Genetics: Chapter 14: Gene Mutation, DNA Repair, and Transposition

Types of Classification of Mutations

-Based on Location of Mutation -Based on Type of Molecular Change -Based on Phenotypic Effects

Human Disorders Caused by Single-Gene Mutations

-Achondroplasia -Marfan Syndrome -Familial Hypercholesterolemia -Cystic Fibrosis -Huntington Disease

Deamination

-DNA base damage -amino group in cytosine or adenine is converted to a keto group -cytosine converted to uracil -adneine converted to hypoxanthine -result in base pairing of original bases -G = C converted to A = U and next generation, A = T

Depurination

-DNA base damage -loss of one of the nitrogenous bases, usually a purine, in an intact double-helical DNA molecule -result in base pairing of original bases -G = C converted to A = U and next generation, A = T

Induced Mutations May Arise from....(2)

-DNA damage caused by: 1. Chemical 2. Radiation -induced from external surfaces/we cause

Oxidative Damage

-DNA may suffer this -occurs by byproducts of normal cellular processes and exposure to high-energy radiation 1. Superoxides (O2-) 2. Hydroxyl radicals (OH) 3. Hydrogen perioxide (H2O2) -reactive oxidants can produce over 100 types of chemical modifications in DNA, such as modifications to bases, loss of bases, and single-stranded breaks

Introduction

-DNA molecule stores, replicates, transmits, and decodes information -Changes in DNA sequences give rise to variations that result in phenotypic variability, adaptation to environmental changes, and evolution -Gene mutations are the source of new alleles and genetic variation in populations but are also the source of genetic changes that can lead to cell death, genetic diseases, and cancer -mutations can be negative if results in disease -mutations can be beneficial if enable organisms to adapt to environment-->evolve

Proofreading

-DNA polymerase II proofreads each step and catches 99 percent of error when nucleotides are incorrectly inserted during DNA replication, recognizing and removing them by reversing direction of error -behaves like an exonuclease, cuts out the incorrect nucleotide and replaces it with the correct one

Spontaneous DNA Replication Errors

-DNA polymerase occasionally inserts incorrect nucleotides but can proofread and correct these errors if detected because it has exo and endonuclease activity in both directions -errors due to mispairing predominantly lead to point mutations -bases can take several forms or tautomers, which increase their chance of mispairing during DNA replication

Most common causes of Spontaneous Mutation (2)

-Depurination and Deamination -result in base pairing of original bases -G = C converted to A = U and next generation, A = T

Missense DNA Mutation

-Disorder: Achondroplasia -Molecular Change: Glycine to arginine at position 380 if FGFR2 gene -much more common -alter amino acid sequence of a protein

Deletion DNA Mutation

-Disorder: Cystic Fibrosis Molecular Change: Three base-pair deletion of phenylalanine codon at position 508 of GTTR gene

Insertion DNA Mutation

-Disorder: Familial Hypercholesterolemia -Molecular Change: various short insertions throughout the LDLR gene

Trinucleotide Repeat Expansions/Sequences

-Disorder: Huntington Disease -Molecular Change: >40 repeats of CAG sequence in coding region of Huntington gene -specific short DNA sequences repeated many times -normal individuals may have fewer than 30 repeats, but some have over 200 repeats within and surrounding specific genes -other disorders: Fragile-X Syndrome, Myotonic Dystrophy

Nonsense DNA Mutation

-Disorder: Marfan Syndrome -Molecular Change: Tryosine to STOP codon at position 2113 of fibrillin-1 gene -30% of mutations -prematurely terminate protein synthesis -trigger rapid decay of mRNA

Spontaneous DNA Slippage

-If a DNA strand loops out and becomes displaced or if DNA polymerase slips, small insertions and deletions can occur -insertions and deletions can lead to frameshift mutations or amino acid insertions and deletion in the gene product -can cause replication slippage

Types of Single Gene Mutations

-Missense -Nonsense -Insertion -Deletion -Trinucleotide Repeat Expansions

Spontaneous Mutations Arise from....(2)

-Replication Errors -Base Modifications

Classification Based on Location of Mutation

-Somatic Mutations -Germ-line Mutations -Autosomal Mutations -X-linked and Y-linked Mutations

Transversions

-a purine and a pyrimidine are interchanged

Transitions

-a pyrimidine replaces a pyrimidine -a purine replaces a purine

Single-Gene Mutations Cause...

