Chapter 6 Transmission Genetics and the Sources of Genetic Variation

Transcription

- the process of copying a DNA sequence into a complementary messenger RNA (mRNA). 1. RNA synthesis is complementary and antiparallel to the template strand. 2. New nucleotides are added to the 3'OH group of the growing RNA, so transcription proceeds in a 5' ---> 3' direction. 3. The non template strand is not usually transcribed.

genetic code

- the way in which 20 different amino acids (and a stop signal) are specified by the 64 possible nucleotide triplets or codons. - specifies the relation between codon triplets and the amino acids for which they code.

Transport proteins

- transport materials within and between cells.

•Mutations are ___________!

- undirected! simply they are random, when happen they fall into this category (beneficial, deleterious, and neutral)

Imagine a hypothetical bone disorder caused by a dominant variant of a gene that affects growth. A man of normal stature whose father has this disorder is worried that his own children could inherit their grandfather's short stature. In this case, should he be concerned?

No, If the man carried a single copy of this gene variant to pass on to his children, he would have the disorder.

Mendel's law of segregation

Only one of an individual's two copies of a particular gene goes into each gamete.

The process of transcription

When RNA polymerase binds to a promoter, double-stranded DNA is unwound, allowing the polymerase to access that segment of DNA and synthesize a complementary RNA molecule.

Eukaryotic DNA is organized into __________.

chromosomes.

The processes of transcription, RNA splicing, and translation in eukaryotes.

- A gene is first transcribed in its entirety, including both the coding exons and the noncoding introns. - The introns are subsequently excised during RNA splicing, and the remaining exons are linked together to form a mature mRNA. - This mRNA is in turn translated to produce a protein.

Mutation: Hypothesis 2: •Acquired inherited resistance.

- At the time of exposure to the phage, all E. coli cells would be phage-sensitive; that is, all the cells would be sensitive to the damaging effects of the phage. - The process of exposure to the phage would induce mutations responsible for phage resistance in a small fraction of the bacterial cells. - This resistance would then be heritable, and the cells with induced resistance would go on to produce colonies of resistant cells. **** predicts that resistance is only induced by the presence of the phage. Resistance arises independently with some probability in each cell once the phage is present, and its distribution clusters around the average.

The process of translation.

- During the process of translation, the ribosome moves in the 3′ direction along an mRNA strand. - Successive tRNA molecules, matching successive codons on the mRNA strand, dock with the ribosome. - The amino acids carried by these tRNA molecules link together to form a growing amino acid chain, which will subsequently fold into an active protein.

Ploidy

- Number of copies of unique chromosomes in a cell, can vary.

Mutation: Hypothesis 1: Random mutation.

- Prior to exposure to the phage, a few resistant E. coli cells would arise by random mutation. - Once exposed to the bacteriophage, most cells would be killed, but the resistant cells would not. These would reproduce and form new resistant colonies. **** predicts that resistant cells arise by random mutation even before the phage is present. In some cultures, a mutation may arise early (arrow), resulting in many resistant cells. In other cultures, a mutation may occur late, resulting in few resistant cells. Thus, under the mutation hypothesis, the number of resistant cells fluctuates widely from culture to culture.

Chromatin structure influences gene expression

- RNA polymerase cannot readily access promoters in the condensed chromatin. Therefore, the chromatin must be decondensed before DNA in a given region can be expressed.

Mutations

- a change to the DNA sequence of the organism.

Nonsynonymous mutation

- a mutation in a gene that changes the amino acid sequence of the protein that gene encodes.

Frameshift mutation

- a mutation in which the addition or deletion of a base pair causes a shift in the reading frame. Unless an addition or deletion involves a number of base pairs that is a multiple of 3, it will cause a ________ _________. - An insertion or deletion of any other length generates a ________ ________.

Nonsense mutation

- a mutation that creates a stop codon where there was not one previously.

codons

- a sequence of three nucleotides specifying an amino acid product.

promoter

- a short DNA sequence located before the transcribed part of the gene-- and the promoter serves as a signal to begin transcription.

