Genome Content (Lec 16) Flashcards
organization and sequence of genetic information contained within a genome is called what?
structural genomics
approximate locations of genes, relative to the location of other genes, based on the rates of recombination is called what?
genetic maps
what are the limitations of genomic maps?
low resolution or detail; do not correspond to physical distances between genes
Define contig
a set of overlapping fragments that form a continuous stretch of DNA
Define single-nucleotide polymorphisms
site in the genome where individual members of a species differ in a single base pair
The specific set of SNPs and other genetic variants observed on a chromosome is called a what?
haplotype
In regards to structural genomics determining the DNA sequences of entire genomes, the number of copies of DNA sequences (greater than 1000 bp) varies from people to people. This is referred to as?
copy-number variations
In regards to structural genomics determining the DNA sequences of entire genomes, markers associated with DNA sequences that are expressed as RNA are called what?
expressed-sequence tags
In regards to structural genomics determining the DNA sequences of entire genomes, molecular bio + computer science = ?
bioinformatics
This aspect of structural genomics may include deletions or duplications; most contain multiple genes and potentially affect the phenotype; have been found to be associated with psoriasis schizophrenia, autism, and mental retardation
Copy-number variations
This aspect of structural genomics may be obtained by isolating RNA from a cell and subjecting it to reverse transcription, producing a set of cDNA fragments; cDNA fragments are sequenced and the sequence identifies the DNA fragment
Expressed-Sequence tags
How does a cDNA sequence differ from the genomic sequence?
no introns
What is the Ab initio approach of bioinformatics?
scans sequence looking for features usually found within a gene
What is the comparative approach of bioinformatics?
looks for similarity between a new sequence and sequences of known genes
Define metagenomics
sequencing genomes of entire communities of organism- for example, the flora of the human gut
Define synthetic biology
the creation from scratch novel organisms
Define functional genomics
characterizes what the sequences do, The Encode project
All the RNA molecules transcribed from a genome are called what?
transcriptome
All the proteins encoded by the genome are called what?
proteome
Genes that are evolutionary related are called what?
homologous
Homologous genes in different species that evolved from the same gene in a common ancestor are called what?
orthologs
Homologous genes arising by duplication of a single gene in the same organism are called what?
paralogs
What is the difference between orthologs and paralogs?
orthologs are in different organisms; parallels are in the same organism
In regards to gene expression and microarrays, using a known DNA fragment as a probe to find a complementary sequence is called what?
nucleic acid hybridization
What is a reporter sequence?
encoding an easily observed product used to track the expression of a gene of interest
What does a microarray consist of?
DNA probes fixed to a glass slide
How can genes encoding a particular trait or function be identified?
mutagenesis screen
In a mutagenesis screen, progeny with normal phenotypes are mated with wild type fish, the following progeny are ____ to reveal ____ mutations
backcrossed; recessive
How do prokaryotic genomes evolve?
genome size and number of genes; horizontal gene transfer; function of genes
Define horizontal gene transfer
exchanging genetic information from closely related distantly related species over evolutionary time
How do eukaryotic genomes evolve?
genome size and number of genes; segment duplications and multilane families; noncoding DNA; transposable elements; protein diversity; homologous genes; collinearity between related genomes
True or false?
A very low degree of homology occurs in eukaryotic genomes
false; tremendous degree
Mice and humans have about ___% of their genes in common
99
About 50% of genes in ___ ___ are homologous to genes in humans
fruit flies
Plants have about ___% of their genes homologous to human genes
18
Define colinearity
presence of many genes in the same order in related genomes due to evolution from a common ancestral genome
Chromosome number in grasses ranges from __ to ___
4; 266
The rice genome consists of only about ___ million bp, whereas the genome of wheat contains ___ billion bp
460; 17
The ___ genome consists of 25 linkage blocks, consisting of groups of linked genes
rice
What is the total average length of gene in the human genome?
27,000 bp
What is the average size of coding region in the human genome?
1,340 bp
What is the average number of exons per gene in the human genome?
8.8
The total length of the entire human genome is how long in bp?
3.2 billion bp
It was previously thought that only 25% of the DNA in the human genome was transcribed into RNA. The percentage is actually probably closer to ___%
80
Less than 2% of the human genome does what?
encodes protein
___ genes are often separated by vast regions of noncoding DNA, much of which consists of repeated sequences derived from ____ elements
Active; transposable
The human genome does not encode substantially more protein domains, but the domains are combined in more ways to produce a relatively ___ ___
diverse proteome
The human genome with approximately 24,000 genes, might encode 72,000 or more mRNAs. How is this possible?
because a single gene often encodes multiple proteins through alternative splicing; each gene encodes on average two or three different mRNAs
Which three chromosomes have the highest densities?
17, 19, and 22
Which chromosomes have the lowest densities?
X, Y, 4, 13, and 18
X,Y, brett favre, kurt warner, peyton manning
Some proteins encoded by the human genome that are not found in other animals include those affecting what?
immune function; neural development; structure and function; intercellular and intracellular signaling pathways in development; hemostasis; apoptosis
True or false?
Transposable element are much more common in the worm, plant, and fruit fly than the human genome
false; more common in human genome
In one region of the X chromosome, __% of the DNA is made up of transposable elements, whereas other regions are largely devoid of these elements
89
The human genome contains a variety of types of transposable elements. Name 4.
LINEs, SINEs, retrotransposons, and DNA transposons
note: most appear to be relatively old and are defective, containing mutations and deletions making them no longer capable of transposition
One technique used in the determination of cellular proteins is called what?
mass spectrometry
Affinity capture (interactome), protein microarrays, and structural proteomics are three techniques that are used to analyze what?
the complete set of proteins found in a cell
True or false?
Protein microarrays can be used to study protein-protein interactions of thousands of proteins at once
true