-a wide range of Human Diseases

Mismatch Repair

-activated if proofreading fails -mismatches are detected, cut, and removed by endonuclease and exonuclease activity -correct nucleotide is inserted by DNA polymerase and the gap is sealed by ligase

Nonhomologous End Joining DSB Repair

-activated in G1 phase of cell cycle -complex of 3 proteins binds to free ends of broken DNA, trims and ligates them together -error-prone for loss of some nucleotides and joining wrong ends

Behavioral Mutations

-affect behavior patterns in organisms -ex. the mating behavior of a fruit fly may be impaired if it cannot beat its wings

Regulatory Mutations

-affect regulation of gene expression

UV Light

-all electromagnetic radiation consists of energetic waves that have different wavelengths -UV radiation creates pyrimidine dimers (two identical pyrimidines) that distort the DNA conformation in such a way that errors tend to be introduced during DNA replication

Visible/Morphological Mutations

-alter normal/wild-type visible phenotype

Mutation

-alteration in DNA sequence -may be 1. single base-pair substitution 2. deletions or insertions of one or more base pairs 3. major alterations in chromosomal structure -may occur within the coding or noncoding regions of a gene (exon and intron sequence) -may or may not bring about detectable changes in phenotype -may occur in somatic or germ cells

Tautomeric Forms

-alternate chemical forms that differ a single proton shift in the molecule -purines and pyrimidines can exist in these forms

Transposable Elements in Humans

-approximately half of human genome is composed of transposable element DNA -1 percent of human genome comprises gene coding-sequence DNA -most appear to be inactive -is possible for a mobile element to transpose from one chromosome to another in gamete-forming cells of the mother, causing a genetic disease

Classifications Based on Type of Molecular Change

-based on type of nucleotide change -point mutation or base substitution which may result in missense mutation, nonsense mutation, or silent mutation -base substitutions classified as transitions or tranversions -frameshift mutations can be very severe

Exposure to ionizing radiation can lead to....

-both strands of DNA being cleaved -results in: 1. chromosomal rearrangements 2. cancers 3. cell death

Tautomeric Shifts

-can change the bonding structure allowing noncomplementary base pairing, which may lead to permanent base-pair changes and mutations -C and A -C and T etc.

Biochemical Mutations

-can have an effect on the well-being and survival of the affected individual -ex. sickle cell anemia, hemophilia

Insertion Sequences (IS Elements)

-can move from one location to another, causing mutation and double-stranded breaks -if inserted into a gene/gene-regulatory region, can cause mutations -all contains two essential features 1. A gene encoding the enzyme transposase makes staggered cuts into DNA, allowing the IS element to insert 2. IS element ends contain inverted terminal repeats (ITRs), which act as recognition sites for the binding of transposase and important for transposition

Neutral Mutation

-can occur either in a protein-coding region or in any part of the genome with a negligible effect -vast majority of mutations are likely to occur in the large portions of the genome that do not contain genes -do not affect gene products or gene expression -effect on genetic fitness of the organism is neutral

Nutritional/Biochemical Mutations

-cause loss in ability to synthesize an amino acid or vitamin

Polygenic

-caused by variations in several genes -most human genetic diseases ex. sickle cell anemia

Replication Slippage

-causes trinucleotide or dinucleotide expansion or contraction during DNA replicaiton -can occur anywhere in the DNA -is more common in repeated sequences -Hot spots for hereditary Diseases such as Fragile X syndrome or Huntington disease -more copies/repeated sequences increases severity of the disease

Point Mutation/Base Substitution

-change of one base pair to another -may result in missense mutation, nonsense mutation, or silent mutation -classified as transitions or transversions -change of one letter

Free Radicals

-chemical species containing one or more unpaired electrons -directly/indirectly affect DNA 1. Alter purines and pyrimidines 2. Break Phosphodiester Bonds between nucleotides 3. Produce deletions, translocations, and fragmentation

Intercalating Agents

-chemicals whose dimensions and shapes allow them to wedge between DNA base pairs, causing base-pair distortions and DNA unwinding ---Ethium Bromide ---Acridine Dyes ---Chemotherapeutic Agents -changes in DNA structure may affect many functions, including transcription, replication, and repair leading to frameshift mutations

Base Excision Repair (BER)

-corrects DNA containing a damaged DNA base -Endonucleases cut the damaged DNA -DNA polymerase fills in the gap -ligase seals the ends

Organisms use DNA Repair Systems to....

