Microbiology: A Systems Approach, 2nd ed. Chapter 9: Microbial Genetics

Microbiology: A Systems Approach, 2nd ed. Chapter 9: Microbial Genetics 1  Outline and Learning Outcomes 9.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity 1. Define the terms genome and gene. 2. Differentiate between genotype...

Microbiology: A Systems Approach, 2nd ed. Chapter 9: Microbial Genetics 1  Outline and Learning Outcomes 9.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity 1. Define the terms genome and gene. 2. Differentiate between genotype and phenotype. 3. Diagram a segment of DNA, labeling all important chemical groups within the molecule. 4. Summarize the steps of bacterial DNA replication and the enzymes used in this process. 5. Compare and contrast the synthesis of leading and lagging strands during DNA replication. 2  9.1 Introduction to Genetics and Genes: Unlocking the Secrets of Heredity Genetics: the study of the inheritance (heredity) of living things – Transmission of traits from parent to offspring – Expression and variation of those traits – The structure and function of the genetic material – How this material changes Takes place on several levels: organismal, chromosomal, molecular 3 Levels of genetic study. The operations of genetics can be observed at the levels of organism, cell, chromosome, and DNA sequence (molecular level). 4 Figure 9.1 The Nature of the Genetic Material Must be able to self-replicate Must be accurately duplicated and separated from each daughter cell 5  The Levels of Structure and Function of the Genome Genome Chromosome Gene 6  Genome The sum total of genetic material of a cell Mostly in chromosomes Can appear in nonchromosomal sites as well In cells- exclusively DNA In viruses- can be either DNA or RNA 7 The general location and forms of the genome in selected cell types and viruses 8 Figure 9.2  Chromosome A discrete cellular structure composed of a neatly packed DNA molecule Bacterial chromosomes – Condensed and secured by means of histone-like proteins – Single, circular chromosome 9  Gene A certain segment of DNA that contains the necessary code to make a protein or RNA molecule Structural genes: code for proteins or code for RNA Regulatory genes: control gene expression Sum of all genes is an organism’s genotype The expression of the genotype creates traits which make up the phenotype. Some genes may not be expressed in the phenotype. All organisms contain more genes in their genotype than are manifested as a phenotype at a given time 10  The Size and Packaging of Genomes Vary greatly in size – Smallest viruses- 4 or 5 genes – Escherichia coli- 4,288 genes – Human cell- 20,000 to 25,000 genes The stretched-out DNA can be 1,000 times or more longer than the cell 11 An Escherichia coli cell disrupted to release its DNA molecule. The cell has spewed out its single, uncoiled DNA strand into the surrounding medium 12 The DNA Code: A Simple Yet Profound Message 1953: James Watson and Francis Crick – Discovered DNA is a gigantic molecule – A type of nucleic acid – With two strands combined into a double helix 13  General Structure of DNA Basic unit: nucleotide – Phosphate – Deoxyribose sugar – Nitrogenous base 14  Nucleotides Covalently bond to form a sugar-phosphate linkage- the backbone of each strand Each sugar attaches to two phosphates One bond is to the 5’ carbon on deoxyribose The other is to the 3’ carbon 15  Nitrogenous Bases Purines and pyrimidines Attach by covalent bonds at the 1’ position of the sugar The paired bases are joined by hydrogen bonds – Easily broken – Allow the molecule to be “unzipped” Pyrimidine: Adenine always pairs with thymine (A..T) Purine: Guanine always pairs with cytosine (G…C) 16  Antiparallel Arrangment One side of the helix runs in the opposite direction of the other- antiparallel One helix runs from 5’ to 3’ direction The other runs from 3’ to 5’ 17 18 DNA Replication: Preserving the Code and Passing it On The process of the genetic code duplicated and passed on to each offspring Must be completed during a single generation time (around 20 minutes in E. coli). 19  The Overall Replication Process Requires the actions of 30 different enzymes – Separate the strands – Copy its template – Produce two new daughter molecules 20 21 Figure 9.5 Simplified steps to show the semiconservative replication of DNA. Circular DNA has a special origin site where replication begins. When strands are separated, two replication forks form, and a DNA polymerase III complex enters at each fork. The DNA polymerases proceed in both directions along the DNA molecule, attaching the correct nucleotides according to the pattern of the template. 22 23 Figure 9.7 Completion of chromosome replication in bacteria. (a) As replication proceeds, one double strand loops away. (b) Final separation is achieved through action of topoisomerase IV and the final release of two completed molecules. The daughter cells receive these during binary fission 24  Outline and Learning Outcomes 9.2 Applications of the DNA Code: Transcription and Translation 6. Explain how the classical view of the “central dogma” has been changed by recent science. 7. Identify important structural and functional differences between RNA and DNA. 8. Illustrate the steps of transcription, noting the key elements and the direction of mRNA synthesis. 9. List the three types of RNA directly involved in translation. 10. Define the terms codon and anticodon, and list the four known start and stop codons. 11. Identify the locations of the promoter, the start codon, and the A and P sites during translation. 12. Indicate how eukaryotic transcription and translation differ from these processes in bacteria and archaea. 13. Explain the relationship between genomics and proteomics. 25  9.2 Applications of the DNA Code: Transcription and Translation Central dogma – Genetic information flows from DNA to RNA to protein The master code of DNA is used to synthesize an RNA molecule (transcription) The information in the RNA is used to produce proteins (translation) 26 Figure 9.8 Summary of the flow of genetic information in microbes. DNA is the ultimate storehouse and distributor of genetic information. (a) DNA must be deciphered into a usable language. It does this by transcribing its code into RNA helper molecules that translate that code into protein. (b) Other sections of the DNA produce very important RNA molecules that regulate genes and their products. 