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Questions and Answers
What is the term for the entirety of genetic material found within a cell or organism?
What is the term for the set of chromosomes found in a particular species?
What is the term for chromosomes that are diploid in all individuals of a species, regardless of sex?
What is the term for the site of spindle attachment during mitosis and the site of constriction between the two sister chromatids in G2 cells?
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What percentage of the genome is non-coding?
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Approximately how many genes are there in the mammalian genome?
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What is the term for a completely sequenced genome isolate that is used as a reference for genetic studies?
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Which arm of the chromosome is longer?
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What are small insertions and deletions usually defined as?
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What type of genetic variation do indels represent?
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What is the characteristic of indels in terms of size?
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What is the primary feature of indels?
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What is the term used to describe small insertions and deletions?
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What is the primary characteristic of small insertions and deletions?
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What type of genetic variation do small insertions and deletions represent?
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What is the term used to describe small insertions and deletions?
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What is the characteristic of small insertions and deletions in terms of size?
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What is the definition of small insertions and deletions?
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What is the primary function of the reverse transcriptase encoded by autonomous transposable elements?
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How do non-autonomous transposable elements, such as SINE elements, achieve transposition?
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Which of the following is an example of the phenotypic effect caused by transposable element insertions?
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Which of the following correctly describes how transposable elements can contribute to disease?
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What type of sequences do autonomous transposable elements, such as LINE elements, usually encode?
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What is the primary purpose of using computational algorithms during the genome sequencing process?
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Which technology currently facilitates the identification of genome variation?
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What is the approximate current cost of sequencing a mammalian genome?
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What type of genomic variation can be identified by analyzing the number of reads mapping to the reference genome?
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What role do computer clusters play in the genome sequencing process?
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Study Notes
Genome and Chromosomes
- A genome is the entirety of genetic material (DNA) found within a cell or organism.
- DNA is made up of four nitrogenous bases: adenine (A), cytosine (C), guanine (G), and thymine (T).
- Chromosomes are linear elements that package DNA.
Karyotype
- A karyotype is the set of chromosomes found in a particular species.
- Mammals have a diploid karyotype, meaning they have two copies of each chromosome.
- Genome size and karyotype vary among mammals and do not relate to organism complexity.
Types of Chromosomes
- Autosomes are chromosomes that are diploid in all individuals of a species, regardless of sex.
- Sex chromosomes confer sexual traits and are different between males and females.
- In mammals, sex chromosomes are known as X and Y, and males are the heterogametic sex.
Chromosomal Structure
- Chromosomes have centromeres, which are the site of spindle attachment during mitosis.
- Chromosomes have telomeres, which are DNA sequences at the ends of chromosomes characterized by a conserved repeat structure.
- A chromosomal arm is the region from the centromere to the end of the telomere.
- The p-arm refers to the shorter of the two chromosome arms, and the q-arm to the longer arm.
Genome Composition
- The majority of the genome (~98%) is non-coding, meaning it does not encode protein-coding gene exons.
- The number of genes (~20,000) is fairly constant among mammals.
Reference Genome
- A reference genome is a completely sequenced genome isolate used as a reference for genetic studies.
- The human reference genome is the best assembled and annotated mammalian reference genome.
- Reference genomes exist for dozens of mammals, including dog, cat, and livestock species.
- Each base in the reference genome has its own unique genome coordinates, e.g., chr18:28,000,000, designating the 28,000,000th base on chromosome 18.
Indels
- Small insertions and deletions in DNA, usually defined as
- Involves insertion or deletion of a small number of nucleotides in a DNA sequence
Indels
- Small insertions and deletions in DNA, usually defined as
- Involves insertion or deletion of a small number of nucleotides in a DNA sequence
Transposable Elements
- Transposable elements are virus-like sequences that copy themselves and move around the genome.
- There are two types of transposable elements: autonomous and non-autonomous.
- Autonomous transposable elements, such as LINE elements, encode genes necessary for transposition, including reverse transcriptase.
- Non-autonomous transposable elements, such as SINE elements, rely on transposition proteins encoded by autonomous elements to support transposition.
- Transposable element insertions can disrupt genes and cause disease.
- An example of a disease caused by transposable element insertions is the merle phenotype observed in dogs.
Genome Variation Detection
- Genome variation is detected through whole genome sequencing.
- The process involves extracting DNA from cells and breaking it down into small, evenly-sized fragments.
- These fragments are then loaded onto a sequencing machine, which produces hundreds of millions of short sequences.
- Computer clusters (many computers working in parallel) are used to map these short sequence 'reads' back to the reference genome.
- Computational algorithms are used to identify variants, which are positions that differ between the sequenced genome and the reference genome.
- Whole genome sequencing can also identify copy number variants by detecting differences in the number of reads mapping to the reference genome.
- The current cost of sequencing a mammalian genome is approximately £1,000.
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Description
Test your knowledge of genomes, chromosomes, and their composition in cells and organisms. Learn about the nitrogenous bases, karyotype, and their variations among mammals.
