DNA and Bacterial Chromosomes Overview

Unique sequences = Found once or a few times in the genome Moderately repetitive sequences = Found a few hundred to a few thousand times Highly repetitive sequences = Found tens of thousands to millions of times Transposable elements = Short segments of DNA that can move within the genome

Genes for rRNA = Moderately repetitive sequences Alu family = Highly repetitive sequences AATAT = Highly repetitive sequences Protein coding genes = Unique sequences

Transposition = Process in which a DNA segment is inserted into a new location Genome complexity = Number of times a particular sequence appears in the genome Centromeric regions = Common location for highly repetitive sequences Introns = Non-coding DNA found within unique sequences

<p>Highly repetitive sequences = Function is not well understood Moderately repetitive sequences = Includes transposable elements Unique sequences = Make up roughly 41% of the human genome Transposable elements = Can move to new locations in the genome</p> Signup and view all the answers

<p>AATATAT in Drosophila = Highly repetitive sequences Protein coding genes = Unique or non-repetitive sequences Genes for rRNA = Moderately repetitive sequences Alu family in humans = Highly repetitive sequences</p> Signup and view all the answers

<p>Genome = All the genetic material of an organism Nucleoid = Region of the cell where bacterial chromosome is found Intergenic regions = Nontranscribed DNA segments between genes Bacterial chromosome = Usually a single circular molecule</p> Signup and view all the answers

<p>Synthesis of RNA = Production of RNA from DNA Replication of chromosomes = Duplication of genetic material Gene regulation = Control of gene expression Chromosome compaction = Fitting DNA within the cell</p> Signup and view all the answers

<p>Escherichia coli = ~ 4.6 million base pairs Haemophilus influenzae = ~ 1.8 million base pairs Bacillus subtilis = ~ 4.2 million base pairs Streptococcus pneumonie = ~ 2.0 million base pairs</p> Signup and view all the answers

<p>Microdomains = Loops extending from the chromosome core Central core = Main structural region of bacterial DNA Origin of replication = Initiation site for DNA replication Cytoplasm = Medium surrounding the nucleoid</p> Signup and view all the answers

<p>Nuclear genome = Eukaryotes Mitochondrial genome = Animals and plants Chloroplast genome = Plants Bacterial genome = Prokaryotes</p> Signup and view all the answers

<p>Protein-encoding genes = Majority of bacterial DNA Repetitive sequences = Roles in DNA folding and regulation Structural genes = Define traits and functions of the cell Noncoding DNA = Segments that do not encode proteins</p> Signup and view all the answers

<p>Compact structure = 1000-fold compaction in the cell Circular shape = Distinctive feature of bacterial chromosomes Length variability = Few million bps in typical bacteria Direct cytoplasmic contact = Nucleoid is not membrane-bound</p> Signup and view all the answers

<p>Genome complexity = Represents full genetic potential Gene density = High in bacterial chromosomes Chromosome number = Typically one in bacteria Genetic recombination = Involves exchange of DNA segments</p> Signup and view all the answers

<p>Negative supercoiling = Compacts the chromosome Positive supercoiling = Creates tension causing DNA strand separation Supercoiling control = Influenced by DNA gyrase and topoisomerase I Topoisomerase I = Relaxes negative supercoils</p> Signup and view all the answers

<p>DNA gyrase = Creates negative supercoils using ATP Topoisomerase I = Relaxes negative supercoils Ciprofloxacin = Inhibits bacterial topoisomerases Coumarins = Another class of topoisomerase inhibitors</p> Signup and view all the answers

<p>Origin of replication = Site where replication starts Centromere = Role in chromosome segregation Kinetochore = Links centromere to spindle apparatus Telomere = Prevents chromosome translocations</p> Signup and view all the answers

<p>Transposons = TEs that move by a 'cut and paste' mechanism. Retrotransposons = TEs that move via retrotranscription. Flanking direct repeats = Sequences adjacent to the inserted TE. Inverted repeats = Palindromic sequences at the ends of TEs.</p> Signup and view all the answers

<p>Eukaryotic genes in yeast = Relatively small with few introns Complex eukaryotic genes = Long with many introns Intron lengths = Can range from less than 100 to over 10,000 bp Gene quantity = Hundreds to thousands per chromosome</p> Signup and view all the answers

<p>Genome size variation = Not necessarily related to complexity Salamander genome sizes = Two-fold difference in closely related species Repetitive DNA sequences = Do not encode proteins Genome compositions = Influenced by number of genes and repetitive sequences</p> Signup and view all the answers

<p>LTR Retrotransposons = Contain long terminal repeats and reverse transcriptase. Non-LTR Retrotransposons = Do not contain long terminal repeats. Autonomous TEs = Complete elements that can transpose independently. Nonautonomous TEs = Incomplete elements that rely on autonomous TEs for movement.</p> Signup and view all the answers

<p>Transposase = Enzyme that catalyzes the removal and reinsertion of TEs. Reverse transcriptase = Enzyme that synthesizes DNA from RNA. Integrase = Enzyme that helps insert TEs into new DNA sites. Endonuclease = Enzyme that cleaves DNA strands during transposition.</p> Signup and view all the answers

<p>Microdomain organization = Formed by NAPs Negative supercoil occurrence = One per 40 turns of the double helix Function of helicases = Unwind DNA for replication Role of supercoiling = Enhances replication and transcription</p> Signup and view all the answers

