L14- genomics and genome projects

Question 1

Why sequence the genome?

Answer 1

Get genetic information available

Question 2

How many base pairs in the human genome

Answer 2

3,000,000,000 base pair

Question 3

How is genome sequence obtained?

Answer 3

Obtain organisms genomic DNA -> break DNA into small fragments -> obtain DNA sequence -> search for overlaps to reconstruct the genome sequence

Question 4

Why do we use model organisms?

Answer 4

Small genome – “value for money”
Easy organisms to manipulate
Provide information on fundamental biological processes
Technology development
Useful for comparative genomics

Question 5

Why do we use smaller organisms like E.coli?

Answer 5

Helps us understand pathogenisis

Question 6

Why do we use single cell eukaryotes?

Answer 6

Easy to manipulate

Question 7

Why do we use c.elegans?

Answer 7

Useful in developmental studies?

Question 8

What is the limitation of using fragments of DNA to sequence the genome?

Answer 8

Unable to identify the chromosome the sequence belongs to

Question 9

In how many days was the genome sequence of a causative bacteria that appeared in europe early summer 2011?

Answer 9

2 days

Question 10

What were the outcomes of genome sequencing of a causative bacteria that appeared in europe early summer 2011?

Answer 10

1) Revealed an unidentified new strain of E. coli.
2) Insight into the antibiotic resistance characteristics.
3) Insight to why the bacteria was so virulent and also why it seemed to be targeting adults.

Question 11

What were the outcomes of the human genome project

Answer 11

Comprehensive Genome Map
Technological Advancements
Scientific Discoveries
Collaborative Efforts

Question 12

What are the main limitations of identifying genes within a genome?

Answer 12

How big is a valid open reading frame
Identification of RNA splice sites

Question 13

How do we define how big is a valid open reading from?

Answer 13

Search for ATG and then stop codon but at a reasonable disatnce?

Question 14

What length do we question validity of an open reading frame?

Answer 14

Around 50 codons (and less)

Question 15

What are RNA splice sites?

Answer 15

Conserved sequences

Question 16

How do we overcome RNA splice sites?

Answer 16

RNA analyses can help but depends on the expression of the gene

Question 17

What are the other limitations of identifying genes within a genome ?

Answer 17

Incomplete Coverage
Genetic Variation
Functional Understanding

Question 18

Why would incomplete coverage be a limitation?

Answer 18

some highly repetitive and structurally complex regions of the genome, such as centromeres
and telomeres. Major ‘gaps’ in 2003 sequencing data. Recent advancement in sequencing technology filled most gaps.

Question 19

Why would genetic variation be a limitation?

Answer 19

Does not capture the full extent of human genetic
diversity.

Question 20

Why would fundamental understanding be a limitation?

Answer 20

understanding the function of every gene and
regulatory element remains a significant challenge

Question 21

Problems in gene identification are emphasised by genome analyses in __________

Answer 21

Saccharomyces cerevisiae

Question 22

The S. cerevisiae is _____ the size of the human genome

Answer 22

0.001

Question 23

In contrast to the human genome, genes are ______________ in the S. cerevisiae genome with
very little repetitive DNA

Answer 23

tightly packed

Question 24

In contrast to the human genome, RNA alternative ____________ S. cerevisiae rarely occurs to complicate gene identification

Answer 24

alternative splicing

Question 25

Simple genetics can be performed in S. cerevisiae to analyse ______________

Answer 25

potential gene function

Question 26

list some advancements due to human genome project

Answer 26

Foundation for precision medicine – cancer treatment, Pharmacogenomics
Gene therapy
Genetic screening
Several open databases being accessible
Comparative genomics- widely popular