Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
Contents
Chapter 1 – The genetics revolution..........................................................................................................4
The birth of genetics..............................................................................................................................4
After cracking the code.........................................................................................................................4
Genetics today.......................................................................................................................................5
Chapter 2 – Single-gene inheritance..........................................................................................................7
Single-gene inheritance patterns............................................................................................................7
The chromosomal basis of single-gene inheritance patterns..................................................................8
The molecular basis of Mendelian inheritance patterns.........................................................................9
Some genes discovered by observing segregation ratios.....................................................................10
Sex-linked single-gene inheritance patterns........................................................................................10
Human pedigree analysis....................................................................................................................10
Chapter 3 – Independent assortment of genes.........................................................................................13
Mendel’s law of independent assortment............................................................................................13
Working with independent assortment................................................................................................14
The chromosomal basis of independent assortment............................................................................15
Polygenic inheritance..........................................................................................................................15
Organelle genes: inheritance independent of the nucleus....................................................................16
Chapter 4 – Mapping eukaryote chromosomes by recombination...........................................................17
Diagnostics of linkage.........................................................................................................................17
Mapping by recombinant frequency....................................................................................................18
Mapping with molecular markers........................................................................................................19
Centromere mapping with linear tetrads..............................................................................................20
Using the chi-square test to infer linkage............................................................................................20
Using recombinant-based maps in conjunction with physical maps....................................................20
Chapter 6 – Gene interaction...................................................................................................................21
Interactions between the alleles of a single gene: variations on dominance........................................21
Interaction of genes in pathways.........................................................................................................22
Inferring gene interactions...................................................................................................................22
Penetrance and expressivity................................................................................................................24
Chapter 8 – RNA: transcription and processing......................................................................................25
RNA....................................................................................................................................................25
Transcription.......................................................................................................................................26
Transcription in eukaryotes.................................................................................................................27
Intron removal and exon splicing........................................................................................................28
Small functional RNAs that regulate and protect the eukaryotic genome...........................................28
Chapter 10 – Gene isolation and manipulation........................................................................................30
Overview: isolating and amplifying specific gene fragments..............................................................30
Generating recombinant DNA molecules............................................................................................30
Using molecular probes to find and analyze a specific clone of interest.............................................33
Determining the base sequence of a DNA segment.............................................................................34
Aligning genetic and physical maps to isolate specific genes.............................................................34
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
Genetic engineering............................................................................................................................35
Chapter 12 – Regulation of Gene Expression in Eukaryotes...................................................................36
Transcriptional regulation in eukaryotes.............................................................................................36
Lessons from yeast: the GAL system..................................................................................................38
Dynamic chromatin.............................................................................................................................39
Activation of genes in a chromatin environment.................................................................................40
Long-term inactivation of genes in a chromatin environment.............................................................41
Gender-specific silencing of genes and whole chromosomes..............................................................42
Post-transcriptional gene repression by miRNAs................................................................................43
Chapter 14 – Genomes and genomics.....................................................................................................44
The genomics revolution.....................................................................................................................44
Obtaining the sequence of a genome...................................................................................................44
Bioinformatics: meaning from genomic sequence..............................................................................45
The structure of the human genome....................................................................................................47
The comparative genomics of humans with other species...................................................................47
Comparative genomics and human medicine......................................................................................48
Functional genomics and reverse genetics...........................................................................................48
Chapter 17 – Large-scale chromosomal changes.....................................................................................52
Changes in chromosome number........................................................................................................52
Changes in chromosome structure.......................................................................................................56
Overall incidence of human chromosome mutations...........................................................................59
Chapter 18 – Population genetics............................................................................................................60
Detecting genetic variation..................................................................................................................60
The gene-pool concept and the Hardy-Weinberg law.........................................................................61
Mating systems...................................................................................................................................62
Genetic variation and its measurements..............................................................................................63
The modulation of genetic variation....................................................................................................63
Biological and social applications.......................................................................................................66
Chapter 19 – The inheritance of complex traits.......................................................................................67
Measuring quantitative variation.........................................................................................................67
A simple genetic model for quantitative traits.....................................................................................68
Broad-sense heritability: nature versus nurture...................................................................................68
Narrow-sense heritability: predicting phenotypes...............................................................................69
Mapping QTL in populations with known pedigrees..........................................................................71
Association mapping in random-mating populations..........................................................................71
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
This summary covers the most important chapters according to our professor for exam (Uni
Amsterdam 2024 genetics)
Introduction to genetic analysis
Chapter 1 – The genetics revolution
The birth of genetics
Genetics seek to understand the rules that govern the transmission of genetic information at three
levels – from parent to offspring within families, from DNA to gene action within and between cells,
and over generations within populations of organisms. 1800s in Europe, people sought to explain the
resemblance between parents and offspring. Blending theory was common, inheritance worked like
the mixing of fluids, eventually a average value of trait will be reached, so it was not right.
