INTRGEN - Essentials of Genetics Chapter 14

gene mutations

base-pair sequence of DNA within individual genes
-alternation in DNA sequence

mutations in germ cells

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

mutations in somatic cells

not transmitted to the next generation but may lead to altered cellular function or tumors

spontaneous mutation

changes in the nucleotide sequence of genes that appear to have no known cause
-often occur during the enzymatic process of DNA replication

induced mutations

result from the influence of extraneous factors
-may be the result of natural or artificial agents

mutation rate

the likelihood that all gene will undergo a mutation in a single generation or in forming a single gamete
-varies between different organisms, genes
-hot spots have high susceptibility to mutation

mutation rate for spontaneous mutation

-exceedingly low for all organisms
-the rate varies between different organisms
-even within the same species, the spontaneous mutation rate varies from gene to gene

variation in mutation rates between organisms

reflects the relative efficiencies of their DNA proofreading and repair systems

Somatic mutations

those occurring in any cell in the body except germ cells

Germ-line mutations

those occurring in gametes

Autosomal mutations

mutations within genes located on the autosomes

x-linked mutations

those within genes located on the X chromosome

somatic mutations will have a greater impact if they are

dominant, or if they are X-linked in males

point mutation, or base-substitution

a change of one base pair to another in a DNA molecule

missense mutation

a change of one nucleotide of a triplet within a protein-coding portion of a gene resulting in the creation of a new triplet that codes for a different amino acid in the protein product

nonsense mutation

a change of one nucleotide of a triplet within a protein-coding portion of a gene resulting in a premature stop codon, terminating the translation of the protein

silent mutation

the point mutation alters the codon but does not result in a change in the amino acid at that position in the protein (due to degeneracy of the genetic code)

frameshift mutation

insertion or deletion of one or more nucleotides at any point within a gene. this causes all of the subsequent 3-letter codons to be changed, unless its in multiples of 3, which would reestablish the reading frame

transition

pyrimidine replaces a pyrimidine or purine replaces purine

transversion

pyrimidine replaces a purine or vice versa

loss-of-function mutations

one that reduces or eliminates the function of the gene product
-can be dominant or recessive

null mutations

mutations that result in complete loss of function

gain-of-function mutation

results in a gene product with enhance or new functions. may be due to a change in the amino acid sequence of the protein that confers a new activity, or it may result from a mutation in a regulatory region of the gene, leading to expression of the gene at higher levels, or the synthesis of the gene product at abnormal times, or places
-most are dominant

visible mutations

affect a morphological trait
-recognized by their ability to alter a normal or wild-type visible phenotype

nutritional mutation

loss of ability to synthesize an amino acid or vitamin
-auxotrophs

biochemical mutation

mutations in biochemical pathway
ex: sickle-cell anemia and hemophilia

behavioral mutation

affect the behavior pattern of an organism
-often difficult to analyze

regulatory mutation

changes gene expression- can disrupt an entire pathway
-can disrupt normal regulatory processes and may inappropriately activate or inactivate expression of a gene

lethal mutation

a mutation that interrupts a process that is essential to the survival of the organism

conditional mutations

the expression depends on the environment in which the organism finds itself

temperature sensitive mutation

conditional mutation
at a "permissive" temperature, the mutant gene product functions normally, but it loses its function at a different, "restrictive" temperature

neutral mutation

a mutation that occur either in a protein-coding region or in any part of the genome, and whose effect on the genetic fitness of the organism is negligible

tautomers

bases that can take several forms

replication slippage

one strand of the DNA template loops out and becomes displaced during replication, or when DNA polymerase slips or stutters during replication
-can occur anywhere in the DNA but seems distinctly more common in regions containing repeated sequences

tautomeric forms

alternate chemical forms that differ only by a single proton shift in the molecule

tautomeric shifts

change the bonding with non complementary bases
-end result is a point mutation

depurination

the loss on one of the nitrogenous bases in an intact double-helical DNA molecule
-most frequently is a purine (A or G)

