Fluent Essays

In your initial post, mention at least one "most interesting fact" from the Genetics lecture.  In addition, investigate pages 5-9 of the paper titled "Theory of..." located in the "supplemental folder" and describe at least one interesting fact related to microbial genetics from that paper.  Pages 5-9 is just one example, there are other relevant parts of the paper too.  600 words.  Please see enclosed Genetics Lecture PowerPoint and pages 5-9. Chapter 8: Microbial Genetics * Plasmids Exist in Cells Separate from Chromosomes Big Picture: Genetics The science of heredity Central dogma of molecular biology Mutations Gene expression controlled by operons Alteration of bacterial genes and/or gene expression Cause of disease Prevent disease treatment Manipulated for human benefit Big Picture: Genetics Structure and Function of the Genetic Material Learning Objectives 8-1 Define genetics, genome, chromosome, gene, genetic code, genotype, phenotype, and genomics. 8-2 Describe how DNA serves as genetic information. 8-3 Describe the process of DNA replication. 8-4 Describe protein synthesis, including transcription, RNA processing, and translation. 8-5 Compare protein synthesis in prokaryotes and eukaryotes. Structure and Function of the Genetic Material Genetics: the study of genes, how they carry information, how information is expressed, and how genes are replicated Chromosomes: structures containing DNA that physically carry hereditary information; the chromosomes contain genes Genes: segments of DNA that encode functional products, usually proteins Genome: all the genetic information in a cell Structure and Function of the Genetic Material The genetic code is a set of rules that determines how a nucleotide sequence is converted to an amino acid sequence of a protein Central dogma: Genotype and Phenotype Genotype: the genetic makeup of an organism Phenotype: expression of the genes DNA and Chromosomes Bacteria usually have a single circular chromosome made of DNA and associated proteins Short tandem repeats (STRs): repeating sequences of noncoding DNA Figure 8.1 A Prokaryotic Chromosome Chromosome The Flow of Genetic Information Vertical gene transfer: flow of genetic information from one generation to the next Horizontal gene transfer: flow of genetic information between individuals of the SAME generation (see the middle portion of the next slide!) Figure 8.2 The Flow of Genetic Information Parent cell DNA Genetic information is used within a cell to produce the proteins needed for the cell to function. Genetic information can be transferred horizontally between cells of the same generation. Genetic information can be transferred vertically to the next generation of cells. New combinations of genes Translation Cell metabolizes and grows Recombinant cell Offspring cells Transcription DNA Replication DNA forms a double helix “Backbone” consists of deoxyribose-phosphate Two strands of nucleotides are held together by hydrogen bonds between A-T and C-G Strands are antiparallel Order of the nitrogen-containing bases forms the genetic instructions of the organism DNA Replication One strand serves as a template for the production of a second strand Topoisomerase and gyrase relax the strands Helicase separates the strands A replication fork is created DNA Replication DNA polymerase adds nucleotides to the growing DNA strand In the 5‘ 3' direction Initiated by an RNA primer Leading strand is synthesized continuously Lagging strand is synthesized discontinuously, creating Okazaki fragments DNA polymerase removes RNA primers; Okazaki fragments are joined by the DNA polymerase and DNA ligase Figure 8.5 A Summary of Events at the DNA Replication Fork REPLICATION Proteins stabilize the unwound parental DNA. The leading strand is synthesized continuously by DNA polymerase. DNA polymerase Enzymes unwind the parental double helix. Primase Parental strand The lagging strand is synthesized discontinuously. Primase, an RNA polymerase, synthesizes a short RNA primer, which is then extended by DNA polymerase. DNA polymerase digests RNA primer and replaces it with DNA. DNA ligase joins the discontinuous fragments of the lagging strand. DNA polymerase DNA polymerase Okazaki fragment DNA ligase RNA primer Replication fork 3' 5' 5' 3' 3' 5' DNA Replication Energy Needs Energy for replication is supplied by nucleotides (remember, ATP is one example of a nucleotide!) Hydrolysis of two phosphate groups on ATP provides energy Figure 8.4 Adding a Nucleotide to DNA New Strand Template Strand Sugar Phosphate When a nucleoside triphosphate bonds to the sugar, it loses two phosphates. Hydrolysis of the phosphate bonds provides the energy for the reaction. DNA Replication Most bacterial DNA replication is bidirectional Each offspring cell receives one copy of the DNA molecule Replication is highly accurate due to the proofreading capability of DNA polymerase Figure 8.6 Replication of Bacterial DNA Check Your Understanding Check Your Understanding 8-3 Describe DNA replication, including the functions of DNA gyrase, DNA ligase, and DNA polymerase. RNA and Protein Synthesis