Chapter 14 - BIO 182
transposable element (transposon)
A DNA sequence that can replicate and move from one location to another in a DNA molecule
Discuss transposable elements and their possible influence on gene expression
A DNA sequence that can replicate and move from one location to another in a DNA molecule When such a large piece of DNA inserts into a gene, it can interfere with transcription, cause errors in RNA processing, or disrupt the open reading frame.
amino acid replacement
A change in the identity of an amino acid at a particular site in a protein resulting from a mutation in a gene.
gene family
A group of genes with related functions, usually resulting from multiple rounds of duplication and divergence.
mismatch repair
A mechanism for repairing nucleotide mismatches in newly replicated DNA.
Illustrate how post replication mismatch repair provides a backup mechanism for mistakes not caught by the proofreading function of DNA polymerase
A mechanism for repairing nucleotide mismatches in newly replicated DNA. Mismatch repair usually, but not always, cleaves the daughter strand, so the corrected strand matches the parental template strand.
deletion
A missing region of a gene or chromosome.
point mutation
A mutation in which a base pair is replaced by a different base pair; this is the most frequent type of mutation; also known as a nucleotide substitution.
frameshift mutation
A mutation in which an insertion or deletion of some number of nucleotides that is not a multiple of three causes a shift in the reading frame of the mRNA, changing all following codons.
Define a point mutation
A mutation in which one base pair is replaced by a different base pair
synonymous (silent) mutations
A mutation resulting in a codon that does not alter the corresponding amino acid in the polypeptide.
nonsense mutation
A mutation that creates a stop codon, terminating translation.
germ-line mutation
A mutation that occurs in eggs and sperm or in the cells that give rise to these reproductive cells and therefore is passed on to the next generation.
somatic mutation
A mutation that occurs in somatic cells.
somatic cell
A nonreproductive cell, the most common type of cell in the body of a multicellular organism.
nonsynonymous (missense) mutation
A point mutation (nucleotide substitution) that causes an amino acid replacement.
tandem repeat
A region along a DNA molecule in which many duplicated copies of a short sequence of nucleotides are adjacent to one another.
duplication
A region of a chromosome that is present twice instead of once.
hotspot
A site in the genome that is especially mutable.
single nucleotide polymorphism
A site in the genome where the base pair that is present differs among individuals in a population.
base excision repair
A specialized repair system in which an incorrect DNA base and its sugar are both removed and the resulting gap is repaired.
Explain the effects of duplications and deletions on gene dosage, and the impact on cellular or organism function
Although large duplications that include hundreds or thousands of genes are usually harmful and quickly eliminated from the population, small duplications including only one or a few genes can be maintained over many generations. Usually, duplication of a region of the genome is less harmful than deletion of the same region. Even though a deletion may eliminate a gene that is essential for survival, the deletion can persist in the population because chromosomes usually occur in homologous pairs. the deletion can be transmitted from generation to generation, as long as the chromosome with the deletion is present along with a normal chromosome.
mutagen
An agent that increases the probability of mutation.
DNA ligase
An enzyme that uses the energy in ATP to close a nick in a DNA strand, joining the 3′ hydroxyl of one end to the 5′ phosphate of the other end.
explain the difference between a homozygous and a heterozygous genotype
An individual who inherits the same allele of a gene from each parent is homozygous. an individual who inherits a different allele of a gene from each parent is heterozygous.
polymorphism
Any genetic difference among individuals that is present in multiple individuals in a population.
mutation
Any heritable change in the genetic material, usually a change in the nucleotide sequence of a gene.
genetic risk factor
Any mutation that increases the risk of a given disease in an individual.
Explain the concept of genetic polymorphism
As we saw earlier, common genetic differences in a population are called polymorphisms, so a difference between two sequences at a single nucleotide position in a DNA sequence is called a single-nucleotide polymorphism (abbreviated as SNP and pronounced "snip"). A SNP is the result of a point mutation that occurred sometime in the past and then increased in frequency so that many individuals in the population now carry it.
homozygous
Describes an individual who inherits an allele of the same type from each parent, or a genotype in which both alleles for a given gene are of the same type.
heterozygous
Describes an individual who inherits different types of alleles from the parents, or genotypes in which the two alleles for a given gene are different.