apurinic site

can occur if the glycosidic bond linking the 1'-C of the deoxyribose and the number 9 position of the purine ring is broken

deamination

an amino group in cytosine or adenine is converted to keto group
-the major effect of these changes is an alteration in the base-pairing specificities of these two bases during DNA replication
-may occur spontaneously or as a result of treatment with chemical mutagens
----change base and causes it to pair incorrectly

mutagens

have the potential to damage DNA and cause mutations
-some are natural, some are unnatural or human-made additions to our modern world

base analogs

compounds that can substitute for purines or pyrimidines

alkylating agent

donates alkyl groups to amino or kept groups in nucleotides
-alters the base pairing of nucleotides

intercalating agents

chemicals that have dimensions and shapes that allow them to wedge between the base pairs of DNA
-cause a distortion to DNA strands unwind

adduct-forming agents

group of chemicals that cause adducts

DNA adduct

a substance that covalently binds to DNA, altering its conformation and interfering with replication and repair

electromagnetic spectrum

full range of wavelengths

one major effect of ultraviolet (UV) radiation

the creation of pyrimidine dimers, particularly those consisting of two thymine residues on the same strand of DNA

pyrimidine dimers

chemical species consisting of two identical pyrimidines
-distort DNA conformation and inhibit normal replication
-can block DNA Replication

ionizing radiation

radiation that penetrates deeply into tissues, causing ionization of the molecules encountered along the way

free radicals

chemical species containing one or more unpaired electrons
-can directly or indirectly affect the genetic material, altering purines and pyrimidines in DNA, breaking phosphodiester bonds, disrupting the integrity of chromosomes, and producing a variety of chromosomal aberrations, such as deletions, translocations, and chromosomal fragmentation.

polygenic

caused by variations in several genes

trinucleotide repeat sequences

specific short DNA sequences that are repeated many times

trinucleotide repeat expansions

abnormally large numbers of repeat sequences

DNA repair

counteract spontaneous and induced DNA damage
-essential to the maintenance of the genetic integrity of organisms and, as such, to the survival of the organism

proofreading

if an incorrect nucleotide is inserted during polymerization, the enzyme can recognize the error and "reverse" its direction. it then behaves as a 3' to 5' exonuclease, cutting out the incorrect nucleotide and replacing it with the correct one

mismatch pair

the mismatch is detected, the incorrect nucleotide is removed, and the correct nucleotide is inserted in its place.

strand discrimination

based on DNA methylation

endonuclease

creates a nick in the backbone of the unmethylated DNA strand, either 5' or 3' to the mismatch

exonuclease

unwinds and degrades the nicked DNA strand, until the region of the mismatch is reached

postreplication repair

responds after damaged DNA has escaped repair and has failed to be completely replicated

SOS repair system

in the presence of a large number of unprepared DNA mismatches and gaps, bacteria can induce the expression of about 20 genes who's products allow DNA replication to occur even in the presence of these lesions
--last resort
-SOS repair itself become mutagenic, although it may allow the cell to survive DNA damage would otherwise kill

photoreactivation enzyme & repair

UV-induced damage to E. coli DNA can partially be reversed if, following irradiation, the cells are exposed briefly to light in the blue range of the visible spectrum
-enzymes mode of action is to cleave the bonds between thymine dimers, thus directly reversing the effect of UV radiation on DNA

excision repair

"cut and paste"
1. recognize error and clipped out by endonuclease
2. A DNA polymerase fills in the gap by inserting nucleotides complementary to those on the intact strand, which it uses as a replicative template. usually performed by DNA polymerase I
3. dna ligase seals the final nick that remains at the 3'-OH end of the last nucleotide inserted, closing the gap

base excision repair

corrects DNA that contains a damaged DNA base
-DNA glycosylase cut the glycosidic bond between the base or the sugar, create a aplyrimidinic or apurinic site
-AP endonuclease recognizes the sugar with the missing base and makes a cut in the phosphodiester backbone at the aplyrimidinic or apurinic site.
-Endonucleases then remove the deoxyribose sugar and the gap is filled by DNA polymerase and DNA ligase

DNA glycosylase

recognizes the altered base in a BER

AP endonuclease

recognizes the sugar with the missing base and makes a cut in the phosphodiester backbone at the aplyrimidinic or apurinic site.