Ribonucleic acid Single-stranded nucleotide 5-carbon ribose sugar Contains uracil (U) instead of thymine (T) Ribosomal RNA (rRNA): integral part of ribosomes Transfer RNA (tRNA): transports amino acids during protein synthesis Messenger RNA (mRNA): carries coded information from DNA to ribosomes Transcription in Prokaryotes Synthesis of a complementary mRNA strand from a DNA template Transcription begins when RNA polymerase binds to the promoter sequence on DNA Transcription proceeds in the 5‘ 3' direction; only one of the two DNA strands is transcribed Transcription stops when it reaches the terminator sequence on DNA Figure 8.7 The Process of Transcription TRANSCRIPTION DNA mRNA Protein RNA polymerase DNA RNA polymerase bound to DNA RNA polymerase RNA nucleotides Template strand of DNA RNA Promoter (gene begins) RNA polymerase RNA RNA synthesis Terminator (gene ends) RNA polymerase binds to the promoter, and DNA unwinds at the beginning of a gene. RNA is synthesized by complementary base pairing of free nucleotides with the nucleotide bases on the template strand of DNA. The site of synthesis moves along DNA; DNA that has been transcribed rewinds. Transcription reaches the terminator. Complete RNA strand RNA and RNA polymerase are released, and the DNA helix re-forms. Promoter Translation mRNA is translated into the “language” of proteins Codons are groups of three mRNA nucleotides that code for a particular amino acid (20 potential amino acids) Each amino acid is coded by several codons… but each codon will code for just one amino acid (the chart on next slide shows you this better): Translation Translation of mRNA begins at the start codon: AUG Translation ends at nonsense codons: UAA, UAG, UGA Codons of mRNA are “read” sequentially tRNA molecules transport the required amino acids to the ribosome tRNA molecules also have an anticodon that base-pairs with the codon Amino acids are joined by peptide bonds Figure 8.9 The Process of Translation Ribosome P Site Start codon Second codon mRNA On the assembled ribosome, a tRNA carrying the first amino acid is paired with the start codon on the mRNA. The place where this first tRNA sits is called the P site. A tRNA carrying the second amino acid approaches. Components needed to begin translation come together. mRNA Anticodon Ribosomal subunit Ribosomal subunit tRNA Figure 8.9 The Process of Translation Peptide bond forms A site mRNA E site mRNA Ribosome moves along mRNA The second codon of the mRNA pairs with a tRNA carrying the second amino acid at the A site. The first amino acid joins to the second by a peptide bond. This attaches the polypeptide to the tRNA in the P site. The ribosome moves along the mRNA until the second tRNA is in the P site. The next codon to be translated is brought into the A site. The first tRNA now occupies the E site. Figure 8.9 The Process of Translation tRNA released mRNA The second amino acid joins to the third by another peptide bond, and the first tRNA is released from the E site. The ribosome continues to move along the mRNA, and new amino acids are added to the polypeptide. mRNA Growing polypeptide chain Figure 8.9 The Process of Translation mRNA Polypeptide released Stop codon When the ribosome reaches a stop codon, the polypeptide is released. Finally, the last tRNA is released, and the ribosome comes apart. The released polypeptide forms a new protein. mRNA New protein Figure 8.10 Simultaneous Transcription and Translation in Bacteria TRANSLATION DNA mRNA Protein DNA RNA polymerase Direction of transcription Peptide Polyribosome Ribosome mRNA Direction of translation 5' In bacteria, translation can begin before transcription is complete Transcription in Eukaryotes In eukaryotes, transcription occurs in the nucleus, whereas translation occurs in the cytoplasm Exons are regions of DNA that code for proteins Introns are regions of DNA that do not code for proteins Small nuclear ribonucleoproteins (snRNPs) remove introns and splice exons together Check Your Understanding 8-5 How does mRNA production in eukaryotes differ from the process in prokaryotes? Figure 8.11 RNA Processing in Eukaryotic Cells The Regulation of Bacterial Gene Expression Constitutive genes are expressed at a fixed rate Other genes are expressed only as needed Inducible genes Repressible genes Catabolite repression Pre-Transcriptional Control Repression inhibits gene expression and decreases enzyme synthesis Mediated by repressors, proteins that block transcription Default position of a repressible gene is on Induction turns on gene expression Initiated by an inducer Default position of an inducible gene is off The Operon Model of Gene Expression Promoter: segment of DNA where RNA polymerase initiates transcription of structural genes Operator: segment of DNA that controls transcription of structural genes Operon: set of operator and promoter sites and the structural genes they control The Operon Model of Gene Expression In an inducible operon, structural genes are not transcribed unless an inducer is present In the absence of lactose, the repressor binds to the operator, preventing transcription In