For Exam 3 Flashcards
Forward Genetics
Start with a phenotype and identify the underlying gene(s)
Reverse Genetics
Stat with the DNA sequence of a gene and identify the encoded phenotype(function)
Uses the genetic code to predict the amino acid sequence of the protein, computational methods to predict protein structure and function, experimental methods to mutate the gene and see the effect on the organism.
DNA sequencing
Common methods of DNA sequencing rely on measuring the sequential incorporation of bases as DNA is synthesized.
The Sanger method used chemically modified nucleosides (ddNTPs) in combination with normal nucleosides (dNTPs).
Synthesis stops when a ddNTP is added by DNA polymerase to a polynucleotide chain because ddNTP has no hydroxyl group at the 3’ position.
The sequence is determined by detecting the terminal (3’) base (A,C,G,or T) at each position in the DNA
What ratio is ddNTPs to dNTPs?
DNTPs is higher rate/ratio then ddNTPs
Components of sequencing reactions:
-dna polymerase
-short(18-22 bases) primer complementary to template stand
-all 2’ deoxynucleoside triphophastes (dATP, dCTP, dGTP, dTTP)
-all 2’, 3’ dideoxynuclosides triphospates (ddNTPs); labeled uniquely so that each can be detected
-template DNA, sequencing reaction reliably read only 100-700 bases of a template
*ration is important
High-throughput sequencing
Used to simultaneously sequence many different template molecules
They involve physical binding of template DNA to a solid surface or to microbeads and amplification of DNA templates by PCR
Thousands or millions of sequencing reactions are run at once: massively parallel DNA sequencing
Sequencing assembly
-sequencing methods produce limited read sizes
-the key to sequencing a genome sequencing is to generate many short sequence fragments
-if a random method is used to generate the fragments, the fragments overlap
-the fragments can be arranged identifying regions of overlapping sequence using computer bases computational methods (genome assembly)
Assembling reads into chromosome sequence
Many individual short reads can be assembled into a longer contig of DNA sequence by orgaizing the overlapping bases
Funcational genomics:
Identify and annotate funcation to various parts of the genome
Open reading frames:
DNA sequence that contains codons for amino acids with no stop codons and thus may encode parts of proteins. Function of the protein can be predicted using computational methods or mutations
Comparative genomics
Compare genomes both writhing and across species
Addresses question: what genes are present in all species, how rapidly nucleotide and amino acid
RNA sequencing
Transcriptome :Subset of the genome that is expressed as RNA in a particular cell or tissue at a particular time
-determination of which genes are expressed in what amount can made by RNA sequencing (RNA-seq)
-DNA copies of the RNAs must first be synthesized using reverse transcriptase from RNA viruses
Protein analysis
Proteomics: study of proteome- the complete complement of proteins produced by an organism
Many genes encode more than one protein; alternative splicing and Posttranslational modifications increase the diversity of proteins derived from one gene.
The proteome can be measured using gel electrophoresis and mass spectrometry or using antibodies
Functional genomics
2d tell elctrophoresis
Mixture of extracted proteins seperated initially based on ionic charge considering different amino acid sequences vary
Secondarily, proteins separated based on mass
Metabolome
Metabolomics: comprehensive analysis of metabolites in a biological specimen
Metabolome: the complete set of small molecules in a cell, tissue, or organism
-primary metabolites: involved in normal cell processes; includes hormones and other signaling molecules
-secondary metabolites- often unique to particular organisms; antibiotics and chemicals made by plants for defense
Prokaryotic genomes
Key features of prokaryote genomes:
Relatively small, usuall one circular chromosome
Compact- mostly protein-coding regions and RNA genes
-most genes do not have introns
Often carry plasmids-small circular DNA molecules
*great diversity amount prokaryote genomes=huge variety of environments they occupy
Comparative genomics
Patterns:
-# of genes shared by all prokaryotes is small(implies only a few hundred genes required for life)
-core genome: containing genes common to all strains of a species
-pan genome is all genes found in a species across all strains
Minimal genome
Mycoplasma genitalium (only 483 protein coding genes)
Gene families
Genes are often present in many copies in eukaryotes as a result of duplication events.
Following duplication, the original and the copy can be mutated. If the gene product is nonfunctional, the gene is called a pseudogene or a mutated copy may be beneficial (on going evolution)
Paralogs: genes that arise via duplication. Two or more paralogs in a genome make up a group of closely related genes called a gene family.