Gregor Mendel discovered the laws of inheritance. Crossing experiments with pea plants, figure 1.3
shows the results. F1 (first generation hybrid) all had purple flowers, just like one of the parents. F2
(second generation hybrid) has a 3:1 ratio.
Mendel proposed that factors that control traits act like particles, passed along generations, today known
as genes. Somatic cells are the two copies of genes that control plant color.
Gametes are the sex cells (eggs and sperm). Two gene variants, alleles, one for each color. A
dominant gene and a recessive gene. Mendel’s theory of inheritance published in 1866. KEY
CONCEPT Mendel demonstrated that genes behave like particles and not fluids. Bateson coined the
term genetics in 1905, the study of genetics.
Chromosome theory of inheritance demonstrated in 1910 by Thomas Morgan, genes are located in
the chromosomes. Multifactorial hypothesis, continuous traits are each controlled by multiple
Mendelian genes. Genes encode enzymes, one-gene-one-enzyme hypothesis. Genes are made of
deoxyribonucleic acid (DNA). Molecular structure DNA is a double helix, with the four bases
adenine, thymine, guanine, cytosine.
A and T bound by double hydrogen bond, G and C bound by triple hydrogen bond. Based on the
complementary shapes and charges of the bases. Genes have regulatory elements that regulate gene
expression, whether a gene is turned on or off. These elements are specific DNA sequences to which
a regulatory protein binds and acts as either an activator or repressor of the expression of the gene. A
string of DNA nucleotides, with four different bases, encodes a set of 20 different amino acids that are
the building blocks of proteins. There is a messenger molecule made of ribonucleic acid (RNA) that
carries information in the DNA in the nucleus to the cytoplasm where proteins are synthesized.
KEY CONCEPT Geneticists learned that genes reside on chromosomes and are made of DNA. Genes
encode proteins that conduct the basic enzymatic work within cells.
Central dogma is a phrase that represents the flow of genetic information within cells from DNA to
RNA to protein. Figure 1.10, DNA replication is the process by which a copy of the DNA is
produced. Transcription is the process of RNA synthesis from a DNA template.
Messenger RNA is the template for protein synthesis. Translation is protein synthesis, the
translation of information in the specific sequence bases in the mRNA into the sequence of amino
acids that compose a protein. Genetic code is written in 3 letter words, codons.
After cracking the code
A model organism is a species used in experimental biology with the presumption that what is
learned from the analysis of that species will hold true for other species, especially closely related
species. Small organisms that are easy and inexpensive to maintain are suitable as model, short
generation time is imperative, small genome is useful, organisms that are easy to cross or mate and
that produce large offspring are the best.
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
KEY CONCEPT Most genetic studies are performed on one of a limited number of model organisms
that have features that make them suited for genetic analysis.
DNA polymerases can make a copy of a single DNA strand by synthesizing a matching strand with
the complementary base sequence. Nucleases can cut DNA molecules in specific locations or degrade
an entire DNA molecule into single nucleotides. Ligases can join 2 DNA molecules together end-to-
end. Geneticists can also clone DNA with these methods. They have also developed methods to insert
foreign DNA molecules into the genomes of many species, transformation. The recipient species
becomes a genetically modified organism (GMO). DNA sequencing is the process used to decipher
the exact sequence of bases.
Genomics is the study of the structure and function of entire genomes.
KEY CONCEPT Progress in genetics has both produces and been catalyzed by the development of
molecular and mathematical tools for the analysis of single gens and whole genomes.
Genetics today
Single nucleotide polymorphisms (SNPs) is genetic variation, any difference between 2 copies
of the same gene or DNA.
KEY CONCEPT Classical transmission genetics provides the foundation for modern medical
genetics . The integration of classical genetics and genomic technologies can allow the causes of
inherited diseases to be readily identified.
