Summary
Summary Computational Biology
- Course
- Institution
- Book
Summary of the lectures and assignments, based on the book. Summary of the lectures and exercises, based on the book.
[Show more]
Connected book
Book Title:
Author(s):
- Edition:
- ISBN:
- Edition:
Seller
Followmichouweimar
Reviews received
Content preview
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
The benefits of buying summaries with Stuvia:
Guaranteed quality through customer reviews
Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.
Quick and easy check-out
You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.
Focus on what matters
Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!
Frequently asked questions
What do I get when I buy this document?
You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.
Satisfaction guarantee: how does it work?
Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.
Who am I buying these notes from?
Stuvia is a marketplace, so you are not buying this document from us, but from seller michouweimar. Stuvia facilitates payment to the seller.
Will I be stuck with a subscription?
No, you only buy these notes for $3.77. You're not tied to anything after your purchase.
Can Stuvia be trusted?
4.6 stars on Google & Trustpilot (+1000 reviews)
67096 documents were sold in the last 30 days
Founded in 2010, the go-to place to buy study notes for 14 years now