Mobile pieces of DNA that can excise itself from a chromosome and re-insert elsewhere in the genome.
Types of transposable elements?
Class I Retrotransposons and Class II DNA transposons
Class I Retrotransposons
Are first transcribed into RNA, which is then reverse transcribed into DNA and inserted into a new location
Class II DNA transposons
Insert themselves, or a DNA copy, into a new location
The transposon is excised from its original location and inserted into a new one.
The original transposon remains and a new copy is generates at the target site.
What type of organisms have transposons?
Almost all organisms have many types of transposable elements
Autonomous transposable element
Capable of transposing itself, It can express a functional transposase and then send it elsewhere in the genome
Nonautomous transposable element
Cannot transpose by itself. They have mutations that stop them from making functional transposases.
Is Ds transposable?
Yes, it is in the presence of Ac activator
Is a transposition enzyme (transposase) that catalyzes excision and integration
When do we get spotted kernals?
A nonautonamous element becomes unstable if the right autonomous element is present in the genome. IE when Ds is integrated into the normally purple maize, the maize id colorless. But id Ac is present, the Ac can kick out the Ds created purple spots on the maize.
Are related to retroviruses. Like retroviruses, a retrotransposon is transposed through an RNA intermediate
Types of transposable elements in the human genome
LINEs, SINEs, DNA transposons
Class I transposable element that encodes a reverse transcriptase. Autonomous
Class I transposable elements that does not encode reverse transcriptase but is thought to use RT encoded by LINEs. Nonautonomous
What effects can transposable elements have on the human genome?
Transposition, transduction, recombination
DNA sequences that closely resemble known genes bu that don�t produce any RNA or protein product.
Byproducts of evolution, prepresenting dead genes (once functional but now inactive because of mutation or regulatory sequences)
Pseudogens that have been forms by retrotransposition (not mutation) which involves transcription, generation of a DNA copy of the mRNA (reverse transcription) and then integration of such DNA back into the genome.
Occurs when more than 1 allele is observed at a single gene within the population. IE � AA, Aa, aa
How do you detect polymorphism?
Historical methods include � visible phenotypes, chromosomal rearrangements, protein variants. Modern molecular methods � single nucleotide polymorphisms, microsatellites, SNP chips, whole genome resequencing
Single Nucleotide polymorphism (SNPs)
If the exact sequence of a gene can be determined, then single base pair differences can be observed
All individuals are the same (invariable)
Genotyping (an individual)
Determing the particular alleles in an individuals genome
What determines how much polymorphism a population has?
A population gene pool is the sum of all alleles in all breeding members
Give the relative number of each genotype in the population
How do you calculate genotype frequency?
Frequency of AA = # of AA/ total of all (AA, Aa, and aa)
Give the relative number of each allele in the population.
How do you calculate allele frequency?
P = frequency of A = AA+AA+Aa/total x 2
The probability that 3 alleles chosen at random from the population are different. The higher this number, the greater the polymorphism. One very common allele = low heterozygosity. Many common alleles = high heterozygosity.
What are the assumptions a population must meet to be able to use Hardy-Weinberg equilibrium?
Large population size, members choose mates randomly, all genotypes have equal survival and reproduction. If all of these are true, then genotype frequencies can be estimated if allele frequencies are known.
What is the Hardy-Weinburg equilibrium formula?
(p+q) = p^2 + 2pq + q^2 = 1
Even without selection, allele frequency can change due to random fluctuations. Over time genetic drift can eventually lead to fixation. Ulimately genetic drift will always lead to fixation of only 1 allele.
When genetic drift leads to the loss of all but one allele of a gene. The probability of a particular allele eventually becoming fixed by genetic drift equals its frequency in the population
Why doesn�t drift eliminate all neutral polymorphism?
Because of mutation. Heterozygosity ends up at a level where mutation adds alleles as fast as drift removes them.
All mutations start off rare in the population and soon disappear.
What is the probability of a new mutation?
What is the per run throughput of high quality bases on the GS junior system? How long does it take including data processing?
35 million, 12 hours
What is the per day throughput of the 5500x1 SOLiD system?
Why are most populations not in Hardy-Weinberg?
Many populations are not small, alleles aren�t usually equally viable, mating is often not random
A certain type of genetic drift that bottlenecks the population and reduces genetic diversity. It can also lead to large differences in allele frequencies between populations.
Individuals do not choose their mates on the basis of a particular heritable character
Nonrandom mating � positive assertive mating
Bias toward phenotypically similar mates. Each successive generation of assertive mating reduces the Aa frequency by half.
Nonrandom mating � negative assertive mating
Bias toward phenotypically different mates
Nonrandom mating - Inbreeding
Bias toward mating with relatives
In reguard to Hardy-Weinberg: Fitness
The average number of offspring produced by the individual. If genotypes have unequal fitness, then allele frequencies will change over time (natural selection)
What is the equation for the mutation selection equilibrium?
mew = sq^2 mew = rate of new mutations, s = selection coefficient, q^2 = freq. of recessive disease.
What is an example of heterozygote advantage?
Sickle cell anemia. Heterozygotes have a higher survival and reproduction than either homozygote.
Individuals with one genotype are more likely to survive and grow to reproduce than individuals with another genotype.
Basic Mendelian genetics. Takes only fixed values � Pea flower color, shape, fly eye color, etc.
Have a spectrum. Ie tree height, blood pressure, enzyme activity, etc. Most of what we see. Continuous traits do not allow us to classify offspring into discrete catagories
What influences the phenotype of an individual?