Point mutations is a change of one letter in the DNA code to another that can occur during DNA
replication. Icelandic study of gene inheritance found that children have on average 63 unique
mutations that do not exist in the parents. Children are inheriting nearly 4 times as many new
mutations from their fathers as their mothers. Older mothers do not pass on more mutations, the
making of eggs takes place largely before a woman is born, older mothers contribute no more new
point mutations to their children than younger mothers. But men are different, the sperm cell divisions
continue throughout a man’s life. There is more risk of new point mutations occurring during these
rounds of cell division and DNA replication with the increase in age of the father. Older fathers were
more likely to have children with autism and schizophrenia.
KEY CONCEPT Genome sequences of parents and their children clarify the factors that contribute to
new point mutations. Fathers contribute four times as many new mutations to their offspring as do
mothers. The number of new mutations passed on from father to child rises with the age of the father.
Quantitative trait locus (QTL) is a genetic locus that contributes incrementally of quantitatively to
variation for a trait. QTL have alleles that usually engender only partial changes, like the difference
between pale purple and medium purple. Ethylene response factors (ERFs) genes encode regulatory
proteins that bind to regulatory elements in other genes and thereby regulate their expression.
Example with rice paddies, normally they try to grow over the flooding (reaching up) but they die.
When the gene that sets this process in actions is shut off by SUB-1, the plant sits tight and can
survive on sugar reserves for up to 2 weeks.
KEY CONCEPT Genetics and genomics are playing a leading role in improving crop plants. The basic
principles of genetics are the foundation for these advances.
One goal of genetics is to understand the rules that govern how genes and the information they
encode change over the generations within populations. The genes change over time for different
reasons. Mutations in the germline can cause a new gene variant or allele to occur in the next
generation, natural selection is another factor. Genetic changes over the past 100 years have enabled
human populations to adept to the different conditions of life on different parts of the globe. 3 factors
have been particularly powerful in shaping the types of gene variants that occur in different human
populations. These factors are pathogens such as malaria and smallpox, local climatic conditions
including solar radiation, temperature and altitude, and the diet of humans.
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
Contents
Chapter 1 – The genetics revolution..........................................................................................................4
The birth of genetics..............................................................................................................................4
After cracking the code.........................................................................................................................4
Genetics today.......................................................................................................................................5
Chapter 2 – Single-gene inheritance..........................................................................................................7
Single-gene inheritance patterns............................................................................................................7
The chromosomal basis of single-gene inheritance patterns..................................................................8
The molecular basis of Mendelian inheritance patterns.........................................................................9
Some genes discovered by observing segregation ratios.....................................................................10
Sex-linked single-gene inheritance patterns........................................................................................10
Human pedigree analysis....................................................................................................................10
Chapter 3 – Independent assortment of genes.........................................................................................13
Mendel’s law of independent assortment............................................................................................13
Working with independent assortment................................................................................................14
The chromosomal basis of independent assortment............................................................................15
Polygenic inheritance..........................................................................................................................15
Organelle genes: inheritance independent of the nucleus....................................................................16
Chapter 4 – Mapping eukaryote chromosomes by recombination...........................................................17
Diagnostics of linkage.........................................................................................................................17
Mapping by recombinant frequency....................................................................................................18
Mapping with molecular markers........................................................................................................19
Centromere mapping with linear tetrads..............................................................................................20
Using the chi-square test to infer linkage............................................................................................20
Using recombinant-based maps in conjunction with physical maps....................................................20
Chapter 6 – Gene interaction...................................................................................................................21
Interactions between the alleles of a single gene: variations on dominance........................................21
Interaction of genes in pathways.........................................................................................................22
Inferring gene interactions...................................................................................................................22
Penetrance and expressivity................................................................................................................24
Chapter 8 – RNA: transcription and processing......................................................................................25
RNA....................................................................................................................................................25
Transcription.......................................................................................................................................26
Transcription in eukaryotes.................................................................................................................27
Intron removal and exon splicing........................................................................................................28
Small functional RNAs that regulate and protect the eukaryotic genome...........................................28
Chapter 10 – Gene isolation and manipulation........................................................................................30
Overview: isolating and amplifying specific gene fragments..............................................................30
