Genetics Chapter 4

a wild type phenotype is produced when an organism…

has two copies of the wild type allele

two types of mutant alleles:

loss of function, gain of function

loss of function allele

significant decrease or loss of functional gene product

gain of function allele

gene product acquires a new function or expresses increases wild type activity, hypermorphic, neomorphic

null/amorphic mutation

loss of function mutation, produce no functional gene product, often lethal when homozygous

leaky/hypomorphic mutation

loss of function mutation, partial loss of function, severity of the phenotype depends on the level of activity of the mutation

hypermorphic mutation

produce more gene activity than normal

neomorphic mutation

acquire novel gene activities not found in the wild type

neomorphic and hypermorphic mutations are usually more or less dominant?

more

multimeric proteins are subject to what mutations

dominant negative

spoiler effect

dominant negative phenomenon, single mutated subunit of a protein complex disrupts the function of the entire complex, in a heterozygous individual both a normal and mutant allele results in both being produced, when they arrange into a complex, the abnormal subunits poison the function of the entire complex

dominant negative in p53 in cancer

mutant p53 complex and wt p53 complex combine but can’t bind DNA, whole complex is spoiled(heterozygous)

haploinsufficiency

half the amount of gene product is not enough

incomplete dominance

one allele is not always dominant over another, blending of phenotypes, offspring does not match either parent

codominance

one allele is not always dominant over another, heterozygote phenotype matches both parents

conditional alleles

dominance is not a universal term, could depend on environmental conditions

pleiotropy

multiple traits are altered by one gene being mutated

traits that produce variable phenotypes from the same genotype

sex-limited traits, sex-influenced traits, incomplete penetrance, variable expressivity

sex limited traits

sex can influence gene expression due to differing hormone profiles, both sexes carry genes for these traits but are only expressed in one

sex influenced traits

the phenotype corresponding to a particular genotype differs based on the sex

incomplete penetrance

traits that are non penetrant in some individuals

variable expressivity

individuals who carry an allele all show the phenotype to a varying degree of severity

difference between penetrance and expressivity

penetrance is number of individuals that show a phenotype, expressivity is the degree to which the phenotype is expressed

classical complementation

if you cross two mutants with the same phenotype and the mutant alleles are on the same gene, there will not be any complement. if the mutant is on a different gene then there will be complementation and evidence of a pathway.

mutants earlier or later in the pathway have a greater chance of being rescued

earlier

what to expect with independent genes in separate pathways

9: double dominant, 3: single dominant, 3: other single dominant, 1: both recessivee

epistasis

two different genes interacting to contribute to the same phenotype

recombination

any process that produces new arrangements of DNA

independent assortment

equal likelihood of each class of gametesif

if linked, recombinants are always the ___ class

small

crossing over generates recombinants from ___ genes

linked

recombination frequency formula

# of recombinants/total, RF, r

map distance formula

RF x 100, map unites, percent recombinations, centiMorgans, should be less than 50%

distance and recombination frequency are ____ correlated

positively

genetic map distances ____ the physical distance between them

underestimate

the further apart linked genes are, the ___ accurate the genetic map distances

less

__ # of crossovers between 2 genes are unobserved

even

recombination hotspot

short genomic regions with high frequency of genetic exchange, enriched in GC

recombination coldspot

regions with low recombination rates, associated with centromeres and telomeres, and closed chromating

genetic markers

typically in noncoding regions of the genome, VNTRs, SNPs, RFLPs

VNTRs

short DNA sequences, 3-20 bases, repeat end-to-end in a chromosomal region, repeat length varies, different chromosomes can carry different repeat numbers

SNPs

more used than VNTRs, variant where one base pair is substituted by another base pair typically in a noncoding region, 3.3 million in human genome

RFLPs

changes in DNA sequence that are detected using restriction endonucleases/enzymes

restriction endonucleases/enzymes

recognize and cut specific sequences of DNA, EcoRI enzyme, DNA pieces resulting from enzyme cutting are restriction fragments, break phosphodiester bond, cuts and creates sticky/overhanging ends

haplotype

specific array of SNPs in a small region on a single chromosome, closely linked variants and tend to be passed on together during meiosis

genome wide association studies

GWAS, detects and locates genes that influence traits, looks for associations between traits and groups of alleles(SNPs) in populations

recombinant DNa

DNA formed from combining DNA from different organisms

restriction exonucleases

cut phosphodiester bonds at the end of a nucleotide polymer

restriction endonucleases

cut interior phosphodiester bonds

to a study a gene/section of DNA you should ___ it

isolate

steps to study DNA with molecular cloning

1. DNA fragments are inserted into a vector

2. insert in biological system to amplify DNA(ecoli)

3. select for organisms with recombinant plasmid

how do you screen out bacteria that aren’t transformed

grow transformants on medium containing antibiotic, cells that got the plasmid are resistant(grow as colonies), cells that didn’t get the plasmid die

transgenic organism

introducing gene from one organism into the genome of another organism, introduced gene is transgene, they needed to contain regulatory sequences to they can be expressed

complications to transgene expression

posttranslational modifications-may not undergo correct ones in host organisms and can lead to complications, codon bias-rare codons can create problems

most plant cells are totipotent, so…

under appropriate conditions a normal plant can be regenerated from a single isolated plant cell; progeny plants can be regenerated from single transformed cellstr

transgenic animals

inject DNA directly into the nucleus of a fertilized egg

homologous recombination

recombines similar(homologous sequences), less frequent, precise insertion

illegitimate recombination

recombines random sequences, more frequent, random insertion