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Questions and Answers
What is the primary function of DNA in organisms?
What is the primary function of DNA in organisms?
What shape is the bacterial chromosome typically?
What shape is the bacterial chromosome typically?
Where is the bacterial chromosome located within the cell?
Where is the bacterial chromosome located within the cell?
What do the nontranscribed segments of DNA between genes in bacterial chromosomes called?
What do the nontranscribed segments of DNA between genes in bacterial chromosomes called?
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How does the bacterial chromosome fit within the cell?
How does the bacterial chromosome fit within the cell?
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What accounts for the majority of bacterial DNA?
What accounts for the majority of bacterial DNA?
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Which of the following defines the nucleoid in bacteria?
Which of the following defines the nucleoid in bacteria?
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What type of genome do plants possess in addition to their nuclear genome?
What type of genome do plants possess in addition to their nuclear genome?
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Who first identified transposable elements, commonly referred to as 'jumping genes'?
Who first identified transposable elements, commonly referred to as 'jumping genes'?
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What mechanism is used for simple transposition of transposons?
What mechanism is used for simple transposition of transposons?
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What do retrotransposons primarily require for their mode of moving across the genome?
What do retrotransposons primarily require for their mode of moving across the genome?
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Which of the following statements is true for non-autonomous transposable elements?
Which of the following statements is true for non-autonomous transposable elements?
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What is the role of transposase in the transposition process?
What is the role of transposase in the transposition process?
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What type of retrotransposons are related to viruses but cannot produce viral particles?
What type of retrotransposons are related to viruses but cannot produce viral particles?
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What additional feature do simple transposons carry besides genes necessary for transposition?
What additional feature do simple transposons carry besides genes necessary for transposition?
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How do non-LTR retrotransposons differ from LTR retrotransposons in terms of structure?
How do non-LTR retrotransposons differ from LTR retrotransposons in terms of structure?
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Which of the following species has the highest percentage of its genome composed of transposable elements?
Which of the following species has the highest percentage of its genome composed of transposable elements?
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Which organism has the lowest reported abundance of transposable elements in its genome?
Which organism has the lowest reported abundance of transposable elements in its genome?
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What characterizes the nonautonomous version of Ds in transposable elements?
What characterizes the nonautonomous version of Ds in transposable elements?
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Which of the following species is reported to have a transposable element composition of approximately 40% in its genome?
Which of the following species is reported to have a transposable element composition of approximately 40% in its genome?
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What percentage of the total genome composition of transposable elements does the fruit fly (Drosophila melanogaster) have?
What percentage of the total genome composition of transposable elements does the fruit fly (Drosophila melanogaster) have?
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What is a characteristic feature of transposable elements (TEs) in the genome?
What is a characteristic feature of transposable elements (TEs) in the genome?
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How do retroelements primarily move within the genome?
How do retroelements primarily move within the genome?
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Which enzyme plays a crucial role in the processing of retrotransposons during transposition?
Which enzyme plays a crucial role in the processing of retrotransposons during transposition?
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What can occur when the number of transposable elements in a genome increases?
What can occur when the number of transposable elements in a genome increases?
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What is the approximate length of Ty elements found in yeast?
What is the approximate length of Ty elements found in yeast?
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What is the role of integrase in the transposition of retrotransposons?
What is the role of integrase in the transposition of retrotransposons?
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Which of the following statements is true regarding the occurrence of transposable elements in different species?
Which of the following statements is true regarding the occurrence of transposable elements in different species?
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What is one of the main functions of bacterial transposon Tn10?
What is one of the main functions of bacterial transposon Tn10?
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What is the primary role of DNA gyrase in bacterial supercoiling?
What is the primary role of DNA gyrase in bacterial supercoiling?
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Which of the following statements about eukaryotic chromosomes is incorrect?
Which of the following statements about eukaryotic chromosomes is incorrect?
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How does negative supercoiling affect DNA function in bacteria?
How does negative supercoiling affect DNA function in bacteria?