Globin gene family
Different members of the gene family are paralogs, because they have arisen through gene duplication.
During human development, different globin genes are expressed at different times and in different tissues.
Non-protein coding DNA
In multicellular eukaryotes less than half of the genome encodes proteins. The rest includes introns, regulatory sequences, RNA genes, pseudogenes, and intergenic (non gene related) regions
The intergenic regions are mostly composed of repetitive DNA sequences including genome parasites such as a transposable elements.
Intergenic regions vs. Genes and gene related sequences
Intergenic regions make up about 60% and genes and gene related sequences 40% of genome
Characteristics of the human genome
Many introns in human genes
A gene can I code several proteins with posttranscriptional mechanisms accounting for the observed protein diversity in humans
Types of DNA sequence variation
Two types of common genetic variation (polymorphisms in DNA sequence): single nucleotide polymorphisms (SNPs): inherited variations involving a single base originating by point mutations
Short tandem repeats(STRs) short repetitive sequences occurring side by side on chromosomes, usually in noncoding regions
Genetic markers
Polymorphisms are used as genetic markers in analyses of humans and other organisms
-sequence differences (alleles) in genetic markers must be identifiable by current DNA analysis methods; codominance is best
-restriction enzymes can be used to identify SNPs (an insertions and deletions) in restriction sites. SNPs can be in toy assayed
-STRs vary in length and there are multiple alleles at each marker locus
Gel Electrophoresis
DNA fragments can be separated by size using gel electrophoresis.
A mixture of fragments is placed in a well of semisolid gel. An electric field is applied across the gel
Negatively charged DNA fragments move towards positive end.
Smaller fragments move through the gel faster than larger ones
Restriction Fragment Length Polymorphisms (RFLPs)
Restriction enzymes cut DNA at specific sequences generating smaller fragments. Mutations at restriction sites that change the ability of the enzyme to cut can be assayed as RFLPs. These are observed as bands on electrophoresis gel following digestion of PCR-amplified target or hybridization of digested DNA with probe.
Genotype to phenotype
Mendelian(or discrete) traits:
-single gene, affecting discrete phenotypic differences
Phenotypic variation is often complex:
-phenotypes vary continuously over a range- quantitative variation
-phenotypic variation is usually due to the action of multiple genes and also influenced by the environment
Darwinian selection LO
Darwin outlined basic principles and supporting evidence that provide a foundation for modern evolutionary theory
Populations evolve through differential survival And reproduction of individuals
Natural selection influences a population through individual differences and fitness Xpress through survival and reproduction connection.
Variation and populations LO
Random combination of alleles to form genotypes of asexual population is modeled by the hardy Weinberg equations enter nonrandom mating can cause a deviation between observed genotype frequencies from the expectations of the hardy
Revolutionary mechanisms LO
Mutation is a source of heritable variation and the substrate for Evolutionaries change. Random genetic drift influences variation and change in populations over generations. Selection causes predictable patterns of change and allele frequencies.
Evolution
Evolution is the genetic and or phenotypic change in populations from generation to generation. Evolutionarily theory is the understanding an application of the mechanisms of Evolutionaries changes to biological problems.
Charles Darwin
Species change over time. Divergent species share a common ancestor – descent with modification. The mechanism that produces this change is natural selection. That explains how some people are similar and different
Darwin Darwinian suction
Darwin propose the slight variation among individuals of had the chain chances of surviving and produce an offspring which he identified as natural selection
Darwin recognized that selective breeding of animals and plants by humans similarly produced changes and characteristics of these breeds through artificial selection. Artificial selection is when humans decide the specific genotype or phenotype’s of an organism instead of the environment
The six components of evolutionarily theory
Evolution changes over generations. Gradualism changes are small. Speciation species diversify split. Common ancestry organisms related through ancestors. Natural selection differential right reproduction mediated by environment. Nonselective mechanisms changes can occur by chance.
Evolution of populations
For a population to evolve its members must possess heritable genetic variation. Genetic makeup of an organism is the genotype. The phenotype is a physical expression of an organism is Junes. The population involves an individuals with different genotypes survive or reproduce at different rates
Adoption is an evolutionarily process
individuals do not evolve. Populations do.
