Mammalian Genome Variation

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Questions and Answers

What is the term for the entirety of genetic material within a cell or organism?

Autosome

Karyotype

Phenotype

Genome (correct)

What is the term for a variant form of a sequence present at a particular locus?

Genotype

Phenotype

Allele (correct)

Locus

What is the process that leads to mutations arising from exposure to natural processes that occur within the cell?

Single nucleotide variants

Endogenous mutational process (correct)

Exogenous mutational process

Linkage

What is the term for the sequence structure at the end of chromosomes?

Telomere Signup and view all the answers

What is the term for the set of chromosomes within a cell?

Karyotype Signup and view all the answers

What is the term for the genetic constitution of a particular individual?

Genotype Signup and view all the answers

What is the term for two loci that are located close together on the same chromosome and are frequently inherited together?

Linkage Signup and view all the answers

What is the term for a mutation that involves the insertion or deletion of a single DNA base?

Single nucleotide variants Signup and view all the answers

What percentage of the mammalian genome is made up of coding exons?

1 - 2% Signup and view all the answers

Which class of genome variation involves large-scale DNA mutations that juxtapose previously unconnected DNA?

Structural variants Signup and view all the answers

What commonly causes indels?

Polymerase slippage Signup and view all the answers

Which type of genome variation involves gaining or losing whole chromosomes?

Cytogenetic variation Signup and view all the answers

Which type of transposable elements encodes the machinery needed for transposition?

Autonomous elements Signup and view all the answers

How is genome variation typically discovered?

Through whole genome sequencing Signup and view all the answers

Which type of genome variation is inherited?

Germline variation Signup and view all the answers

Which statement is true about balanced structural variants?

They do not lead to gain or loss of DNA Signup and view all the answers

What typically joins sister chromatids together?

Centromere Signup and view all the answers

What type of chromosome is an autosome?

Any chromosome that is not a sex chromosome Signup and view all the answers

In mammals, what are the sex chromosomes?

X and Y chromosomes Signup and view all the answers

What term describes a specific fixed genomic position where a gene is located?

Locus Signup and view all the answers

What does a reference genome represent?

A completely sequenced genome used for comparison Signup and view all the answers

What mutation can result from exposure to ultraviolet light?

Exogenous mutational process Signup and view all the answers

How would you describe a diploid cell?

Contains two copies of each chromosome Signup and view all the answers

What is the result when spontaneous deamination of 5-methylcytosine occurs?

Endogenous mutation Signup and view all the answers

Study Notes

Genome Variation and Karyotypes

Mammals have varying karyotypes and genome sizes, but a similar number of genes, which make up approximately 1-2% of the genome.
Genome variation can be classified into five categories: single nucleotide variants (SNVs), small insertions and deletions (indels), structural variants, transposable element insertions, and cytogenetic variants.

Types of Genome Variation

Single nucleotide variants (SNVs): the mutation of a single DNA base into a different base.
Small insertions and deletions (indels): insertions and deletions less than 100 base pairs in length, frequently caused by polymerase slippage.
Structural variants: large-scale DNA mutations that juxtapose DNA that was previously not connected, can be inter-chromosomal or intra-chromosomal.
Transposable element insertions: autonomous (encode the machinery needed for transposition) or non-autonomous (use the transposition machinery of a different class of transposable element).
Cytogenetic variants: the gain or loss of one or more entire chromosomes, causing aneuploidy.

Effects of Genome Variation

Most genome variation is non-pathogenic, but a small subset of genetic variants cause or contribute to disease.
Genome variation can be caused by exogenous or endogenous mutational processes.
Unbalanced structural variants can lead to copy number variation.

Genome Analysis and Repair

Genome variation is discovered by whole genome sequencing, which involves shearing DNA into small segments and aligning these to the reference genome.
The cell has DNA repair mechanisms, and those genome variants that we observe are those that escape repair.
Genome variation can be germline (inherited) or somatic (private to the individual).

Glossary

Genome: the entirety of genetic material (DNA) within a cell or organism.
Karyotype: the set of chromosomes within a cell.
Autosome: any chromosome that is not a sex chromosome.
Telomere: the sequence structure at the end of chromosomes.
Centromere: the region of the chromosome that attaches to the mitotic spindle, and the region where two sister chromatids are joined.
Reference genome: a completely sequenced genome isolate from a particular species that is used as a reference for genome analysis.
Genotype: the genetic constitution of a particular individual.
Phenotype: the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.
Locus: a specific fixed genomic position in the genome where a particular gene or genetic marker is located.
Allele: a variant form of a sequence present at a particular locus.
Linkage: two loci which are located close together on the same chromosome and which are frequently inherited together.

Genome and Chromosomes

Genome: the entirety of genetic material (DNA) within a cell or organism
Karyotype: the set of chromosomes within a cell
Diploid: two copies of each chromosome are present
Tetraploid: four copies of each chromosome are present
Autosome: any chromosome that is not a sex chromosome
Sex chromosome: X and Y chromosomes (in mammals)

Chromosome Structure

Telomere: the sequence structure at the end of chromosomes
Centromere: the region of the chromosome that attaches to the mitotic spindle, and the region where two sister chromatids are joined
Sister chromatids: identical copies of a duplicated chromosome, joined at the centromere

Genome Analysis

Reference genome: a completely sequenced genome isolate from a particular species that is used as a reference for genome analysis
Genotype: the genetic constitution of a particular individual

Characteristics and Variations

Phenotype: the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment
Locus (plural loci): a specific fixed genomic position in the genome where a particular gene or genetic marker is located
Allele: a variant form of a sequence present at a particular locus
Linkage: two loci which are located close together on the same chromosome and which are frequently inherited together

Mutations

Single nucleotide variants (SNVs): the mutation of a single DNA base into a different base
Exogenous mutational process: a process that leads to mutations that arises from exposure to exogenous agents, such as cigarette smoke carcinogens or ultraviolet light
Endogenous mutational process: a process that leads to mutations that arises from exposure to natural processes that occur within the cell, such as spontaneous deamination of 5-methylcytosine
Small insertions and deletions (indels): a mutation that involves insertion or deletion of a small sequence of DNA bases

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Description

Learn about the differences in karyotypes and genome size among mammals, as well as the types of genome variation and their effects on disease.