breastfeeding recently. “You are right, this is thrush,” said Dr. Warner. “Everybody has microbes in their mouth, including the organism that causes thrush. In healthy people the growth of the yeast, Candida albicans that causes thrush is kept in check by other microbes living in the mouth.” “Also,” continued Dr. Warner, “milk is such a rich source of organic compounds such as carbohydrates and proteins, the very nutrients that the yeast uses to grow.” “So why did the microbes in Amica’s mouth not prevent this overgrowth?” asked Harold. “Is she sick?” “No, she is not sick. Infants just have an underdeveloped microbiome in their mouth. It takes time for the balance to be established. If Naomi experiences discomfort during breastfeeding, she probably has the yeast on her skin and it gets passed back and forth between Naomi and Amica. Both should be treated at the same time.” “Naomi has been using ointments” said Harold. “I know” said Dr. Warner. “She should stop for now. Most of the time thrush disappears on its own, but since you say it’s been going on for two weeks now, I will prescribe something and give you instructions for both Naomi and Amica so they can both get better.” “And what about the diaper rash?” asked Harold. “The diaper rash is caused by the same microbe. Make sure to keep the diaper area as dry as possible and wash your hands thoroughly before and after diaper changes. You may use a wet wash cloth to wipe Amica’s tongue gently after feeding to remove excess milk.” replied the Dr. Warner. Questions 1.Could the patches in Amica’s mouth, and Noami’s discomfort be related? 2.What is the role of carbohydrates and proteins in cells?