chapter 20 lecture 15 Flashcards
structural genetics
organization and sequence of genetic information contained within a genome
genetic maps
- (linkage map) approximate locations of genes, relative to the location of other genes, based on the rates of recombination
- limitations
- -low resolution or detail – do not correspond to physical distances between genes
physical maps
based on direct analysis of DNA, and place genes in relation to distances measured in number of base pairs, kilobases, or megabases
- higher resolutions and more accurate than genetic maps
~limitations~
- doesn’t tell us order or precise location of the restriction sites
What are some of the limitations of genetic maps
- low resolution or detail
- do not correspond to physical distances between genes
What was the first step in mapping the human genome?
detailed physical and genetic maps
how was genome assembled?
sequence of entile chromosomes assembled bu piecing together small overlapping fragments to create large contigs that were eventually combined into a long linear sequence anchored by previously established markers
A contig is :
a. a set of molecular markers used in genetic mapping
b. a set of overlapping fragments that form a continuous stretch of DNA
c. a set of fragments generated by a restriction enzyme
d. a small DNA fragment used in sequencing
b. a set of overlapping fragments that form a continuous stretch of DNA
single- nucleotide polymorhisms (SNPs)
a site in the genome where individual members of a species differ in a single base pair
haplotype
specific set of SNPs and other genetic variants observed on a chromosome
Use of SNPs
valuable markers in linkage studies
- when a SNP is close to a disease it tends to be inherited with disease
- leads to people with disease to have different SNPs than healthy people
copy-number variations (CNV_
number of copies of DNA sequences varies from people to people (greater than 1000 bp)
- 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
expressed-sequence tags (ESTs)
markers associated with DNA sequences that are expressed as RNA
- obtained by isolating RNA from a cells and subjecting it to reverse transcription, producing a set of cDNA fragments
0 cDNA fragments are sequenced and the sequence (tag) identifies the DNA fragment
bioinformatics
molecular biology + computer science
How will the cDNA sequence differ from the genomic sequence ?
Genome is the whole thing and cDNA is just a fragment with no introns!
What was the goal of the HapMap project
to catalog and map SNPs and other human genetic variants
the ab initio approach finds genes by looking for
a. common sequences found in most genes
b. similarity in sequence with known genes
c. mRNA with the use of in situ hybridization
d. mutant phenotypes
a. common sequences found in most genes
metagenomics
sequencing genomes of entire communities of organisms
- ex. human gut flora
synthetic biology
novel organisms created by stitching together functions genomic sequences
functional genomics
characterizes what the sequences do
- the Encode project aims to ID all functional elements in the human genome
transcriptome
all the RNA molecules transcribed from a genome
proteome
all the proteins encoded by the genome
Encode project purpose
to carry out a project to identify all functional elements in the human genome sequence
homologous
genes that are evolutionarily related
- ex. NKX2,5
orthologs
homologous genes in different species that evolved from the same gene in a common ancestor
- when speciation happens
- NKX2,5 in flies vs. humans
Paralogs
homologous genes arising by duplication of a single gene in the same organism
What is the difference between orthologs and paralogs?
a. orthologs are homologous sequences; paralogs are analogous sequences
b. orthologs are more similar than paralogs
c. orthologs are in the same organism; paralogs are in different organisms
d. orthologs are in different organisms; paralogs are in the same organism
d. orthologs are in different organisms; paralogs are in the same organism
Gene expression and micro arrays
nucleic acid hybridization: using a known DNA fragment as a probe to find a complementary sequence
- can be used to determine which RNA and DNA sequences are present in a mixture of nucleic acids
- capable of determining which RNA molecules are being synthesized and can thus be used to examine changes in gene expression
gene expression and reporter sequences
reporter sequence: encoding an easily observed product used to track the expression of a gene of interest
- patterns of gene expression studied using a reporter gene to study promoter function
genomewide mutagenesis
mutagenesis screen
- genes affecting a particular characteristic or function can be identified
- when coupled with positional cloning can be used to ID genes that affect a specific characteristic or function
What will happen if an essential gene is mutated?
a lot will die bu some will live and show new characterisitcs
- if mutation not dormant will find characterisitc in 2nd or 3rd generation
which is the correct order of steps in a mutagenesis screen?
a. positional cloning, mutagenesis, identification, of mutants, verification of genetic basis
b. mutagenesis, positional cloning, identification if mutants, verification of genetic basis
c. mutagenesis, identification of mutants, verification of genetic basis, positional cloning
d. identification of mutants, positional cloning, mutagenesis, verification of genetic basis
c. mutagenesis, identification of mutants, verification of genetic basis, positional cloning
comparative genomics
compares the content and organization of whole genomic sequences from different organisms
prokaryotic genomes
small genomes usually ranging from 1 million to 3 million base pairs
- several 1,000 genes
0ones with smallest genomes tent to occupy restricted habitats, largest in more complex environments
- horizontal gene transfer has palyed a major role in bacterial genome evolution
what is the relation between genome size and gene number in prokaryotes?
species with larger genomes generally have more genes than species with smaller genomes, and so gene density is quite constant
eukaryotic genomes
genome size varies greatly - for multicellular organisms there is no clear relation between organismal complexity and amount of NDA or gene number.
- a substantial part of the genome consists of repetitive DNA, much of which is derived from transposable elements
- many genomes have homologous genes in common
- genes are often in same order in the genomes of related organisms
segmental duplication play an important role in evolution by
a. giving rise to new genes and multigene families
b. keeping the number of genes in a genome constant
c. eliminating repetitive sequences produced by transposition
d. controlling the base content of the genome
a. giving rise to new genes and multigene families
colinearity
presence of many genes in the same order in related genomes due to evolution from a common ancestor genome
Why is knowledge of a proteins structure important
structure often provides important information about how a protein functions and the types of proteins with which it is likely to interact
what are some unique proteins encoded by the human genome that are not found in other animals include hose affecting:
- immune function
- neural development
- structure and functiono
- intercellular and intracellular signaling pathways in development
- hemostasis
- apoptosis
what % of the DNA is transcribed into RNA
probably more like 80% instead of previously thought 25%
2d-PAGE
will separate on accumulated pH based on the charge they carry and then by size
mass spectrometryq
can ID the components of a protein while it’s in a mixture
- must be in small fragments before ionization
affinity capture
method of separating biochemical mixtures based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand
interactome
the whole set of molecular interactions in a particular cell
- specifically refers to physical interactions among molecules (ie protein-protein interactions) but can also describe sets of indirect interactions among genes (gene interactions)
protein microarrays
can be used to study protein-protein interactions of thousand of proteins at once
- useful for diagnosis cancers
- ex heart attack because know certain proteins are released and shouldn’t be these unless there is a problem
