Exam 4 Chapter 10 Flashcards
What approach is this: use information from gene and DNA marker mapping studies to align large cloned DNA inserts in a an arrangement that reflects their order along the chromosome, a contig. Then sequence selected ones of these and combine the data to reflect the entire sequence.
the clone by clone approach
What approach is this: Make a huge number of clones with small inserts, a genomic library, then sequence many random clones, and align overlapping sequences; build up the sequence by overlapping the data from millions of these clones
This is now the standard approach for new genome sequence determination
the shotgun cloning approach
Goals of the genome projects:
- Create genetic maps of the human genome and those of other creatures
- Identify and map DNA markers (SNPs, STRs)
- Find the locations of all the genes in these genomes
- Compile lists of genes and nonexpressed sequences
- Identify the proteins encoded by the genes and their distribution in different cell types/environments
- Discover function of all genes and sequences
- Compare genes and proteins between species
- Identify DNA differences between species
- Identify DNA differences between individuals of the same species
- Set up and manage databases to store the information
What other animals genes have we sequenced?
ancient humans, neanderthal and denisovan, gorilla, chimpanzee, rhesus monkey, mouse, rat, fruit fly, yeast, thousands of bacterial genomes (many pathogens)
What is a genetic map?
A genetic map shows the order and the relative position of genes on a chromosome
How many nucleotides are on the human genome?
3.2 billion nucleotides (25,000 genes, more than 500,000 proteins)
What are bioinformatics?
Bioinformatics created software, web-based databases, and tools to collect, analyze and store the information
What are genomics?
comparative study of genomes arose as the sequences from many species became available
How much of the human genome was sequenced by 2003?
85%
What is proteomics?
the study of protein distribution, structure and function
How do we use the DNA sequence?
Having the DNA sequence allow new approaches to screen for mutant alleles and to isolate and clone the important regions of the genome
What are microarrays?
Microarrays are grids of many thousands of different oligonucleotides (single stranded pieces of DNA about 20-50 bases in length)
Genes that are close together on the same chromosome tend to be inherited together and show ___
linkage
How can the linkage map of a chromosome be constructed?
The linkage map of a chromosome can be constructed based on the gene order and the frequency of recombination between each pair of genes
What were the first autosomal genes to be linked to one another?
ABO blood group and nail-patella syndrome
What do linkage maps contain?
the order of genes on a chromosome and distance between them
Genetic markers/DNA markers were identified that show differences in:
Restriction enzyme cutting sites/fragment lengths (RFLPs) and number of repeated DNA sequences (STRs)
Where are the recombinant DNAs placed?
in a DNA sequencer
What do assemblers (specialized software) do?
they produce sequence of genome by overlapping the data
What elements are necessary for DNA sequencing?
One needs template DNA, a primer that is known to bind to a single site in the template, four normal nucleotides, four dideoxynucleotides to halt DNA synthesis when they get incoroporated, and DNA polymerase
How are genes found from the sequence?
1) Software programs scan sequences, searching for ORFs(Open Reading Frames) where there are no stop codons, these may be genes that encode proteins or parts of genes.
2) DNA sequences made from cDNA clones correspond to messenger RNAs, help identify genes
3) Amino acid sequence in the protein is determined by matching the nucleotide codon triplets to the corresponding amino acids
combined these approaches identify the proteins in the proteome
What have we learned about the Human Genome?
- 3.2 billion nucleotides of DNA
- Only small fraction actually encodes proteins
- Many remnants of the genome’s evolutionary history remain in the genome (gene families, pseudogenes, synteny)
- > Half the genome is repetitive DNA, jumping genes (transposable genetic elements) and simple sequence features
What is synteny?
Similar gene orders in related species
What are pseudogenes?
inactive genes that are still there
How can Genome Info be used?
- To find location of genes associated with different genetic disorders
- to work out the function of the protein encoded by this gene
- To study how the mutated gene or its protein product results in a disorder
- To allow development of treatments and medications and genetic tests
How are genes transferred?
- cells removed from the body
- normal gene copies inserted using virus vector
- checked that normal gene is actively making protein
- transgenic cells transferred back into the body
What are some of the problems with gene therapy?
- some patients developed leukemia
- some patients had massive immune reactions to vector proteins
- multiple people have died
- scientists working to develop better vectors and procedures for using them
- need to develop new approaches to use genes to treat genetic diseases