Nucleotide Excision Repair

repair bulky lesions in DNA that alter or distort the double helix, such as the UV-induced pyrimidine dimers discussed previously

xeroderma pigmentosum (xp)

a rare recessive genetic disorder that predisposes individuals to severe skin abnormalities, skin cancers, and a wide range of other symptoms
-results of studies suggest that the XP phenotype is caused by defects in NER pathways and by mutations in more than one gene

unscheduled DNA synthesis

elicited in normal cells by UV radiation
DNA synthesis other than that occurring during chromosome replication

heterokaryon

a single cell with two nuclei from different organisms but a common cytoplasm

complementation

occurs because the heterokaryon has at least one normal copy of each gene in the fused cell

DNA double-strand break repair

responsible for reattaching two broken DNA strands

homologous recombination repair

-involves the activity of an enzyme that recognizes the double-strand break, then digests back the 5' ends of the broken DNA helix, leaving overhanging 3' ends. One 3' end searches for a region of sequence complementary on the sister chromatic and then invades the homologous DNA duplex, aligning the complementary sequences. Once aligned, DNA synthesis proceeds from the 3' overhanging ends, using the undamaged DNA strands as templates
-relatively error free

non homologous end joining

activated in G1, during DNA replication
-proteins bind to the free ends of the broken DNA, trim the ends, and ligate them back together. Some nucleotide sequences are lost in the process of end joining, so it is an error-prone

Ames test

uses a number of different strains of the bacterium Salmonella typhimurium that have been selected for their ability to reveal the presence of specific types of mutations. Each strain contains a mutation in one of the genes of the histidine operon
mutant (his-)
Wild type (his+)
The assay measures the frequency of reverse mutations that occur within the same mutant gene, yielding wild type
**Allows scientists to estimate the mutagenicity and cancer-causing potential of chemical agents by following the rate of mutation in specific strains of bacteria
-Used to identify potential mutagens

carcinogens

cancer causing agents

Transposable elements

DNA sequences that can move or transpose within and between chromosomes, inserting themselves into various locations within the genome

insertion sequences

transposable elements in bacteria that can move from one location to another and, if they insert into a gene or gene-regulatory region, may cause mutations

two features of IS elements that are essential to their movement

1. the contain a gene that encodes an enzyme called transposase
2. the ends of IS elements contain inverted terminal repeats

transposase

responsible for making staggered cute in chromosomal DNA, into which the IS element can insert

inverted terminal repeats

short segments of DNA that have the same nucleotide sequence as each other but are oriented in the opposite direction

Tn elements

bacterial transposons
larger than IS elements and contain protein-coding genes that are unrelated to their transposition

R factors

bacterial plasmids that may contain many Tn elements conferring simultaneous resistance to heavy metals, antibiotics, and other drugs

mobile controlling genes

transposable elements

the source of all genetic variation

mutation

somatic mutations

arise in somatic cells- passed to daughter cells by mitosis

germ line mutations

arise in cells that make gametes--passed to future generations

most frequent form of mutation

insertion/deletion

forward mutation

changes wild type allele

reverse mutation

changes a mutant allele back to wild-type

null

complete loss

LOF tend to be

recessive

GOF tend to be

dominant

suppressor mutation

hides the impact of another mutation
-2nd mutation allows wild type to be restored without actually fixing the mutation

intergenic suppressor

occurs in a different gene

base analog

basically imitates a base
-can get attached to backbone and incorporated into DNA
-Can destabilize DNA

Tautomer becomes _____ in replication

stable in replication

strand slippage tends to

be common in areas where there is repetition--long enough run of the same nucleotide

trinucleotide repeats

if it gets expanded past a certain range it becomes a problem

reactive forms of oxygen can be

mutagenic