lei xie phd lxie@sdsc edu n.
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Lei Xie, PhD lxie@sdsc.edu. Structural Genomics and Human Health. Enter the Genome & IT Era. Background –. Proteins are the worker molecules that make possible every activity in your body. Background – Generic Codes. Background – From DNA to Protein.

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background
Background –

Proteins are the worker molecules that make possible every activity in your body

background from dna to protein
Background – From DNA to Protein
  • DNA carries the genetic information of a cell and consists of thousands of genes
  • genes are transcribed into RNA (transcription)
  • proteins are built based upon the code in the RNA (translation).
background1
Background -

3D shape enables proteins to accomplish their function in your body

Proteins are made of amino acids like beads on a necklace.

To become active, proteins must fold into their final shape

background snps
Background - SNPs
  • Definition – must occur in > 1% of population
  • Accounts for > 90% of all genetic variation
  • Est. 1.4M in initial map of the genome
  • 60,000 in coding regions
  • A synonymous SNP does not change the protein; non-synonymous does
  • Synonymous still important in regulation eg transcription factor binding etc.
  • See http://www.ornl.gov/TechResources/Human_Genome/faq/snps.html
example sickle cell anemia
Example: Sickle cell anemia
  • Sickle cell anemia (SCA) is an autosomal recessive disease caused by a point mutation (SNP) in the hemoglobin beta gene (HBB) found in region 15.5 on the short arm (p) of chromosome 11
  • The hemoglobin protein (HBB) is 146 aa long and has a molecular weight of ~15,867 Da
example sickle cell anemia1
Example: Sickle cell anemia
  • Hemoglobin (HBB), found in red blood cells, is responsible for carrying oxygen around the body
  • It is made up of two different types of protein chains: alpha and beta
  • Normal adult HBB is a tetrameric protein consisting of two alpha chains and two beta chains (see PDB structure)
  • The hemoglobin beta gene (HBB)codes for the beta chain found in hemoglobin (often called ‘beta globin’)
  • A point mutation (SNP) in beta globin is responsible for the sickling of red blood cells seen in SCA
example sickle cell anemia2
Example: Sickle cell anemia
  • In SCA the hydrophobic aa valine takes the place of hydrophilic glutamic acid at the 6th aa position of the HBB beta polypeptide chain
  • This is caused by a SNP in which a T is substituted for an A in the middle position of codon 6
  • The SNP converts the GAG codon (encoding Glu) to a GTG codon (encoding Val)
example sickle cell anemia3
Example: Sickle cell anemia
  • Normal deoxy hemoglobin:
  • 4 grey clusters are non-covalently bonded heme groups which bind oxygen
  • Gold spheres are phosphate groups
  • Green and blue chains are alpha, gold and turquoise chains are beta.
  • Red box highlights the region in which the sixth glutamic acid residue is located (i.e. where the SNPs lies)
example sickle cell anemia4
Example: Sickle cell anemia
  • The SNP substitution creates a hydrophobic region on the outside of the protein’s structure
  • This region then ‘sticks’ to the hydrophobic region on adjacent hemoglobin molecule’s beta chain
  • This polymerization of mutant hemoglobin molecules results in the formation of rigid fibers
example sickle cell anemia5
Example: Sickle cell anemia
  • Polymerization of mutant hemoglobin only occurs after red blood cells have released their oxygen molecules
  • As these red blood cells re-bind oxygen, the long fibers of mutant hemoglobin depolymerize and break apart into single molecules
  • Cycling between polymerization and depolymerization causes red blood cell membranes to become rigid
example sickle cell anemia6
Example: Sickle cell anemia
  • The rigidity of the red blood cells, and their distorted shape when not carrying oxygen, can block small blood vessels
  • This blocking can produce micro vascular occlusions which can cause necrosis (death) of the tissue
example sickle cell anemia7
Example: Sickle cell anemia
  • SCA is an autosomal recessive genetic disorder. For it to be expressed, a person must inherit two copies of the mutant (Hb S) variant or one copy of the mutant (Hb S) and one copy of another genetic variant
  • Carriers who have the normal HBB gene (Hb A) and one copy of the mutant (Hb S) are described as having sickle cell trait, but do not express the disease symptoms.
snp profiles
SNP profiles
  • There is now a concentrated effort to identify all the different SNPs in the human genome - hapmap
  • This will be used to generate a single map of the entire human genome and where each all the SNPs lie
  • The genomes of individuals will therefore contain a unique map of SNPs, thus providing individual SNP profiles
snp profiles1
SNP profiles
  • These SNP profiles will be important for analyzing responses to disease treatments
  • SNP profiles are also thought to be important in explaining patients differential responses to drug treatment
  • Since SNPs are also good gene markers, SNP profiles will also be important in identifying the collection of genes that contribute to the development of complex diseases states
conclusions
Conclusions
  • Many SNPs have no effect on cell function, but others could pre-dispose people to disease states or influence drug treatment responses
  • SNPs can either effect a proteins structure/function or they can effect regulatory aspects of gene expression
  • Mapping SNPs to the genome will produce useful individual SNP profiles and identify multiple genes associated with diseases
  • This makes SNPs extremely important for biomedical research and for developing pharmaceutical products or medical diagnostics
useful links
Useful Links
  • http://www.ornl.gov/TechResources/Human_Genome/medicine/pharma.html
  • PDB ( http://www.rcsb.org )
navigation by data source http www ncbi nlm nih gov about glance story discovery html
Navigation By Data Sourcehttp://www.ncbi.nlm.nih.gov/About/glance/story_discovery.html

LocusLink

Chromosome

location

Genbank

All public

DNA sequences

RefSeq

Non-redundant

Sequences for

major organisms

Click on the computers to go to the resources

navigation by data source http www ncbi nlm nih gov about glance story discovery html1
Navigation By Data Sourcehttp://www.ncbi.nlm.nih.gov/About/glance/story_discovery.html

Omim

Relate gene to

phenotype with

emphasis on disease

PubMed

The literature

reference to

all databases

PDB

3D Structure

Click on the computers to go to the resources