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Genetic Variation and Mutation, Lecture notes of Cell Biology

Silliman University (SU)Cell Biology

Genetic variation and mutation, including the definition of mutation, wild-type strain, and mutant. It also covers genotype and phenotype nomenclature, sources of genetic variation, point mutations, consequences of point mutations, gene duplication and divergence, genome duplication, exon shuffling, transposition of mobile genetic elements, and horizontal gene transfer. The document also explains how genetic mutations are passed through sexual reproduction.

Typology: Lecture notes

2022/2023

Available from 01/23/2024

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CYTOGENETICS
Lesson
12
[TRANS] LESSON 12: GENETIC VARIATION
TERMS ON GENETIC VARIATION
MUTATION
●Heritable change in the base sequence of that
genome
WILD-TYPE STRAIN
● Organisms isolated from nature
MUTANT
● Organisms derived from the WT with mutations
GENOTYPE NOMENCLATURE
●hisC gene
PHENOTYPE NOMENCLATURE
●HisC gene
SOURCES OF GENETIC VARIATION
MUTATION WITHIN A GENE
●Mutation within a gene
●Substitutions, deletions or duplication of one or
more nucleotides
●May affect the transcript or product of the gene
●“An existing gene can be modified by a mutation that
changes a single nucleotide or deletes or duplicates
one or more nucleotides. These mutations can alter
the splicing of a gene’s RNA transcript or change the
stability, activity, location, or interactions of its
encoded protein or RNA product.”
MUTATION WITHIN REGULATORY DNA SEQUENCES
●Nucleotide changes in DNA sequences that
regulate the gene's activity
●Results in upregulation or downregulation
●“When and where a gene is expressed can be
affected by a mutation in the stretches of DNA
sequence that regulate the gene’s activity (described
in Chapter 8). For example, humans and fish have a
surprisingly large number of genes in common, but
changes in the regulation of those shared genes
underlie many of the most dramatic differences
between those species.”
POINT MUTATIONS
●Changes that affect a single nucleotide pair
●Types:
○Substitutions
■Transitions - replacement with
same base category
■Transversions- replacement
with different base category
○ Insertion/Deletions - Indels
● May alter gene expression or gene function
● Neutral mutations
○ Most common outcome of point
mutations
● Mutations occur in:
○ Non-coding sequences (introns)
○ Third positions in codons
■ Does not change amino acid
CONSEQUENCES OF POINT MUTATIONS
●DNA is made up of four bases: adenine,
thymine, guanine, and cytosine. Changes in the
order and number of these bases can result in
different point mutations, including frameshift,
silent, nonsense, and missense.
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CYTOGENETICS

Lesson

[TRANS] LESSON 12: GENETIC VARIATION

TERMS ON GENETIC VARIATION

MUTATION

● Heritable change in the base sequence of that genome WILD-TYPE STRAIN ● Organisms isolated from nature MUTANT ● Organisms derived from the WT with mutations GENOTYPE NOMENCLATURE ● hisC gene PHENOTYPE NOMENCLATURE ● HisC gene SOURCES OF GENETIC VARIATION MUTATION WITHIN A GENE ● Mutation within a gene ● Substitutions, deletions or duplication of one or more nucleotides ● May affect the transcript or product of the gene ● “An existing gene can be modified by a mutation that changes a single nucleotide or deletes or duplicates one or more nucleotides. These mutations can alter the splicing of a gene’s RNA transcript or change the stability, activity, location, or interactions of its encoded protein or RNA product.” MUTATION WITHIN REGULATORY DNA SEQUENCES ● Nucleotide changes in DNA sequences that regulate the gene's activity ● Results in upregulation or downregulation ● “When and where a gene is expressed can be affected by a mutation in the stretches of DNA sequence that regulate the gene’s activity (described in Chapter 8). For example, humans and fish have a surprisingly large number of genes in common, but changes in the regulation of those shared genes underlie many of the most dramatic differences between those species.”

POINT MUTATIONS

● Changes that affect a single nucleotide pair ● Types: ○ Substitutions ■ Transitions - replacement with same base category ■ Transversions- replacement with different base category ○ Insertion/Deletions - Indels ● May alter gene expression or gene function ● Neutral mutations ○ Most common outcome of point mutations ● Mutations occur in: ○ Non-coding sequences (introns) ○ Third positions in codons ■ Does not change amino acid CONSEQUENCES OF POINT MUTATIONS ● DNA is made up of four bases: adenine, thymine, guanine, and cytosine. Changes in the order and number of these bases can result in different point mutations, including frameshift, silent, nonsense, and missense. 1

