MCB2004 Microbiology Lecture 3 PDF

# MCB2004: Microbiology ## Lecture 3: Chemical Principles and Biochem ### Chemistry Background * Ch2, pp25-35 of *Microbiology: An Introduction* has a review of chemical principles that will be useful as background. * Structure of atoms * Chemical elements * Chemical bonds...

# MCB2004: Microbiology ## Lecture 3: Chemical Principles and Biochem ### Chemistry Background * Ch2, pp25-35 of *Microbiology: An Introduction* has a review of chemical principles that will be useful as background. * Structure of atoms * Chemical elements * Chemical bonds * Ionic bonds * Covalent bonds * Hydrogen bonds * Chemical reactions * Energy in chemical reactions * Synthesis reactions → Anabolism, making new, larger compounds * Decomposition reactions → Catabolism, breaking down compounds * Exchange reactions * Important inorganic compounds * Water * Acids, Bases, pH * Salts * Organic compounds * Carbon skeleton * Functional groups * You should read these pages and review these concepts. ### Important Biological Molecules * Organic compounds contain carbon and hydrogen (e.g., CO2 is usually considered inorganic) * Inorganic compounds typically lack carbon ### Bacterial Cell - What organic building blocks, or "macromolecules," are required to make all the parts of a cell? * What is in the cell wall? * The cell membrane? * The cytoplasm? * The genetic material? - Learning about organic "macromolecules" will prepare you to understand the anatomy and physiology of both prokaryotic and eukaryotic cells ### Composition of an *E. coli* Cell | Component | % by wt | Ave. MW | No/cell | Types | | :---------------- | :------ | :------- | ---------- | -------- | | Water | 70 | 18 | 4 x 10^10 | 1 | | Inorganic Ions | 1 | 40 | 3 x 10^8 | 20 | | Small Molecules | 1 | 500 | 6 x 10^7 | 450 | | Carbohydrates | 3 | 150 | 2 x 10^8 | 200 | | Lipids (fats) | 2 | 750 | 3 x 10^7 | 50 | | Proteins | 15 | 40,000 | 1 x 10^6 | 4288 | | Nucleic Acids: | | | | | | DNA | 1 | 3 x 10^9 | 2 | 1 | | RNA: tRNA | 1 | 25,000 | 4 x 10^5 | 47 | | RNA: rRNA | 5 | 5 x 10^5 | 1 x 10^5 | 3 | | RNA: mRNA | 0.06 | 1 x 10^6 | 10,000 | ~1000 | ### Carbohydrates - Are important for structure and as energy sources - Consist of C, H, and O with the formula (CH2O)n - Monosaccharides are simple sugars with three to seven carbon atoms. Mostly common are hexoses (e.g., glucose, fructose) and pentoses. ![A diagram of a glucose molecule] - Disaccharides are formed when two monosaccharides are joined in dehydration synthesis. - Disaccharides can be broken down by hydrolysis. ![A diagram showing glucose and fructose combining to form sucrose through dehydration synthesis] - Oligosaccahrides consist of 2 to 20 monosaccharides - Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis. - Starch, glycogen, dextran, and cellulose are polymers of glucose that are convalently bonded differently. - Chitin is a polymer of two sugars repeating many times. ![A diagram showing how a chain of monomers form a polysaccharide] - **Functions of Polysaccharides** * Storage Molecules - starch and glycogen * Structural Molecules - cellulose, chitin, peptidoglycan (also called murein) * Lubrication - hyaluronic acid (extracellular matrix) ### Lipids - Primary components of cell membranes - Also consist of C, H, and O - Fuel storage (fat tissue) - Vitamins and hormones - "Nonpolar" and insoluble in water ![A diagram showing the components of a cell membrane] - **Simple Lipids** - Called fats or triglycerides; contain glycerol & fatty acids; formed by dehydration synthesis. - Saturated fats have no double bonds in the fatty acids. - Unsaturated fats have one or more double bonds in the fatty acids. ![A diagram showing glycerol and fatty acids combining to form a fat molecule] - **Complex Lipids** - Contain C, H, and O + P, N, or S - Cell membranes are made of phospholipids * Phosphate (polar) * Glycerol (polar) * 2 Fatty acids (nonpolar) ![A diagram showing the components of a phospholipid structure] ### Steroids - Consist of four carbon rings with an -OH group attached to one ring. - Are part of membranes ![A diagram showing the structure of a steroid molecule] ### Proteins - Composed of 20 different amino acids, linked together with peptide bonds. - Amino acids contain an alpha-carbon that has an attached: * Carboxyl group (-COOH) * Amino group (NH2) * Side group ![A diagram of a generalized amino acid structure] - Linear polymers - Folded into specific conformation-its native state - Are essential in cell structure and function - **Types of proteins in bacterial cells** * Enzymes are proteins that speed chemical reactions ("catalysis"). * Transporter proteins move chemicals across membranes. * Flagella are made of proteins. * Some bacterial toxins are proteins. - **Consist of subunits called amino acids.