Microbiology: Basic and Clinical Principles PDF

Microbiology: Basic and Clinical Principles Second Edition Chapter 2 Biochemistry Basics Presented by Janet Dowding, Ph.D. St. Petersburg College Copyright © 2023 Pearson Education, Inc. All Rights Reserved Clinical Case Copyright © 2023 Pearson Education, Inc. All Rights Reserved From Atoms...

Microbiology: Basic and Clinical Principles Second Edition Chapter 2 Biochemistry Basics Presented by Janet Dowding, Ph.D. St. Petersburg College Copyright © 2023 Pearson Education, Inc. All Rights Reserved Clinical Case Copyright © 2023 Pearson Education, Inc. All Rights Reserved From Atoms to Macromolecules (1 of 2) After reading this section, you should be able to: • Define the term atom and identify an atom’s parts. • Determine the atomic mass, atomic number, and chemical symbol of an element using the periodic table. • Explain the difference between an anion and a cation and state how they are formed. • Describe isotopes and their importance in medicine. • Distinguish between a molecule, compound, and isomer. • Interpret and write a molecular formula. Copyright © 2023 Pearson Education, Inc. All Rights Reserved From Atoms to Macromolecules (2 of 2) After reading this section, you should be able to: • Differentiate between organic and inorganic compounds and identify selected functional groups. • Compare acids and bases and discuss their effects on pH. • Explain what the pH scale reflects and list its features. • Define the term buffer and state why buffers are important in biological systems. Copyright © 2023 Pearson Education, Inc. All Rights Reserved What Are Atoms? (1 of 4) • Atoms are the smallest units of elements, which are pure substances that make up ordinary matter. Copyright © 2023 Pearson Education, Inc. All Rights Reserved What Are Atoms? (2 of 4) • The center of an atom is called the atomic nucleus and contains protons and neutrons • Around the nucleus is a cloud of electrons Copyright © 2023 Pearson Education, Inc. All Rights Reserved What Are Atoms? (3 of 4) • Protons are positively charged particles • Neutrons are noncharged (neutral) particles • Electrons are negatively charged particles Copyright © 2023 Pearson Education, Inc. All Rights Reserved What Are Atoms? (4 of 4) • Atoms can vary their number of neutrons and/or electrons, but protons remains constant • Number of protons is a defining feature and equal to the element’s atomic number • Each element has a unique atomic number • Elements are organized by their atomic number in the periodic table • The periodic table of elements includes the chemical symbol, atomic number, and atomic mass Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.2 The Periodic Table Copyright © 2023 Pearson Education, Inc. All Rights Reserved The Periodic Table • Atomic mass is the mass of the protons and neutrons in the atom (electrons have negligible mass) • Atomic mass is the average mass of 6.022 ´ 1023 atoms, or one mole, of the element Copyright © 2023 Pearson Education, Inc. All Rights Reserved Ions and Isotopes: Variations of Atoms (1 of 2) • Two forms of atoms are ions and isotopes • All elements exist as a variety of isotopes, while only certain elements form ions Copyright © 2023 Pearson Education, Inc. All Rights Reserved Ions and Isotopes: Variations of Atoms (2 of 2) • Ions are charged atoms that have an unequal number of protons and electrons • Cations are atoms that have lost electrons and consequently have an overall positive charge • Anions are atoms that have gained electrons and consequently have an overall negative charge Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.3 Ion Formation Copyright © 2023 Pearson Education, Inc. All Rights Reserved Isotopes • Isotopes are elements with the same number of protons but different numbers of neutrons • All elements exist as a mixture of isotopes – Isotopes are denoted by their atomic mass – For example, carbon atoms: ▪ 99% are C-12 with 6 protons and 6 neutrons ▪ <1% are C-13 with 6 protons and 7 neutrons ▪ <1% are C-14 with 6 protons and 8 neutrons Copyright © 2023 Pearson Education, Inc. All Rights Reserved What Are Molecules? • Molecules are formed when two or more atoms bond together • Compounds are molecules that are made of more than one type of element Copyright © 2023 Pearson Education, Inc. All Rights Reserved Molecular Formulas (1 of 3) • Molecules are often noted by their molecular formula (or chemical formula) – Reveal the ratio of elements in a molecule Copyright © 2023 Pearson Education, Inc. All Rights Reserved Molecular Formulas (2 of 3) • Rules for