Biology Chapter: DNA and Genetics

Chapter 9: An Introduction to Microbial Genetics

• Talaro's Foundations in Microbiology, 12th Edition, Barry Chess
• Book discusses microbial genetics
• Learning changes everything

Genetics and Genes

• Genetics is the study of heredity
• Genetics explores:
  • Transmission of traits from parent to offspring
  • Expression and variation of traits
  • Structure and function of genetic material
  • How genetic material changes

Levels of Structure and Function of the Genome

• Images of Enterobius vermicularis, Ascaris, and Drosophila polytene chromosomes shown
• Shows cell structure
• Access alternative text for image descriptions

Microbial Genomes

• Genome - the sum total of genetic material (DNA) in a cell
• Most exists as chromosomes
• Some appear in non-chromosomal sites:
  • Mitochondria
  • Chloroplasts
  • Plasmids
• Genome of cells = DNA
• Genome of viruses = DNA or RNA

Chromosomes

• Chromosome - discrete cellular structure composed of neatly packaged DNA
• Eukaryotic chromosomes are located in the nucleus and are multiple and linear
• Bacterial chromosomes are a single circular loop

Chromosomes 2

• Diagram of eukaryotic and prokaryotic cells and viruses, illustrating DNA, chromosomes, plasmids, and locations

Genotypes and Phenotypes 1

• Chromosome subdivided into genes = fundamental unit of heredity responsible for a given trait
• Site on chromosome that provides information for a specific cell function
• Segment of DNA containing the necessary code to make a protein or RNA molecule
• Three basic categories of genes:
  • Structural genes (code for proteins)
  • Genes that code for RNA
  • Regulatory genes (control gene expression)

Genotypes and Phenotypes 2

• All types of genes comprise the genetic makeup (genotype)
• Genotype expression creates observable traits (phenotype)

Size and Packaging of Genomes

• Smallest virus - 4 to 5 genes
• E. coli - single chromosome containing 4,288 genes
• Human cell - 46 chromosomes containing 31,000 genes
• Sophisticated packaging allows genome to fit inside cell

The Packaging of DNA 1

• DNA molecule compacted in the cell by supercoils (superhelices)
• In prokaryotes, DNA gyrase coils the chromosome tightly
• DNA gyrase introduces reversible twists in the DNA molecule
• Eukaryotes have more complex coiling, starting with nucleosomes (DNA around histone proteins)

The Packaging of DNA 2

• Images showing the different levels of DNA packaging, starting with DNA double helix, nucleosomes, chromatin fiber, and metaphase chromosomes

The Structure of DNA: Double Helix 1

• Basic unit of DNA structure is the nucleotide:
  • Deoxyribose sugar
  • Phosphate group
  • Nitrogenous base: adenine (A), guanine (G), thymine (T), cytosine (C)
• Nucleotides covalently bond to form a sugar-phosphate backbone

The Structure of DNA: Double Helix 2

• Diagram of DNA structure showing deoxyribose sugar, nitrogenous base, phosphate, and hydrogen bonds between base pairs

The Structure of DNA: Double Helix 3

• Nitrogenous bases covalently bond to the 1' carbon of each base, spanning the molecule's center to pair with a complementary strand
• Adenine (A) to thymine (T) with 2 hydrogen bonds
• Guanine (G) to cytosine (C) with 3 hydrogen bonds

The Structure of DNA: Double Helix 4

• Diagram of DNA double helix with deoxyribose-phosphate backbone, base pairs, and hydrogen bonds

The Structure of DNA: Double Helix 5

• Antiparallel arrangement of DNA strands
• Each strand provides a template for new strand synthesis
• Order of bases constitutes the DNA code

Significance of DNA Structure

• Maintenance of code during reproduction
• Base pairing ensures code retention; when separated, each strand is a template for replication.
• Provides variety to order bases, leading to RNA and protein synthesis (phenotype).