Its genotype and its environment. Differences between parental stains are due to genetic differences. Differences between individuals within each strain (offspring siblings � F1) are due to the environment. In F2 generation variance is caused by both.
Features of simple inheritance
Traits are catagorical- each individual clearly falls into a particular group (ie purple or white flowers) Trait value is determined by only 1 or 2 genes. Environmental effects on gene are minimal. Crosses yield Mendelian ratios in offspring.
Features in complex inheritance
Traits are nor categorical, but can take on any of a continuous range of values. Multiple genes determine the trait. The trait is significantly influenced by the environment. Crosses do not yield Mendelian ratios. These traits are known as quantitative or continuous traits.
Portrays the variation of a complex trait. In a distribution the average indicated the central tendency or location of the distribution. The variance indicated the dispersion or width of the distrivbution. The mean = the sum of all individual measurements/the number of measurements. Variance = the sum of squared deviates from the mean/ the number of measurements.
Quantitative trait loci (QTLs)
Genes that influence a quantitative trait. QTLs are hard to find, because there are many for each trait, and each one may only have a small effect. Also, the chromosomal region containing a QTL can be found using linkage maps with many molecular markers.
Identifying the locations of QTLs along chromosomes by genetic linkage mapping, using genetic markers. Can use backcrossing to map.
In QTL mapping, if genetic marker is closely linked to the QTL:
There is a small rate of recombination between the 2 loci. The heterozygotes are usually smaller. There is a statistical association between marker genotype and phenotype in the BC1 generation.
In QTL mapping, if genetic marker is unlinked to the QTL:
There is a high rate of recombination. There is no statistical association between marker genotype and phenotype in the BC generation.
Log odds ratio (LOD score)
Lod score = log10 (likelihood that loci are linked/likelihood that loci are unlinked). The higher the Lod score, the more likely that the data are due to loci that are linked rather than unlinked. In humans the cut off is 3.3
Essential in embryogenesis and patterning of the embryonic spine.
Part of the eukaryotic promoter structure. A/T rich region located ~ 30 base pairs. Not found on all genes.
Promoter proximal elements
Part of the eukaryotic promoter structure. Upstream promoter elements are DNA sequences that increase transcription activity. The Spq box is GC rich and common.
Basal transcriptional complex
Occurs using 3 distinct RNA polymerases. All are large multi-subunit enzymes. RNA polymerase I, II, III
RNA polymerase II
Transcribes all protein-coding genes and small nuclear RNA�s, very sensitive to alpha-amanitin, requires 7 assembly factors, TFIIA-J to recruit RNA pol III to promoter
A multimeric protein consisting of a 1)TATA box binding protein 2)TATA-binding protein-associated factors (TAFs)
One of the most highly conserves eukaryotic proteins. It creates a saddle structure that deforms DNA upon binding. It creates a platform for other TFII proteins
TBP associated factors (TABs)
Stabilize TBP binding to the promoter region, function as co-activators � bridging the enhancer-bound proteins to the transcription complex through protein-protein interactions, TAFs are specific to the transcription factors they bind.
mRNAs are capped at the 5� end by capping enzymes that add a 7-methyl guanosine to the phosphate end.
The introns are removed by a spliceosome loop structure. This involves conserved sequences for the splice donor and splice acceptor that are the signal sites for intron splicing.
Is the GT or GU sequence at the 5� end of the intron that signals for splicing.
Is the AG sequence at the 3� end of the intron that signals for splicing.
Alternative DNA splicing
Exons can be spliced together in different ways, specific to a developmental cell type. The genetic control of this process is still relatively not well understood. It also generates further complexity from the genome.
Can be encoded in stand-alone genes or within introns of protein coding genes. They regulate gene expression in 2 ways: translational repression by microRNAs (the microRNA inhibits the ribosome from translating) and RISC (RNA induced silenceing complex) which destroys double stranded RNA. They can also block initiation, de-adenylate (make an endonuclease digest the poly-A tail), cause proteolysis (degredation of a close peptide)
Definition � proteins that are able to promote or inhibit transcription through the direct binding with DNA and proteins at the gene locus.
Basal transcription proteins
RNA polymerases and general transcription factors. Present in all cells. Act directly upstream of the transcription start site.
Differential induction of the transcription
Can be induced to act on transcription based on environmental signals (heat-shock, hormones), regulated developmentally (tissue-specific transcription factors), or cell cycle.
What do transcription factors bind?
Enhancers. This binding can leas to either activation or inhibition.
A DNA sequence that activates the use of the promoter, controls the efficiency and rate of the transcription from the promoter. Can be 3� or 5� or even within a gene. Orientation does not matter.
Prevent enhancer activation by blocking enhancers from activating cis genes. This limits the actions of enhancer sequences. Insulator binding of DNA may make it conformationally difficult for enhancer bound TFs to help nucleate the promoter complex.
Sequences that repress transcription. Ie, the NRSE sequence binds to histone deacetylase which condenses nucleosomes
Acetylation of histone tails (HATs)
Enhances transcription by uncondensing nucleosomes, making the DNA available. Acetylation of the lysine residues at the N terminus of histone proteins removes the positive charges, thereby reducing the affinity between the histones and DNA. This makes it easier for RNA polymerase and transcription factors to access the promoter regions.
Histone deacetylation (HDACs)
Increases DNA affinity to histones and represses transcription
Methylation of histone tails
Condenses nucleosomes and decreases transciprion
Splicing, 5� cap and polyA tail, microRNA regulation