writing molecular formulas… – Carbon-containing molecules: ▪ Carbon (C) is listed first ▪ Followed by hydrogen (H) ▪ Then other elements in alphabetical order – If carbon is not present: ▪ Alphabetical order is usually followed – For ionic compounds: ▪ Positive ion is listed first followed by the negative ion Copyright © 2023 Pearson Education, Inc. All Rights Reserved Molecular Formulas (3 of 3) • Isomers are molecules with the same molecular formula but different molecular structures • A majority of biological molecules have at least one isomer • For example: – C6H12O6 is the molecular formula for glucose, fructose, and galactose Copyright © 2023 Pearson Education, Inc. All Rights Reserved Organic versus Inorganic Molecules • Organic molecules contain carbon and hydrogen (e.g.,C6H12O6 ) • Inorganic molecules may contain carbon, but will lack the associated hydrogen (e.g., CO2 ) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Functional Groups • Functional groups are molecules with shared chemical properties; they often participate in chemical reactions • Organic molecules are classified and named based in part on the functional groups they contain Copyright © 2023 Pearson Education, Inc. All Rights Reserved Table 2.1 Selected Biologically Important Functional Groups (1 of 3) Functional Group Formula Notes (R = the remainder of a molecule; often a carbonbased addition to the molecule) A molecule has the following structure: R is single bonded to O on the upper right that is single bonded to H on the right or R, single bond, O H. Alcohol Found in all alcohols and added to steroids to make sterols; the suffix “ol” on a molecule name often means an alcohol group is present (examples: cholesterol, ethanol, glycerol); alcohol groups (also called hydroxyl groups) are OH groups tagged onto organic molecules. These are not to be confused with the hydroxide ion OH- , which is an inorganic ion that is not bonded to carbon and instead tends to be free in a solution. O H super minus, A molecule has the following structure: R is single bonded to N on the right and N is single bonded to H on the upper right and on the lower right or R, single bond, N H sub 2. Amine Important in many organic molecules including amino acids and the nitrogen bases of nucleotides A molecule has the following structure: R is single bonded to C on the upper right and C is double bonded to O above and single bonded to O H on the lower right or R, single bond, C O O H. Carboxyl Found in a variety of organic acids such as amino acids and fatty acids; it’s considered an acid because it ionizes to form R - COO- and release H+ R, single bond, C O O super minus H super plus Copyright © 2023 Pearson Education, Inc. All Rights Reserved Table 2.1 Selected Biologically Important Functional Groups (2 of 3) Table 2.1 [continued] Functional Group Formula Ester A molecule has the bonded to C on the upper right. C is double bonded to O above and single bonded to O on the lower right that is single bonded to R prime on the upper right or R, single bond, C O O, single bond, R prime. Notes (R = the remainder of a molecule; often a carbon-based addition to the molecule) following structure: R is single In biology, esters tend to be formed by the condensation of an alcohol and an acid, by removing water (dehydration synthesis); lipids contain esters; phospholipids in bacteria and eukaryotic cell membranes have ester linkages. A molecule has the following structure: R is single bonded to O on the upper right and O is single bonded to R prime on the lower right or R, single bond, O, single bond, R prime. Ether Common linkage in carbohydrates; found in plasma membranes of archaea A molecule has the following structure: A central C atom is single bonded to R on the left and H above, below, and on the right or R, single bond, C H sub 3. Methyl Common in many organic molecules, especially in hydrocarbon chains; added to DNA to regulate gene expression (DNA methylation) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Table 2.1 Selected Biologically Important Functional Groups (3 of 3) Table 2.1 [continued] Functional Group Formula Notes (R = the remainder of a molecule; often a carbonbased addition to the molecule) A molecule has the following structure: R is single bonded to O on the right, O is single bonded to P on the right, and P is single bonded to O super minus on the right, double bonded to O above, and single bonded to O super minus below or R, single bond, P O 4 super 2 minus. Phosphate Found in DNA, RNA, ATP, and added to lipids, carbohydrates, and proteins; phosphate