<p>Barbara McClintock = First to identify transposable elements in corn. Jumping genes = Common term used to describe transposable elements. Antibiotic resistance gene = Example of a gene carried by simple transposons. 7SL RNA gene = Origin of the Alu sequence in humans.</p> Signup and view all the answers

<p>Quinolones = Inhibit bacterial topoisomerases Coumarins = Target bacterial gyrase Ciprofloxacin = Used in anthrax treatment Topoisomerase inhibitors = Do not affect eukaryotic topoisomerases</p> Signup and view all the answers

<p>Transposase gene = Gene necessary for transposition. Long terminal repeats = Structural features of LTR retrotransposons. Inverted repeats = Sequences that flank transposons. Direct repeats = Repetitive sequences adjacent to TEs post-insertion.</p> Signup and view all the answers

<p>Microdomains = Organized into macrodomains NAPs = Form DNA bridges Chromosomal DNA in bacteria = Primarily negatively supercoiled Supercoiling tension = Facilitates strand separation</p> Signup and view all the answers

<p>Simple transposition = Involves a 'cut and paste' mechanism. Retrotransposition = Involves transcribing TE to RNA before DNA synthesis. TE increase = Occurs during retrotransposition. Excision = Removal of the TE from its original location.</p> Signup and view all the answers

<p>Corn = Complete Ac element. Ds element = Nonautonomous element needing transposase. 7SL RNA gene = Source for human Alu sequences. Bacteria = Example of a diverse group harboring TEs.</p> Signup and view all the answers

<p>Complete TEs = Also known as autonomous TEs. Incomplete TEs = Referred to as nonautonomous TEs. Transcription = The process involved in retrotransposition. Genome = The overall structure where TEs can move.</p> Signup and view all the answers

<p>Transposon = Uses a DNA template for transposition Retrotransposon = Uses an RNA intermediate for transposition Insertion Element = Commonly found in multiple copies Antibiotic Resistance Transposon = Carries genes for antibiotic resistance</p> Signup and view all the answers

<p>E. coli = IS1 S. cerevisiae = Ty elements Drosophila = P elements Humans = Alu</p> Signup and view all the answers

<p>Transcription = Produces RNA from retrotransposon Reverse Transcriptase = Synthesizes dsDNA from RNA Integrase = Catalyzes insertion of the TE into the genome RNA Template = Serves as a blueprint for DNA synthesis</p> Signup and view all the answers

<p>IS1 = $768$ bp Tn10 = $9300$ bp Alu = $300$ bp L1 = $6500$ bp</p> Signup and view all the answers

<p>Ac/Ds = Found in corn and other plants P elements = Absent from M strains of Drosophila Ty elements = About 35 copies per genome in S. cerevisiae L1 = About 500,000 copies in the human genome</p> Signup and view all the answers

<p>Transposition = Movement of transposable elements within the genome Replication = Transposable elements can replicate around this time Mutation = Transposable elements can influence genetic variability Proliferation = Rapid increase in the number of transposable elements</p> Signup and view all the answers

<p>IS1 = Transposon Ty elements = Retrotransposon L1 = Retrotransposon Ac = Transposon</p> Signup and view all the answers

<p>An insertion element usually in E. coli = IS1 Known for providing antibiotic resistance = Tn10 Found in the human genome at high copy numbers = Alu Commonly found in corn = Ac</p> Signup and view all the answers

<p>Frog (Xenopus laevis) = 77% Corn (Zea mays) = 60% Human (Homo sapiens) = 45% Fruit fly (Drosophila melanogaster) = 20%</p> Signup and view all the answers

<p>Chromosome breakage = Excision of a TE Gene inactivation = Insertion of a TE into a gene Mutation = Incorrect excision of TEs Gene duplications = Insertion of a gene into a transposon</p> Signup and view all the answers

<p>Chromosomal rearrangements = Homologous recombination between TEs Alteration in gene regulation = Transposition next to regulatory sequences Alteration in exon content = Insertion of exons into a gene Hybrid dysgenesis = Drosophila crosses with P elements</p> Signup and view all the answers

<p>Selfish DNA hypothesis = Exist because they can Advantage hypothesis = Offer beneficial functions Insertion of exons = Exon shuffling Antibiotic-resistance genes = In bacteria</p> Signup and view all the answers

<p>Corn (Zea mays) = 60% Human (Homo sapiens) = 45% Nematode (Caenorhabditis elegans) = 12% Bacterium (Escherichia coli) = 0.3%</p> Signup and view all the answers

<p>Radiation = Can cause transposition Mutagens = Increase mutations Hormones = Influence growth Temperature = Affect genetic stability</p> Signup and view all the answers

<p>Exon shuffling = New gene functions Gene inactivation = Loss of function Mutation = Change in sequence Chromosomal abnormalities = Structural changes</p> Signup and view all the answers

<p>Transposase = Enzyme facilitating transposition Nonautonomous TEs = Lack functional transposase gene Autonomous TEs = Can move independently TEs = Transposable elements</p> Signup and view all the answers

<p>Can proliferate like parasites = Selfish DNA hypothesis Deleterious transpositions eliminated = Advantage hypothesis Insertion into coding region = New functions via exons Impact on chromosome structure = Harmful outcomes</p> Signup and view all the answers