Concept Check: (1)

• In DNA, adenine pairs with thymine and cytosine pairs with guanine

Concept Check: (2)

• In DNA, adenine pairs with thymine and cytosine pairs with guanine

The Overall Replication Process 1

• Replication occurs simultaneously on both DNA strands
• Semiconservative process:
  • Uncoil parent DNA molecule
  • Separate two strands to expose nucleotide sequence
  • Synthesize two new complementary strands using single strands as templates

The Overall Replication Process 2

• Diagram of DNA replication showing replication fork, parental template strands, and synthesized daughter strands

The Overall Replication Process 3

• Diagram of DNA replication showing origin of replication, replication forks, and termination site; with DNA replication being semiconservative.

The Overall Replication Process 4

• Explanation of the figure for "Replication of a bacterial chromosome," describing replication start at the origin, moving replication forks, and termination at a site, the process is semiconservative.

Events in DNA Replication 1

• All chromosomes have a specific origin of replication site where it starts.
• The origin is AT-rich, making separation easier.
• Two replication forks synthesize new DNA, each with its own enzymes.

Events in DNA Replication 2

• Detailed process of DNA replication illustrated with steps. Helicase, primase, DNA polymerase III, DNA polymerase I, ligase, and gyrase act in the process of replication. Shows leading and lagging strands.

Events in DNA Replication 3

• Explanation of the figure of "replication of a circular bacterial chromosome," including the origin of replication, the bidirectional movement of replication forks, and their meeting at a termination site. Also specifies the semiconservative nature of the replication process.

Events in DNA Replication 4

• Description of events in DNA replication, including the location of the origin of replication, the movement of the replication forks, and their meeting at the termination site, with specification of the semiconservative nature of the process.

Enzymes Involved in DNA Replication and their Function

• Table of enzymes and their functions in DNA replication showing the activity of each in the process.

DNA Polymerase III

• Graphic illustration of DNA polymerase III at work in a DNA molecule during replication.

Concept Check: (3)

• The lagging strand of DNA is replicated in short pieces due to the DNA polymerase working in only one direction.

Concept Check: (4)

• The lagging strand of DNA is replicated in short pieces because the DNA polymerase works in only one direction,

Applications of the DNA Code 1

• Genetic information in DNA conveyed to RNA through transcription
• RNA information used to produce proteins via translation
• Specialized RNAs regulate gene function

Applications of the DNA Code 2

• Diagram of the process of transcription and translation, with DNA, RNA, ribosomes, and proteins.

Gene-Protein Connection

• Each structural gene is a sequence of nucleotides coding for a protein's primary structure.
• Groups of three consecutive bases on DNA become triplets (codons) on RNA, each specifying an amino acid.
• Protein's primary structure determines its shape and function.
• Proteins contribute to the cell phenotype as enzymes and structural components.

DNA-Protein Relationship

• Diagram showing DNA triplets, mRNA codons, and corresponding amino acids.

RNAs: Major Participants in Transcription and Translation

• RNA structure differs from DNA:
  • Single-stranded
  • Contains uracil (U) instead of thymine (T)
  • Riboses sugar instead of deoxyribose sugar
• RNA takes on secondary and tertiary levels of complexity giving different specialized forms of RNA (mRNA, tRNA, and rRNA)

Major Types of RNA

• Table of RNA types, their roles, and whether they are translated to protein

Messenger RNA (mRNA) 1

• mRNA is a transcribed version of genes in DNA.
• Synthesis is similar to the leading strand during DNA replication.
• Message is in codons (triplets).

Messenger RNA (mRNA) 2

• Illustrates single-strandedness and use of uracil instead of thymine. mRNA sequence GC-U-A-C-G-G-A-G-C-U-U-C-G-G-A-G-C-U-A-G. Codons shown.

Transfer RNA: tRNA 1

• Acts as a messenger translating mRNA code into protein.
• Structure a complex helix with cloverleaf structure and hairpin loops.
• Bottom loop is an anticodon.
• Binding site for amino acids specific to each anticodon.

Transfer RNA: tRNA 2

• tRNA strand loops back producing a cloverleaf structure.
• Anticodon specifies the attachment of a particular amino acid.

