Chapter 21: Genomes and their evolution Flashcards
when was the human genome published
2006
what is the goal of the human genome project
complete the nucleotide sequence
when did the human genome project begin
1990
who invented the whole genome shotgun approach
J. Craig Venter
what was the whole-genome approach?
- cut the DNA into overlapping fragments
- clone the fragments in plasmid
- sequence
- order the sequences into one sequence
how are newer techniques of sequencing beneficial
- they are faster paced and have a lowered cost of genome sequencing
what do next generation cloning techniques not requ
a cloning step
what is genomics
the study of whole sets of genes and their interactions
what information can comparing genes give us
provide insight into evolution and their biological processes
what is bioinformatics
storage, analysis and distribution of biological data, most often DNA and amino acid sequences
what does NLM stand form
national library of medicine
what does NIH stand for
National institutes of Health
who maintains the NCBI
NLM and NIH
what is GenBank
the NCBI data base of sequences that is constantly updated
what does the NCBI blast allow software users to search for
- specfic dna sequence
- protein sequence
- common stretches of amino acids
- 3D protein structures
what can the NCBI give insight on
common stretches of amino acidcs
what is proteomics
studying large sets of proteins
what is a proteome
entire set of proteins expressed by a cell or group of cells
what have scientists begun to compile in systems bio
catalogs of genes and proteins
what is systems biology
the computer software that is used to map genes and to produce a functional map of their interactions
how can geneticists study genes directly
using available DNA sequences
what is gene annotation
the identification of protein-coding genes within DNA sequences in a database
what do the computers search in the protein
- translational start and stop signals
- RNA splicing sites
- promotor sequences
what can help provide clues about a proteins function
comparing sequences of unknown genes with those of known genes
how can you show the gene function is altered
knocking out the function
who published the pan cancer atlas
the cancer genome atlas project in 2018
what was the pan cancer atlas
- many interacting genes and gene products were analyzed
how did the pan cancer atlas contribute to medicine
showed how, where, and why tumors arise
what is used to analyze the gene expression patterns in patients with cancers or other diseases
- DNA microarrays
- silicon chips
- RNA seq
why is it good to analyze what genes are overexpressed or underexpressed in cancer
- allows physicians to tailor the treatment to unique genetic makeup of the patient and the caner
how many genes do free-living bacteria and archae
1500-7500 genes
what is not correclated to genome size
the number of genes
what species has the lowest gene density
humans or other mammals
what is gene density
the # of genes in a given length of DNA
what do multicellular eukaryptes have
- many introns within genes
- large amount of noncoding dna between genes
what did sequencing of the human geneome reveal
- 98.5% does not code for proteins, rRNAs or tRNAs
what % do the gene regulatory sequences and introns account for
5
what are some noncoding DNA that is found between genes
- pseudogenes
- repetitive DNA
what is a pseudogene
former genes that have accumulated mutations and are not functional
what is repetitive dna
dna that is present in multiple copies in the genome
what is there a high level of in noncoding genes
sequence conservation which suggests that these regions have important functions
what are transposable elements
stretches of dna that can move from one location to another
how much of the human dna is made up of transposable elements
75%
what are the two types of transposable elements
transposons
retrotransposons
what is the retrotransposon
move by means of rna intermediate and they use a reverse transcriptase
what is the transposon
move by means of DNA intermediate and require a transposase enzyme
what is the most abundant transposable element in the human genome
the retrotransposon
what sequence does the retrotransposon contain
Line-1 (L1)
what are come characteristics of the L1 sequence
- low rate of transposition that can affect gene expression
what is the basis of change at the genomic level
mutation
what has happened to th esize of genomes over evolutionary time
they have increased, with extra genetic material providing raw material for gene diversification
what is polyploidy and how can it be achieved
one or more extra sets of chromosomes
-accidents in meiosis
what can happen to chromosomes that are polyploidy
- extra sets diverge by accumulating mutations
- variations persist if the organism carrying them survives and reproduces
what can unequal crossing during prophase 1 result in
one chromosome with a deletion and another with a duplication of a particular region
what can transposable elements show
sites for crossover
what do multiple copies of similar transposble element causd
facilitate recombination/ crossing over
what can an insertion of transposable element w. protein coding sequence do
block protein production
what can increase protein production
insertion of a transposable element with the regulatory sequence
what is present in one copy per haploid set of chromosomes
eukaryotic genes
what is a multigene family
collection of 2 or more identical or very similar genes
what is an example of multigene families
- nonidentical genes that code for globins
what are alpha and beta globins
polypeptides of hemoglobin coded by genes on different human chromosomes
how many pairs of chromosomes do humans have
23
how many chromosomes do chimpanzees have
24 pairs
what contributes to the generation of new species
chromosomal rearrangements
what did the lysozyme gene evolve into and how
- gene was duplicated and evolved into the gene that codes for alpha-lactalbumin
what us lysozyme
an enzyme that protects animals against bacterial infection
what is alpha-lactalbumin
nonenzymatic protein that allows for milk production in mammals
what do comparisons of closely related species help with
shed light on recent evolutionary events
what is a highly conserved gene
the gene that has changed very little over time
how can highly conserved genes be studied
in model organisms and the results can be applied to another organism
what genes from both mouse and human species encode the same amino acids
FOXP2 GENE
what does the the foxp2 gene regulate
genes that function in vocalization in
vertebrates
what is the result of a mutation of the foxp2 gene
produce severe language and speech impairment in humans
what is an effect of the damaged foxp2 gene in muce
malformed brains and fail to emit
normal ultrasonic vocalization
what is evolutionary development biology (Evodevo
compares developmental processes of
different multicellular organisms
what has the analysis of the homeotic genes in Drosophilia shown
that they all include a sequence called a a homeobox (DNA seq)
what does the homeobox do
encodes genes that specify
identity of body segments of the fly
where have similar homeobox genes been found
regulatory genes of yeasts and plants
what homeotic genes in animals called
Hox genes
what do homeobox genes code for
a domian
what is the homeodomain
is the part of the protein that binds
to the DNA, where the protein functions as a transcription factor
are homeotic genes conserved
yes
