Bacterial Metabolism and Genetics Lecture PDF

Bacterial Metabolism and Genetics  Bacterial Metabolism Metabolism : refers to all the biochemical reactions that occur in a cell or organism Catabolism (Dissimilation) : - Pathways that breakdown organic substrates into smaller -releasesmolecules en...

Bacterial Metabolism and Genetics  Bacterial Metabolism Metabolism : refers to all the biochemical reactions that occur in a cell or organism Catabolism (Dissimilation) : - Pathways that breakdown organic substrates into smaller -releasesmolecules energy (used to form ATP) for growth and maintenance Anabolism (Assimilation) a building and bond-making process that forms larger macromolecules from smaller ones (cellular components) (biosynthesis) -requires the input of energy (ATP)  Metabolic Pathways Most biochemical reactions are part of a series of reactions referred to as a metabolic pathway: Pathways can be catabolic or anabolic Each reaction is catalyzed by its own enzyme. It usually takes multiple reactions to make "end-point“.  Enzymes and Their Role in Metabolism ❖ Enzymes, organic catalysts of a highly molecular structure, are produced by the living cell. ❖ They are of a protein nature, are strictly specific in action, and play an important part in the metabolism of microorganisms. ❖ proteins that accelerate the rate of a reaction without being changed themselves. ❖ Their specificity is associated with active centres formed by a group of amino acids.  SOURCES OF METABOLIC ENERGY The bacterial cell is a highly specialized energy transformer. Chemical energy generated by substrate oxidations is conserved by formation of high-energy compounds Such as adenosine diphosphate (ADP) and adenosine triphosphate (ATP). Or compounds containing the thioester bond such as acetyl CoA. How is ATP produced? In most organisms, energy from a “food source” is converted to energy in ATP by glycolysis followed by 1 of 2 processes: FERMENTATION (low ATP yield) RESPIRATION (high ATP yield)  SOURCES OF METABOLIC ENERGY The three major mechanisms for generating metabolic energy are: Fermentation Respiration Photosynthesis At least one of these mechanisms must be used if an organism is to grow.  SOURCES OF METABOLIC ENERGY Photosynthesis is similar to respiration. The difference in the two processes is that in photosynthesis, the reductant and oxidant are created photochemically by light energy absorbed by pigments in the membrane 6CO2 + 6H2O + sunlight 🡪 C6H12O6 + 6O2  Energy Production Depending on the biochemical mechanism used, bacterial metabolism can be categorized into three types: aerobic respiration, anaerobic respiration, and fermentation  Aerobic respiration -a series of reactions that converts glucose to CO2 and allows the cell to recover significant amounts of energy -utilizes glycolysis, the Krebs cycle, and the electron transport chain -relies on free oxygen as the final electron and hydrogen acceptor - used by all aerobic bacteria Aerobic respiration in prokaryotes  Anaerobic respiration Anaerobic respiration is the metabolic process in which inorganic compounds other than molecular oxygen serve as the terminal electron acceptors. Depending on the species, acceptors can be molecules such as nitrate or sulfate. Anaerobic respiration can be used as an alternative to aerobic respiration in some species (facultative organisms). Anaerobic respiration -involves glycolysis, the Krebs cycle, and the electron transport chain -uses NO3 - SO, 4 2- 3 , CO 3- , Fermentation -incomplete oxidation of glucose -oxygen is not required -organic compounds are final electron acceptors  Products of Fermentation in Microorganisms Alcoholic beverages: ethanol and CO2 Solvents: acetone, butanol Organic acids: lactic acid, acetic acid Vitamins, antibiotics, and hormones Catabolism of various organic molecules  Anabolism: Formation of Macromolecules Biosynthesis of polysaccharides Glucose Glycogen, Peptidoglycan (in bacteria) Biosynthesis of simple lipids Biosynthesis of amino acids Amination or transamination Bacterial genetics  Useful terms 🡪 Gene Segment of DNA coding for a functional product Usually 1 gene codes for 1 protein 🡪 Chromosome Structure made of DNA that contains the genes Carries hereditary info 🡪 Genome All the genetic info in a cell 🡪 Genotype The genes of an organism 🡪 Phenotype Expression of the genes  Bacterial chromosomes Bacteria are haploid they have a single chromosome and therefore a single copy of each gene. Eukaryotic cells are diploid they have a pair of each chromosome and therefore have two copies of each gene. In diploid cells, one copy of a gene (allele) may be expressed as a protein (i.e., be dominant), whereas another allele may not be expressed (i.e.,be recessive). The genetic material of a typical bacterium The genetic material of a typical bacterium, Escherichia coli, consists of a single circular DNA molecule with a molecular weight of about 2 × 109 and is composed of approximately 5 × 106 base pairs. This amount of genetic information can code for about 2000 proteins with an average molecular weight of 50,000. The DNA of the smallest free-living organism Mycoplasma has a molecular weight of 5 × 108. The DNA of human cells contains about 3 × 109 base pairs and encodes about 100,000 proteins  The flow of genetic information (Central Dogma) DNA Transcription mRNA Translation Protein Transcriptio n Copying of the sense strand of the DNA into mRNA Translatio n Transformation of the nucleotide sequence carried by the mRNA into the polypeptide amino acid sequence at the 70S ribosomes Translation Codon s How many codons are there? 