is denoted as PO43in an inorganic form or as PO42- when bonded to an organic molecule as a functional group P O 4 super 3 minus P O 4 super 2 minus A molecule has the following structure: R is single bonded to S on the right and S is single bonded to H on the lower right or R, single bond, S H. Sulfhydryl In cysteine and methionine (amino acids); important in building disulfide bonds in organic molecules Copyright © 2023 Pearson Education, Inc. All Rights Reserved Acids, Bases, and Salts (1 of 5) • Solvents are dissolving agents • Solutes are dissolved substances • Most cellular chemistry occurs in an aqueous solution where water is the solvent Copyright © 2023 Pearson Education, Inc. All Rights Reserved Acids, Bases, and Salts (2 of 5) • Acids add hydrogen ions (H+ ) • Bases add hydroxide ions (OH- ) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Acids, Bases, and Salts (3 of 5) • Salts form when acids and bases react with each other; the acid contributes the anion of a salt, while the base contributes a cation Copyright © 2023 Pearson Education, Inc. All Rights Reserved Acids, Bases, and Salts (4 of 5) • The concentration of a solution is determined by the amount of solute dissolved in a specific volume of solvent Copyright © 2023 Pearson Education, Inc. All Rights Reserved Acids, Bases, and Salts (5 of 5) • Molarity is a measure of the concentration of a given solute in a liter of solvent (mol/L) • Weight-volume proportion is a measure of solute in mass in a given volume of solvent (e.g., mg/mL) • Intravenous solutions are typically labeled as having a particular percentage of a given solute (e.g., 0.9% saline contains 9 grams of NaCl per L) Copyright © 2023 Pearson Education, Inc. All Rights Reserved pH: A Measure of Acidity (1 of 6) • H+ and OH- ions determine the overall acidity or basicity of a solution or pH • pH scale describes the acidity and basicity of a solution • pH values typically fall between 0–14 Copyright © 2023 Pearson Education, Inc. All Rights Reserved pH: A Measure of Acidity (2 of 6) • Due to the logarithmic (log10 ) nature of the pH scale there is a 10-fold difference in H+ ions for every whole-number increment on the scale Copyright © 2023 Pearson Education, Inc. All Rights Reserved pH: A Measure of Acidity (3 of 6) • Pure water – Equal concentration of H+ and OH– Chemically neutral (pH 7) • Basic, or alkaline, solutions – More OH- ions than H+ ions – pH greater than 7 • Acidic solutions – More H+ ions than OH- ions – pH less than 7 Copyright © 2023 Pearson Education, Inc. All Rights Reserved pH: A Measure of Acidity (4 of 6) • When an acid is added to a basic solution the pH will decrease • When a base is added to an acidic solution the pH will increase Copyright © 2023 Pearson Education, Inc. All Rights Reserved pH: A Measure of Acidity (5 of 6) • pH indicators can be added to growth media to observe acidic, neutral, or basic by-products • For example, phenol red: Copyright © 2023 Pearson Education, Inc. All Rights Reserved pH: A Measure of Acidity (6 of 6) • Most microbes grow best at a pH of 6.5-8.5 • Humans arterial blood has a pH of 7.35-7.45 – Acidosis is lower than normal blood pH – Alkalosis is higher than normal blood pH • Buffers are compounds that stabilize pH by absorbing or releasing H+ ions Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Bonds (1 of 2) After reading this section, you should be able to: • Define the term valence electron and explain how valence electrons relate to bonding. • Compare and contrast ionic and covalent bonds. • Describe electrolytes and their importance in biological systems. • Discuss the process of polar covalent bonding and how it sets the stage for hydrogen bonding. • Identify the characteristics of hydrogen bonds. Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Bonds (2 of 2) After reading this section, you should be able to: • Describe van der Waals interactions. • Define the terms hydrophobic, hydrophilic, and amphipathic, and explain how these qualities relate to micelle formation. Copyright © 2023 Pearson Education, Inc. All Rights Reserved Electrons Determine What Bonds Can Form (1 of 3) • Chemical bonds are the “glue” or forces that bind atoms in molecules • Atoms contain electrons organized in electron shells around their atomic nucleus – Each shell has a maximum number of electrons – The outermost shell is the valence shell Copyright © 2023 Pearson Education, Inc. All Rights Reserved Electrons Determine What Bonds Can Form (2 of 3) • Valence electrons (electrons in the valence shell) participate in chemical reactions Copyright © 2023 