Chapter 7 Microbial Biochemistry Fall II 2024 Final PDF

Chapter 7 Microbial Biochemistry  Chemical Elements in living cells Macronutrients (99% dry weight of a cell) Hydrogen (H), most abundant Carbon (C) Oxygen (O) Nitrogen (N) Phosphorous (P) Sulfur (S) C, N, O, H are the four most abundant elements in...

Chapter 7 Microbial Biochemistry  Chemical Elements in living cells Macronutrients (99% dry weight of a cell) Hydrogen (H), most abundant Carbon (C) Oxygen (O) Nitrogen (N) Phosphorous (P) Sulfur (S) C, N, O, H are the four most abundant elements in living matter have low atomic numbers (are light elements) form strong bonds with other atoms to produce molecules Carbon forms four chemical bonds, nitrogen forms three, oxygen forms two, and hydrogen forms one.  Molecular compounds Atoms form molecules by combining to fill their outermost shells A molecule is formed by two or more atoms If a molecule has more than two different atoms is called a compound. All compounds are divided into two classes they can be either organic or inorganic Both types are essential to life  Isomers and stereoisomers Isomers (structural isomers): organic molecules that have the same molecular formula but a different bonding arrangement among the atoms. Stereoisomers: organic molecules that have identical molecular formulas and arrangements of atoms, but have different spatial orientation of groups in the molecule.  Isomers and Stereoisomers Glucose and galactose, are stereoisomers. Fructose is an isomer of glucose and galactose. They all have the same chemical formula (C6H12O6), but differ in their physical and chemical properties.  Enantiomers Enantiomers are stereoisomers that exhibit chirality. Their chemical structures are nonsuperimposable mirror images of each other. (a) D-glucose and L-glucose are monosaccharides that are enantiomers. (b) The enantiomers D-alanine and L-alanine are enantiomers found in bacterial cell walls and human cells, respectively.  Biological Molecules Organic compounds always contain carbon and hydrogen; typically structurally complex (proteins, sugars, amino acids). Covalent bonds mostly. Inorganic compounds typically lack carbon; usually small and structurally simple (water, molecular oxygen, carbon dioxide, salts, acids and bases). Mostly ion bonds.  Organic compounds Always contain carbon and hydrogen. Covalent bonds Carbon has 4 electrons and 4 empty spaces in it outer shell. It can combine with a variety of other atoms or other carbon in order to fill the empty shell space Carbon atoms can form chains and rings. Carbon chains form the basic structure of organic compound (sugars, amino acids, vitamins, proteins) They are chemically stable Organic compounds Butane Glucosamine Chlorocyclohexane  Functional groups bond to carbon skeletons and are responsible for most of the chemical and physical properties of a particular organic compound  Hydroxyl group Hydroxyl group is present in alcohols, monosaccharides, amino acids and nucleic acids  More than one different functional group can be present in a molecule Identify the functional groups in the glycine amino acid Amino Carboxyl group group glycine amino acid  Macromolecules (polymers) Small organic molecules can combine into large macromolecules Macromolecules are polymers consisting of many small repeating molecules called monomers Carbon chains form the skeletons of most organic molecules Functional groups combine with carbon skeletons to form biomolecules Held together by covalent bonds They are chemically stable  Biomolecules: assembled in the cell Mostly assembled via dehydration synthesis Carbohydrates Lipids Proteins Nucleic acids  Dehydration Synthesis Monomers join by dehydration synthesis or condensation reactions (water is released) Dehydration (de=from hydro=water): elimination of a hydrogen atom from one monomer and a hydroxyl group from the other, they combine to produce water.  Dehydration synthesis of maltose In this dehydration synthesis reaction, two molecules of glucose are linked together to form maltose. In the process, a water molecule is formed. Organic Macromolecules: Carbohydrates All are composed of carbon, hydrogen, and oxygen (CH2O)n Some may also have nitrogen, phosphorous and or sulfur Functions Long-term storage of chemical energy Ready energy source (principal function) Part of backbones of nucleic acids (Ribose and Deoxyribose) Structural components of cells, form cell wall (cellulose and chitin) Chitin also form the exoskeleton of Arthropods Involved in intracellular interactions between animal cells  Types of Carbohydrates Monosaccharides: can contain 3-7carbon (glucose & fructose) Disaccharides: sucrose , lactose & maltose Polysaccharides: cellulose & glycogen Monosaccharides Disaccharides Water molecule released in the reaction Tortora, Funke and Case. Microbiology an Introduction 13th edition  Polysaccharides (Glycans) Tortora, Funke and Case. Microbiology an Introduction 13th edition  Starch, glycogen, and cellulose are three of the most important polysaccharides. In the top row, hexagons represent individual glucose molecules. Micrographs (bottom row) show wheat starch granules stained with iodine (left), glycogen granules (G) inside the cell of a cyanobacterium (middle), and bacterial cellulose fibers (right). (credit “iodine granules”: modification of work by Kiselov Yuri; credit “glycogen granules”: modification of work by St.ckel J, Elvitigala TR, Liberton M, Pakrasi HB; credit “cellulose”: modification of work by American Society for Microbiology)  Chitin Chitin is formed by chains of N-acetylglucosamine (NAG), an amide derivative of glucose  Organic Macromolecules: Lipids Consist primarily of C and H May also contain O2, N2, Sulfur and phosphorous Are all hydrophobic (because they are non polar molecules) They can dissolve in non polar solvents like ether and chloroform Essential components of the cell membranes Energy storage, source of nutrients Four groups Simple Fats Phospholipids Waxes Isoprenoids and Steroids  Fatty acids Building blocks of lipids Molecule consists of long chains of H and C with a terminal COOH functional