the presence of lactose, metabolite of lactose–allolactose (inducer)–binds to the repressor; the repressor cannot bind to the operator and transcription occurs Figure 8.12 An Inducible Operon Control region Structural genes Operon I P O Z Y A DNA Regulatory gene Promoter Operator Structure of the operon. The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I) Figure 8.12 An Inducible Operon RNA polymerase I P Z Y A Transcription Translation Repressor mRNA Active repressor protein Repressor active, operon off. The repressor protein binds with the operator, preventing transcription from the operon. Figure 8.12 An Inducible Operon (3 of 3) Allolactose (inducer) I P O Z Y A Transcription Translation Transacetylase Permease β-Galactosidase Inactive repressor protein Repressor inactive, operon on. When the inducer allolactose binds to the repressor protein, the inactivated repressor can no longer block transcription. The structural genes are transcribed, ultimately resulting in the production of the enzymes needed for lactose catabolism. Operon mRNA The Operon Model of Gene Expression In repressible operons, structural genes are transcribed until they are turned off Excess tryptophan is a corepressor that binds and activates the repressor to bind to the operator, stopping tryptophan synthesis Figure 8.13 A Repressible Operon Control region Structural genes Operon I P O E C A DNA Regulatory gene Promoter Operator Structure of the operon. The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I) D B Figure 8.13 A Repressible Operon (2 of 3) RNA polymerase I P O E D C B A Transcription Repressor mRNA Translation Inactive repressor protein Polypeptides comprising the enzymes for tryptophan synthesis Operon mRNA Repressor inactive, operon on. The repressor is inactive, and transcription and translation proceed, leading to the synthesis of tryptophan. Figure 8.13 A Repressible Operon (3 of 3) I P E D C B A Active repressor protein Tryptophan (corepressor) Repressor active, operon off. When the corepressor tryptophan binds to the repressor protein, the activated repressor binds with the operator, preventing transcription from the operon. Positive Regulation Catabolite repression inhibits cells from using carbon sources other than glucose Cyclic AMP (cAMP) builds up in a cell when glucose is not available cAMP binds to the catabolic activator protein (CAP) that in turn binds the lac promoter, initiating transcription and allowing the cell to use lactose Figure 8.14 The Growth Rate of E. Coli on Glucose and Lactose Bacteria growing on glucose as the sole carbon source grow faster than on lactose. Bacteria growing in a medium containing glucose and lactose first consume the glucose and then, after a short lag time, the lactose. During the lag time, intra-cellular cAMP increases, the lac operon is transcribed, more lactose is transported into the cell, and β-galacto-sidase is synthesized to break down lactose. Glucose Lactose All glucose consumed Glucose used Lag time Lactose used Figure 8.15 Positive Regulation of the Lac Operon Promoter lacZ lacl DNA Operator RNA polymerase can bind and transcribe cAMP Inactive CAP Active CAP Inactive lac repressor Lactose present, glucose scarce (cAMP level high). If glucose is scarce, the high level of cAMP activates CAP, and the lac operon produces large amounts of mRNA for lactose digestion. CAP-binding site CAP-binding site DNA lacl Promoter lacZ Operator RNA polymerase can't bind Inactive CAP Inactive lac repressor Lactose present, glucose present (cAMP level low). When glucose is present, cAMP is scarce, and CAP is unable to stimulate transcription. Epigenetic Control Methylating nucleotides turn genes off Methylated (off) genes can be passed to offspring cells Not permanent Changes in Genetic Material Mutation: a permanent change in the base sequence of DNA Mutations may be neutral, beneficial, or harmful Mutagens: agents that cause mutations Spontaneous mutations: occur in the absence of a mutagen Types of Mutations Base substitution (point mutation) Change in one base in DNA Missense mutation Base substitution results in change in an amino acid Nonsense mutation Base substitution results in a nonsense (stop) codon Frameshift mutation Insertion or deletion of one or more nucleotide pairs Shifts the translational “reading frame” Chemical Mutagens & radiation Nitrous acid: causes adenine to bind with cytosine instead of thymine Nucleoside analog: incorporates into DNA in place of a normal base; causes mistakes in base pairing Glyphosate / RoundUp has also been seen to be directly mutagenic (again, see paper in supplemental folder) Ionizing radiation (X-rays and gamma rays) causes the formation of ions that can oxidize nucleotides and break the deoxyribose-phosphate backbone UV radiation causes thymine dimers Repair of mutations can happen: Photolyases separate thymine dimers Nucleotide excision repair: Enzymes cut out incorrect bases and fill in correct bases Ultraviolet light Exposure to ultraviolet light causes adjacent thymines to become cross-linked, forming a thymine dimer and disrupting their normal base pairing. Thymine