Population genetics

- a subdiscipline in evolutionary biology that investigates how allele frequencies and genotypes frequencies change overtime. - investigates how the genotype frequencies in an offspring population are related to the genotype frequencies in a parental population.

Synonymous mutation

- also called a silent mutation. - a base pair substitution that does not change the amino acid that a codon normally produces.

Epigenetic inheritance

- alter gene expression without changes in DNA sequence.

Bind to DNA

- and help regulation expression of DNA.

Chemical signals

- communication within and between cells.

Structural functions

- cytoskeleton or elements of the extracellular matrix.

Alleles

- different variants of the same gene.

Homozygotes

- each plant contained alleles (gene variants) for only one trait for any given character, in this case, a specific flower color.

Blending inheritance

- in which the characteristics of the parents were averaged in some way to determine the characteristics of each offspring. - would result in the sort of resemblance between parent and offspring that is needed for heredity, and thus for evolution. The problem is that blending of this sort also eliminates variation.

Regulatory elements

- influence the rate at which RNA molecules are transcribed from DNA, affecting the levels of gene expression, and ultimately the phenotype.

Enzymes

- initiate and regulate chemical reactions

DNA

- is a double-stranded molecule held in place with hydrogen bonds. The two strands are wound together so that they are oriented in opposite directions. - each strand is called a 5' end with a terminal phosphate group and a 3' end with a terminal hydroxyl group.

Crossing-over

- occurs between one of the red ABC chromatids (that is, chromosome copies) and one of the blue abc chromatids at a location between the B locus and the C locus.

Transitions

- occurs when a purine is replaced by another purine or a pyrimidine is replaced by another pyrimidine.

Transversion

- occurs when a purine replaces a pyrimidine or vice versa.

Recombination

- remixes existing variation, present in parents, into new genetic combinations that appear in their offspring.

gametes

- sex cell of an organism.

amino acids

- specified by nucleotide triplets, these molecules are the building blocks of protein.

Methylation

- the addition of a methyl group to a C-G base pair in DNA.

Genotype

- the combination of alleles that an individual has at a given locus (sometimes includes multiple loci).

Transmission genetics

- the mechanisms by which genes are passed from parents to offspring.

Particulate inheritance

- the phenotypic effects of the particles carrying heritable information may blend, the particles themselves remain distinct, and they can be separated again in future reproductive events.

Locus

- the physical location of a gene on a chromosome.

Mutation rates and fitness consequences

1. Beneficial - increase fitness 2. Deleterious - decrease fitness 3. Neutral - no effect on fitness

Proteins Functions:

1. Enzymes 2. Chemical signals 3. Bind to DNA 4. Structural functions 5. Transport proteins

Place the following steps in the order Mendel performed them in his studies of flower color inheritance in pea plants.

1. Generate a true-breeding population of purple flowers and a true-breeding population of white flowers. 2. Perform crosses between purple-flowered and white-flowered plants. 3. Score F1 plants for flower color. 4. Self-fertilize F1 plants. 5. Score F2 plants to determine the proportion of each flower color.

Luria and Delbruck

1. Inoculate nutrient broth with 50-500 phage-sensitive E. coli cells. 2. Incubate and allow E. coli to grow to high density. 3. Plate E. coli onto agar covered by a large number of phage particles. 4. Count the number of E. coli colonies that appear in 24-48 hours. ***Phage resistance was likely to be a product of random mutations that occurred at different times prior to the presence of the phage.

