Exam 4 Chapter 10

Question 1

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.

Answer 1

the clone by clone approach

Question 2

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

Answer 2

the shotgun cloning approach

Question 3

Goals of the genome projects:

Answer 3

1. Create genetic maps of the human genome and those of other creatures
2. Identify and map DNA markers (SNPs, STRs)
3. Find the locations of all the genes in these genomes
4. Compile lists of genes and nonexpressed sequences
5. Identify the proteins encoded by the genes and their distribution in different cell types/environments
6. Discover function of all genes and sequences
7. Compare genes and proteins between species
8. Identify DNA differences between species
9. Identify DNA differences between individuals of the same species
10. Set up and manage databases to store the information

Question 4

What other animals genes have we sequenced?

Answer 4

ancient humans, neanderthal and denisovan, gorilla, chimpanzee, rhesus monkey, mouse, rat, fruit fly, yeast, thousands of bacterial genomes (many pathogens)

Question 5

What is a genetic map?

Answer 5

A genetic map shows the order and the relative position of genes on a chromosome

Question 6

How many nucleotides are on the human genome?

Answer 6

3.2 billion nucleotides (25,000 genes, more than 500,000 proteins)

Question 7

What are bioinformatics?

Answer 7

Bioinformatics created software, web-based databases, and tools to collect, analyze and store the information

Question 8

What are genomics?

Answer 8

comparative study of genomes arose as the sequences from many species became available

Question 9

How much of the human genome was sequenced by 2003?

Answer 9

85%

Question 10

What is proteomics?

Answer 10

the study of protein distribution, structure and function

Question 11

How do we use the DNA sequence?

Answer 11

Having the DNA sequence allow new approaches to screen for mutant alleles and to isolate and clone the important regions of the genome

Question 12

What are microarrays?

Answer 12

Microarrays are grids of many thousands of different oligonucleotides (single stranded pieces of DNA about 20-50 bases in length)

Question 13

Genes that are close together on the same chromosome tend to be inherited together and show ___

Answer 13

linkage

Question 14

How can the linkage map of a chromosome be constructed?

Answer 14

The linkage map of a chromosome can be constructed based on the gene order and the frequency of recombination between each pair of genes

Question 15

What were the first autosomal genes to be linked to one another?

Answer 15

ABO blood group and nail-patella syndrome

Question 16

What do linkage maps contain?

Answer 16

the order of genes on a chromosome and distance between them

Question 17

Genetic markers/DNA markers were identified that show differences in:

Answer 17

Restriction enzyme cutting sites/fragment lengths (RFLPs) and number of repeated DNA sequences (STRs)

Question 18

Where are the recombinant DNAs placed?

Answer 18

in a DNA sequencer

Question 19

What do assemblers (specialized software) do?

Answer 19

they produce sequence of genome by overlapping the data

Question 20

What elements are necessary for DNA sequencing?

Answer 20

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

Question 21

How are genes found from the sequence?

Answer 21

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

Question 22

What have we learned about the Human Genome?

Answer 22

1. 3.2 billion nucleotides of DNA
2. Only small fraction actually encodes proteins
3. Many remnants of the genome’s evolutionary history remain in the genome (gene families, pseudogenes, synteny)
4. > Half the genome is repetitive DNA, jumping genes (transposable genetic elements) and simple sequence features

Question 23

What is synteny?

Answer 23

Similar gene orders in related species

Question 24

What are pseudogenes?

Answer 24

inactive genes that are still there

Question 25

How can Genome Info be used?

Answer 25

1. To find location of genes associated with different genetic disorders
2. to work out the function of the protein encoded by this gene
3. To study how the mutated gene or its protein product results in a disorder
4. To allow development of treatments and medications and genetic tests

Question 26

How are genes transferred?

Answer 26

1. cells removed from the body
2. normal gene copies inserted using virus vector
3. checked that normal gene is actively making protein
4. transgenic cells transferred back into the body

Question 27

What are some of the problems with gene therapy?

Answer 27

1. some patients developed leukemia
2. some patients had massive immune reactions to vector proteins
3. multiple people have died
4. scientists working to develop better vectors and procedures for using them
5. need to develop new approaches to use genes to treat genetic diseases