Chapter 18-21 test Flashcards
What are genomics?
An approach where scientists can study whole sets of genes and their interactions
What is bioinformatics?
the application of computational methods to the storage and analysis of biological data
What is the whole genome shotgun approach?
An approach to sequencing the human genome that starts with cloning and sequencing of DNA fragments from randomly cut DNA. Powerful computer programs then assemble the large number of overlapping short sequences into a single continuous sequence
Which 2 processes helped complete the sequencing of the whole human genome?
The initial methodical approach built on a storehouse of human genetic info and the whole-genome shotgun approach
What are the most modern sequencing techniques and how do they work? How is it different from the whole genome shotgun approach
Sequencing by synthesis. Many very small base pair fragments are sequenced at the same time. Cloning is not required, unlike the whole genome shotgun approach
What is metagenomics?
DNA from a group of species is collected from an environmental sample and sequenced
How is protein function that an unknown gene codes for determined?
Biochemical studies are done on the 3 dimensional structure to locate binding sites and other attributes. Functional studies are done to see how blocking or disabling the gene to see how phenotype is affected
What is proteomics?
An approach where scientists study full sets of proteins encoded by genomes
What is the systems biology approach? How is this approach made possible?
An approach that aims to model the dynamic behavior of whole biological systems based on the study of interactions among the system’s parts. This approach is made possible by bioinformatics because of the large amount of information involved
What is the typical genome size range for archaea and bacteria? how does this compare to eukaryotic genomes?
1-6 million base pairs. Eukaryotic organisms have much bigger genomes
Which eukaryotes have a large range of genome sizes and which dont?
Protists, insects, amphibians and plants have a large range of genome size and mammals and reptiles have a smaller range
Does genome size reveal anything about phenotype in eukaryotes?
no
Why is the number of genes in eukaryotes usually lower than expected?
They have large genomes, but not as many genes as base pairs
What allows organisms with a larger genome to get away with having the same number of genes as organisms with a much smaller genome?
Organisms with bigger genomes use more RNA splicing and get “more bang for their buck”, they make more proteins with fewer genes. Post translational modifications add diversity, and miRNAs and other small RNAs that serve as regulators add variety
Which organisms have the highest and lowest gene densities?
Eukaryotes have lower densities, other less complex organisms have higher densities
Why do eukaryotes have lower gene density?
They have more introns(noncoding DNA) and more non protein coding DNA between genes
How much of the human genome is gene related regulatory sequences and introns? What is the rest?
5%-20%. The rest is unique noncoding DNA such as fragments and pseudovenes(including repetitive genes)
What are pseudogenes?
Former genes that accumulated mutations over a long period of time and no longer produce functional proteins
What is most of repetitive DNA made up of?
transposable elements and sequences related to them
Which evidence suggests that noncoding DNA is important?
The high degree of sequence conservation between species.
What does genome organization tell us?
It tells us about how genomes evolved and continue to evolve
What are transposable elements?
Stretches of DNA present in Eukaryotes and prokaryotes that can move from one location to another in the genome in a process called transposition
How does transposition work?
The original and new DNA sites are brought close together by enzymes, the elements never completely detach from the cell’s DNA
Who discovered transposable elements and how?
Barbara McClintock, she identified changes in colors of corn kernels that only made sense of transposable elements existed
What are the type types of transposable elements?
Transposons: can move within the genome by means of a DNA intermediate by cut and paste or copy and paste
Retrotransposons: can move by means of an RNA intermediate that is a transcript of retrotransposon DNA, always leave a copy behind
Which enzymes is involved with transposons?
transposase
What are Alu elements?
A family of transposable element sequences that are about 300 nucleotides long(shorter than most functional transposable elements) and they do not code for protein. Many of these elements are transcribed into RNA of unknown function(if any)
What is LINE-1? compare to Alu family
Aka L1, these are retrotransposons that are much longer than Alu elements, about 6500 base pairs long. They have a low rate of transposition
What are some possibilities of the function of L1?
They effect gene expression, potentially in developing neurons
How does repetitive DNA, excluding transposable elements, arise? How much of the human genome consists of these genes?
Mistake during DNA replication or recombination. These make up 14% of the human genome
What is simple sequence DNA?
Many copies of repeated, short DNA sequences
What is Short tandem repeat?
(STR) When the unit of repeating nucleotides in simple sequence DN contains 2-5 nucleotides
What is a genetic profile?
The diversity in the number of repeating nucleotide sequences in repetitive DNA, unique to each individual since humans are diploid
How much of he human genome is made up of simple sequence DNA? Where are these genes usually found and why is this important?
3%, located at the chromosomal telomeres and centromeres, suggesting that this DNA plays a structural role and helps organize chromatin in the interphase in the nucleus(centromeres) and prevents telomere degredation
What are multigene families?
Collections of two or more very identical genes
What are the characteristics of multigene families with identical and nonidentical DNA sequences?
Identical: Clustered tandemly and have RNAs as final products(except for histone protein genes)
Nonidentical: effect gene expression by expressing versions of the same genes at different times
How are new species formed?
Meoitic accidents resulting in different numbers of chromosomes
What is evidence of unequal crossing over and template slippage?
multigene families
What are examples of genes where a gene was altered to the point where it had a totally different section?
genes for lysozyme and a-lactalbumin
What is an example of genes evolving with related functions?
Globin families
What are domains?
Functional regions of proteins, coded for by exons
What is in example of a protein coding gene with multiple copies of exons?
collagen
How do transposable elements contribute to genome evolution?
Promote recombination, disrupt cellular genes/control elements and carry entire genes/exons to new locations
What do transposable elements of similar sequence do?
