Mutations: Types, Causes, and Consequences - PDF

Mutations What is a mutation? A change in the nucleotide sequence of DNA. Are mutations good or bad? Mutations usually result in changes that lead to reduced function or lack of function of RNAs and proteins. Mutations throughout evolution have resulted in an increase in the number of sp...

Mutations What is a mutation? A change in the nucleotide sequence of DNA. Are mutations good or bad? Mutations usually result in changes that lead to reduced function or lack of function of RNAs and proteins. Mutations throughout evolution have resulted in an increase in the number of species, species better adapted to certain environmental conditions, and generation of more complex organisms. Are mutations heritable? Yes, if they are not repaired before the DNA is replicated, daughter cells will inherit the change. Do mutations happen randomly or do they occur because of selective pressure? Luria and Delbrück experiment Figure 18.02  Mutations happen randomly, not as a consequence of selective pressure. Some mutations will result in organisms better adapted to some conditions.  Classification of mutations Very large mutations, like chromosomal aberrations ▪ Changes in hundreds of thousands or millions of nucleotides ▪ Can be observed by microscopy Intermediate mutations, like those caused by transposable elements ▪ Changes in hundreds of nucleotides Small mutations ▪ Point mutations strictly refer to changes of 1 nucleotide in the sequence Point mutations Substitutions ▪ Transitions: purine purine G A, A G pyrimidine pyrimidine C T, T C ▪ Transversions: purine pyrimidine pyrimidine purine Ex: A T, A C, C G, TA Insertions Deletions When one base changes in one strand, both strands will end up having the mutation  Classification of mutations based on changes in the amino acid sequence These terms only apply to mutations in the open reading frame part of a gene A G T C Point mutation Substitution Transition  Classification of mutations based on changes in the amino acid sequence These terms only apply to mutations in the open reading frame part of a gene T A A T Point mutation Substitution Transversion  Classification of mutations based on changes in the amino acid sequence These terms only apply to mutations in the open reading frame part of a gene G A C T Point mutation Substitution Transition  Classification of mutations based on changes in the amino acid sequence These terms only apply to mutations in the open reading frame part of a gene Point mutation Insertion  Classification of mutations based on changes in the amino acid sequence These terms only apply to mutations in the open reading frame part of a gene Point mutation Deletion Insertions or deletions of nucleotides in a number that is not a multiple of three within the ORF result in frame-shift mutations regardless of the position of insertion/deletion  Classification of mutations based on functional changes Loss-of-function- The cell loses some function ▪ The mutation causes the amino acid sequence of the protein to change and that reduces protein functionality or ▪ The mutation causes lower levels of the protein to be produced and therefore the cell loses some of the function performed by the protein ▪ Loss-of-function mutations may occur in any part of a gene Loss-of-function mutations may occur in the promoter region of the gene  Loss-of-function mutations may occur in the 5’-UTR region of the gene An increase in the number of trinucleotide repeats in the 5’-UTR of the Fragile Mental Retardation (FMR1) gene in the X chromosome causes lack of transcription of the gene and results in Fragile X-syndrome. normal number of repeats normal amounts of mRNA and protein large number of repeats decreased transcription and amount of protein Loss-of-function mutations may occur in the introns of the gene ß-globin gene in humans Loss-of-function mutations may occur in: the open reading frame the promoter region of the gene the 5’-UTR the introns the 3’-UTR (have not seen example yet)  Gain-of-function- The cell gains some function ▪ Generally the mutation causes higher levels of the protein to be produced and therefore the cell gains the function performed by the protein ▪ Rarely the mutation causes the amino acid sequence of the protein to change and that results in the protein acquiring a new function ▪ Gain-of-function mutations generally occur in the regulatory regions of a gene (promoter) Loss-of-function mutations are more common than gain-of-function mutations  Example of gain-of-function mutations Constitutive expression of human genes encoding proteins that promote cell division can lead to tumor formation and cancer. Example of gain-of-function mutations Ectopic expression of the eyeless gene in Drosophila results in additional eyes produced in antenna, legs and wings. Eyes produced on antenna and legs  Forward and reversion mutations Forward- first, original mutation Reversion- second mutation that restores the original function in the cell ▪ True reversion- restores the original function in the cell by restoring the sequence of the gene (strictly speaking) or of the protein encoded by the gene ▪ Suppression- restores the original function in the cell without restoring the original sequence o Intragenic suppression- the second mutation occurs in the same gene as the forward mutation o Intergenic suppression- the second mutation occurs in a different gene than the forward mutation Reverts to the original amino acid sequence of the protein  or intragenic suppression G C Both forward and reversion mutations happen in the same gene  or intergenic suppression First, forward mutation happens in gene A Second, reversion mutation happens in gene B  Suppressor tRNAs The mutation in the gene encoding the tRNA is an intergenic suppression, because it will restore the amino acid sequence of the forward protein being translated and nonsense mutation negate the effect of the forward nonsense mutation reversion intergenic suppression  If the forward mutation is a G deletion, the reversion must be C an insertion. It does not have to be in the same position. If the forward mutation is an insertion, the reversion must be a deletion. It does not have to be in the same position. From easier to harder to have a reversion: Deletions/insertions Transitions Transversions  Spontaneous mutations Example: In a population of 668,000 individuals 41 individuals who did not have a genetic disorder in their ancestry show the disease due to a new mutations in certain gene. The rate of mutation for that gene would be -5.  