Generating recombinant DNA molecules............................................................................................30
Using molecular probes to find and analyze a specific clone of interest.............................................33
Determining the base sequence of a DNA segment.............................................................................34
Aligning genetic and physical maps to isolate specific genes.............................................................34
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
Genetic engineering............................................................................................................................35
Chapter 12 – Regulation of Gene Expression in Eukaryotes...................................................................36
Transcriptional regulation in eukaryotes.............................................................................................36
Lessons from yeast: the GAL system..................................................................................................38
Dynamic chromatin.............................................................................................................................39
Activation of genes in a chromatin environment.................................................................................40
Long-term inactivation of genes in a chromatin environment.............................................................41
Gender-specific silencing of genes and whole chromosomes..............................................................42
Post-transcriptional gene repression by miRNAs................................................................................43
Chapter 14 – Genomes and genomics.....................................................................................................44
The genomics revolution.....................................................................................................................44
Obtaining the sequence of a genome...................................................................................................44
Bioinformatics: meaning from genomic sequence..............................................................................45
The structure of the human genome....................................................................................................47
The comparative genomics of humans with other species...................................................................47
Comparative genomics and human medicine......................................................................................48
Functional genomics and reverse genetics...........................................................................................48
Chapter 17 – Large-scale chromosomal changes.....................................................................................52
Changes in chromosome number........................................................................................................52
Changes in chromosome structure.......................................................................................................56
Overall incidence of human chromosome mutations...........................................................................59
Chapter 18 – Population genetics............................................................................................................60
Detecting genetic variation..................................................................................................................60
The gene-pool concept and the Hardy-Weinberg law.........................................................................61
Mating systems...................................................................................................................................62
Genetic variation and its measurements..............................................................................................63
The modulation of genetic variation....................................................................................................63
Biological and social applications.......................................................................................................66
Chapter 19 – The inheritance of complex traits.......................................................................................67
Measuring quantitative variation.........................................................................................................67
A simple genetic model for quantitative traits.....................................................................................68
Broad-sense heritability: nature versus nurture...................................................................................68
Narrow-sense heritability: predicting phenotypes...............................................................................69
Mapping QTL in populations with known pedigrees..........................................................................71
Association mapping in random-mating populations..........................................................................71
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
This summary covers the most important chapters according to our professor for exam (Uni
Amsterdam 2024 genetics)
Introduction to genetic analysis
Chapter 1 – The genetics revolution
The birth of genetics
Genetics seek to understand the rules that govern the transmission of genetic information at three
levels – from parent to offspring within families, from DNA to gene action within and between cells,
and over generations within populations of organisms. 1800s in Europe, people sought to explain the
resemblance between parents and offspring. Blending theory was common, inheritance worked like
the mixing of fluids, eventually a average value of trait will be reached, so it was not right.
Gregor Mendel discovered the laws of inheritance. Crossing experiments with pea plants, figure 1.3
shows the results. F1 (first generation hybrid) all had purple flowers, just like one of the parents. F2
(second generation hybrid) has a 3:1 ratio.
Mendel proposed that factors that control traits act like particles, passed along generations, today known
as genes. Somatic cells are the two copies of genes that control plant color.
Gametes are the sex cells (eggs and sperm). Two gene variants, alleles, one for each color. A
dominant gene and a recessive gene. Mendel’s theory of inheritance published in 1866. KEY
CONCEPT Mendel demonstrated that genes behave like particles and not fluids. Bateson coined the
term genetics in 1905, the study of genetics.
Chromosome theory of inheritance demonstrated in 1910 by Thomas Morgan, genes are located in
the chromosomes. Multifactorial hypothesis, continuous traits are each controlled by multiple
Mendelian genes. Genes encode enzymes, one-gene-one-enzyme hypothesis. Genes are made of
deoxyribonucleic acid (DNA). Molecular structure DNA is a double helix, with the four bases
adenine, thymine, guanine, cytosine.
A and T bound by double hydrogen bond, G and C bound by triple hydrogen bond. Based on the
complementary shapes and charges of the bases. Genes have regulatory elements that regulate gene
expression, whether a gene is turned on or off. These elements are specific DNA sequences to which
a regulatory protein binds and acts as either an activator or repressor of the expression of the gene. A
string of DNA nucleotides, with four different bases, encodes a set of 20 different amino acids that are
the building blocks of proteins. There is a messenger molecule made of ribonucleic acid (RNA) that
carries information in the DNA in the nucleus to the cytoplasm where proteins are synthesized.