They facilitate recombination between different chromosomes by providing homologous regions for crossing over
What is a benefit of comparing closely related species?
The genes of one species can accelerate the gene mapping of another species
Which genes tend to evolve fastest?
Genes coding for transcription factors
What is FOXP2?
A transcription factor that functions in vocalization of vertebrates and is said to be rapidly evolving
What are single nucleotide polymorphisms?
(SNP’s) Single base pair sites where variation is found in at least 1% of the population
What is evo-devo?
the field of evolutionary developmental biology
What is a homeobox?
a 180 nucleotide sequence that specifies a 60 amino acid hemeodomain. These have to do what body development
How do genes with homeodomains regulate development?
Coordinating the transcription of batteries of developmental genes, switching them on or off
What is the Hox gene?
A gene responsible for development of of axes in insects and crustaceans, it also turns on different genes at different times in different species
What is the formal definition of evolution?
descent with modification
What is scala naturae?
A scale that aristotle concluded that all life could be placed on in terms of complexity and each organism had its own fixed rung on the ladder
What did Carolus Linneaus do? How did Darwin argue this?
He developed a two part format to naming species in terms of similarity into increasingly general categories. Darwin argued that classification should be based on evolutionary relationships and that scientists using the Linnaean system often group organisms this way
What are strata?
layers of sedimentary rock in which fossils are usually found
What do Georges Cuvier do?
He examined strata and noticed that species in older ones were dissimilar to newer ones and that each new sediment layer was a catastrophic event. He inferred that extinctions were common and that new organisms migrated to replace old ones
What did James Hutton and Charles Lyell do?
They proposed that geological events slowly changed earth over time continuously
What two principles did Lamarck use to explain his findings that were accepted at the time
- Use and disuse
2. Inheritance of acquired characteristics
What book did Darwin write and publish his natural selection theory in?
On the origin of species by means of natural selection, aka The origin of species
What is artificial selection?
Modifying species over many generations by selecting individuals with desired traits
What are Darwin’s 2 observations/inferences?
Observation 1: Members of a population often vary in inherited traits
Observation 2: All species can produce more offspring than their environment can support and many of these offspring fail to survive
Inference 1: Individuals whose inherited traits give them a better chance of surviving and reproducing in a given environment tend to leave more offspring than others
Inference 2: The unequal ability of individuals to survive and reproduce will lead to accumulation of favorable traits in the population over generations
Who experiences evolution?
Populations(not individuals)
How does methicillin work and which disease became immune to it?
It deactivates protein that bacteria use to synthesize their cell walls. MRSA became immune to it
What is homology?
Similarity resulting from common ancestry
What are homologous structures?
Structures that represent a variation on a structural theme that was present in a common ancestor
What is convergent evolution?
the independent evolution of similar features in different lineages. This results in analogous resemblance
What does endemic mean?
They are located in place and no where else in the world
What are the pieces of evidence that support evolution?
- Direct observations of evolutionary change
- Homology
- The fossil record
- Biogeography
What is phylogeny?
the evolutionary history of a species or group of species
What is systematics?
A discipline focused on classifying organisms and determining their evolutionary relationships
Who came up with the binomial, scientific naming system of naming organisms?
Carolus Linnaeus
What is the order of taxonomy classifications from largest to smallest groups?
Domain Kingdom Phylum Class Order Family Genus Species
What is a taxon?
The named taxonomic unit at any level of hierarchy
What is the flaw with Linnaean classification?
It doesnt reflect evolutionary history
What are sister taxa?
groups of organisms that share an immediate ancestor, and are therefore each others closest relatives
What does it mean if a phylogenetic tree is rooted?
The branch point farthest to the left represents the most recent common ancestor of the whole tree
What is a basal taxon?
Taxon that diverges early in the history of a group
What is a polytomy?
A branch point from which more than 2descendants emerge
What is the point of phylogenetic trees? What can they be mistaken to reflect?
to reflect ancestry, no phenotype
What are homoplasies?
Analogous structures that arose independelty
How can you distinguish between analogous and homologous similarities?
More elements that are similar in 2 complex structures=homologous along with fossil evidence and ancestral genetic similarities
What is cladistics and what are clades?
Cladistics is an approach in systematics where common ancestry is the primary criterion to classifying organisms. Biologists places species into groups called clades that include ancestral species and their descendants
What does monophyletic, paraphyletic, and polyphyletic mean? Which one is equal to a taxon?
Monophyletic: clade consisting of an ancestor and ALL of its descendants. = to a taxon
Paraphyletic: consists of ancestral species and some of its descendants, most recent ancestor IS apart do the group
Polyphyletic: Includes taxa with different ancestors, most recent ancestor is NOT apart of group
What is a shared derived character?
An evolutionary trait unique to a clade
What is the outgroup and the ingroup?
Outgroup: species or group of species from an evolutionary lineage that is known to habe diverges before the lineage that includes the species being studied
Ingroup: Species being studied
What is the principle of maximum parsimony?
A principle used to narrow the possibilities in a data set when making a phylogenetic tree, starting with the organism with the fewest evolutionary changes
What is a molecular clock?
A concept that is an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates assuming that number of nucleotide substitutions in related genes is proportional to the time that has elapsed since the genes branched from their common ancestor
What causes differences in molecular clock speed?
Whether a gene change is neutral or not
What are problems with molecular clocks?
They are very uncertain, especially when you go far back. They do not run smoothly because of natural selection and non neutral mutations.
What is the horizontal gene transfer?
a process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and fusions of organisms. This is how genes moved between organisms of different domains