Define copy- number variation as a difference in the number of copies of a large genome region which may include one or more genes
Differences among individuals in the number of copies of a region of the genome.
copy-number variations
Differences among individuals in the number of copies of a region of the genome.
genetic variation
Differences in genotype among individuals in a population.
Define chromosomal deletions and duplication
Duplication: A region of a chromosome that is present twice instead of once. Deletion: A missing region of a gene or chromosome.
neutral
Genetic changes that have no effect or negligible effects on the organism, or whose effects are not associated with differences in survival or reproduction.
Discus why germ-line mutations, but not somatic mutations, are transmitted to progeny and play a role in genetic variation relevant to evolution
Germ-line mutations are important to the evolutionary process because, as they are passed from one generation to the next, they may eventually come to be present in many individuals descended from the original carrier. In contrast, mutations in nonreproductive cells are called somatic mutations, and for these mutations, what matters is the rate of mutations per nucleotide per replication. Although somatic mutations are not transmitted to future generations, they are transmitted to daughter cells in mitotic cell divisions
explain the effects of neutral, harmful, and beneficial mutations on the survival and reproduction of organisms
Harmful mutations are often eliminated in one or a few generations because they decrease the survival or reproduction of the individuals that carry them. Less harmful mutations may persist in a population. Mutations that have negligible effects on survival or reproduction are considered neutral. Many mutations are neutral because they occur in noncoding DNA. Neutral mutations are therefore especially likely to occur in organisms with large genomes and abundant noncoding DNA. neither beneficial or harmful. a few mutations are beneficial. provide some sort of advantage to the organism. In human populations, beneficial mutations are often discovered through their effects in protecting against infectious disease.
Explain why DNA ligase is an important tool for molecular biologists.
In addition to their role in DNA replication and repair, ligases are an important tool in research in molecular biology because they allow DNA molecules from different sources to be joined to produce recombinant DNA
Discuss how the effects of small insertions and deletions depend on where in the genome they occur
In noncoding DNA, such mutations have little or no effect. In protein-coding regions, their effects depend on their size. A small deletion or insertion that is an exact multiple of three nucleotides results in a polypeptide with fewer (in the case of a deletion) or more (in the case of an insertion) amino acids as there are codons deleted or inserted. Small deletions or insertions that are not exact multiples of 3 can cause major changes in amino acid sequence of the corresponding proteins because they do not insert or delete entire codons. frameshift mutations so profoundly alter the amino acid sequence, the mutant protein does not fold properly into its tertiary structure and becomes nonfunctional.
Discuss experimental evidence that demonstrates that mutations are random and without regard to the needs of an organism
In the Lederbergs' experiments, isolating antibiotic-resistant bacteria from the original plate showed that the mutation for antibiotic resistance existed in the bacteria before they were ever exposed to antibiotic. This result supported the hypothesis that mutations occur spontaneously without regard to the needs of the organisms. The environment does not create specific mutations, but instead selects for them. The principle the Lederbergs demonstrated is true of all organisms so far examined.
Describe how base excision repair corrects individual nucleotides by involving several DNA repair enzymes working together
In the first step of base excision repair, an abnormal or damaged base is cleaved from the sugar in the DNA backbone. Then, the baseless sugar is removed from the backbone, leaving a gap of one nucleotide. Finally, a repair polymerase inserts the correct nucleotide into the gap
reciprocal translocation
Interchange of parts between nonhomologous chromosomes.
Describe the similarities and differences between nucleotide excision repair and mismatch repair.
Nucleotide excision repair is similar to mismatch repair, with the difference being the number of mismatched bases. Nucleotide excision repair can recognize thousands or nucleotides that are mismatched or damaged, whereas mismatch repair can recognize only one mismatched base.
spontaneous
Occurring in the absence of any assignable cause; most mutations are spontaneous.
Describe damage that affects the bases themselves, such as changes in the side groups that form hydrogen bonds or the addition of side groups that interfere with base pairing.
Other types of damage alter the chemical structure of the bases themselves, making them prone to mispairing. Chemicals that are highly reactive also tend to be mutagenic, often because they add bulky side groups to the bases that hinder proper base pairing. The main environmental source of such chemicals is tobacco smoke. Other chemicals can perturb the DNA replication complex and cause the insertion or deletion of one or occasionally several nucleotides.