-counteract mutations/genetic damage that would result in genetic diseases and cancer -maintain the integrity of genetic material susceptible to spontaneous and induced damage

Conditional Mutations

-expression depends on the environment of organism -Ex. temperature-sensitive mutation -mutant gene product functions at one temperature but not another -temperature sensitive coat color variations in Siamese cats and Himilayan rabbits

Spontaneous Mutations

-happen naturally and randomly -usually linked to normal biological or chemical processes in the organism -alters the structure of nitrogenous bases -often occur during the enzymatic process of DNA replication

Germ Cell Mutations

-heritable -are the basis for the transmission of genetic diversity and evolution as well as genetic diseases

Transposons Effects on Genes

-insertions can lead to translation disruptions -promoters and enhancers can have effects on nearby genes -cause abberant splicing and early termination of transcription -exon shuffling -recombination between transposons can lead to chromosomal rearrangements, resulting in phenotypic changes or diease -ability to alter genes and chromosomes, may contribute to the variability that underlies evolution -may also affect the evolution of genomes by altering gene-expression in ways that are retained by the host

Lethal Mutations

-interrupts an essential process -results in death -various inherited biochemical disorders -ex. Tay-Sachs Disease, Huntington Disease

Photoreactivation Repair

-involves a photoreactivation enzyme (PRE) -cleaves the bonds between thymine dimers -requires exposure to light -enzyme must absorb a photon of light to cleave the damaged DNA -enzyme is found in bacteria, fungi, plants, and some vertebrates but not in humans

Transposable Elements/Transpoons

-jumping genes -DNA sequences that can move or transpose within and between chromosomes -insert themselves into various locations within the genome -present in all organisms -function is still unknown -used in genetic research as mutagens, cloning tags, and vehicles for introducing foreign DNA into model organisms -do occur in humans -can have a wide range of effects on genes

Bacterial Transpoons (Tn Elements)

-larger than IS elements -can introduce multiple drug resistance onto bacterial plasmids (R factors) -can move from plasmids onto bacterial chromosomes, spreading multiple drug resistance between different bacterial strains

rate of mutation

-likelihood that a gene will undergo a mutation in a single generation or in forming a single gamete -exceedingly low for all organisms -varies between different organisms -humans and Drosophilia have higher mutation rates than Neurospora (fungi), viruses, and bacteria -even within same species, spontaneous mutation rate varies from gene to gene

Classification Based on Phenotypic Effects

-loss of function mutations/null mutations -gain of function mutations -visible/morphological mutations -nutritional/biochemical mutations -biochemical mutations -behavioral mutations -regulatory mutations -lethal mutations -conditional mutations, such as temperature-sensitive mutation -neutral mutation

There is a strong link between....

-mismatch repair and cancer -Ex. ---Hereditary Nonpolyposis Colon ---Leukemia ---Lymphoma ---Tumors of the ovary, prostate, and endometrium

Frameshift Mutations

-much more common -alter protein sequence -create internal nonsense codons

Base Analogs

-mutagenic chemicals -can substitute for purines or pyrimidines during nucleic acid replication -Ex. 5-bromouracil (5-BU) behaves as a thymine analog ---increases tautomeric shifts ---increases sensitivity to UV light, also mutagenic

Adduct-Forming Agents

-mutation-causing chemicals that covalently bind to DNA -alter its conformation -interferes with replication and repair 1. Acetaldehyde: composition of cigarette smoke 2. Heterocyclic amines (HCAs): cancer-causing chemicals created during cooking of meats (beefs, chicken, and fish); 17 different HCAs linked to cancers of stomach, colon, and breast

Mutagens

-natural or artificial agents that induce mutations -Fungal toxins -Cosmic Rays -Ultraviole Light -Industrial Pollutants -Medical Xrays -Chemicals in Tobacco Smoke

Alkylating Agents

-naturally occuring or human made chemicals -donate an alkyl group (CH3 or CH3CH2) to amino or keto groups in nucleotides to alter base-pairing affinity -leads to transition mutations

Missense Mutation

-new triplet code for a different amino acid

Silent Mutation

-new triplet code still codes for same amino acid

Somatic Mutations

-occur in any cell except germ cells -not heritable -recessive autosomal mutation occurs in somatic cell of diploid organism, unlikely to result in a detectable phenotype -have greater impact if they are dominant

Germ-line Mutations

-occur in gametes -are inherited

Autosomal Mutations

-occur within genes -located on autosomes -inherited dominant autosomal mutations will be expressed phenotypically in the first generation -due to heterozygosity, autosomal recessive mutation of either males or females may go unnoticed for many generations until chance mating brings two copies together

X-linked and Y-linked

-occur within genes located on the X and Y chromosome -have greater impact in males if X-linked since they are immediately expressed -more noticeable if they occur early in development, with undifferentiated cells giving rose to several differentiated tissues or organs -X-linked recessive mutations arising in gametes of a homogametic female (such as human) may be expressed in a hemizygous male (such as human) offspring

