lec 1.4 - mutations

mutations are

periment charges in DNA seq

mutations may occur

spontaneously or may be induced by mutagens

• chemically or naturally induced

point mutation

change in single base pair

• can be caused by the chemical conversion of one base into another or by errors that occur during replication

transition and transversion mutations

transition: replaces purine with purine or pyrimidine with pyrimidine

• i.e. G-C base pair w A-T base pair or vice versa

transversion: replaces a purine with a pyrimidine

• changing A-T to T-A

• worse than transition

insertions and deletions

addition or deletion of bases and can result from the movement of transposable elements or certain chemicals

• insertions can revert by deletion of the inserted material, but deletions cannot revert

forward mutations

alter gene function

back mutations

aka revertants, reverse the effects of forward mutations

• back to original sequence

• hard/rare

true reversion

mutation that restores the original sequence of the DNA

• very rare

second-site reversion

second mutation (at a second site) suppressing the effect of a first mutation within the same gene

suppression

when a mutation in a second gene bypasses the effect of mutation in the first gene

• usually when 2 diff proteins interact w/ each other

loss and gain of function mutations

• recessive mutations are due to loss of function by the polypeptide product

• dominant mutations result from a gain of function

what is required to test whether a gene is essential to life

• testing whether a gene is essential requires a null mutation (one that completely eliminates its function).

• need to completely knock it out/no functional protein to see if it is needed for a viable organism

mutations are usually ______ to the wild-type allele

recessive to the wild-type allele

• mutations damage gene function

• genes encode proteins; dominance is explained by the properties of mutant proteins

complementation test

test that determines whether two mutations are alleles of the same gene

1. cross two different recessive mutations that have the same phenotype

2. determine whether the wild-type phenotype can be produced

3. if the mutations are in the same gene then there will be no complementation (mutation shows). if there is complementation=WT phenotype is expressed that means the alleles are on different genes

cistron

• alternative term for gene

• genetic unit defined by complementation test, equivalent to a gene

existence of multiple alleles allows for

the possibility of heterozygotes that represent any pairwise combination of alleles

• in other words, the genetic diversity in a population allows for various combinations of alleles to exist in individuals

• i.e. in drosophila, many recessive mutations that read to diff eye colours all the way to no colour

polymorphic distribution

when a locus has a distribution of alleles where no individual allele can be considered to be the sole wild type

• codominance/both alleles ae expressed

• i.e. ABO human blood group locus encodes a galactosyltransferase whose specificity determines the blood group

  • inheriting two A alleles (AA) or one A one O (AO): blood type A, expressing the A antigen on their red blood cells

  • inheriting two B alleles (BB) or one B one O (BO): blood type B, expressing the B antigen

  • inheriting A allele and one B allele (AB): blood type AB, expressing both A and B antigens

  • if they inheriting two O alleles (OO): blood type O, which does not express A or B antigens

recombination

• when in meiosis does this occur?

result of crossing over that occurs at a chiasma (pl. chiasmata) during meiosis and involves two of the four chromatids (two non-sister chromatids)

• at prophase 1

• no difference if sister chromatids cross (because they are identical), must be non-sister

frequency of recombination between two genes is proportional to

their physical distance - used to map the distance between genes

• recombination between genes that are very closely linked is rare because they are always inherited as a single unit therefore no recombination

recombination in genes on diff chromosomes

• genes on different chromosomes show 50% recombination

  • recombination due to independent assortment

  • genes on different chromosomes segregate independently so that all possible combinations of alleles are produced in equal proportions (25% each combination)

recombination in genes on same chromosome

genes may or may not segregate depending on their distance from one another

• 50% recombination if genes are far apart

• linkage is 100% between genes if they are close on the chromosomes

  • recomb. elsewhere between other genes, just not with respect to genes under observation

in terms of distance between genes, what is more accurate in determining the recombination frequency and why?

smaller distances are more accurate because the larger ones have multiple sites of crossing over

codons

• start codon

triplet nucleotides that the genetic code is read in

• triplets are nonoverlapping and are read from a fixed starting point

  • start codon: AUG

frameshift mutations

mutations that insert or delete 1 or 2 individual bases causing a shift in the triplet sets after the site of mutation

• combinations of mutations that together insert or delete three bases (or multiples of three) insert or delete amino acids, but do not change the reading of the triplets beyond the last site of mutation

  • protein can still fold and be functional (just might do so differently now)

open reading frame (ORF)

usually only one of the three possible reading frames is translated (the one starting at base 1) and the other two are closed by frequent termination signals (usually the ones starting at base 2 and 3)

• ORF is a DNA sequence consisting of triplets that can be translated into amino acids, starting w/ initiation codon (AUG) ending w/ term. codon (UAA, UAG, UGA)

closed (blocked) reading frame and unidentified reading frame (URF)

• closed (blocked) reading frame – reading frame that cannot be translated into polypeptide because of the occurrence of termination codons

  • shorter protein

• unidentified reading frame (URF) – open reading frame with as yet undetermined function

  • looks like an ORF but we are not sure what it codes yet

gene expression

the process by which the information in a sequence of DNA in a gene is used to produce an RNA or polypeptide, involving transcription and (for polypeptides) translation

mRNA regions

each mRNA consists of a:

• untranslated 5′ region (5′ UTR or leader)

  • has no codons

• coding region

  • codes for protein

• untranslated 3′ UTR or trailer

  • has no codons

introns

parts of the gene with codons that are not represented in the polypeptide product as they do not code for anything

• introns are removed from the pre-mRNA transcript by splicing to give an mRNA that is collinear w/ the polypeptide product

• not present in mature mRNA

RNA processing

modifications to RNA transcripts of genes.

• This may include alterations to the 3′ and 5′ ends and the removal of introns

pre-mRNA

the nuclear transcript that is processed by modification and splicing to give an mRNA (nuclear RNA)

exon

any segment of an uninterrupted gene that is represented in mature RNA product

ribosome

large assembly of RNA and proteins that synthesizes polypeptides under direction from an mRNA template

• combo of rRNA and RNA proteins

ribosomal RNAs (rRNAs)

major component of the ribosome

transfer RNA (tRNA)

intermediate in polypeptide synthesis that interprets the genetic code

• each tRNA molecule can be linked to an amino acid

• tRNA has an anticodon seq. that is complementary to a triplet codon representing the AA

proteins are ____-acting

• what are ___-acting mutations

trans-acting : regulatory proteins that bind to DNA

• trans-acting mutations identify sequences of DNA that produce proteins that bind to other DNA sequences to cause an effect

  • trans-acting mutations are expressed as RNA or polypeptide

• control sites in DNA provide binding sites for proteins; coding regions are expressed via the synthesis of RNA

sites on DNA are ___-acting

• what are ___-acting mutations

cis-acting: DNA sequences in the vicinity of the structural portion of a gene that are required for gene expression.

• a promotor

• cis-acting mutations identify sequences of DNA that are targets for recognition by trans-acting products

  • they are not expressed as RNA or polypeptide and affect only the contiguous stretch of DNA

    • contiguous: multiple DNA sequences next to each other