Transfer RNA: tRNA 3

• Diagrams showing the structure of tRNA with amino acid attachment site, hairpin loops, and anticodon

Ribosomal RNA: rRNA

• Prokaryotic 70S Ribosome, complex.
• Ribosome composed of rRNA and proteins. Has a structure that contributes to reading the mRNA code, facilitating tRNA interaction, and quickly producing proteins.

Transcription: The First Stage of Gene Expression

• Synthesis of RNA using DNA codes (template) in 3 stages:
  • Initiation: RNA polymerase binds to promoter region upstream of the gene.
  • Elongation: RNA polymerase adds complementary nucleotides (Uracil replaces Thymine) in the 5' to 3' direction from the DNA template strand.
  • Termination: RNA polymerase recognizes the "STOP" sign on DNA and releases the transcript (100-1,200 bases).

Major Events in Transcription (1)

• Each gene has specific promoter and leader sequence (initiating transcription)
• Ends with terminal sequences to stop translation.
• Initiation: RNA polymerase, bound by sigma factor, locates and unwinds DNA in the promoter region. Only the template strand is used for transcription reading 3' to 5'.

Major Events in Transcription (2)

• Elongation: RNA polymerase moves along the DNA strand.
• The mRNA strand forms following a 5' to 3' rule.
• Termination: RNA polymerase reaches termination site, releases the mRNA transcript.

Major Events in Transcription (3)

• Detailed illustration of stages in transcription.

Translation: The Second Stage of Gene Expression

• Elements (mRNA, tRNA, amino acids) needed to synthesize protein brought together in ribosomes.
• Translation occurs in 5 stages:
  • Initiation
  • Elongation
  • Termination
  • Protein folding and processing

The Master Genetic Code 1

• mRNA codons and corresponding amino acids shown.
• Code universal, redundant (multiple codons for same amino acid)

The Master Genetic Code 2

• Table of mRNA codons and corresponding amino acids. Shows the first, second and third base in the mRNA codon triplet. The START codon is AUG. Stop codons are UAA, UAG, and UGA..

Interpreting the DNA Code

• mRNA molecules are a complementary copy of DNA genes.
• tRNAs use anticodons to interpret mRNA codons and bring in specific amino acids.

Translation 1

• Ribosomes assemble on the 5' end of an mRNA transcript.
• Ribosome scans for the start codon (usually AUG).
• tRNA molecule and methionine (amino acid) enter ribosome and bind.

Translation 2

• Illustration of tRNA entrances into the ribosome. Methionine and leucine are two amino acids used.

Translation 3

• Illustration shows initial tRNA entries into the ribosome.

Translation 4

• Peptide bond formation (connecting amino acids)

Translation 5

• First tRNA is released to allow for the ribosome to move.

Translation 6

• tRNA enter the A site and another peptide bond is formed.

Translation 7

• Illustration shows a peptide bond forming

Translation 8

• Process continues until the ribosome reaches a stop codon.

Translation 9

• Illustration shows formation of a peptide bond and ribosome movement and the translation of further amino acids.

Translation Termination

• UAA, UAG, and UGA are stop codons.
• Ribosome falls off when a stop codon is reached.

Concept Check: (5)

• tRNA acts as a translator of mRNA codons into amino acids; the genetic code to mRNA.

Concept Check: (6)

• tRNA acts as a translator of mRNA codons into amino acids.

Polyribosomal Complex

• Multiple ribosomes on a single mRNA molecule.

Eukaryotic Transcription and Translation

• Transcription in the nucleus, translation in cytoplasm - Do not occur simultaneously
• Eukaryotic start codon has AUG (not formyl-methionine)
• Eukaryotic mRNA encodes a single protein (unlike bacterial mRNA, which encodes intervening sequences ).
• Eukaryotic DNA contain introns, noncoding sequences requiring splicing.

Splicing of Eukaryotic pre-mRNA 1

• Interrupted gene coding sequences called exons in eukaryotes
• Introns are transcribed but not translated; they are removed before translation
• Splicing does not occur in prokaryotes

Splicing of Eukaryotic pre-mRNA 2

• Illustrates the splicing of introns from the primary mRNA transcript.

