Samenvatting

Summary BIF20306 Introduction to bioinformatics

2 keer verkocht

Instelling
Wageningen University (WUR)

This is a concise but complete summary of the course 'Introduction to bioinformatics'. The summary contains information from the reading materials, the lectures, and the practicals. It provides a good preparation for the exam.

[Meer zien]

Voorbeeld 2 van de 13 pagina's

Bekijk voorbeeld

Heel boek samengevat? Ja
Geupload op 13 oktober 2021
Aantal pagina's 13
Geschreven in 2021/2022
Type Samenvatting

€5,49

In winkelwagen

Op verlanglijstje

100% tevredenheidsgarantie
Direct beschikbaar na je betaling
Lees online óf als PDF
Geen vaste maandelijkse kosten

Summary Introduction to
bioinformatics
BIF20306

Table of contents
Week 1. Introduction and databases......................................................................................................1
Week 2. Sequences................................................................................................................................3
Week 3. Evolution...................................................................................................................................5
Week 4. Structure and function..............................................................................................................9
Week 5. Omics......................................................................................................................................12

Week 1. Introduction and databases
Amino acid Three-letter code One-letter code Comment
Non-polar Glycine Gly G Only -H as side
chain
Alanine Ala A
Valine Val V
Leucine Leu L
Isoleucine Ile I
Proline Pro P Side chain to N
bond
Phenylalanine Phe F
Methionine Met M
Tryptophan Trp W
Cysteine Cys C Forms disulfide
bonds
Polar Asparagine Asn N Amide N polar
Glutamine Gln Q Amide N polar
Serine Ser S -OH group polar
Threonine Thr T -OH group polar
Tyrosine Tyr Y -OH group polar
Acidic Aspartic acid Asp D
Glutamic acid Glu E
Basic Histidine His H
Lysine Lys K
Arginine Arg R
The relationship between DNA, RNA and proteins has been described as the central dogma of
molecular biology. The information of DNA is transcribed into RNA in the process of transcription,
which is subsequently converted into proteins in the process of translation.
The genetic code refers to the correspondence between the 4-letter nucleotide alphabet of DNA and
the 20-letter amino acid alphabet of proteins.
The primary structure of a polypeptide is the amino acid sequence from the N- to the C-terminus.
The secondary structure of a protein is a description of its structure in terms of local alignments:
sheets, helices, turns.

1

, Turns are built up from 3 to 6 amino acids and cover a huge conformational space of the protein
backbone. They are important for the protein globularity.
Loops are structural elements that consist of multiple turns and connects helices and sheets.
The tertiary structure describes the 3D arrangement and placement of secondary structural
elements. It specifies protein properties.
The amino acid interactions include hydrogen bonds, disulfide bridges, ionic bonds and hydrophobic
interactions.
The quaternary structure is the arrangement of several polypeptide subunits. The assembly is carried
out through noncovalent interactions.
mRNA is produced from 5’ (N-terminus) to 3’ (C-terminus). DNA read from 3’ to 5’.
The genome is the total pool of genomic DNA in an organism.
The transcriptome is the total pool of mRNA in an organism.
The proteome is the total pool of proteins in an organism.

DNA and RNA differ in composition of their nucleotides. While in DNA deoxyribose is found as sugar
residue, in RNA this is replaced by ribose. Furthermore, in RNA, the base uracil replaces thymine.
DNA is present as a complementary double strand, whereas RNA is single-stranded.
In DNA, the base pairings A-T and C-G are seen. A purine ring (Adenine or Guanine) is paired with a
corresponding pyrimidine (Thymine, Cytosine or Uracil). Two hydrogen bonds are formed in the base
pairing of A-T, whereas three such bonds are formed in the pairing of C-G.

Primary databases contain primary sequence information and accompanying annotation information
regarding function, bibliographies, and so on.
Secondary databases summarize the results from analyses of primary protein sequence databases.

Biological databases
Primary databases DNA sequences Genbank, ENA, DDBJ
Protein sequences Uniprot (Swissprot=annotated and reviewed),
TrEMBL=annotated, not reviewed, PIR)
Protein structures PDB
Secondary databases Motifs Prosite
Profiles/domains Pfam
Protein folds SCOP, CATH
Other databases Multiple sequence MAFFT
alignment
Phylogenetic trees MegaX
Amino acid composition PIR
Calculate maximum IQ tree
likelihood trees and their
bootstrap analysis
Secondary structure 2struc, raptorX, TMHMM, expasy
3D structure PDBsum

Motifs are short sequence regions that are conserved in related proteins and usually have a key role
in the protein’s function.
A profile is a pattern that evaluates the probability of the appearance of a given amino acid, an
insertion, or a deletion at every position in a protein sequence.
Binary files are all the files that are non-text files.
Redundancy occurs when the same sequence is deposited multiple times or when several databases

2

Dit zijn jouw voordelen als je samenvattingen koopt bij Stuvia:

Bewezen kwaliteit door reviews

Studenten hebben al meer dan 850.000 samenvattingen beoordeeld. Zo weet jij zeker dat je de beste keuze maakt!

In een paar klikken geregeld

Geen gedoe — betaal gewoon eenmalig met iDeal, creditcard of je Stuvia-tegoed en je bent klaar. Geen abonnement nodig.

Direct to-the-point

Studenten maken samenvattingen voor studenten. Dat betekent: actuele inhoud waar jij écht wat aan hebt. Geen overbodige details!

Veelgestelde vragen

Wat krijg ik als ik dit document koop?

Je krijgt een PDF, die direct beschikbaar is na je aankoop. Het gekochte document is altijd, overal en oneindig toegankelijk via je profiel.

Tevredenheidsgarantie: hoe werkt dat?

Onze tevredenheidsgarantie zorgt ervoor dat je altijd een studiedocument vindt dat goed bij je past. Je vult een formulier in en onze klantenservice regelt de rest.

Van wie koop ik deze samenvatting?

Stuvia is een marktplaats, je koop dit document dus niet van ons, maar van verkoper Rebeccaveenstra. Stuvia faciliteert de betaling aan de verkoper.

Zit ik meteen vast aan een abonnement?

Nee, je koopt alleen deze samenvatting voor €5,49. Je zit daarna nergens aan vast.

Is Stuvia te vertrouwen?

4,6 sterren op Google & Trustpilot (+1000 reviews)

Afgelopen 30 dagen zijn er 68175 samenvattingen verkocht

Opgericht in 2010, al 15 jaar dé plek om samenvattingen te kopen

Begin nu gratis

Samenvatting

Summary BIF20306 Introduction to bioinformatics

Document informatie

Onderwerpen

Gekoppeld boek

Geschreven voor

Verkoper

Voorbeeld van de inhoud