Pearson Education, Inc. All Rights Reserved Electrons Determine What Bonds Can Form (3 of 3) • Atoms with Full valence shells – Stable electron configuration – Nonreactive (inert) – Examples: noble gases (e.g., helium, neon) • Atoms with Not Full valence shells – Reactive – Electrons can be gained, lost, or shared Copyright © 2023 Pearson Education, Inc. All Rights Reserved Ionic Bonds (1 of 2) • Ionic bond – Electrostatic force of attraction that exists between oppositely charged ions – Forms when electrons are transferred from one atom to another to make ions Copyright © 2023 Pearson Education, Inc. All Rights Reserved Ionic Bonds (2 of 2) • When ionic compounds dissolve, the free ions are called electrolytes Copyright © 2023 Pearson Education, Inc. All Rights Reserved Covalent Bonds (1 of 2) • Covalent bonds are the electrostatic force of attraction between atoms that share one or more pairs of electrons Copyright © 2023 Pearson Education, Inc. All Rights Reserved Covalent Bonds (2 of 2) • Carbon – Core atom of organic molecules – Can form four covalent bonds – Capable of catenation (the ability of atoms of the same element to form long chains) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Polar Covalent Bonds (1 of 2) • Polar covalent bonds result from unequal sharing of electrons (without a full transfer of electrons) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Polar Covalent Bonds (2 of 2) • Highly electronegative atoms (e.g., O, N, F) hog the electrons of the covalent bond • The asymmetric charge distribution creates two poles—a dipole because the electronegative atom takes on a partial negative charge and the other atom takes on a partial positive charge Copyright © 2023 Pearson Education, Inc. All Rights Reserved Hydrogen Bonds: Noncovalent Interactions (1 of 2) • Hydrogen bonds are a noncovalent electrostatic attraction between 2 or more molecules or within a single large molecule Copyright © 2023 Pearson Education, Inc. All Rights Reserved Hydrogen Bonds: Noncovalent Interactions (2 of 2) • Intermolecular hydrogen bonds are formed between 2 or more individual molecules (e.g., water molecules) • Intramolecular hydrogen bonds can occur within a single large molecule (e.g., protein) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Van Der Waals Interactions • Some molecules have temporary dipoles that exhibit a force of attraction called van der Waals interactions • These interactions are weaker than hydrogen bonds but when added up across a complex molecule they are significant stabilizers of molecular structures Copyright © 2023 Pearson Education, Inc. All Rights Reserved Water Prefers to Interact With Polar Molecules • Polar covalent bonds of water allow water molecules to form hydrogen bonds with each other and with other polar substances • Water is a great solvent for dissolving polar substances • Water is not good at dissolving nonpolar substances (e.g., fats) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Hydrophobic, Hydrophilic, and Amphipathic Molecules (1 of 2) • Hydrophilic substances are “water loving” and readily dissolve in water • Hydrophobic substances are “water fearing” and do Not readily dissolve in water Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.11 Polar and Nonpolar Molecules Copyright © 2023 Pearson Education, Inc. All Rights Reserved Hydrophobic, Hydrophilic, and Amphipathic Molecules (2 of 2) • Amphipathic molecules have both hydrophobic and hydrophilic properties (e.g., micelles and phospholipids) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Reactions After reading this section, you should be able to: • Identify the reactants and products in a chemical equation. • Describe catalysts and their importance in biological systems. • Explain synthesis, decomposition, and exchange reactions. • Distinguish between dehydration synthesis and hydrolysis reactions. • Describe activation energy and how it can be lowered in biochemical reactions. • Compare and contrast endergonic and exergonic reactions. • Explain what is meant by a reversible reaction the concept of equilibrium. Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Reactions Make and Break Chemical Bonds • Chemical reactions involve making and/or breaking chemical bonds • Reactants are the ingredients of a chemical reaction • Products are the substances generated as a result of the reaction Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Equations: Recipes for Reactions • Catalysts are an organic or inorganic substance that increases the rate of a chemical reaction Copyright © 2023 Pearson Education, Inc. All Rights Reserved Synthesis Reactions (1 of 2) • Synthesis reactions build substances by combining two or more reactants A + B ® AB Copyright © 2023 Pearson Education, Inc. All Rights Reserved Synthesis Reactions (2 of 2) • Dehydration synthesis reactions bring reactants together in a way that releases water Copyright © 2023 Pearson Education, Inc. All Rights Reserved Decomposition Reactions (1 of 2) • Decomposition reactions break a substance down into simpler components AB ® A + B Copyright © 2023 Pearson Education, Inc. All Rights Reserved Decomposition Reactions (2 of 2) • Hydrolysis reactions add water to break the covalent bonds in complex molecules Copyright © 2023 Pearson Education, Inc. All Rights Reserved Exchange Reactions • Exchange reactions involve swapping one or more components in a compound A + BC ® AC + B Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Reactions Consume or Release Energy (1 of 2) • Reactions involve collisions between atoms or molecules • Reactions require reactants to be properly oriented to interact • Reactions require energy to cause the change • Activation energy can be lowered in biochemical reactions with catalysts Copyright © 2023 Pearson Education, Inc. All Rights Reserved Chemical Reactions Consume or Release Energy (2 of 2) • Activation energy is the minimum amount of energy needed to get a reaction started Copyright © 2023 Pearson Education, Inc. All Rights Reserved Endergonic versus Exergonic Reactions • Exergonic reactions occur when reactions release more energy than is spent to start the reaction – Products have a lower final energy than the reactants • Endergonic reactions occur when reactions use more energy than is released – Products have a higher final energy than the reactants Copyright © 2023 Pearson Education, Inc. All Rights Reserved Reaction Reversibility • Some chemical reactions are reversible reactions • When forward and reverse reactions occur at the same rate and the reaction is at equilibrium CH3 CO2 H + H2O É CH3CO2- + H3O + Copyright © 2023 Pearson Education, Inc. All Rights Reserved Biologically Important Macromolecules After reading this section, you should be able to: • Identify the four main groups of biomolecules and their building blocks. • Describe glycosidic bonds, peptide bonds, and phosphodiester bonds. • Explain the structural and functional characteristics of carbohydrates, lipids, nucleic acids, and proteins. • Summarize how saturation affects a lipid’s characteristics. • Compare and contrast deoxyribonucleotides and ribonucleotides. • Describe the four levels of protein structure. • State what chaperone proteins do and why they are important. Copyright © 2023 Pearson Education, Inc. All Rights Reserved There Are Four Main Classes of Biomolecules (1 of 3) • Carbohydrates, lipids, nucleic acids, and proteins are the four main classes of biomolecules Table 2.2 The Four Main Classes of Biomolecules Biomolecule Examples Building Blocks Notes Carbohydrates Glucose Simple sugars Glucose is a monosaccharide (a simple sugar) Carbohydrates Sucrose Simple sugars Sucrose is a disaccharide (built by bonding two simple sugars) Carbohydrates Glycogen Simple sugars Glycogen is a polysaccharide (polymer of many simple sugars) Nucleic Acids Deoxyribonucleic acid (DNA) Nucleotides DNA is a polymer of deoxyribonucleotides Ribonucleic acid (RNA) Nucleotides RNA is a polymer of ribonucleotides Nucleic Acids Copyright © 2023 Pearson Education, Inc. All Rights Reserved There Are Four Main Classes of Biomolecules (2 of 3) Table 2.2 [continued] Biomolecule Examples Proteins Enzymes Antibodies Lipids Fats and oils Building Blocks Notes Amino acids Enzymes are proteins that serve as catalysts; antibodies are proteins made as part of an immune response Glycerol and up to 3 fatty acids Monoglycerides = Glycerol + one fatty acid Diglycerides = Glycerol + two fatty acids Triglycerides = Glycerol + three fatty acids Lipids Waxes Long-chain alcohol and fatty acid Mycolic acid is a type of wax found in acid-fast bacterial cell walls Lipids Steroids Fused hydrocarbon rings Cholesterol is incorporated into certain cell plasma membranes Copyright © 2023 Pearson Education, Inc. All Rights Reserved There Are Four Main Classes of Biomolecules (3 of 3) • Biological macromolecules are built by a series of synthesis reactions and broken down by a series of decomposition reactions • Biomolecules often contain multiple functional groups that contribute to their chemical properties. • Polymerization is the process of covalently bonding together monomers to build many macromolecules