Population
A group of individuals of the same species that live and interbreed and a particular geographic area
Members of a population become adapted to the environment in which they live
Adaptation
The process by which useful characteristics evolve and the characteristics them self
Gene pool
The sum of all copies of all alleles at all loci in a population it is the source of genetic variation that produces the phenotypic traits on which natural selected shit OK I’m at. If there is no variation and there is no evolution. Measures of genetic variation estimate the composition of the gene pool
Individual fitness
Natural selection acts on the phenotype rather than directly on the genotype. The reproductive contribution of a phenotype to subsequent generations relative to other phenotypes is called fitness. Fitness of a phenotype is determined by the rate or amount of survival and reproduction of individuals with that phenotype relative to others
Sexual selection on reproductive success
Sexual selection acts on characteristics that determine reproductive success. If an individual survives but does not reproduce it makes no contribution to the next generation. Sexual selection favors traits that increase the chances of reproduction.
Intrasexual selection
Traits such as bright colors Longhorns and elaborative court shit displays many improve ability to compete for meets
Intersexual selection
To be more attractive to the opposite sex
Natural selection on the phenotypic characters
Natural selection can act on characters with quantitative variation and three ways: stabilizing selection – preserves average phenotype, directional selection – favors individuals that vary in one direction, disruptive selection – favors individuals that vary in opposite directions from the main
Stabilizing selection
If it ain’t broke don’t fix it. Stabilizing selection reduces variation in population but does not change the mean example as human birthweights. Read to evolution are slow because neutral selection and natural selection is usually stabilizing. For specific genes stabilizing selection is often called purifying selection because there’s selection I can delete tryst invitations
Directional selection
Positively favored to increase frequency. Directional selection occurs when individuals at one extreme are more successful. At a single gene locus, directional selection may result in favoring a particular genetic variant called one selective positive selection for that variant
Disruptive selection
Disruptive selection individuals that either stream are more success successful than average individuals
A gene Pool and allele frequencies
Allele frequencies or their proportion and 13 pool, alleles and a sample of individuals P equals the number of copies of an allele in the population divided by the sum of alleles in a population. If a locus has two alleles a and B there could be three genotypes a a a B and BB the population is polymorphic I feel like us
Monomorphic
No evolution is happening there at that locus in the allele is said to be fixed.
Hardy Weinberg model
Frequency is a genetic of different alleles at each locus in frequencies a genotypes and a Mendelian population to make up the genetic structure of a population. Hardy Weinberg equilibrium describes of model population and which allele and genotype frequencies do not change. If they fit the model then no evolution will happen
Hardy Weinberg model assumptions
Mating is random. Population size is infinitive. No gene flow no migration into or out of the population. No mutation natural selection does not affect survival of any genotypes. If these conditions hold allele frequencies remain constant after one generation genotype frequencies occur in the proportion P2 to PQQ to
Deviations from hardy Weinberg equilibrium
Short term deviations and genotype of portions relative the hardy Weinberg expectations are nonrandom mating and gene flow. Long-term deviations from hardy Weinberg equilibrium is that mutation genetic drift and natural selection almost be very strong to cause a short to cause it deviation
Nonrandom mating
Occurs when sexual reproduction is biased in someway by choice or by geographical distance. If individuals meet with the same genotype pass it on homozygotes frequencies will increase. Self in or self fertilization is a common form of nonrandom mating it does not change allele frequencies in the population
Mutation
Creates new alleles in its source of genetic variation. Mutations are random with respect to the adaptive needs of an organism, selection acting on the random variation results and adaption. Origins of mutations are random. Most mutations are harmful or neutral most likely to mess something up then be beneficial. If you were beneficial or if conditions change and a little because it could become advantageous. Mutation rate is really low mutations only cause long-term deviations from hardy Weinberg equilibrium not a very strong force equals very long term hardy Weinberg equilibrium
Genetic drift
Results from random changes in allele frequency. Operate independent of fitness, harmful alleles me increasing frequency and rare advantages of alleles may be lost. Strength of genetic drift inversely related to population size larger changes and small populations in smaller changes and large
The random walk
P equals one or zero are the only Staples seat states are the only stable states. Vaccination is one loss is zero random genetic drift causes the loss of genetic variation
Random genetic drift
A temporary reduction in population size is considered a bottleneck in much genetic variation is lost during the bottleneck. The founder effect is equivalent to a population bottleneck but applies to small populations that colonize in the region. The small colonizing population is likely to contain only a subset of genetic. Ocean and descendent generations will exhibit elevated frequencies of the alleles present and founder individuals. Genetic drift dramatically change is frequency of alleles during temporary reductions in population size which can have lasting impacts
Neutral variance
Many mutations do not affect the function of the resulting proteins i.e. silent mutations. No real that does not affect fitness as a neutral allele things affected by drift and only by drift. Mutual alleles can increase in frequency by genetic drift. This can be used to study divergence of population and species
Natural selection affect an allele frequencies
Eliosa influence individual fitness survival and reproduction are subjected to natural selection. Natural selection on individual phenotypes increases the frequency of alleles conferring high fitness and decreases the frequency of alleles conferring low fitness
Balancing selection
Balancing a selection neutral selection natural selection acts to maintain immediate frequencies of alleles at the locus because heterozygotes are favored heterozygous advantage is stable equilibrium is reached based on genotype frequent fitnesses
Phylogeny
Evolutionarily history of relationships among organisms or their genes. Just portrayed in a diagram called a pile Leo genetic tree each split or no represents the common point at which lineage diverged the common ancestor of all organisms is the tree
Tree of life
One of the greatest unifying concepts in biology is that all life is connected through revolutionary history. The tree of life is the complete evolutionarily history of life. Knowledge of evolutionarily relationships is essential for making comparisons in biology.
