Resumen
Summary Computational Biology
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Samenvatting van de colleges en opdrachten, gebaseerd op het boek. Summary of the lectures and exercises, based on the book.
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LecturesBuilding blocks of life
Molecular biology primer (from gene to protein)
Central dogma molecular biology
mRNA longer & heavier
Proteins synthesized in cytoplasm
Proteins more abundant, why study DNA?
DNA (&RNA) sequencing can be automated
Seq technologies
1st generation: Sanger seq
- Short read
- Infer nucleotide identity using dNTPs
- Visualize with electrophoresis
2nd gen (NGS): Illumina
- Short read
- High throughput from parallelization of seq reactions
3rd gen: Oxford Nanopore
- Long read
- Seq native DNA in real time with single molecule resolution
Longer read length higher error
Combine long & short read tech to cover gaps & correct seq errors
Genome => full set of chromosomes or genes in a gamete of diploid organism
Regular somatic cell contains 2 full sets of genomes (& mtDNA)
Haploid organisms: cell contains 1 set of genome
Mt & chloroplast genome: also 1 set
,Size of genomes: does not correlate with complexity
Gene => DNA based unit that can exert its effect on organism through RNA or
protein products
1 gene 1 protein
Programmable unit that can give rise to multitude of products: proteins &
RNA products through splicing
Translation
1. Initiation
2. Elongation
3. Termination
Bioinformatics = gene encoded in 1 strand + scan model takes 1 st ATG as start
codon
ORF finding program
Reading frame => way of dividing seq of nucleotides in DNA or RNA molecule
into a set of consecutive, non-overlapping triplets
Open reading frame (ORF) => spans of DNA seq between start & stop codons
,Amino acids
Why study aa?
20 aa
Lock & key property
Serine proteases
- Chymotrypsin cuts after Phe, Trp & Tyr
- Trypsin cuts after Lys & Arg
- Elastase cuts after Ala, Gly & Val
Composition helps predict
- Protein structure
- Possible biochemical structure
- Protein functionality
- Mutability & evolution
Secondary structure
Alpha helix
Beta strand
(beta) turn
Proteins
Macromolecules made up from 20 aa
Heart of aa = C alpha, bound to:
- Amino group (backbone)
- Carboxyl group (backbone)
- Hydrogen (backbone)
- Side chain R
Di-peptide
Binding of aa to form protein: 2 protons from NH3 & 1 O from carboxyl
join form water
Peptide bond: C=O at one side & N-H at other side
- Only ends of chain are NH3 or carboxylic charged
Amino acid sequence = primary structure
Order of aa in protein chain
Always read from N term to C term of protein
- N term = +H3N
- C term = COO-
, 20 aa
Side chain (R) determines differences in structural & chemical properties
of 20 natural aa
Several aa in >1 category
Characterisation: multiple ways
- Hydrophobicity
- Size
- Charge
- Secondary structure preference
- Alcoholicity
- Aromaticity
- Special characteristics: bridge forming by cysteines, rigidity of prolines,
titrating at phys pH of histidine, flexibility of glycines
Amino acid characteristics
Glycine (G) & alanine (A)
Small & neutral
G (Gly)
- Smallest residue, hydrophobicity undetermined (no R)
- Turns 😊 no R flexible backbone > strands 😐 > helix ☹
- No chiral center: <4 different groups bound to it, 2 protons on C alpha
A (Ala)
- Small hydrophobic residue
- R = methyl group
- Alpha helix 😊 > beta strands 😐 > beta turns ☹
- Subset of all other aa
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