Bioquestion

From SungsamGong

Contents 1 Genetic Code 1.1 Why is the genetic code redundant? 1.2 Is the genetic code universal? 1.3 How has the genetic code been fixed? 1.4 First things first 1.5 Any relation between codon redundancy and mutational tolerance? 1.6 If there is any propensity to mutations? 1.7 What is Codon Adaptation Index(CAI)? 2 Chromosome 3 Genetic Polymorphisms 3.1 Polymorphism vs Mutation vs SNP 3.2 Disease Association of SNP 4 Protein Folding 5 Protein Evolution 5.1 What are the driving forces of protein evolution? 6 BioDatabase 6.1 Ensemble 7 Statistics 7.1 Regression 8 TLB 8.1 Joy 8.2 ESST

Genetic Code

Why is the genetic code redundant?

Why is it triplet?
Why not 4 or 2 letter code?

Is the genetic code universal?

Why or why not?

How has the genetic code been fixed?

What if it it different from the existing one?
Simulation, Entropy, Evolution?

First things first

Why only 4 nucleotides?
Why only 20 amino acids?

Any relation between codon redundancy and mutational tolerance?

How much?

If there is any propensity to mutations?

Then, how do they keep maintained?
Breaking of Weismann Barrier

What is Codon Adaptation Index(CAI)?

>Sharp P, Li W. 1987. the codon Adaptation Index- a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-95
>Also, read this one
>this one too [1]

Chromosome

Why do we have 23 + XX?Y? sets of chromosome? (chromosome evolution?)
Are genes of a same fuction located in the same chromosome? Why or why not?

Genetic Polymorphisms

Polymorphism vs Mutation vs SNP

Difference amongst polymorphism and mutation and SNP?
read this for the difference btween poly. and mutation [2]

Disease Association of SNP

How can we tell a SNP is associated with a certain type of disease?
How can we reason the intrinsic factors that cause a certain type of disease (at DNA level)?

Protein Folding

How similar or dissimilar is protein folding from protein-protein interaction?

Protein Evolution

What are the driving forces of protein evolution?

1. the degree to retain proper three dimensional structure (to avoid protein misfolding)
   
2. to maintain protein's function by keeping
   
   1. protein interaction (protein-protein, protein-nucleic acid, protein-ligand)
      
   2. catalytic activity of enzyme proteins)
3. catalytic activity of enzyme proteins)

References

Can we measure the relative contribution of those factors?

BioDatabase

Ensemble

1. Exon (ENSE): Starg Phasge?, EndPhase?

Statistics

Regression

What is Principal Component Regression (PCR)?
>Mandel J. 1982 Use of the singular value decomposition in regression analysis. Am Stat 36:15-24
>Drummond DA. Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23: 327-37

TLB

Joy

ESST

1. Why 64 environments? (why 4*2*2^3)
   1. Is the number optimal?
2. How different are 64 ESSTs in terms of substitution patterns?

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