V. Lab | 77. In silico tools in molecular biology

Question 1

I. Background information
1. What are in silicon methods?

Answer 1

In silico methods refer to methods conducted via computer-based reach.

Question 2

I. Background information
2. What does In silico methods include?

Answer 2

In silico methods refer to methods conducted via computer-based reach. The methods include:
- searching in computerized databases
- computer-based design
- modelling and simulation of chemical, biochemical reactions
- in vivo cellular processes such as signaling, molecular networks governing cell growth, division and differentiation
=> taken together, in silico methods have become indispensable both for medical
practice as well as basic or applied biomedical research

Question 3

I. Background information
3. What is the main attributor of genetic variations?

Answer 3

• Common individual differences are largely attributable to genetic variations, i.e. polymorphisms and mutations in the human genome.
• A trait or disease is attributed to their genetic variations among individuals

Question 4

I. Background information
4A. What are the features of monogenic disease?

Answer 4

1. Monogenic diseases: 1 gene variation (locus) => 1 trait /disease
2. Examples
   - Phenylketonuria
   - Sickle cell anemia
   - Cystic fibrosis

Question 5

I. Background information
4B. What are the features of Polygenic disease?

Answer 5

Polygenic diseases: many gene variations and environmental factors both attribute
to the disease
- Malignant tumors
- Diabetes
- Cardiovascular diseases

Question 6

I. Background information
5. What are the features of length polymorphism?

Answer 6

Length polymorphism: (differ in length)
- Microsatellites (short tandem repeats, 2-10 bp)
- Minisatellites (variable number of tandem repeats – VNTR, 10-1000 bp)population

Question 7

II. Experiment
1. What is the aim of using in silica tools in THIS LAB?

Answer 7

The aim of the experiment is to genotype a SNP in ourselves that is critically involved in sensing the bitter taste of phenylthiocarbamide (PTC), a naturally occurring compound. The TAS2R38 gene has 3 SNPs, which are critical in sensing bitter taste.

Question 8

II. Experiment
2A. What are the tools we will use in this experiment?

Answer 8

• OMIM (online Mendelian Inheritance in Man) is a database, where we can find the gene sensitive to PTC -> TAS2R38
• Also use NCBI nucleotide database to determine the amino acid sequence encoded
  by both haplotypes
• Genomic sequences with SNP will be amplified by polymerase chain reaction (PCR)
• Will analyze SNP by PCR-RFLP -> select appropriate restriction endonuclease by the NEBcutter -> design the forward and reverse primer by NCBI Primer-BLAST

Question 9

II. Experiment
2B. What is OMIM?

Answer 9

OMIM (online Mendelian Inheritance in Man) is a database, where we can find the gene sensitive to PTC => TAS2R38

Question 10

II. Experiment
2C. What is NCBI?

Answer 10

Also use NCBI nucleotide database to determine the amino acid sequence encoded by both haplotypes

Question 11

II. Experiment
3. What are the steps in this lab?

Answer 11

First, genomic sequences encompassing the SNP of interest will be amplified by polymerase chain reaction (PCR)
=> then the amplicon will be cleaved by the appropriate restriction endonuclease in a sequence-specific manner
=> then we resolve the digestion fragments by agarose gel electrophoresis