Questions and Answers
Who proposed the germ-plasm theory in 1893?
Weismann
What is the ultimate source of all genetic variation?
Evolution progresses by only random changes in gene frequencies.
False
Human somatic cells have ____ copies of each chromosome.
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Match the following cell types with their chromosome count:
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What is a locus?
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What is an allele?
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Genes on different chromosomes are transmitted dependently.
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In sexual reproduction, a paternal haploid sperm fertilizes a maternal haploid ______ to form a diploid zygote.
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Define genotype.
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What is another name for Short Tandem Repeats (STRs)?
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Which type of STRs usually manifest extensive polymorphism?
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Trinucleotide STRs are commonly used as genetic markers.
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What is the mutation rate for STR loci approximately per meiosis?
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How are STR assays usually conducted?
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What is the name of the first highly polymorphic DNA locus described in 1980?
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RFLPs are observed using a method known as PCR.
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A __________ is a specific place on a chromosome where a DNA sequence resides.
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Who proposed the first comprehensive theory of evolution based on inheritance of acquired characteristics?
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Jean Baptiste de Lamarck believed that characteristics acquired for survival are passed on to the next generation.
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What is the term used to describe the process by which species gradually change over time?
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Somatic cells proliferate by ________.
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Match the following cell types with their chromosome count:
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Define locus.
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What is an allele?
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Genes on different chromosomes are transmitted dependently. (True/False)
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In sexual reproduction, a paternal haploid sperm fertilizes a maternal haploid ovum to form a diploid ______.
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Match the genetic terms with their definitions:
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What are the two main families of VNTRs?
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What is characteristic of STR loci?
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What is the basis of DNA fragment length polymorphism in STRs?
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What is the frequency order of repeats in STRs?
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Trinucleotide STRs are often used as genetic markers.
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What is the mutation rate for STR loci?
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What is the purpose of STR assays?
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What is the basis of contemporary DNA profiling?
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What is the D1S80 minisatellite locus characterized by?
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Who described the first highly polymorphic DNA locus in 1980?
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Who coined the term 'minisatellites'?
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What is the basis of RFLPs?
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What is a locus?
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What is an allele?
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What is a haplotype?
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Study Notes
Population Genetics and Molecular Evolution
- Welcome to the unit, where many new ideas will be introduced, and the mind will be stretched to understand the concepts of evolution, genetics, and molecular biology.
The Evolution of Evolution
- The universe has undergone many changes since Darwin's time, and our understanding of evolution has also evolved significantly.
- The scala naturae, or the scale of nature, was a concept developed by Aristotle, where living organisms were ranked in order of complexity, with God at the top and minerals at the bottom.
- Carl Linnaeus, a Swedish botanist, developed the modern binomial nomenclature of species and believed that species were created by God and reproduced in their original form.
The Paradox of Linnaeus
- Linnaeus proposed that species were created anew by God, implying that they are independent of each other.
- However, he also developed a hierarchical structure based on degrees of similarity, which suggests a shared ancestry.
Early Proponents of Evolution
- Erasmus Darwin, Jean Baptiste de Lamarck, Alfred Russel Wallace, and Charles Darwin were all early proponents of evolution.
- Jean Baptiste de Lamarck proposed the inheritance of acquired characteristics, where characteristics acquired for survival are passed on to the next generation.
- Lamarck's theory was later discredited, but it is now being revisited.
Evolution by Natural Selection
- Evolution requires inherited variation, and it progresses by the preferential reproduction of individuals with genotypes manifesting greater fitness.
- Fitness is measured by the propensity of individuals to produce thriving offspring.
- Evolution occurs in the prevailing environment, including physical, local, social, and cultural environments.
Evolution in Recent Human History
- Evolution is not only limited to ancient times; it has also occurred in recent human history, such as changes in disease resistance, fecundity, and cognitive behavior.
Somatic Cells vs Germ Cells
- Somatic cells make up tissues and have two copies of each chromosome (diploid), while germ cells (sperm and ova) have only one copy of each chromosome (haploid).
- Germ cells are formed by meiosis, which involves two sequential cell divisions.
Recombination of Homologous Chromosomes in Meiosis
- Recombination of homologous chromosomes is a source of genetic diversity in most eukaryotic organisms.
Weismann's Barrier
- Weismann's barrier proposes that only germ cells pass genetic information to the next generation, and somatic cells do not.
Definitions
- Locus: The location of a sequence or place of interest on a chromosome.
- Allele: Each of two or more alternative forms of a gene.
- Genotype: The genetic constitution of an organism, including all the genes present.
- Dihybrid: A hybrid that is heterozygous with respect to two independent genes.
- True breeding: Producing offspring with phenotypes identical to those of the parents.
Mendel's Laws
- Segregation: An offspring receives a random copy of an allele from each of its parents.
- Independent Assortment: Genes on different chromosomes are transmitted independently.
Punnett Squares
- Punnett squares are used to predict the probability of different genotypes and phenotypes in offspring.
Genetic Variation in Species
- Populations exhibit genetic variation, where alleles occur at different frequencies.
- This genetic variation determines the proportions of genotypes in the population.
