Burton's Microbiology for the Health Sciences Section III. Chemical and Genetic Aspects of Microorganisms Burton's Microbiology for the Health Sciences Chapter 6. Biochemistry: The Chemistry of Life 1
Chapter 6 Outline Introduction Organic Chemistry Carbon Bonds Cyclic Compounds Biochemistry Carbohydrates Lipids Proteins Nucleic Acids Copyright 2011 Wolters Kluwer Health Lippincott Williams & Wilkins Introduction A microbe can be thought of as a bag of chemicals that interact with each other in a variety of ways; even the bag itself is composed of chemicals. Everything a microorganism is and does is related to chemistry. Organic chemistry is the study of compounds that contain carbon. Inorganic chemistry involves all other chemical reactions. Biochemistry is the chemistry of living cells. 2
Organic Chemistry Organic compounds contain carbon. Organic chemistry is the branch of science that studies organic compounds. Organic compounds are not necessarily related to living organisms; although some organic compounds are associated with living organisms, many are not. Organic chemistry involves the following chemical substances. Which ones are not directly related to living things? fossil fuels, dyes, drugs, paper, ink, paints, plastics, gasoline, rubber tires, food, and clothing. Organic Chemistry Carbon & Carbon Bonds All elements are listed on the periodic table. The atomic number indicates the number of protons. This equals the number of electrons. The elemental symbol is 1, 2, or 3 letters, with the first letter capitalized. The atomic weight is the number of protons plus the number of neutrons 3
Organic Chemistry Carbon Bonds Carbon atoms have a valence of 4, meaning that they can bond to four other atoms. 4
Organic Chemistry Carbon Bonds There are 3 ways in which carbon atoms can bond to each other: single bond, double bond, and triple bond. Organic Chemistry Carbon Bonds A covalent bond is one in which a pair of electrons is shared. 5
Organic Chemistry Carbon Bonds When atoms of other elements attach to available carbon bonds, compounds are formed. Organic Chemistry Carbon Bonds A series of carbon atoms bonded together is referred to as a chain. 6
Organic Chemistry Carbon Bonds, cont. If only hydrogen atoms are bonded carbon bonds, hydrocarbons are formed. Therefore, a hydrocarbon is an organic molecule that contains only carbon and hydrogen atoms; some examples of simple hydrocarbons are shown here: Organic Chemistry Cyclic Compounds When carbon atoms link to other carbon atoms to close a chain, they form rings or cyclic compounds. Benzene is a cyclic compound with six carbons and six hydrogens. 7
Biochemistry Biochemistry is the study of biology at the molecular level; it is the chemistry of living organisms. Biochemistry involves biomolecules present within living organisms; biomolecules are usually large molecules called macromolecules. Macromolecules include carbohydrates, lipids, proteins, and nucleic acids. Other examples: vitamins, enzymes, hormones, and energy-carrying molecules such as adenosine triphosphate (ATP). Biochemistry, cont. Humans obtain their nutrients from the foods they eat. Carbohydrates, fats, nucleic acids, and proteins contained in the foods are digested; their components are absorbed and carried to every cell in the body, where they are broken down and rearranged. Microorganisms also absorb their essential nutrients into the cell. The nutrients are then used in metabolic reactions as sources of energy and as building blocks for enzymes, structural macromolecules, and genetic materials. 8
Biochemistry Carbohydrates Carbohydrates are biomolecules composed of carbon, hydrogen, and oxygen (in the ratio 1:2:1). Examples include: Glucose, fructose, sucrose, lactose, maltose, starch, cellulose, and glycogen. 9
Biochemistry Carbohydrates Categories of carbohydrates include monosaccharides, disaccharides, and polysaccharides. Carbohydrates Monosaccharides Monosaccharides are the smallest and simplest of the carbohydrates. Mono means one, referring to the number of rings in the structure. Glucose (C 6 H 12 O 6 ) is the most important monosaccharide in nature; it may occur as a chain or in alpha or beta ring configurations. 10
Carbohydrates Monosaccharides, cont. The main source of energy for body cells is glucose. The three forms of glucose are shown above. Glucose is carried in the blood to cells where it is oxidized to produce energy-carrying ATP. ATP is the main energy source used to drive most metabolic reactions. Carbohydrates Disaccharides Di means 2; disaccharides are double-ringed sugars that result from the combination of 2 monosaccharides (with the removal of a water molecule) this is known as a dehydration synthesis reaction. Sucrose (table sugar), lactose and maltose, are examples of disaccharides. 11
