chapter 20: genomics and proteomic Flashcards
define genomics
Field of genetics that attempts to uderstand the content, organization function and evolution of the genetic information in whole genomes
genetic maps
- approximation of the location of genes relative to other genes
- based on recombination
-use cM or map units
what are come characteristics of genetic maps
- low resolution
-not always accurate - based on rates of crossing over
physical maps
based on the direct analysis of dna and they place genes in relation to distances
- measured in number of base pairs, kilobases, or mega base
high recombination=
father genes
- List some problems associated with sequencing of an entire genome
- whole genome sequencing
- only small fragments can be sequenced at a time
- must fragment genome into millions of small overlapping fragments
- how to order them after fragments are sequenced
goals of human genome project
- developing sequencing technology
- sequence genomes of model organims
- determine sequence of the human genome
- identify all genes in human genome
what were the two projects of the human genome project
- internatinoal human genome sequencing (public effor)
- celera genomics (private effort)
- Give the percent similarity between two humans
99.99%
- Define single nucleotide polymorphisms and haplotype (fig 20.8)
SNP: mutation where a single base pair in a DNA sequence differs
haplotype: A haplotype is a group of alleles in an organism that are inherited together from a single parent. Haplotypes are groups of SNPs that are inherited as a single block.
- Explain how SNPs can be used for genome wide association studies
- can help tell you the overall risk of developing a disease
how many base pairs in the human genome
3.2 billion
how many base pairs difference between you and your neighbor
4000cM
○ What is a contig
§ Set of two or more overlapping dna fragments that form a continuous stretch of dna
what is bioinformatics
molecular biology + computer science
- identify genes
-annotate genes
how is bioinformatics useful to identify a gene
-exract the useful information from sequencing projects
- ab initio approach
define annotation in bioinformatics
○ Linking its sequence information to other information about its function and expression
○ The protein it encodes and similar genes in other species
Computer programs are available for determining whether similar sequences have been found
Define metagenomics
§ Sequencing genomes of a entire group of organisms that share a common environment
Applied mostly to microbial communities
What issues does metagenomics address
Study of microbes that can’t be cultured in a lab
Study of the structure of microorganisms
why does this field exist
- some bacteria can’t be cultured in a lab
- it can extract DNA from their environment to answer multiple ques
how are snps helpful in studying the genome
use them across the genome to find genes of interest
what is functional genomics
- characterizes what sequence do their function
-goal is transcriptome and proteome
what is trnascriptome
rna molecules transcribed from a genome
what is proteome
all the proteins encoded by a genome
Define homology search and explain how this can be used to understand the function of a gene
○ Conmparisons of dna and protein sequeinces from the same species and from different species
○ Computational methods that search for similar evolutionary related homologous genes
Genes that are related = homologous genes
differentiate between ortholog and paralog
ortholog: Homologous genes in a different species that evolved from a common ancestor
paralogs: § Homologous genes in the same organism that arose through duplication
list two techniques that can be used to study the expression of a gen
- microarrays
- rna sequencing
describe how microarrays can be used to examine gene expression
○ Used to study expression of so many genes
○ A microarray consists of dna probes fixed to s olid support such as a nylon membrane or glass slide
○ Each spot consists of a different dna probe
describe the process of rna seq as below
collect total cellular rna from cells (isolate)
-isolate mRNA
- reverse transcribe into cDNA
-fragment cDNA
sequence with next gen sequencing
-assemble sequences into rna transcripts