dimer An endonuclease cuts the DNA, and an exonuclease removes the damaged DNA. New DNA DNA polymerase fills the gap by synthesizing new DNA, using the intact strand as a template. DNA ligase seals the remaining gap by joining the old and new DNA. The Frequency of Mutation Spontaneous mutation rate = 1 in 109 replicated base pairs or 1 in 106 replicated genes Mutagens increase the mutation rate to per 10-5 or 10-3 replicated gene Identifying Mutants Positive (direct) selection detects mutant cells because they grow or appear different than unmutated cells Negative (indirect) selection detects mutant cells that cannot grow or perform a certain function Auxtotroph: mutant that has a nutritional requirement absent in the parent Identifying Chemical Carcinogens The Ames test exposes mutant bacteria to mutagenic substances to measure the rate of reversal of the mutation Indicates degree to which a substance is mutagenic IMPORTANT: If the Ames test suggests no mutagenicity, this is NOT a “for-sure” negative– sometimes chemicals react with a human protein to yield a carcinogen ! Genetic Transfer and Recombination Learning Objectives 8-14 Describe the functions of plasmids and transposons. 8-15 Differentiate horizontal and vertical gene transfer. 8-16 Compare the mechanisms of genetic recombination in bacteria. Genetic Transfer and Recombination Genetic recombination: exchange of genes between two DNA molecules…in particular, between 2 same-aged individuals instead of from parent to offspring; creates genetic diversity especially among microbes (which do not normally sexually reproduce…sexual reproduction / meiosis and fertilization is the norm for most multicellular creatures, but unicellular organisms cannot do that) Vertical gene transfer: transfer of genes from an organism to its offspring Horizontal gene transfer: transfer of genes between cells of the same generation Plasmids and Transposons Transposons = Mobile genetic elements Move from one chromosome to another or from one cell to another Occur in prokaryotic and eukaryotic organisms Plasmids are self-replicating circular pieces of DNA 1 to 5% the size of a bacterial chromosome Often code for proteins that enhance the pathogenicity of a bacterium Plasmids Conjugative plasmid: carries genes for sex pili and transfer of the plasmid Dissimilation plasmids: encode enzymes for the catabolism of unusual compounds Resistance factors (R factors): encode antibiotic resistance Transposons Transposons are segments of DNA that can move from one region of DNA to another Contain insertion sequences (IS) that code for transposase that cuts and reseals DNA Complex transposons carry other genes (e.g., in antibiotic resistance) Transformation in Bacteria Transformation: genes transferred from one bacterium to another as “naked” DNA Figure 8.28 The Mechanism of Genetic Transformation in Bacteria a b c d DNA fragments from donor cells Recipient cell A D B C Chromosomal DNA Recipient cell takes up donor DNA. Donor DNA aligns with complementary bases. Recombination occurs between donor DNA and recipient DNA. A D B C A D B C Degraded unrecombined DNA Genetically transformed cell a b c d b c d B C D a 5' 3' 5' 3' Conjugation in Bacteria Conjugation: plasmids transferred from one bacterium to another Requires cell-to-cell contact via sex pili Figure 8.30a Conjugation in E. coli RECOMBINATION Bacterial chromosome Mating bridge Replication and transfer of F factor F factor F+ cell F– cell When an F factor (a plasmid) is transferred from a donor (F+) to a recipient (F–), the F– cell is converted to an F+ cell. F+ cell F+ cell Transduction in Bacteria DNA is transferred from a donor cell to a recipient via a bacteriophage Generalized transduction: Random bacterial DNA is packaged inside a phage (virus that infects bacteria) and transferred to a recipient cell Specialized transduction: Specific bacterial genes are packaged inside a phage and transferred to a recipient cell Figure 8.32 Transduction by a Bacteriophage RECOMBINATION Phage protein coat Phage DNA Bacterial chromosome A phage infects the donor bacterial cell. Phage DNA and proteins are made, and the bacterial chromosome is broken into pieces. Occasionally during phage assembly, pieces of bacterial DNA are pack- aged in a phage capsid. Then the donor cell lyses and releases phage particles containing bacterial DNA. Phage DNA Bacterial DNA A phage carrying bacterial DNA infects a new host cell, the recipient cell. Recipient cell Donor bacterial DNA Recipient bacterial DNA Recombinant cell reproduces normally Recombination can occur, producing a recombinant cell with a genotype different from both the donor and recipient cells. Many cell divisions Donor cell Genes and Evolution Mutations and recombination create cell diversity Diversity is the raw material for evolution Natural selection acts on populations of organisms to ensure the survival of organisms fit for a particular environment Check Your Understanding Check Your Understanding 8-17 Natural selection means that the environment favors survival of some genotypes. From where does diversity in genotypes come?