Carbohydrates Disaccharides Disaccharides react with water in a process called a hydrolysis reaction This causes them to break down into 2 monosaccharides. The Dehydration Synthesis and Hydrolysis of Sucrose 12
Carbohydrates Disaccharides, cont. Recall that peptidoglycan is found in the cell walls of all members of the Domain Bacteria Peptidoglycan is a repeating disaccharide attached by proteins to form a lattice that surrounds and protects the bacterial cell. Carbohydrates Polysaccharides The definition of a polysaccharide varies from one reference book to anothe. In this book, polysaccharides are defined as carbohydrates that are composed of many monosaccharides. Most contain hundreds. Examples: starch and glycogen Polysaccharides serve 2 main functions: Storage of energy (e.g., glycogen in animal cells; starch in plant cells) Provide a tough molecule for structural support and protection (e.g., bacterial capsules) 13
Carbohydrates Polysaccharides, cont. Polysaccharides are examples of polymers molecules that consist of many similar subunits. In the presence of the proper enzymes or acids, polysaccharides may be hydrolyzed or broken down into disaccharides, and then into monosaccharides. Hydrolysis of Starch Carbohydrates Polysaccharides, cont. Plant and algal cells have cellulose (a polysaccharide) cell walls to provide support. Some protozoa, fungi, and bacteria have enzymes that can break down cellulose. 14
Lipids An important class of biomolecules. Most lipids are insoluble in water, but soluble in fat solvents, such as ether, chloroform, and benzene. Lipids are essential constituents of most living cells. Lipids can be classified into the following categories: -Waxes -Fats and oils -Phospholipids -Glycolipids -Steroids -Prostoglandins and leukotrienes The general structure of some categories of lipids. 15
Lipids Fatty Acids Fatty acids are the building blocks of lipids; they are long-chain carboxylic acids that are insoluble in water. Lipids Fatty Acids Saturated fatty acids contain 1 single bond between carbon atoms; they are solid at room temperature. 16
Lipids Fatty Acids Monounsaturated fatty acids have 1 double bond in the carbon chain; found in butter, olives, and peanuts. Lipids Fatty Acids Fatty acids are the building blocks of lipids; they are long-chain carboxylic acids that are insoluble in water. 17
Lipids Waxes A wax consists of a saturated fatty acid and a long-chain alcohol. Examples: the wax coating on fruits; leaves; skin, fur, and feathers of animals. The cell wall of Mycobacterium tuberculosis (the causative agent of tuberculosis) contains waxes. These waxes protect M. tuberculosis from digestion following phagocytosis by white blood cells. These waxes make M. tuberculosis difficult to stain and de-stain; explains why M. tuberculosis is acid-fast. Lipids Fats and Oils Fats and oils are the most common types of lipids. They are also known as triglycerides because they are composed of glycerol and 3 fatty acids. Fats are solid at room temperature. Oils are liquids at room temperature. Most fats come from animal sources (e.g, beef); most oils come from plant sources (e.g., olive oil). 18
Lipids Phospholipids Phospholipids contain glycerol, fatty acids, a phosphate group, and an alcohol. There are 2 types: The Lipid Bilayer Structure of Cell Membranes 19
Lipids Phospholipids, cont. The outer membrane of Gram-negative bacterial cell walls contains lipoproteins and lipopolysaccharide (LPS). LPS consists of a lipid and a polysaccharide portion. The cell walls of Gram-positive organisms do not contain LPS. Proteins Proteins are the most essential chemicals in all living cells; considered the substance of life. Some proteins are the structural components of membranes, cells and tissues; others are enzymes and hormones. All proteins are polymers of amino acids. All proteins contain carbon, hydrogen, oxygen, and nitrogen (and sometimes sulfur). 20
Proteins Amino Acids Amino acids contain carbon, hydrogen, oxygen and nitrogen; some also have sulfur in the molecule. The basic structure of an amino acid is shown here: Copyright 2011 Wolters Kluwer Health Lippincott Williams & Wilkins The Formation of a Dipeptide. 21