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What is a common characteristic of repetitive DNA sequences in eukaryotic genomes?
What is a common characteristic of repetitive DNA sequences in eukaryotic genomes?
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Which statement is true about the structure of bacterial chromosomes?
Which statement is true about the structure of bacterial chromosomes?
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What is the role of nucleoid-associated proteins (NAPs) in bacterial DNA structure?
What is the role of nucleoid-associated proteins (NAPs) in bacterial DNA structure?
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What defines topoisomers in the context of DNA structure?
What defines topoisomers in the context of DNA structure?
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Which of the following drug classes serves as a target for bacterial topoisomerases?
Which of the following drug classes serves as a target for bacterial topoisomerases?
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In eukaryotic species, how many genes can a single chromosome typically contain?
In eukaryotic species, how many genes can a single chromosome typically contain?
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What is the typical structure of eukaryotic chromosomes?
What is the typical structure of eukaryotic chromosomes?
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What does the selfish DNA hypothesis propose about transposons?
What does the selfish DNA hypothesis propose about transposons?
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What are potential consequences of unregulated transposon activity?
What are potential consequences of unregulated transposon activity?
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Which of the following outcomes results from incorrect excision of transposons?
Which of the following outcomes results from incorrect excision of transposons?
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How can transposons contribute to antibiotic resistance in bacteria?
How can transposons contribute to antibiotic resistance in bacteria?
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Which phenomenon involves the insertion of exons into the coding region of other genes?
Which phenomenon involves the insertion of exons into the coding region of other genes?
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What is likely to occur if transposons stimulate chromosomal rearrangements?
What is likely to occur if transposons stimulate chromosomal rearrangements?
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Which effect does the insertion of a transposon into a gene typically cause?
Which effect does the insertion of a transposon into a gene typically cause?
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What can occur due to homologous recombination between transposons?
What can occur due to homologous recombination between transposons?
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Study Notes
DNA: The Genetic Material
- DNA is the genetic material, storing information for producing an organism
- DNA's instructions are carried out through its base sequence
- DNA is necessary for synthesizing RNA and cellular proteins
- DNA also replicates chromosomes, ensuring proper chromosome segregation and compaction within the cell (fitting the cell).
Bacterial Chromosomes
- Typically circular and a few million base pairs long
- Examples, E. coli ~4.6 million base pairs, Haemophilus influenzae ~1.8 million base pairs
- Contain thousands of genes, mostly protein-encoding
- Intergenic regions are non-transcribed DNA segments between genes
- Repetitive sequences play roles in DNA folding, gene regulation and genetic recombination.
Chromosomes and Genomes
- Chromosomes are structures containing genetic material; a genome is all genetic material in an organism
- Bacterial genomes are typically a single circular chromosome
- Eukaryotic genomes include a nuclear genome (complete set of nuclear chromosomes) and potential additional mitochondrial and chloroplast genomes (in plants).
Bacterial Chromosome Structure
- Located in the nucleoid region of the cell
- Not surrounded by a membrane
- DNA is in direct contact with the cytoplasm
Bacterial Chromosome Compaction
- DNA must be compacted ~1000-fold to fit within the bacterial cell
- The chromosome has a central core with loops called microdomains emanating from the core.
- Microdomains are typically ~10,000 bp in length.
- Adjacent microdomains are typically organized into macrodomains, which are 800-1000 kbp long
- Nucleoid-associated proteins (NAPs) form the micro and macro domains.
- NAPs act as bridges, compressing DNA and helping to organize it into distinct regions.
DNA Supercoiling
- Twisting forces on DNA result in supercoiling, where DNA coils around each other
- Supercoiling can either be positive (overwinding) or negative (undertwisting), differing in supercoiling levels
- DNA structures differing in supercoiling are topoisomers of one another
- Supercoiling is a structural strain related to DNA conformation (coiling patterns)
- Supercoiling relieves tension from helical stress, which occurs during processes like DNA replication and transcription when DNA separates.
- Negative supercoiling is common in bacteria, contributing to chromosome compaction and enhancing processes like DNA replication and transcription.