EXAMPLES OF POINT MUTATIONS

● Reversal of His mutations in E. coli ● “ Mutation rates can be measured in the laboratory. In this experiment, an E. coli strain that carries a deleterious point mutation in the His gene—which is needed to manufacture the amino acid histidine—is used. The mutation has converted a G-C nucleotide pair to an A-T, resulting in a premature stop signal in the mRNA produced from the mutant gene (left box). “ GENE DUPLICATION AND DIVERGENCE ● Duplications of genes or genomes ● Duplicated DNA can acquire mutations of their own ○ Resulting in gene families ● Some genes lose their function - pseudogenes ● “An existing gene, or even a whole genome, can be duplicated. As the cell containing this duplication, and its progeny, continue to divide, the original DNA sequence and the duplicate sequence can acquire different mutations and thereby assume new functions and patterns of expression.” GENOME DUPLICATION ● Happens rarely ● Result in cells with multiple copies of the genome ● “ Many crop plants have undergone whole-genome duplication. Many of these duplications, which arose spontaneously, were propagated by plant breeders because they rendered the plants easier to cultivate or made their fruits larger, more flavorful, or devoid of indigestible seeds. N indicates the ploidy of each type of plant: for example, wheat and kiwi are hexaploid—possessing six complete sets of chromosomes (6N).”

EXON SHUFFLING

● Exchange of exons from originally separate genes ● Caused by crossovers in the intron sequences ● May result in a new functional gene ● “Two or more existing genes can be broken and rejoined to make a hybrid gene containing DNA segments that originally belonged to separate genes. In eukaryotes, such break- ing and rejoining often occurs within the long intron sequences, which do not encode protein. Because these intron sequences are removed by RNA splicing, the breaking and joining do not have to be precise to produce a functional gene.” TRANSPOSITION OF MOBILE GENETIC ELEMENTS ● Specialized DNA sequences (mobile genetic elements) move from one location to another ● May alter the activity or regulation of a gene ● May promote gene duplication, exon shuffling, and other changes HORIZONTAL GENE TRANSFER ● Direct transfer of genetic material from one cell to another ● Commonly seen in prokaryotes ○ Transduction ○ Transformation ○ Conjugation HOW GENETIC MUTATIONS ARE PASSED SEXUAL REPRODUCTION ● Only germ line ● (gametes) mutations are passed to progeny ● Mutations in somatic cells can be detrimental but do not affect the offspring

HUMAN GENOME

● ~3.2 × 109 nucleotide pairs ● Only <2% of the human genome codes for proteins ○ ~19,000 genes ● ~50% are mobile genetic elements ● “ Mobile genetic elements can move exons from one gene to another. Genes are sparsely distributed in the human genome. ” INTER-HUMAN GENETIC DIFFERENCES ● ~0.1 % difference between individuals ● single-nucleotide polymorphisms (SNPs) ○ A nucleotide difference found in at least 1% of humans ○ May be linked to heritable difference between humans TAKEAWAYS ● By comparing the DNA and protein sequences of contemporary organ- isms, we are beginning to reconstruct how genomes have evolved in the billions of years that have elapsed since the appearance of the first cells. ● Genetic variation—the raw material for evolutionary change—arises through a variety of mechanisms that alter the nucleotide sequence of genomes. These changes in sequence range from simple point mutations to larger-scale deletions, duplications, and rearrangements. ● Genetic changes that give an organism a selective advantage are likely to be perpetuated. Changes that compromise an organism’s fit- ness or ability to reproduce are eliminated through natural selection. ● Gene duplication is one of the most important sources of genetic diversity. Once duplicated, the two genes can accumulate different mutations and thereby diversify to perform different roles. ● Repeated rounds of gene duplication and divergence during evolu- tion have produced many large gene families. ● The evolution of new proteins is thought to have been greatly facilitated by the swapping of exons between genes to create hybrid proteins with new functions. ● The human genome contains 3.2 × 109 nucleotide pairs distributed among 23 pairs of chromosomes—22 autosomes and a pair of sex chromosomes. Less than a tenth of this DNA is transcribed to pro- duce protein-coding or otherwise functional RNAs. ● Individual humans differ from one another by an average of 1 nucleotide pair in every 1000 ; this and other genetic variation underlies most of our individuality and provides the basis for identifying individuals by DNA analysis. ● Nearly half of the human genome consists of mobile genetic elements that can move from one site to another within a genome. Two classes of these elements have multiplied to especially high copy numbers. ● Viruses are genes packaged in protective coats that can move from cell to cell and organism to organism, but they require host cells to reproduce. ● Comparing genome sequences of different species provides a powerful way to identify conserved, functionally important DNA sequences. ● Related species, such as human and mouse, have many genes in common; evolutionary changes in the regulatory DNA sequences that affect how these genes are expressed are especially important in determining the differences between species.