Regulation of Protein Synthesis and Metabolism

• Genes are regulated to be active only when necessary.
• Prokaryotes regulate gene expression through operons (set of genes regulated as a single unit).

Operons

• Two types:
  • Inducible operons - turned ON by a substrate (catabolic operons); when nutrients are needed, enzymes are made.
  • Repressible operons - turned OFF by the product synthesized; (anabolic operons); stops producing when not needed.

Lactose (lac) Operon: Inducible Operon

• Made of 3 segments:
  • Regulator: gene that codes for repressor(protein).
  • Control locus: promoter and operator.
  • Structural locus: 3 genes for lactose-metabolizing enzymes
    • galactosidase
    • permease
    • galactosidase transacetylase

Lac Operon 1

• Normally off; repressor binds in absence of lactose to operator region to block transcription downstream structural genes.

Lac Operon 2

• Operon Off: No Lactose - repressor protein binds to the operator of the operon, preventing RNA polymerase from transcribing the structural genes (lacZ, lacY, and lacA) that encode lactose-processing enzymes.

Lac Operon 3

• Lactose acts as an inducer, binding to the repressor.
• Binding changes repressor shape, causing it to detach from the operator.
• RNA polymerase binds to the promoter allowing transcription of structural genes.

Lac Operon 4

• Illustration showing lactose turning operon on.

Arginine Operon: Repressible 1

• Operon normally on; only turned off when not needed. This happens when arginine (its product) builds up and acts as a corepressor.

Arginine Operon: Repressible 2

• Diagram of arginine operon in its on state, showing RNA polymerase transcribing structural genes and enzymes synthesizing arginine.

Arginine Operon: Repressible 3

• Operon is turned off when excess arginine is present to block RNA synthesis.

Arginine Operon: Repressible 4

• Diagram showing arginine operon in its repressed or off state.

RNA and Gene Expression 1

• Riboswitch regulates translation of mRNA to protein.
• RNA interference (noncoding RNA) regulates eukaryotes gene expression, through interactions.

RNA and Gene Expression 2

• Illustration showing riboswitch on and off states, with or without ligand causing translation to happen or be inhibited.

Concept Check: (7)

• If the operon repressor is active, transcription does NOT occur.

Concept Check: (8)

• If the operon repressor is active, transcription does NOT occur.

Mutations: Changes in the Genetic Code

• A change in phenotype due to a change in genotype is called a mutation.
• Wild-type (natural, nonmutated) characteristic of an organism is a normal characteristic.
• Mutant strain have variations in morphology, nutritional and genetic control mechanisms.

Isolating Mutants

• Replica plating technique used to identify mutants.
• By transferring colonies on master plates (complete vs incomplete mediums)
• Identify missing colonies from incomplete mediums show they are mutants.

Causes of Mutations 1

• Spontaneous mutations - random DNA changes due to errors in replication.
• Induced mutations - caused by mutagens (physical or chemical agents).

Causes of Mutations 2

• Table showing examples of chemical and radiation mutagens and their effects.

Categories of Mutations

• Point mutation (addition, deletion, or substitution of bases)
• Missense mutation (changes single amino acid)
• Nonsense mutation (changes codon to stop codon)
• Silent mutation (alters base but not amino acid)
• Back-mutation (mutated gene reverses to original).
• Frameshift mutations alter the reading frame of mRNA.

Effect of Major Types of Mutations 1

• Wild-type sequence as an example - THE BIG BAD CAT ATE THE FAT RED BUG - this is a natural unaltered characteristic. This is a common example used for sequencing comparison with changes.

Effect of Major Types of Mutations 2

• Missense mutations alter a single amino acid. Effects can range from negligible to severe

Effect of Major Types of Mutations 3

• Nonsense mutations introduce a stop codon prematurely. This usually leads to non-functional proteins. A severe effect from a mutation

Effect of Major Types of Mutations 4

• Frameshift mutations shifts the reading frame of mRNA altering virtually all amino acids after mutation usually giving rise to a non-functional protein.

Repair of Mutations

• Cells have repair mechanisms to correct damaged DNA
  • DNA polymerase proofreads during replication
  • Mismatch repair corrects mismatched nitrogen bases
  • Light repair corrects UV damage
  • Excision repair removes segments with incorrect sequences.

