Mol Lecture #17

Question 1

Omics

Answer 1

biological study of the totality of the types of a specific macromolecule or unit there of in a specific cell, tissue or organism. (suffix we can put at the end of macromolecule terms)

Question 2

Genomics

Answer 2

• study of the genes in a given sample → whole genome

Question 3

Transcriptomics

Answer 3

• study of all expressed genes→ usually, protein coding genes (mRNA)

Question 4

Proteomics

Answer 4

• study of all proteins in a given sample

Question 5

‘Omics’

Answer 5

• Full understanding of cell biology requires a parts list (idea behind omics)
• Omics are often times driven by technological advances

Question 6

Process of omics

Answer 6

1) identify parts (genomes, proteomics)
2) characterize the function of the parts (takes the most amount of time)
3) Comparing parts between species

Question 7

Genomics

Answer 7

• Characterize the whole genome
  –>Get the sequence→ mark up the sequence (annotating the genome) → labeling genes, regulatory elements, etc. (transposons,…)
• Determine the function of the genes and regulatory elements→ expressed (when, where), and the function of proteins
• Study how genomes evolve to understand evolution as a process and understand how organisms differ in attributes

Question 8

Genomic Sequence Determination and Annotation

Answer 8

• Sequence determination uses molecular biology tools followed by computer-based approaches to organize and analyze data.
• Molecular bio approaches
• Dideoxy sequencing

Question 9

Molecular bio approaches

Answer 9

• takes advantage of base-pairing characteristics of nucleotides and various enzymes involved in nucleotide polymerization reactions

Question 10

Dideoxy sequencing→ whole genomes

Answer 10

Massively parallel sequencing method

Question 11

Dideoxy Method of Sequencing DNA

Answer 11

→ Novel nucleotide type (dideoxy ribonucleic acid)
- Reaction : Template, DNA polymerase, dNTPs, primer (DNA), Fluorescently labelled ddNTP, pH buffer & salt
- (Process) The ddATP doesn’t have a 3’ OH group so it stops the reaction
- (Process)Get the coordinate information (length), and put in the last nucleotide in order to get the sequencing information. (laser tells you the fluorescence)
- This method is only useful for small pieces and not very efficient
- Fragment -< 1500 bp/ 1 well or two

Question 12

Whole genome shotgun sequencing

Answer 12

• Fragment a large piece of DNA for sequencing
• Plasmid sequence is known→ use a primer
• Use computational skills to align all fragments of the genomes (lots of mistakes, so it is done multiple times, individual reactions) (randomly fragmenting copies of the genome)
• Now, we ligate a known sequence onto the end of the plasmid, which allows us to have a primer sequence complimentary to it.

Question 13

Illumina/ Solexa sequencing → Massively parallel DNA sequencing (to dideoxy and whole genome sequencing) I.

Answer 13

• Many reactions run simultaneously in a chip format (silicon chip)
• Adapter gives us our known sequence
• Amplify the chip so that the whole region has the same DNA piece

Question 14

II.

Answer 14

• Everytime we add on a new nucleotide base (fluorescent), the laser can stop and read the nucleotide. It then reverses the stop reaction and continues. (Cannot do that with dideoxy because of the H group)
  → (Able to do many reactions on the chip within the same space)
• 1 billion fragments simultaneously
• Decrease sequencing costs

Question 15

Gene Production and Annotation

Answer 15

1) Blast searches or homology searches
→ using sequence info from already annotated genomes to annotate the unknown genome
- Using homologous sequences
2) Look for parts of the genomes that are expressed using transcriptomics.

Question 16

Determination of Gene Function

Answer 16

What is the function of a given gene?
1) Homology searches (using knowledge of gene function in other species)
2) Gene expression analysis - when? Where?
3) Functional analysis- using genetic or biochemical methods to demonstrate the function of a gene fragment.