- DNA gyrase (topoisomerase II) and topoisomerase I control supercoiling in bacteria; topoisomerase I relaxes negative supercoils, while DNA gyrase creates negative supercoils using energy from ATP
- Supercoiling is targeted by certain drugs for curing bacterial diseases.
Eukaryotic Chromosomes
- Consist of one or more sets of chromosomes
- Each set contains several different linear chromosomes.
- Chromosomes are tens or hundreds of millions of base pairs long
- Contain origins of replication, centromeres (segregation during mitosis and meiosis), kinetochore proteins, and telomeres (prevent translocation and maintain chromosome length).
Eukaryotic Genes
- Located between telomeric regions
- Single chromosome has hundreds to thousands of genes
- Less complex eukaryotes (like yeast) have relatively short genes concentrated on primarily coding polypeptides.
- More complex eukaryotes like mammals have longer genes, with many introns (non-coding intervening sequences).
Sizes of Eukaryotic Genomes
- Genome size varies considerably amongst species (sometimes due to more genes)
- Size variation in closely related species is often due to repetitive DNA sequences (not extra genes).
- Repetitive sequences may not have coding functions for proteins.
Sequence Complexity
- Complexity refers to the number of times a particular base sequence appears in a genome.
- Classifications of repetitive sequences include: unique/non-repetitive, moderately repetitive, and highly repetitive.
Unique and Repetitive Sequences
- Unique/(non-repetitive) sequences: Found once or a few times, including protein-coding genes and other non-coding DNA
- Moderately repetitive sequences: Found a few hundred to thousands of times, including rRNA genes and transposable elements (TEs).
- Highly repetitive sequences: Found tens of thousands to millions of times, often found in centromeric regions, and with functions not fully understood.
- TEs are segments of DNA that can move, sometimes increasing the number of copies in several different locations within a genome.
Transposition Pathways
- Two transposition pathways exist: simple and retrotransposition.
- Simple transposition: Mechanism: A cut-and-paste mechanism where the transposable element (TE) is removed from its original location and inserted into a new location.
- Retrotransposition: Mechanism: A TE is transcribed into RNA, then reverse transcriptase creates a DNA copy that is inserted into a new location.
- These TEs are called transposons or retroelements.
Transposons
- Simple transposons consist of flanking direct repeats, inverted repeats, and a transposase gene
- Example: antibiotic resistance gene is found in a transposon.
- Retrotransposons (e.g., LTRs and non-LTRs) are based on RNA intermediates using reverse transcription
- Autonomous elements include all necessary information for transposition, whereas non-autonomous elements lack necessary information and rely on autonomous elements.
Transposase
- Enzyme responsible for cutting and rejoining DNA during transposition
- Binds to inverted repeats (IRs), causing DNA cleavage between IRs and direct repeats (DRs).
- Excises TE from the chromosome and inserts it into another location
Transposable Elements Influence on Mutation and Evolution
- Researchers have discovered that transposable elements are present in most species' genomes.
- They can rapidly enter and proliferate within a genome
- Transposable sequences can affect chromosome structure, gene expression, and other processes.
Biological Significance of Transposable Elements
- Selfish DNA hypothesis: TEs exist due to their capability to proliferate within a host organism without substantially harming it (like parasitic behavior)
- TEs can offer adaptive advantages, such as carrying antibiotic resistance genes, causing exon shuffling in genes to enhance functionality by adding exons
- TEs can be harmful, e.g causing hybrid dysgenesis and disruptions of chromosomal structure (and gene activity)
Negative Effects of Transposable Elements
- Transposition can disrupt chromosomal structure and gene expression
- Transposition can be stimulated by radiation, mutagens, or hormones and cause chromosomal issues such as abnormalities and sterility.
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Description
Explore the fundamental role of DNA as the genetic material in organisms. Understand the structure and function of bacterial chromosomes, including examples and the significance of intergenic regions. Dive into the relationship between chromosomes and genomes in both bacterial and eukaryotic cells.