Copyright © 2023 Pearson Education, Inc. All Rights Reserved Carbohydrates Include Simple Sugars and Polysaccharides • Carbohydrate refers to organic molecules consisting of one or more sugar monomers • Single sugars are built from carbon, hydrogen, and oxygen and follow the formula (CH2O)n • Single sugars can be polymerized to make larger molecules called polysaccharides (e.g., glycogen) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Carbohydrate Structures (1 of 2) • Monosaccharides are one sugar unit • Disaccharides consist of two monosaccharides linked together by a glycosidic bond Copyright © 2023 Pearson Education, Inc. All Rights Reserved Carbohydrate Structures (2 of 2) • Glycosidic bonds are formed by a dehydration synthesis reaction • Glycosidic bonds can be broken by enzymatically adding water (hydrolysis) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Carbohydrate Functions (1 of 3) • Carbohydrate functions – Energy sources – Structural biomolecules – Cellular adhesion – Communication – Environmental sensing Copyright © 2023 Pearson Education, Inc. All Rights Reserved Carbohydrate Functions (2 of 3) • Cellulose – Most abundant polysaccharide on the planet – Major structural macromolecule in plant and algal cell walls • Chitin – Structural polysaccharide in fungal cell walls • Peptidoglycan – Part of bacterial cell walls Copyright © 2023 Pearson Education, Inc. All Rights Reserved Carbohydrate Functions (3 of 3) • Capsules – Carbohydrate-based structure made by some bacteria – Used to adhere to surfaces and provides protection from our immune system Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipids Include Fats, Oils, Waxes, and Steroids • Lipids are a collection of biomolecules that includes fats, oils, waxes, and steroids • All lipids are organic molecules made up of carbon, hydrogen, and oxygen • Lipids are predominantly hydrophobic • Some lipids contain modifications (e.g., functional groups) that make them amphipathic • Lipids have diverse structures that range from long chains to complex cyclical structures Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipid Structures (1 of 3) • Saturated lipids lack double bonds in their fatty acid chains • Pack tightly together and therefore usually solid at room temperature • Examples include butter and lard Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipid Structures (2 of 3) • Unsaturated lipids contain double bonds in 1 or more of the hydrocarbon chains of their fatty acids • Kinks and bends in their chains prevent them from tightly packing • Examples include corn oil and olive oil Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipid Structures (3 of 3) • Monounsaturated fats have one double bond in their fatty acid chains • Polyunsaturated fats have more than one double bond in their fatty acid chains Copyright © 2023 Pearson Education, Inc. All Rights Reserved Structure of Fats and Oils • Fats and oils are built by combining glycerol with up to 3 fatty acids through an ester bond • Fatty acids are long hydrocarbon chains with a carboxylic acid functional group – Monoglyceride has one linked fatty acid – Diglycerides contain two fatty acid chains – Triglycerides have three fatty acid chains Copyright © 2023 Pearson Education, Inc. All Rights Reserved Structure of Waxes • Waxes contain fatty acids linked to a long-chain alcohol (instead of a glycerol) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Structure of Steroids • Steroids contain 4 fused hydrocarbon ring structures • Sterols are modified steroids with an attached alcohol functional group (e.g., cholesterol) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.18 Types of Lipids Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipid Functions (1 of 3) • Lipid functions – Energy sources – Cell structure components – Mediate cell signaling Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipid Functions (2 of 3) • Phospholipids – Common ingredients of the cellular membrane – Amphipathic – Organize into lipid bilayers • Glycolipids – Lipids and oils linked to carbohydrates • Lipoproteins – Lipids and oils linked to proteins Copyright © 2023 Pearson Education, Inc. All Rights Reserved Lipid Functions (3 of 3) • Lipopolysaccharide (LPS) – Toxic portion of the Gram-negative bacterial cell wall • Mycolic acid – Part of the acid-fast bacterial cell wall (e.g., Mycobacterium tuberculosis and M. leprae) – Increases bacterial pathogenicity. • Cholesterol – Abundant in animal cell plasma membranes Copyright © 2023 Pearson Education, Inc. All Rights Reserved Nucleic Acids