Types of mutation

1. Point mutation 2. Insertion 3. Deletion

•NS is a two-stage process:

1. Random generation of variation 2. Differential replication of certain variants

Hardy-Weinberg equilibrium Three important conclusions

1. The frequencies of the A1 and A2 allele do not change overtime. - tells us how allele frequencies change in the absence of evolutionary processes. 2. Given the frequencies of A1 and A2 alleles, we can predict the equilibrium frequencies of the A1A1, A1A2, and A2A2 genotypes when mating is random, referred to as Hardy-Weinberg equilibrium frequencies. - tells us how genotype frequencies relate to allele frequencies in the absence of evolutionary processes. 3. A locus that is initially not at HArdy-Weinberg equilibrium will reach Hardy-Weinberg equilibrium in a single generation. - tells us how long it takes to reach these genotype frequencies.

Mendel's Law

1. The law of segregation 2. The law of independent assortment

Unstable equilibrium two conditions hold:

1. When at this point, the system does not change. 2. If perturbed or displayed by some small amount, the system will move further away from its initial position at rest.

Neutral equilibrium conditions hold:

1. When at this point, the system does not change. 2. If perturbed or displayed by some small amount, the system will stay in its displaced position, rather than returning to the original position as it would in a stable equilibrium or moving further away as it would in an unstable equilibrium.

From DNA to proteins

1. a section of DNA is unwound, and portions are copied into RNA by the process of transcription. 2. the RNA is "read" by ribosomes and converted into a string of amino acids.

Stable equilibrium two conditions hold:

1. ensures that we have an equilibrium 2. ensures that our equilibrium is stable.

Hardy-Weinberg model

A null model how genotype frequencies relate to alleles in large populations and how they change overtime in the absence of natural selection, mutation, migration, assortative mating and genetic drift.

Mendel's law of segregation describes the pattern whereby which occurs?

Allele at a single diploid locus are distributed into haploid gametes.

The figure below depicts the results of an experiment designed to estimate the distribution of fitness effects of mutations induced in a viral genome. Fitness values are expressed in comparison to the fitness of the wild-type virus. Which of the following statements is true of these results?

Beneficial mutations were less common than neutral mutations.

The graph below depicts patterns of epigenetic modification of genes associated with eye development in the cave fish Astyanax mexicanus, a species in which cave populations have undergone eye degeneration relative to populations that live near the water's surface.

Consistent Transcription factors bind more readily to these promoters in the surface population than in the cave population. Inconsistent The proportion of inactivating mutations, in these eye-development genes is higher for the cave population than for the surface population. Expression of these three genes is higher in cave-dwelling populations than in surface populations.

Which of the following statements accurately describes hoe epigenetic effects on gene expression differ from genetic effects?

Epigenetic effects do not involve changes in DNA sequence.

In-frame mutations

Insertions or deletions of 3 nucleotides, or multiples of 3 nucleotides, do not shift the reading frame.

The law of segregation

Mendel's principle is that each individual (of a diploid species) has two gene copies at each locus and these gene copies segregate during gamete production. At each locus, only one gene copy goes to each gamete, and an offspring receives one gene copy at each locus from each parent.

The law of independent assortment

Mendel's principle states that which allele is passed down to the next generation at one locus is independent of which allele is passed down at other loci, such as loci on different chromosomes.

What is meant when we say that a mutation is undirected?

Mutations arise randomly with respect to their effects on fitness.

Place the following steps in the order they occur during transcription of a eukaryotic protein-coding gene.

RNA polymerase binds to the promoter The DNA double helix is unwound RNA polymerase catalyzes the synthesis of an RNA polymer that is complementary to the DNA template strand Introns are removed and exons are spliced together into a molecule of mRNA that can be trnaslated into the amino acid sequence of a protein.

Which class of mutations in a protein-coding gene is least likely to have a phenotypic effect?

Synonymous

Mendel's law of independent assortment

The gene copy that goes into a gamete at one locus does not depend on which copy goes into that gamete from a second locus on a different chromosome.

Drag each statement to the correct box to indicate whether it is true or false of Mendel's conclusions on flower-color inheritance in pea plants.

True A purple-flowered plant in the parental generation has only alleles for purple flowers. Each plant in the F1 generation has alleles for both purple and white flower color. False White flowers in the F2 generation must be the consequence of new mutations.