Homologous Recombination DSB Repair

-occurs during the late S or early G2 phase of cell cycle

Dominant mutations in cells of adult tissue

-often masked by the activity of thousands of nonmutant cells in the same tissue

Xeroderma Pigmentosum (XP)

-rare genetic disorder that arises due to defects in the NER pathways and to mutations in more than one gene -affected individuals exhibit severe skin abnormalities, skin cancers, and a wide range of other symptoms, including developmental and neurological defects -severe, may be lethal -early detection and protection from sunlight can arrest it

Double Strand Break Repair (DSB Repair)

-reattaches two broken DNA strands -two types: 1. Homologous Recombination 2. Nonhomologous End Joining -defects may underlie familial disposition to breast and ovarian cancer -several human disease syndromes result from defects 1. Fanconi's Anemia 2. Ataxia Telangiectasia

Loss of Function/Null Mutations

-reduce/eliminate function of gene product

Nucelotide Excision Repair (NER)

-repairs bulky lesions that alter/distort the double helix -specific number of nucleotides are removed, including the lesion -DNA polymerase and ligase complete the repair

Excision Repair

-required by light-independent DNA repair mechanisms in all prokaryotes and eukaryotes -endonuclease recognizes and cuts the distortion/error -DNA polymerase inserts the complementary nucleotides in the missing gap -DNA ligase seals the final nick -two types: 1. Base Excision Repair (BER) 2. Nucleotide Excision Repair (NER) -polymerase I & II involved -at least seven different genes involved in humans -complex is responsible for the excision of approximately 28-nucleotide-long fragments from the DNA strand that contains the lesion

Postreplication Repair

-responds after damaged DNA has escaped repair and failed to be completely replicated -when DNA bearing a lesion is replicated, DNA polymerase may skip over the lesion, leaving it an unreplicated gap on the newly synthesized strand -through recombination processes, the correct complementary sequence is recruited from the parental strand and inserted into the gap opposite the lesion -new gap is filled by DNA polymerase and ligase

Frameshift Mutations

-result from insertions or deletions of a base pair, altering the triplet reading frame -can be very serious, especially if: ---they occur early in the coding sequence ---one of the many altered triplets will be UAA, UAG, UGA which are stop or translation termination codons -except multiples of threes, which would reestablish the initial frame of reading -loss or gain of one letter

Induced Mutations

-result from the influence of an extravenous factor, either natural or artificial -ex. radiation, UV light, natural and synthetic chemical -we cause the induction to occur

Gain of Function Mutations

-result in a gene product with enhanced/new function

Monogenic

-single base-pair change in one of the approximately 20,000 human genes can lead to serious inherited disorders

Other disease-associated mutations affect: (3)

-the sequence of gene promoters -mRNA splicing signals -other noncoding sequences that affect the transcription, processing, and stability of mRNA or protein

Nonsense Mutation

-triplet code for a stop codon -translation terminated prematurely

Pyrimidine Dimer

-two identical pyrimidines -created by UV radiation -distorts DNA conformation in such a way that errors are introduced during DNA replication -formed between adjacent thymidine residues along a DNA strand

Save Our Soul/ SOS Repair System

-well studied in E. Coli -last resort to minimize DNA damage -Bacteria can induce the expression of about 20 genes whose products allow DNA replication to occur even in the presence of these lesions -DNA synthesis becomes error-prone, inserting random and incorrect nucleotides in places that would normally stall DNA replication -can itself become mutagenic but allows cells to survive with DNA damage that would otherwise kill itself

Ionizing Radiation

-x rays -gamma rays -cosmic rays -more energetic than UV radiation -penetrates deeply into tissue -is mutagenic -stable molecules and atoms are transformed into free radicals

Bacteria Have Two Types of Transpoons

1. Insertion Sequence (IS Elements) 2. Bacterial Transpoons (Tn Elements)

Two types of mutations

1. Spontaneous 2. Induced -reactions (metabolic, food etc.) ---> intermediates/byproducts can be radicals -create changes in DNA/mutations

Types of Light

Radio Waves 10^3 m ---> 10^9 nm (1m) Microwaves 10^9 (1m) ---> 10^6 nm Infrared 10^6 nm ---> 10^3 nm Visible Spectrum (wavelength) 750 nm ---> 380 nm -light from sun passed through prism UV 10^3 nm ---> 1 nm X Rays I nm ---> 10^-3 nm Gamma Rays 10^-3 nm ---> 10^-5 nm Cosmic Rays 10^-5 nm---> Decreasing Wavelength and increasing energy as you go down