Spontaneous mutations DNA replication ▪ DNA polymerases can make mistakes, but they usually have proof- reading ability based on their 3’ 5’ exonuclease activity.  Spontaneous mutations DNA replication ▪ The tautomeric (alternative) forms of the bases may result in DNA pol leaving the wrong base in the new strand. Common form Tautomeric form Easy to remember: A–T A–C In the tautomeric form each base still pairs with a C–G C–A base of the other type, but G–C G–T not the normal one: T–A T–G purine-pyrimidine pyrimidine- purine This causes transition mutations. Figure 18.08  Spontaneous mutations DNA replication ▪ Repeated sequences may cause slippage or sliding of the template or new strand, leading to deletions or insertions respectively. o The repeated single nucleotide, dinucleotide, trinucleotide, etc… will be deleted or inserted. o If the repeat is not of a trinucleotide or made of a number of bases multiple of three, and the slippage occurs in the ORF of the gene, this will cause a frame-shift mutation. Figure 18.16  Spontaneous mutations DNA structure ▪ Depurination, breakage of bond between deoxyribose and purine ▪ Results in substitutions, either transitions or transversions  Spontaneous mutations DNA structure ▪ Deamination, removal of an amino group, most commonly from cytosine ▪ Results in transitions  Hot spots Sequences of DNA that accumulate a higher number of mutations than others Sequences with repeats because the slippage of DNA strands causes frequent mutations. Sequences with high proportion of methylated cytosines, because deamination changes methylated cytosines to thymines, and these mutations are not repaired as easily as others. ▪ In prokaryotes there are specific sequences in which the Cs are methylated. Enzymes produced by the bacterial species and digest foreign DNA cannot digest the bacterial’s own DNA. ▪ In eukaryotes the Cs in CG sequences may be methylated. This methylation may correlate with gene expression. More methylation Note: You willlevels lower not know by looking at a sequence where or if the Cs in that of expression. sequence would be methylated, so hot spots in your examples will contain repeats that you should be able to identify. Induced mutations  Induced mutations Radiation ▪ High energy, ionizing radiation, for example X-rays or emitted by radioactive isotopes, can break phosphodiester bonds and cause chromosomal abnormalities, such as deletions, inversions or translocations. ▪ Lower energy, non-ionizing radiation, for example, UV rays. o Mostly cause formation of thymine dimers. o If these dimers are not repaired the altered DNA structure will result in problems during DNA replication and mutations. How do we know if a compound is mutagenic? We use the Ames test Tests for reversion of His- mutants of Salmonella tiphimurium, by plating them in minimal medium. Minimal medium Minimal medium with histidine His+ bacteria Growth Growth His- bacteria No growth Growth (auxotrophic) It includes a control, in which reversion is tested without adding the potential mutagenic compound Uses two different types of His- mutants, with either substitutions or frameshift mutations, because a particular mutagen, depending of its mode of action, will cause either substitutions or frame-shift mutations. Therefore any mutagen will only be able to revert substitutions or The Ames test The Ames Test for Potential Mutagenicity of Chemical Compounds  Everyday mutagens Heterocyclic amines (HAs) 2-amino-3-methylimidazo[4,5—f]quinoline (IQ) 2-amino-3,4-dimethylimidazo[4,5—f]quinoline (MeIQ), 2-amino-3,8-dimethylimidazo[4,5—f]quinoxaline (MeIQx) 2-amino-3,4,8-trimethylimidazo[4,5—f]quinoxaline (DiMeIQx) 2-amino-1-methyl-6-phenylimidazo[4,5 — b]pyridine (PhIP)  HAs Found in overcooked or barbecued meats and fried foods. Modification of these amines by liver enzymes produce compounds that bind to the DNA and form adducts. Adducts result in mistakes made during DNA replication and mutations.  Everyday mutagens Nitrosamines N-Nitrosonornicotine N-nitro4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone Nitrosodimethylamine  Nitrosamines Produced from nitrites in food, such as beer, fish, meat and cheeses. Formed from nicotine in tobacco. Bind to DNA and form adducts. Adducts result in mistakes made during DNA replication and mutations.  Everyday mutagens Polycyclic aromatic hydrocarbons (PAHs) Benzopyrene  PAHs Produced by incomplete combustion of fuel. Also produced by meats cooked at high temperature. Bind to DNA and form adducts. Adducts result in mistakes made during DNA replication and mutations.  Mutagens used in research to produce mutations Base analogs Base modifying agents ▪ Deaminating ▪ Hydroxylating ▪ Alkylating Intercalating agents  Base analogs 5- Bromouracil is an analog of Amino purine is an analog of adenine thymine A–T A–C B–A B–G Base analogs cause transition mutations A G T C Mostly A:T base pairs to G:C base pairs  Base modifying agents ▪ Deaminating Example: nitrous acid It can deaminate o adenine into hypoxanthine which pairs best with cytosine A G T C o cytosine into uracil which pairs best with adenine o guanine into xanthine which still pairs best with cytosine Note: You need to know the mode of action of the mutagens given as examples.  Base modifying agents A G ▪ Hydroxylating T C Example: hydroxylamine  Base modifying agents ▪ Alkylating Example: Ethyl methane sulfonate (EMS) It can alkylate A G o guanine to ethylguanine which pairs best with thymine T C o Thymine to ethylthymine which pairs best with guanine  Intercalating agents Examples: ethidium bromide proflavine Cause insertions and deletions A:T  G:C Most common type of spontaneous mutations: transitions Most common type of mutations induced by mutagens used in research: transitions A transition in the third position of the codon within the ORF is likely to be a silent mutation.