KEY CONCEPT Geneticists learned that genes reside on chromosomes and are made of DNA. Genes
encode proteins that conduct the basic enzymatic work within cells.
Central dogma is a phrase that represents the flow of genetic information within cells from DNA to
RNA to protein. Figure 1.10, DNA replication is the process by which a copy of the DNA is
produced. Transcription is the process of RNA synthesis from a DNA template.
Messenger RNA is the template for protein synthesis. Translation is protein synthesis, the
translation of information in the specific sequence bases in the mRNA into the sequence of amino
acids that compose a protein. Genetic code is written in 3 letter words, codons.
After cracking the code
A model organism is a species used in experimental biology with the presumption that what is
learned from the analysis of that species will hold true for other species, especially closely related
species. Small organisms that are easy and inexpensive to maintain are suitable as model, short
generation time is imperative, small genome is useful, organisms that are easy to cross or mate and
that produce large offspring are the best.
, Summary an introduction to genetic analysis 11th edition griffiths 9781464109485
KEY CONCEPT Most genetic studies are performed on one of a limited number of model organisms
that have features that make them suited for genetic analysis.
DNA polymerases can make a copy of a single DNA strand by synthesizing a matching strand with
the complementary base sequence. Nucleases can cut DNA molecules in specific locations or degrade
an entire DNA molecule into single nucleotides. Ligases can join 2 DNA molecules together end-to-
end. Geneticists can also clone DNA with these methods. They have also developed methods to insert
foreign DNA molecules into the genomes of many species, transformation. The recipient species
becomes a genetically modified organism (GMO). DNA sequencing is the process used to decipher
the exact sequence of bases.
Genomics is the study of the structure and function of entire genomes.
KEY CONCEPT Progress in genetics has both produces and been catalyzed by the development of
molecular and mathematical tools for the analysis of single gens and whole genomes.
Genetics today
Single nucleotide polymorphisms (SNPs) is genetic variation, any difference between 2 copies
of the same gene or DNA.
KEY CONCEPT Classical transmission genetics provides the foundation for modern medical
genetics . The integration of classical genetics and genomic technologies can allow the causes of
inherited diseases to be readily identified.
Point mutations is a change of one letter in the DNA code to another that can occur during DNA
replication. Icelandic study of gene inheritance found that children have on average 63 unique
mutations that do not exist in the parents. Children are inheriting nearly 4 times as many new
mutations from their fathers as their mothers. Older mothers do not pass on more mutations, the
making of eggs takes place largely before a woman is born, older mothers contribute no more new
point mutations to their children than younger mothers. But men are different, the sperm cell divisions
continue throughout a man’s life. There is more risk of new point mutations occurring during these
rounds of cell division and DNA replication with the increase in age of the father. Older fathers were
more likely to have children with autism and schizophrenia.
KEY CONCEPT Genome sequences of parents and their children clarify the factors that contribute to
new point mutations. Fathers contribute four times as many new mutations to their offspring as do
mothers. The number of new mutations passed on from father to child rises with the age of the father.
Quantitative trait locus (QTL) is a genetic locus that contributes incrementally of quantitatively to
variation for a trait. QTL have alleles that usually engender only partial changes, like the difference
between pale purple and medium purple. Ethylene response factors (ERFs) genes encode regulatory
proteins that bind to regulatory elements in other genes and thereby regulate their expression.
Example with rice paddies, normally they try to grow over the flooding (reaching up) but they die.
When the gene that sets this process in actions is shut off by SUB-1, the plant sits tight and can
survive on sugar reserves for up to 2 weeks.
KEY CONCEPT Genetics and genomics are playing a leading role in improving crop plants. The basic
principles of genetics are the foundation for these advances.
One goal of genetics is to understand the rules that govern how genes and the information they
encode change over the generations within populations. The genes change over time for different
reasons. Mutations in the germline can cause a new gene variant or allele to occur in the next
generation, natural selection is another factor. Genetic changes over the past 100 years have enabled
human populations to adept to the different conditions of life on different parts of the globe. 3 factors
have been particularly powerful in shaping the types of gene variants that occur in different human
populations. These factors are pathogens such as malaria and smallpox, local climatic conditions
including solar radiation, temperature and altitude, and the diet of humans.