Drag each statement to the correct box to indicate whether it is true or false regarding the fitness effects of mutations.

True Although mutation is undirected, most mutations that arise are neutral or deleterious. Modern molecular techniques allow evolutionary geneticists to estimate the distribution of fitness effects of mutations. False Given that natural selection can cause adaptive evolution, most mutations must therefore increase fitness. Work in Drosophilia indicates that the distribution of fitness effects is highly variable across different genetic backgrounds, making it difficult to generalize about the relative frequencies of neutral, harmful, and advantageous mutations.

Drag each statement to the correct box to indicate whether it is true or false based on the figure demonstrating the results of a cross between plants that breed true for red flower color and white flower color.

True If blending inheritance were the explanation for pink-flowered F1 offspring, we would not expect any red- or white-flowered offspring in the F2. Blending inheritance would pose a problem for the theory of natural selection because it would erode heritable genetic variation in fitness-related traits. False Only blending inheritance can explain the observation that F1 flowers are pink since red must be dominant to white.

The figure below depicts results from a study by researcher Claudia Bank and her colleagues who induced point mutations in the coding region of a heat shock protein (HSP90) in yeast and estimated the distribution of fitness effects at two different temperatures. Drag each statement below to the correct box to indicate whether it is true or false of these results.

True Nonsense mutations tend to fall in the deleterious or lethal peak of the distribution. HSP90 is likely more crucial for fitness at 36°C than at 25°C. False The peak corresponding to the neutral mutations is hogher at 36°C than at 25°C.

Which of the following options best describes what is meant by the phrase "distribution of fitness effects" with regard to mutations in nature?

the relative frequencies of deleterious, beneficial, and neutral mutations among all mutations that occur across the whole genome or some subset of the genome.

recessive trait

a trait that is expressed only when both copies at a locus code for the trait.

dominant trait

a trait that is expressed when one or both gene copies at a locus code for the trait.

A ____ is a DNA sequence that does for a functional product such as a protein. The synthesis of an RNA strand that is complementary to such a sequence in a template DNA strand is called ____. In eukaryotes, the RNA synthesized from a protein-coding sequence contains coding regions called ___ and noncoding regions called ___. The noncoding regions are removed and the coding regions are spliced together before the mature mRNA can serve as the template for protein synthesis, or ____. The mRNA is read in three-nucleotide chunks called ____, each of which corresponds to either an amino acid or a signal to start or stop the process.

gene transcription exons introns translation codons

Brachydactyly

ia a malformation or shortening of the digits and is inherited as a dominant trait. BB and Bb individuals show malformed or shortened fingers, whereas bb individuals have normal fingers.

Cave-dwelling and surface-dwelling populations of the Pachon cave fish (Astyyanax mexicanus) show no functionally significant nucleotide differences in key eye- development genes. Given this observation, which of the following modifications most likely drives eye degeneration in blind fish from cave-dwelling populations?

methylation of DNA in promoters of eye-development genes.

Point mutation in a DNA sequence in which a purine is replaced by a purine (or a pyrimidine by a pyrimidine) are called ____. These mutations are about twice as common as ___, in which a purine is replaced by a pyrimidine or vice versa. Chromosomal mutations include ____, in which a segment of a chromosome flips 180°. Addition or deletion of entire sets of chromosomes can change the ____ of an organism, which is usually lethal in animals but is common in plants.

transitions transversions inversions ploidy

translocation

mutation in which a section of one chromosome moves to a different chromosome

transition

mutation that changes an adenine to guanine

nonsynonymous mutation

mutation that changes the amino acid specified by a codon

Biological evolution

occurs when genotype frequencies change over time.

Translation

process, in which a nucleotide sequence of mRNA specifies the sequence of amino acids to be linked together to form a particular protein.

locus

the physical position of a gene on a chromosome.

frameshift mutation

two-nucleotide insertion in a protein-coding gene