64 codons Sense codons – 61(code for AMINO ACIDS) Nonsense codons – 3 codons (STOP CODONS) Start codon – AUG codes for methionine Stop codons -UAG, UAA, UGA  Mutation s 🡪 Mutation is a stable, heritable change in the genomic nucleotide sequence Mutations may be neutral Beneficial Harmful (mostly) Mutagen Agent that causes mutations Spontaneous mutations Occur in the absence of a mutagen  Types of Gene Mutations Point mutations (most common) – A single base at one point in the DNA sequence is inserted, deleted, or substituted by another base Frameshift mutations – (a type of point mutation) One or several base pairs are deleted or inserted into the DNA sequence Transposons or insertion sequences are integrated into the DNA. Types of Gene Mutations Point mutations – 3 types 1.Silent Mutation - the change in the codon but no change in amino acid 2. Missense Mutation - the change in the codon changes the amino acid thus the protein 3. Nonsense Mutation - the change in the codon change amino acid to Stop codon  MUTATION S (1) The base substitution silent mutation. This occurs when one base is inserted in place of another. It takes place at the time of DNA replication  Base substitution - missense mutation When the base substitution results in a codon that simply causes a different amino acid to be inserted  Base substitution - nonsense mutation When the base substitution generates a termination codon that stops protein synthesis prematurely Nonsense mutations almost always destroy protein function.  frameshift mutation The second type of mutation is the frameshift mutation. This occurs when one or more base pairs are added or deleted, It shifts the reading frame on the ribosome and results in incorporation of the wrong amino acids “downstream” from the mutation in the production of an inactive protein.  Gene transfer Genetic Recombination Vertical gene transfer Horizontal gene transfer Vertical gene transfer Occurs during reproduction between generation of cells Horizontal gene transfer The transfer of genes between cells of the same generation Plasmid s Can be integrated with Chromosomal DNA Episomes -Integrated form of plasmid with DNA Types of Plasmids F (fertility) factor Carries genes for sex pili and transfer of the plasmid R (resistance) factor Encodes antibiotic resistance Bacteriocin factor – Encodes for toxin that kills bacterial cell of the same or similar species that lack that factor Virulence factor – Encode for enzymes, structures or toxins that make bacteria pathogenic  Transposon s Small DNA segments "Jumping genes" Can move on same chromosome or to different chromosomes or plasmids Copy of their DNA and inserting the copy at another site in the bacterial chromosome or the plasmid. TRANSFER OF DNA BETWEEN BACTERIAL CELLS The transfer of genetic information from one cell to another can occur by three methods: conjugation transduction transformation From a medical viewpoint, the two most important consequences of DNA transfer are: (1) that antibiotic resistance genes are spread from one bacterium to another primarily by conjugation and (2) that several important exotoxins are encoded by bacteriophage genes and are transferred by transduction.  Bacterial Conjugation Conjugation is the mating of two bacterial cells DNA is transferred from the donor to the recipient cell The mating process is controlled by an F (fertility) plasmid (F factor), which carries the genes for the proteins required for conjugation. One of the most important proteins is pilin, which forms the sex pilus (conjugation tube). Conjugatio n  High Frequency Recombination -Hfr Some F+ cells have their F plasmid integrated into the bacterial DNA These cells are called Hfr (high-frequency recombination) cells During this transfer, the single strand of DNA that enters the recipient F– cell contains a piece of the F factor at the leading end followed by the bacterial chromosome and then by the remainder of the F factor. The donor cell genes can integrate at several different sites in the bacterial DNA. The newly acquired DNA can recombine into the recipient’s DNA and become a stable component of its genetic material. ▪Conjugation Hfr plasmid Conjugation Hfr plasmid incorporates directly into the host genome so increases probability of recombination  Transductio n Virus (bacteriophage) acts as a genetic vector, passing DNA from donor to recipient Donor DNA incorporates into recipient DNA Donor and recipient SAME SPECIES 2 Types: Generalized Transduction (random) Specialized Transduction (only specific genes) Transduction has been found to occur in variety of prokaryotes, including certain species of Bacteria: Escherichia coli, Pseudomonas, Salmonella, Staphylococcus, etc. The bacteriophage containing the bacterial DNA is called transduced DNA.  Transductio n Within the recipient cell, the phage DNA can integrate into the cell DNA and the cell can acquire a new trait—a process called lysogenic conversion. This process can change a nonpathogenic organism into a pathogenic one. Diphtheria toxin, botulinum toxin, cholera toxin, and erythrogenic toxin (Streptococcus pyogenes) are encoded by bacteriophages and can be transferred by transduction. Bacteriophage life cycle  Transformatio n Transformation is the transfer of DNA itself from one cell to another. Naked DNA transferred from dead donor into COMPETENT recipient Competent recipient is young, actively dividing or has receptors Donor and recipient usually closely related Donor DNA recombines with recipient Can confer: Virulence factors, antibiotic resistance  Transformatio n This occurs by either of the two following methods. In nature, dying bacteria may release their DNA, which may be taken up by recipient cells. There is little evidence that this natural process plays a significant role in disease. In the laboratory, an investigator may extract DNA from one type of bacteria and introduce it into genetically different bacteria. When purified DNA is injected into the nucleus of an eukaryotic cell, the process is called transfection. Transfection is frequently used in genetic engineering procedures. Transformatio n Comparison of Conjugation, Transduction, and Transformation References: Gerard J. Tortora, Berdell R. Funke, Christine L. Case - Microbiology_ an introduction-Pearson (2018) Chapter 5 and 8