Polymorphisms at the Molecular Level
- Genetic polymorphisms refer to differences in DNA base sequences at a particular locus, which can be observed when looking at a collection of human chromosomes.### Structural Variations
- Submicroscopic variations: Copy Number Variations (CNVs), Single Nucleotide Polymorphisms (SNPs), small indels
- Microscope-visible variations: > 3Mb CNVs
- DNA sequence length: 1 kb to 100 kb to 1 Mb to 100 Mb to 1 Gb
Genetic Polymorphisms
- Base substitutions: SNPs, RFLPs, small indels
- Copy Number Variations (CNVs):
- Small size: VNTRs, STRs, minisatellites
- Large size: chromosome fragments, viral insertions, dispersed repeats (LINEs and SINEs)
Chromosome Translocations
- Occur when chromosomes break and rejoin incorrectly
- Can result in changes to the genome
Single Nucleotide Polymorphisms (SNPs)
- Aka “SNP”
- Arise from a mutation at a specific residue site
- Can be a base mutation or an indel (insertion or deletion)
- Convention: a mutation becomes a SNP when its frequency is ≥0.01
- Can be synonymous or non-synonymous
- Usually identified by direct, automated sequencing of a DNA fragment
- Usually di-allelic and codominant
Variable Number Tandem Repeat (VNTR) Polymorphisms
- Characterized by variation in the number of tandemly repeating sequence motifs
- Two main families: minisatellites (LTRs) and microsatellites (STRs)
- Dispersed Repeats: LINEs and SINEs
Short Tandem Repeats (STRs)
- Aka “microsatellites”
- STR loci usually manifest extensive polymorphism
- Characterized by DNA fragment length polymorphism due to variable numbers of tandemly repeating (VNTR) short motifs (1 to ~7 base pairs)
- Genotyped by PCR with locus-specific primers
- May be used for disease gene mapping
Features of STRs
- Dinucleotide frequency > Trinucleotide frequency > Tetranucleotide frequency > 5, 6, 7 bp
- May be genotyped by PCR with locus-specific primers
- Trinucleotide STRs often cause disease, so not used as genetic markers
- Mutation rate high: ~10-3 to 10-4 per meiosis
- Assays usually multiplexed
- Polymorphic loci exhibit from 2 to >50 alleles
- Used for disease gene mapping (by linkage analysis)
Minisatellite Locus
- D1S80 minisatellite locus: 24 repeats of a 16bp motif
- May be amplified by PCR
- Allele length ≈ 200 - 1000bp
- Oligonucleotide primers are used
History of VNTR Loci
- 1980: Ray White and David Botstein describe the first highly polymorphic DNA locus (D2S44)
- 1985: Alec Jeffreys discovers and patents the first two DNA probes in the human myoglobin gene
- 1985: Alec Jeffreys coins the term “minisatellites”
- 1985: First paper on PCR (Mullis et al)
- 1991: First paper on microsatellites (short tandem repeats; STRs) by James Weber
RFLPs
- Restriction Endonucleases bind to specific nucleotide sequences, resulting in reproducible cleavage of the DNA
- The presence or absence of these RE sensitive sites forms the basis of a diallelic, codominant system of genetic variation
- RFLPs were observed by a method known as DNA hybridization following Southern blotting
- Can perform gel electrophoresis or capillary electrophoresis if no other method available
Locus, Allele & Haplotype
- Locus: a specific place on a chromosome where a DNA sequence resides
- Allele: the sequence of DNA at a specified locus; an alternative form or variant of a DNA sequence at a given locus
- Haplotype: the combination of loci on a single chromosome, or part of a chromosome
Population Genetics and Molecular Evolution
- Welcome to the unit, where many new ideas will be introduced, and the mind will be stretched to understand the concepts of evolution, genetics, and molecular biology.
The Evolution of Evolution
- The universe has undergone many changes since Darwin's time, and our understanding of evolution has also evolved significantly.
- The scala naturae, or the scale of nature, was a concept developed by Aristotle, where living organisms were ranked in order of complexity, with God at the top and minerals at the bottom.
- Carl Linnaeus, a Swedish botanist, developed the modern binomial nomenclature of species and believed that species were created by God and reproduced in their original form.
The Paradox of Linnaeus
- Linnaeus proposed that species were created anew by God, implying that they are independent of each other.
- However, he also developed a hierarchical structure based on degrees of similarity, which suggests a shared ancestry.
Early Proponents of Evolution
- Erasmus Darwin, Jean Baptiste de Lamarck, Alfred Russel Wallace, and Charles Darwin were all early proponents of evolution.
- Jean Baptiste de Lamarck proposed the inheritance of acquired characteristics, where characteristics acquired for survival are passed on to the next generation.
- Lamarck's theory was later discredited, but it is now being revisited.
Evolution by Natural Selection
- Evolution requires inherited variation, and it progresses by the preferential reproduction of individuals with genotypes manifesting greater fitness.
- Fitness is measured by the propensity of individuals to produce thriving offspring.
- Evolution occurs in the prevailing environment, including physical, local, social, and cultural environments.