The Ames Test 1

• Chemical compounds capable of mutating bacterial DNA can also mutate mammalian DNA.
• Ames test is to screen for mutagenic compounds.
• Indicator organism - Salmonella missing the ability to synthesise histidine.

The Ames Test 2

• Detailed explanation of Ames test procedure. Shows the control plate and the test plate to determine the level of mutagenicity. Shows how the back-mutated are counted and used to detect likely carcinogens.

Positive and Negative Effects of Mutations

• Harmful mutations lead to non-functional proteins.
• Beneficial mutations allow adaptation and survival in environmental changes, leading to change in population and genetic variation.

Concept Check: (9)

• Deletion mutation causes a frameshift mutation.

Concept Check: (10)

• A deletion mutation causes a frameshift mutation

DNA Recombination Events

• Genetic recombination occurs when an organism expresses genes from another organism.
• Three means in bacteria:
  • Conjugation
  • Transformation
  • Transduction

Conjugation 1

• Transfer of plasmids or chromosomal fragments between donor and recipient cells via direct contact.
• Gram-negative cells use a fertility plasmid (F factor) and conjugative pilus for transfer.

Conjugation 2

• Illustration of physical conjugation mechanism in gram-negative bacteria.

Conjugation 3

• High-frequency recombination involves integrating the donor's fertility plasmid into the recipient's chromosome.

Conjugation 4

• Illustration showing F-factor transfer during conjugation.

Conjugation 5

• Illustration showing high-frequency recombination (Hfr transfer)

Transformation 1

• Recipient cell acquires DNA fragments from a lysed donor cell.
• Donor and recipient cells can be unrelated.
• Useful tool in recombinant DNA technology.

Transformation 2

• Illustration of transformation showing DNA fragment uptake via a receptor.

Transformation 3

• DNA fragment uptake into the cell and how it is incorporated into the receiving chromosome.

Griffith's Work on Transformation

• Illustration of Griffith's experiment demonstrates transformation. Living S cells cause pneumonia, while living R cells do not. Heat killed S cells don't cause pneumonia, but living R cells mixed with heat killed S cells results in pneumonia causing living S cells.

Transduction 1

• Bacteriophages transfer DNA between bacterial cells.
• Two types:
  • Generalized transduction
  • Specialized transduction

Transduction 2

• Illustration comparing generalized vs specialized transduction in bacteria.

Recombination: Intermicrobial DNA Exchange

• Three modes of microbial genetic recombination shown (conjugation, transformation, transduction). A table showing the mode, factors involved in each mode, and the types of genes transferred during each mode.

Transposons 1

• Special DNA segments capable of moving within a genome.
• Cause genetic rearrangement.
• Can move between chromosomes, plasmids, or from plasmid to chromosome.
• May have beneficial or harmful effects.

Transposons 2

• Illustration showing transposon movement.

Genetics of Animal Viruses

• Viral genome (DNA or RNA) encodes genes needed for new virus production and metabolic machinery.
• Viruses use host cells to synthesize new viral particles.
• Replication of DNA viruses typically occurs in the nucleus.
• Replication of RNA viruses often occurs in cytoplasm.
• Viruses translate viral mRNA into proteins using host cell ribosomes and tRNA.

Replication of dsDNA Viruses

• Illustration showing replication cycle of double-stranded DNA viruses. The viruses enters the nucleus and their DNA is replicated and used to produce new viral proteins.

Replication of ssRNA Viruses

• Illustration showing replication cycle of single-stranded RNA viruses. The virus RNA is delivered into the cytoplasm where its proteins are synthesized.

Concept Check: (11)

• Conjugation is genetic transfer via direct cell-to-cell contact involving plasmids.

Concept Check: (12)

• Conjugation is genetic transfer via direct cell-to-cell contact involving plasmids.

Test your knowledge on the fundamental concepts of DNA and genetics with this quiz. Explore topics such as gene functions, DNA replication mechanisms, and the roles of various enzymes involved in genetic processes. Perfect for students delving into biological sciences.