Convergent evolution
Some more features can involve an unrelated groups of organisms. Convergent evolution is independently of all trades subjected to similar selection pressures that may become superficially similar. Similar traits generated by convergent evolution an evolutionarily reversals I called homeo plastic traits Romeo pasties.
Homologous characteristics
Feature is shared by two or more species that we’re headed from a common ancestor are homologous pair a characteristic of an August trait that was presented in the ancestral group is incest real. A characteristic of a Maga straight found in the descendent the differs from the ancestral trait is called arrived
Shared derived characteristics
Derived characteristics of homologous traits shared among a group arbutus evidence of the common ancestry of the group and are known as Cine Morpheus which means share to change. Cinemark snap Murphy’s can be used to him for a common ancestry I’m using that the derived characteristic involved in the common ancestor of the group
Phylogenetic econstruction
Assume no convergent evolution and no derived traits have been lost. The group of primary interest is the end group and group is come paired with an outgroup a closely related species or group known to be phonetic genetically outside the group of
Parsimony principal
The simplest explanation of observe data is the preferred explanation. This minimizes the number of Evolutionaries changes that must be assumed the fewest homoplasty’s. I’ll come supervisor the best explanation that’s the data with the fewest
Gene Homeology
I am August feature is shared by two or more species and it was inherited from a common ancestor. Only about half of all genes exist in a single copy per haploid cell others are members of June families. Before genes and proteins can be compared Magus positions the nucleotide amino acid sequences are aligned.
Taxonomic classification
A taxon is in a group of organism that is treated as a unit such as all insects. Species and genre are further grouped into a hierarchical classification system. Genre are grouped into families families to orders orders into classes classes until Baila and five learn to Kingdom
Clade
a taxon
Problematic taxonomy
Many taxonomic name is applied before detailed file in general information was available. A group that does not include all the sentence of a common ancestor is pair of the Latic. They group that does not include its common ancestor is polyphyletic.
Molecular clock
Uses the average rate at which a given gene or proteins accumulates changes to gauge the timing of divergencies. They must be calibrated using independent data such as fossil record no divergencies biogeographical dates
Neutral molecular evolution
A neutral theory of molecular evolution selection does not care of neutral or mutant. The majority of mutations are neutral and may fix in populations through genetic drift. Small populations will go towards fixation fast. Rita fixation of neutral mutations but a genetic drift is independent of population size read affixation is equal to the neutral mutation rate.
Molecular evolution
Study of mechanisms and consequences of the evolution of macromolecules. The relationships between the structure of genes and proteins and organism function. Using molecular variation to reconstruct evolutionarily history. You seem like your data to figure out who is related to who to determine evolutionarily history
Substitutions and protein coding regions
Many nucleotides changing coding regions have no effect to other protein level because most amino acids are specified by more than one codon. A substitution that does not change the amino acid that is specified is a synonymous or silent substitution. A substitution that does collagen a change in the amino acid specified as a non-synonymous substitution for my Mrs. mutation. These are often do Litras but protein shape and function is not always altered so it may be selectively neutral or possibly beneficial.