27  The Gene-Protein Connection The Triplet Code and the Relationship to Proteins – Three consecutive bases on the DNA strand- called triplets – A gene differs from another in its composition of triplets – Each triplet represents a code for a particular amino acid A protein’s primary structure determines its characteristic shape and function Proteins ultimately determine phenotype DNA is mainly a blueprint that tells the cell which kinds of proteins and RNAs to make and how to make them 28 Simplified view of the DNA-protein relationship. The DNA molecule is a continuous chain of base pairs, but the sequence must be interpreted in groups of three base pairs (a triplet). Each triplet as copied into mRNA codons will translate into one amino acid; consequently, the ratio of base pairs to amino acids is 3:1. 29 Figure 9.9 The Major Participants in Transcription and Translation Number of components participate, but most prominent: – mRNA – tRNA – regulatory RNAs – ribosomes – several types of enzymes – storehouse of raw materials RNAs: Tools in the Cell’s Assembly Line – RNA differs from DNA Single stranded molecule Helical form Contains uracil instead of thymine The sugar is ribose – Many functional types, from small regulatory pieces to large structural ones – Only mRNA is translated into a protein molecule 30 31  Outline and Learning Outcomes 9.3 Genetic Regulation of Protein Synthesis 14. Define the term operon and explain one advantage it provides to a bacterial cell. 15. Differentiate between repressible and inducible operons and provide an example of each. 16. List several antibiotic drugs and their targets within the transcription and translation machinery. 32  9.3 Genetic Regulation of Protein Synthesis and Metabolism Control mechanisms ensure that genes are active only when their products are required – Enzymes are produced as they are needed – Prevents the waste of energy and materials Prokaryotes organize collections of genes into operons – Coordinated set of genes regulated as a single unit – Either inducible or repressible Inducible- the operon is turned in by the substrate of the enzyme for which the structural genes code Repressible- contain genes coding for anabolic enzymes; several genes in a series are turned off by the product synthesized by the enzyme 33  The Lactose Operon: A Model for Inducible Gene Regulation in Bacteria Lactose (lac) operon Regulates lactose metabolism in Escherichia coli 34  A Repressible Operon Normally the operon is in the “on” mode and will be turned “off” only when the nutrient is no longer required The excess nutrient serves as a corepressor needed to block the action of the operon Example, arg operon 35 corepressor : is a substance that inhibits the expression of genes  Antibiotics that Affect Transcription and Translation Some infection therapy is based on the concept that certain drugs react with DNA, RNA, or ribosomes and alter genetic expression Based on the premise that growth of the infectious agent will be inhibited by blocking its protein-synthesizing machinery selectively Antibiotics often target the ribosome- inhibiting ribosomal function and ultimately protein synthesis 36  Outline and Learning Outcomes 9.4 DNA Recombination Events 17. Explain the defining characteristics of a recombinant organism. 18. Describe three forms of horizontal gene transfer used in bacteria. 37  9.4 Mutations: Changes in the Genetic Code Genetic change is the driving force of evolution Mutation: when phenotypic changes are due to changes in the genotype An alteration in the nitrogen base sequence of DNA Wild type: a microorganism that exhibits a natural, nonmutated characteristic Mutant strain: when a microorganism bears a mutation 38  Causes of Mutations Spontaneous mutation: random change in the DNA arising from errors in replication Induced mutation: results from exposure to known mutagens 39 40  Categories of Mutations Point mutations: involve addition, deletion, or substitution of single bases Frameshift mutations: mutations that occur when one or more bases are inserted into or deleted from a newly synthesized DNA strand – Changes the reading frame of the mRNA – Nearly always result in a nonfunctional protein 41  Repair of Mutations Most ordinary DNA damage is resolved by enzymatic systems specialized for finding and fixing such defects DNA that has been damaged by UV radiation – Restored by photoactivation or light repair – DNA photolayse- light-sensitive enzyme Excision repair – Excise mutations by a series of enzymes – Remove incorrect bases and add correct one 42 Excision repair of mutation by enzymes. (a) The first enzyme complex recognizes one or several incorrect bases and removes them. (b) The second complex (DNA polymerase I and ligase) places correct bases and seals the gaps. (c) Repaired DNA 43 Figure 9.21  Positive and Negative Effects of Mutations Mutations are permanent and inheritable Most are harmful but some provide adaptive advantages 44  Outline and Learning Outcomes 9.5 Mutations: Changes in the Genetic Code 19. Define the term mutation and discuss one positive and one negative example 45  9.5 DNA Recombination Events Recombination: when one organism donates DNA to another organism The end result is a new strain different from both the donor and the original recipient Bacterial plasmids and gene exchange Recombinant organism: Any organism that contains (and expresses) genes that originated in another organism 46  Transmission of Genetic Material in Bacteria Usually involves small pieces of DNA (plasmids or chromosomal fragments) Plasmids can replicate independently of the bacterial chromosome Three means of genetic recombination in bacteria – Conjugation – Transformation – Transduction 47 3 types of DNA transfer 48 Conjugation: Bacterial “Sex” 49 Transformation: Capturing DNA from Solution 50 51 Biomedical Importance of Conjugation Resistance (R) plasmids, or factors- bear genes for resisting antibiotics Can confer multiple resistance to antibiotics to a strain of bacteria R factors can also carry resistance to heavy metals or for synthesizing virulence factors 52