Evolution in Recent Human History
- Evolution is not only limited to ancient times; it has also occurred in recent human history, such as changes in disease resistance, fecundity, and cognitive behavior.
Somatic Cells vs Germ Cells
- Somatic cells make up tissues and have two copies of each chromosome (diploid), while germ cells (sperm and ova) have only one copy of each chromosome (haploid).
- Germ cells are formed by meiosis, which involves two sequential cell divisions.
Recombination of Homologous Chromosomes in Meiosis
- Recombination of homologous chromosomes is a source of genetic diversity in most eukaryotic organisms.
Weismann's Barrier
- Weismann's barrier proposes that only germ cells pass genetic information to the next generation, and somatic cells do not.
Definitions
- Locus: The location of a sequence or place of interest on a chromosome.
- Allele: Each of two or more alternative forms of a gene.
- Genotype: The genetic constitution of an organism, including all the genes present.
- Dihybrid: A hybrid that is heterozygous with respect to two independent genes.
- True breeding: Producing offspring with phenotypes identical to those of the parents.
Mendel's Laws
- Segregation: An offspring receives a random copy of an allele from each of its parents.
- Independent Assortment: Genes on different chromosomes are transmitted independently.
Punnett Squares
- Punnett squares are used to predict the probability of different genotypes and phenotypes in offspring.
Genetic Variation in Species
- Populations exhibit genetic variation, where alleles occur at different frequencies.
- This genetic variation determines the proportions of genotypes in the population.
Polymorphisms at the Molecular Level
- Genetic polymorphisms refer to differences in DNA base sequences at a particular locus, which can be observed when looking at a collection of human chromosomes.### Structural Variations
- Submicroscopic variations: Copy Number Variations (CNVs), Single Nucleotide Polymorphisms (SNPs), small indels
- Microscope-visible variations: > 3Mb CNVs
- DNA sequence length: 1 kb to 100 kb to 1 Mb to 100 Mb to 1 Gb
Genetic Polymorphisms
- Base substitutions: SNPs, RFLPs, small indels
- Copy Number Variations (CNVs):
- Small size: VNTRs, STRs, minisatellites
- Large size: chromosome fragments, viral insertions, dispersed repeats (LINEs and SINEs)
Chromosome Translocations
- Occur when chromosomes break and rejoin incorrectly
- Can result in changes to the genome
Single Nucleotide Polymorphisms (SNPs)
- Aka “SNP”
- Arise from a mutation at a specific residue site
- Can be a base mutation or an indel (insertion or deletion)
- Convention: a mutation becomes a SNP when its frequency is ≥0.01
- Can be synonymous or non-synonymous
- Usually identified by direct, automated sequencing of a DNA fragment
- Usually di-allelic and codominant
Variable Number Tandem Repeat (VNTR) Polymorphisms
- Characterized by variation in the number of tandemly repeating sequence motifs
- Two main families: minisatellites (LTRs) and microsatellites (STRs)
- Dispersed Repeats: LINEs and SINEs
Short Tandem Repeats (STRs)
- Aka “microsatellites”
- STR loci usually manifest extensive polymorphism
- Characterized by DNA fragment length polymorphism due to variable numbers of tandemly repeating (VNTR) short motifs (1 to ~7 base pairs)
- Genotyped by PCR with locus-specific primers
- May be used for disease gene mapping
Features of STRs
- Dinucleotide frequency > Trinucleotide frequency > Tetranucleotide frequency > 5, 6, 7 bp
- May be genotyped by PCR with locus-specific primers
- Trinucleotide STRs often cause disease, so not used as genetic markers
- Mutation rate high: ~10-3 to 10-4 per meiosis
- Assays usually multiplexed
- Polymorphic loci exhibit from 2 to >50 alleles
- Used for disease gene mapping (by linkage analysis)
Minisatellite Locus
- D1S80 minisatellite locus: 24 repeats of a 16bp motif
- May be amplified by PCR
- Allele length ≈ 200 - 1000bp
- Oligonucleotide primers are used
History of VNTR Loci
- 1980: Ray White and David Botstein describe the first highly polymorphic DNA locus (D2S44)
- 1985: Alec Jeffreys discovers and patents the first two DNA probes in the human myoglobin gene
- 1985: Alec Jeffreys coins the term “minisatellites”
- 1985: First paper on PCR (Mullis et al)
- 1991: First paper on microsatellites (short tandem repeats; STRs) by James Weber
RFLPs
- Restriction Endonucleases bind to specific nucleotide sequences, resulting in reproducible cleavage of the DNA
- The presence or absence of these RE sensitive sites forms the basis of a diallelic, codominant system of genetic variation
- RFLPs were observed by a method known as DNA hybridization following Southern blotting
- Can perform gel electrophoresis or capillary electrophoresis if no other method available
Locus, Allele & Haplotype
- Locus: a specific place on a chromosome where a DNA sequence resides
- Allele: the sequence of DNA at a specified locus; an alternative form or variant of a DNA sequence at a given locus
- Haplotype: the combination of loci on a single chromosome, or part of a chromosome
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Test your knowledge of population genetics and molecular evolution concepts, covering topics from genetic variation to evolutionary processes.