** | Amino Acid | Abbreviation | Three-letter Abbreviation | Structure | | :----------------- | :------------- | :------------------------ | :-------------------------- | | Glycine | Gly, G | Gly | Hydrogen atom | | Alanine | Ala, A | Ala | Unbranched chain | | Valine | Val, V | Val | Branched chain | | Leucine | Leu, L | Leu | Branched chain | | Isoleucine | Ile, I | Ile | Branched chain | | Serine | Ser, S | Ser | Hydroxyl (-OH) group | | Threonine | Thr, T | Thr | Hydroxyl (-OH) group | | Cysteine | Cys, C | Cys | Sulfer-contaning (-SH) group | | Methionine | Met, M | Met | Thioether (SC) group | | Glutamic acid | Glu, E | Glu | Additional carboxyl group | | Aspartic acid | Asp, D | Asp | Additional carboxyl group | | Lysine | Lys, K | Lys | Additional amino (-NH) group | | Arginine | Arg, R | Arg | Additional amino (-NH) group | | Asparagine | Asn, N | Asn | Additional amino (-NH) group | | Glutamine | Gln, Q | Gln | Additional amino (-NH) group | | Phenylalanine | Phe, F | Phe | Cyclic | | Tyrosine | Tyr, Y | Tyr | Cyclic | | Histidine | His, H | His | Heterocyclic | | Tryptophan | Trp, W | Trp | Heterocyclic | | Proline | Pro, P | Pro | Heterocyclic | - **Peptide bonds** between amino acids are formed by dehydration synthesis. ![A diagram showing two amino acids connecting through dehydration synthesis] - **Levels of Protein Structure** - **Primary Structure**: polypeptide strand (amino acid sequence) - the sequence of amino acids ina polypeptide chain. - **Secondary Structure**: helix and pleated sheet (with three polypeptide strands)- the folding pattern of the polypeptide backbone. - **Tertiary Structure**: helix and pleaded sheets fold into a 3D shape - the overall three-dimensional shape of a single polypeptide chain. - **Quaternary Structure**: the relationship of several folded polypeptide chains, forming a protein - the structure that results when multiple polypeptide chains interact to form a functional protein. ![A diagram showing the levels of protein structure] - **Proteins can fail!** - Called denaturation. - Denaturation occurs when proteins encounter hostile environments, such as temperature and pH, and therefore lose their shapes and functions. ### Level of Protein Structure - Conjugated proteins consist of amino acids and other organic molecules (post-translational modifications) - Glycoproteins - Nucleoproteins - Lipoproteins ### Nucleic Acids - **Mononucleotides** (e.g., AMP, ADP, ATP) * Provide chemical energy - ATP. * Enzyme cofactors (e.g., NAD & FAD) - **Nucleic Acids** * DNA - The genetic material. * RNA - Structural, enzymatic, informational - **Consist of nucleotides**. - **Nucleotides consist of**: * Pentose sugar * Phosphate group * Nitrogen-containing (purine or pyrimidine) base. ![A diagram showing the structure of a nucleotide] - **Base Pairing** ![A diagram showing base pairing in DNA] ### DNA - deoxyribonucleic acid - Has deoxyribose (pentose sugar) - Exists as a double helix. - A (adenine) hydrogen bonds with T (thymine) - C (cytosine) hydrogen bonds with G (guanine) - Order of the nitrogen-containing bases forms the genetic instructions of the organism. ![A diagram showing the structure of DNA] ### RNA - Has ribose (pentose sugar) - Is usually single-stranded - A hydrogen bonds with U (uracil) - C hydrogen bonds with G - Several kinds of RNA play a special role in protein synthesis. ![A diagram showing the structure of RNA] ### DNA vs RNA | | DNA | RNA | | :---------- | -------- | -------- | | Sugar | Deoxyribose | Ribose | | Bases | Thymine | Uracil | | Structure | Double-stranded | Single-stranded | | Stability | Stable | Unstable | ![A diagram comparing DNA and RNA] ### ATP - Stores the chemical energy released by some chemical reaction. - Releases phosphate groups by hydrolysis to liberate useful energy for the cell. - Has ribose, adenine, and three phosphate groups. ![A diagram showing the structure of ATP] - Is made by dehydration synthesis. - Is broken by hydrolysis to liberate useful energy for the cell. - When you exercise, you "burn," aka hydrolyze ATP. ![A diagram showing the hydrolysis of ATP]