Describe the effect of a reciprocal translocation on gene dosage and meiosis
Proper gene dosage requires the presence of both parts of the reciprocal translocation, however, as well as one copy of each of the normal homologous chromosomes. Problems can arise in meiosis because both chromosomes involved in the reciprocal translocation may not move together into the same daughter cells, resulting in gametes with only one part of the reciprocal translocation. This inequality does upset gene dosage, because these gametes have extra copies of genes in one of the chromosomes and are missing copies of genes in the other.
DNA typing/ fingerprinting
The analysis of a small quantity of DNA to uniquely identify an individual
allele
The different forms of a gene, corresponding to different DNA sequences in each different form.
explain how an allele relates to a gene
The different forms of any gene are called alleles, and they correspond to different DNA sequences (polymorphisms) in the genes.
phenotype
The expression of a physical, behavioral, or biochemical trait; an individual's observable phenotypes include height, weight, eye color, and so forth.
genotype
The genetic makeup of a cell or organism; the particular combination of alleles present in an individual.
define the relationship between genotype and phenotype
The phenotype results in part from the genotype. For example, a genotype with a mutation that affects expression of an enzyme that normally metabolizes lactose can lead to the phenotype of lactose intolerance.
describe how the phenotype of an organisms is a complex interplay between the genotype and the environment
The phenotype results in part from the genotype. For example, a genotype with a mutation that affects expression of an enzyme that normally metabolizes lactose can lead to the phenotype of lactose intolerance. However, the environment also commonly plays an important role in the expression of the genotype, so it is most accurate to say that a phenotype results from an interaction between the genotype and the environment.
Discuss the significance of polymorphisms in the population
The polymorphism is the result of a mutation that occurred in the past, spread through the population, and is now shared among a subset of individuals in a population.
duplication and divergence
The process of creating new genes by duplication followed by change in sequence over evolutionary time.
nucleotide excision repair
The repair of multiple mismatched or damaged bases across a region; a process similar to mismatch repair, but over a much longer piece of DNA, sometimes thousands of nucleotides.
germ cell
The reproductive cells that produce sperm or eggs and the cells that give rise to them.
Define inversion
The reversal of the normal order of a block of genes.
inversion
The reversal of the normal order of a block of genes.
Explain how gene duplication followed by evolutionary divergence results in gene families made up of genes with related but not identical functions
The term "divergence" refers to the slow accumulation of different mutations in duplicate copies of a gene that occurs on an evolutionary time scale. Multiple rounds of duplication and divergence can give rise to a group of genes with related functions known as a gene family. The largest gene family in the human genome includes approximately 400 genes and encodes proteins that detect odors. These proteins are structurally very similar, but differ in the region that binds small odor molecules. It is the diversity of the odorant binding sites that allows us to identify so many different smells.
Describe different types of DNA structural damage, such as stranded or double-stranded breaks, cross-linked thymine dimers, or missing bases.
These include breaks in the sugar-phosphate backbone, one of the main mutagenic effects of X-rays. Breaks can occur in just one or both strands of a DNA molecule and can result in the types of chromosomal mutations described earlier. Ultraviolet light can cause cross-links between adjacent pyrimidine bases, especially thymine, resulting in the formation of thymine dimers that warp the backbone. loss of a base from one of the deoxyribose sugars, resulting in a gap in one strand where no base is present. Other types of damage alter the chemical structure of the bases themselves, making them prone to mispairing.
Explain why the effect of a point mutation depends on its location in the genome
many point mutations in noncoding DNA have no detectable effects on the organism. This example is typical in that the synonymous codons differ at their third position (the 3′ end of the codon). A quick look at the genetic code shows that most amino acids can be specified by synonymous codons, and that in most cases the synonymous codons differ in the identity of the nucleotide at the third position. A change in the identity of an amino acid at a particular site in a protein resulting from a mutation in a gene. a nonsense mutation, which creates a stop codon that terminates translation.
Discuss the utility of DNA typing in identifying a particular individual with high probability
that each genotype yields a distinct pattern of bands, so these patterns can be used to identify the genotype of any individual for a particular region of DNA. If six or eight of these polymorphisms match between two samples, it is very likely that the samples come from the same individual
Explain the relationship between the commonality of mutations in eukaryotes and the size of their genomes and number of cell division sin their life cycle
while humans have the lowest rate of mutation per nucleotide per replication, humans also have the highest number of mutations per genome per generation. This seeming paradox arises because humans have a large genome and undergo many cell divisions over their lifetime, providing more opportunities for mutations to occur.