Proteins Enzymes Enzymes are protein molecules produced by living cells. They are known as biological catalysts - that is, they catalyze metabolic reactions. A catalyst is an agent that speeds up a chemical reaction without being consumed in the reaction. Almost every chemical reaction in a cell requires a specific enzyme. Some protein molecules function as enzymes by themselves; other proteins, called apoenzymes, only function when linked with a nonprotein cofactor such as Ca 2+, Fe 2+, Mg 2+, Cu 2+ or a coenzyme. Proteins Enzymes Some apoenzymes require vitamin-type compounds called coenzymes; examples are vitamin C, flavinadenine dinucleotide (FAD), and nicotinamide-adenine dinucleotide (NAD). The combination of an apoenzyme plus a cofactor is called a holoenzyme (i.e., a whole enzyme). Enzymes are usually named by adding the ending - ase to the word. Hemolysins and lysozyme are examples of enzymes not ending in ase. The specific molecule on which an enzyme acts is referred to as that enzyme s substrate. 22
Nucleic Acids Function DNA is the hereditary molecule the molecule that contains the genes and genetic code. Information in DNA must flow to the rest of the cell for the cell to function properly the flow is accomplished by RNA. RNA molecules participate in the conversion of the genetic code into proteins and other gene products. Nucleic Acids Structure In addition to the elements C, H, O, and N, DNA and RNA also contain phosphorus, P. The building blocks of nucleic acid polymers (DNA and RNA) are called nucleotides. Nucleotides are more complex monomers than amino acids. DNA contains dexoyribose as its pentose, whereas RNA contains ribose as it pentose. 23
DNA Structure For a double-stranded DNA molecule to form, the nitrogenous bases on the two separate strands must bond together. A always bonds with T via 2 hydrogen bonds. G always bonds with C via 3 hydrogen bonds. A-T and G-C are known as base pairs. The bonding forces of the double-stranded polymer cause it to assume the shape of a double alpha-helix, similar to a right-handed spiral staircase. Base pairs that occur in doublestranded DNA molecules. 24
Double-stranded DNA molecule, also known as a double helix. DNA Replication When a cell is preparing to divide, all DNA molecules in the chromosomes of the cell must duplicate, to ensuring that the same genetic information is passed on to both daughter cells. This is called DNA replication. http://youtu.be/hfz8o9d1tus DNA replication occurs by separation of the 2 DNA strands and the building of complementary strands by the addition of the correct DNA nucleotides. DNA polymerase is the most important enzyme required for DNA replication. 25
Semiconservative DNA Replication. DNA Replication Gene Expression A gene is a particular segment of a DNA molecule or chromosome. A gene contains the blueprint that will enable a cell to make what is known as a gene product. It is the sequence of the four nitrogenous bases of DNA (i.e., A, G, C, and T) that spell out the instructions for a particular gene product. Most genes code for proteins Some code for rrna and trna. 26
DNA Replication Gene Expression, cont. The Central Dogma explains the flow of genetic information within a cell (proposed by Francis Crick in 1957). DNA mrna protein. Also known as one gene one protein hypothesis. One gene of a DNA molecule is used to make one molecule of mrna by a process known as transcription. The genetic information in the mrna is then used to make one protein by a process known as translation. DNA Replication Gene Expression, cont. The process by which the genetic code within the DNA molecule is transcribed to produce an mrna molecule is called transcription. The primary enzyme involved is RNA polymerase. 27
DNA Replication Gene Expression, cont. In eucaryotes, transcription occurs within the nucleus; the newly formed mrna molecules then travel through the pores of the nuclear membrane into the cytoplasm, where they are used to produce proteins. http://youtu.be/983lhh20rgy http://youtu.be/41_ne5ms2ls In procaryotes, transcription occurs in the cytoplasm; ribosomes attach to the mrna molecules as they are being transcribed at the DNA thus both transcription and translation may occur simultaneously. Viral gene expression Reverse transcriptase (enzyme that does reverse transcription) http://youtu.be/by35navuwgy Viral replication http://youtu.be/styodr8houu DNA Replication Gene Expression, cont. The process of translating the message carried by mrna, whereby particular trnas bring amino acids to be bound together in the proper sequence to make a protein, is called translation. The base sequence of the mrna molecule is read in groups of 3 bases, called codons. The 3-base sequence codon can be read by a complementary 3-base sequence (the anticodon) on a trna molecule. 28
Chart to illustrate the sequence of 3 bases (GGC) in the DNA template that codes for a particular codon (CCG) in mrna, which in turn, attracts a particular anticodon (GGC) on the trna carrying an amino acid (proline). DNA mrna trna Amino Template (Codon) (Anticodon) Acid G C G G C G Proline C G C 29
Translation (protein synthesis) http://youtu.be/-zb6r1mmtkc 30