Include DNA and RNA • Nucleic acids are macromolecules that serve as the genetic material of cells and viruses • Two main categories of nucleic acids: – Deoxyribonucleic acid (DNA) ▪ Double-stranded helical molecule – Ribonucleic acid (RNA) ▪ Single-stranded molecule Copyright © 2023 Pearson Education, Inc. All Rights Reserved Nucleic Acid Structures (1 of 3) • Nucleic acids are polymers of nucleotides consisting of three ingredients: – A five-carbon sugar (deoxyribose in DNA; ribose in RNA) – One to three phosphate groups – A single nitrogenous base (adenine, guanine, cytosine, thymine, or uracil) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.19 Nucleotides Copyright © 2023 Pearson Education, Inc. All Rights Reserved Nucleic Acid Structures (2 of 3) • DNA – Made of deoxyribonucleotides (contain deoxyribose sugar) – Contain: adenine, guanine, cytosine, thymine • RNA – Made of ribonucleotides (contain ribose sugars) – Contain: adenine, guanine, cytosine, uracil Copyright © 2023 Pearson Education, Inc. All Rights Reserved Nucleic Acid Structures (3 of 3) • Both DNA and RNA nucleotides are connected by phosphodiester bonds – Creates a sugar and phosphate backbone Copyright © 2023 Pearson Education, Inc. All Rights Reserved Nucleic Acid Functions • DNA is the genetic blueprint of all cells • RNA directs the production of proteins • Specialized RNAs can catalyze reactions (e.g., ribozymes) • Most ribonucleotides can serve as energy sources in cells (e.g., ATP) Copyright © 2023 Pearson Education, Inc. All Rights Reserved ATP: A Special Ribonucleotide • Adenosine triphosphate (ATP) is a vitally important ribonucleotide • When phosphates are cleaved off ATP, energy is released Copyright © 2023 Pearson Education, Inc. All Rights Reserved Proteins Are Cellular Workhorses • Genes in DNA encode proteins • At some level every cellular process involves a protein Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (1 of 12) • Proteins are polymers of amino acids – 22 are genetically encoded – 20 “standard”’amino acids – 2 “nonstandard” amino acids (selenocysteine and pyrrolysine) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (2 of 12) • Each amino acid consists of an: – Amine group (NH2 ) – Carboxyl group (COOH) – Side groups (R groups) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (3 of 12) • More on R groups: – Polar – Nonpolar – Acidic properties – Basic properties • The properties of each amino acid contribute to the overall structure and function of the final protein Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.22 (1 of 2) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.22 (2 of 2) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (4 of 12) • Amino acids are covalently connected by peptide bonds – Amino group of one amino acid is attached to the carboxyl group of the next • Peptides are short amino acid chains • Polypeptides are long chains of amino acids Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (5 of 12) • Protein folding refers to the process whereby proteins take on higher-order structure Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (6 of 12) • There are four levels of protein structure: – Primary – Secondary – Tertiary – Quaternary Copyright © 2023 Pearson Education, Inc. All Rights Reserved Figure 2.23 Protein Structure Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (7 of 12) • Primary structure is the linear sequence of amino acids in a protein Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (8 of 12) • Primary structure lays the foundation for all higher-order structure of a protein • Mutations, or errors that arise in genetic material, can lead to changes in a protein’s primary structure • Can have devastating effects on overall protein structure and function Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (9 of 12) • Secondary Structure includes: – Alpha-helices ▪ Spiral structures that have specified dimensions – Beta-pleated sheets ▪ Accordion-like folds Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (10 of 12) • Tertiary Structure is established by folding into a 3D structure – Noncovalent interactions (e.g., ionic bonds, hydrogen bonds, van der Waals interactions) – Covalent bonds (e.g., disulfide bridges) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (11 of 12) • Quaternary Structure arises when 2 or more separate polypeptide chains combine Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Structures (12 of 12) • A variety of factors impact protein folding, making the process quite complex • Some protein structures are so sophisticated that they