group Non polar  Fatty acids (2) Saturated fat: no double bonds in the fatty acids Chain contains the maximum number of H atoms Unsaturated fat: one or more double bonds in the fatty acids Cis: H atoms on the same side of the double bond Trans: H atoms on opposite sides of the double bond  Simple Fats A fat molecule is formed when a glycerol Glycerol molecule combines carboxyl group with one to three fatty acid molecules by Fatty acid dehydration synthesis  Molecule of fat (triglyceride) Glycerol Ester linkage Palmitic acid (saturated) Oleic acid (C15H31COOH) (unsaturated) + H2O Also called triacylglycerol (C17H33COOH) Primary components of + H2O adipose tissue (body fat) and sebum Energy reserve molecule can provide double of caloric content of proteins and carbohydrates Stearic acid (saturated) (C17H35COOH) + H2O cis configuration Tortora, Funke and Case. Microbiology an Introduction 13th edition  Complex Lipids Contain fatty acids, glycerol and at least one additional compound (e.g. phosphate goup) Cell membranes are made of complex lipids called phospholipids Glycerol, two fatty acids, and a phosphate group Phospholipids have polar as well as nonpolar regions, they are components of the cell membrane  Tortora, Funke and Case. Microbiology an Introduction 13th edition This illustration shows a phospholipid with two different fatty acids, one saturated and one unsaturated, bonded to the glycerol molecule. The unsaturated fatty acid has a slight kink in its structure due to the double bond.  Isoprenoids (terpenoids) Derive from isoprene molecule Have been found in all organisms (mostly present in plants) Branched lipids Many diverse physiological functions Many pharmacological (capsaicin) and industrial applications fragrances (menthol, camphor, lemon) antimicrobial (both Gram - and Gram+) and antifungal properties  Different types of terpenoids and their properties Classification Carbon atoms Species Medicinal uses produced from Monoterpenes C10 Quercus ilex Fragrances, repellent Sesquiterpenes C15 Helianthus Treat malaria, annuus treat bacterial infections, and migraines Diterpenes C20 Euphorbia, Anti- salvia inflammatory, miltiorrhiza cardiovascular diseases Triterpenes C30 Centella Wound healing, asiatica increases circulation Adapted from : Cox-Georgian, Destinney et al. “Therapeutic and Medicinal Uses of Terpenes.” Medicinal Plants: From Farm to Pharmacy 333–359. 12 Nov. 2019, doi:10.1007/978-3-030-31269-5_15  Waxes Contain one long-chain fatty acid covalently linked to long-chain alcohol by ester bond Completely insoluble in water; lack hydrophilic head In humans is a component the sebum  STEROIDS Very different from lipids Characterized by 4 interconnected carbon rings Sterols: when a steroid has an OH (alcohol) attached. Important components of plasma membrane of animals can also be found in plants and fungi Found in Bacteria of the genus Mycoplasma  Steroids Distinctive because its 4 carbon rings STEROID ALCOHOL Organic Macromolecules: Proteins Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur Functions Structure Enzymatic catalysis Regulation (hormones) Transportation Receptors Defense and offense  Amino Acids The monomers that make up proteins Contain at least on carboxyl (–COOH) group and one amino (-NH2) group attached to the same carbon atom Most organisms use 20 amino acids in the synthesis of proteins Side groups affect how amino acids interact and how a protein interacts with other molecules A covalent bond (peptide bond) is formed between amino acids by dehydration synthesis reaction  Amino acids One carbon atom ( carbon) has a carboxyl (–COOH) group, an amino (-NH2), and one H group attached to it.  Linkage of amino acids by peptide bonds Dehydration synthesis Carboxyl Amino group group Peptide bond Amino acid 1 Amino acid 2 Dipeptide Peptide bond occurs between the C of the carboxyl group of one amino acid and the N of the amino group of another amino acid  Protein Structure Directly related to their function Four levels of organization: primary, secondary, tertiary and quaternary  Primary structure The primary structure of a protein is the sequence of amino acids. (credit: modification of work by National Human Genome Research Institute)  Secondary structure The secondary structure of a protein may be an α-helix or a β-pleated sheet, or both. Hydrogen bonding occurs between amine and the carbonyl groups when the peptide chain is long enough.  Tertiary Structure The tertiary structure of proteins is determined by a variety of attractive forces, including hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages in the R part of amino aids that are far apart in the chain Three-dimensional shape of a single polypeptide chain, defines the function of the protein  Quaternary Structure Formed by protein subunits A hemoglobin molecule has two α and two β polypeptides together with four heme groups.  Protein structure has four levels of organization. (credit: modification of work by National Human Genome Research Institute) Conjugated Proteins  Identification of microorganisms Morphology Inclusions Biochemical characteristics Genotypic characteristics  FAME ANALYSIS Fatty acids are extracted from phospholipids of membranes (phospholipid derived fatty acid) and then analyzed using FAME. Fatty acid methyl ester (FAME) analysis in bacterial identification results in a chromatogram unique to each bacterium. Each peak in the gas chromatogram corresponds to a particular fatty acid methyl ester and its height is proportional to the amount present in the cell. (credit “culture”: modification of work by the Centers for Disease Control and Prevention; credit “graph”: modification of work by Zhang P. and Liu P.)  Serological tests Antibodies antigens complexes In 1933 Rebecca Lancefield developed a Streptococci classification system based on the chemical composition of a polysaccharide in their cell wall components  Proteomics Study of all accumulated proteins of an organism Proteins from pathogen are extracted and analyzed using mass spectrometry, then compare to databases of known microorganisms’ proteomic profiles.