require chaperones to mediate folding Copyright © 2023 Pearson Education, Inc. All Rights Reserved Protein Functions • Protein functions – Structural scaffolds in cells – Enzymes (facilitate chemical reactions) – Cellular transporters – Cell recognition – Communication Copyright © 2023 Pearson Education, Inc. All Rights Reserved Visual Summary: Biochemistry Basics Copyright © 2023 Pearson Education, Inc. All Rights Reserved Think Clinically: Be S.M.A.R.T. About Cases (1 of 6) • Summary of the case: – 3-month-old infant was admitted to the hospital after parents tried to limit night time feeding and he began to convulse – Initial examination showed the infant was unconscious, exhibited impaired breathing, low body temperature, hepatomegaly – Patient had a history of hypoglycemia – Blood work revealed low blood sugar, elevated pyruvate, fatty acids, triglycerides, and cholesterol – Referred to a specialist and diagnosed with von Gierke’s disease, or type I glycogen storage disease (GSD) Copyright © 2023 Pearson Education, Inc. All Rights Reserved Think Clinically: Be S.M.A.R.T. About Cases (2 of 6) • Summary of the case: – GSD is a rare genetic disorder (occurs in 1 of every 43,000 live births) – Patients can’t break down glycogen due to a deficiency of the enzyme glucose-6-phosphatase – Patients have trouble stabilizing their blood glucose levels when fasting – Patients suffer from an enlarged liver and kidneys, low blood sugar within a few hours of eating, chronic fatigue, muscle cramps, stunted growth, delayed puberty, and high levels of lactate, triglycerides, cholesterol, and uric acid in the blood – No cure but treatment with cornstarch helps to minimize drops in blood sugar Copyright © 2023 Pearson Education, Inc. All Rights Reserved Think Clinically: Be S.M.A.R.T. About Cases (3 of 6) Henry’s Blood Work Results Blank Observed Levels Normal Ranges for Children Under 1 Year Glucose 38 mg/dL 60–105 mg/dL Lactate (plasma) 3.9 mmol/L 1 to 3.3 mmol/L Pyruvate 0.4 mmol/L 0.05 to 0.10 mmol/L Free fatty acids 3.2 mmol/L Below 2.3 mmol/L Triglycerides 200 mg/dL 20–150 mg/dL Cholesterol 150 mg/dL 50–120 mg/dL Blood pH 7.28 7.34 to 7.44 Copyright © 2023 Pearson Education, Inc. All Rights Reserved Think Clinically: Be S.M.A.R.T. About Cases (4 of 6) 1. Is glycogen an organic or inorganic compound? Explain your response. 2. Write the chemical equation for the reaction catalyzed by glucose6-phosphatase (be sure to use molecular formulas, but don’t worry about writing a balanced equation). After writing the reaction out, name the elements that make up the reactants and specify how many atoms of each element are present in the reactants. 3. Explain what the notations mg/dL and mmol/L mean in the blood work results. 4. How would you describe Henry’s blood pH in comparison with normal ranges? In relation to his observed blood pH, what would he be described as manifesting? Copyright © 2023 Pearson Education, Inc. All Rights Reserved Think Clinically: Be S.M.A.R.T. About Cases (5 of 6) 5. How would you describe the polarity of the enzyme glucose-6phosphatase, knowing it is a transmembrane protein? 6. Why do patients with GSD exhibit hepatomegaly? 7. Hundreds of mutations in the enzyme glucose-6-phosphatase have been discovered; most result in small errors in amino acid sequence. Based on your introductory exposure to protein structure, explain why this would impact the enzyme’s function. 8. What kind of bond do you think is broken to digest cornstarch (be specific)? 9. In the cornstarch therapy, what is the solvent and what is the solute? Copyright © 2023 Pearson Education, Inc. All Rights Reserved Think Clinically: Be S.M.A.R.T. About Cases (6 of 6) 10. Henry’s blood work reveals increases in a number of compounds. Using the diagram, explain the increases in cholesterol, triglycerides, free fatty acids, lactate, and pyruvate. 11. Based on the diagram to the right, explain why GSD type I patients are discouraged from consuming carbohydrates such as fructose, galactose, and lactose. Copyright © 2023 Pearson Education, Inc. All Rights Reserved Copyright This work is protected by United States copyright laws and is provided solely for the use of instructors in teaching their courses and assessing student learning. Dissemination or sale of any part of this work (including on the World Wide Web) will destroy the integrity of the work and is not permitted. The work and materials from it should never be made available to students except by instructors using the accompanying text in their classes. 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