Function in biology

Complex term. Function can be said as what something (e.g., molecule) does.

Under the evolutionary umbrella, function has no a purpose.

Functional terms

Synonyms: keywords, glossaries, vocabularies, etc.

Ontologies

  • Ontology: a more complex case of a controlled vocabulary: formal naming and definition of the categories, properties and relations between the concepts, data and entities that substantiate one, many or all domains of discourse. (Ref)

Gene Ontology

Browsing tools:

Actually 3 ontologies:

Terms are linked by different kind of relationships: is a, part of, regulates, etc.

Graph representations

Types of graphs - https://commons.wikimedia.org/wiki/File:Types_of_graphs_in_biology.png

Types of graph in biology:

  • Simple Directed: Taxonomy (1 parent)
  • Acyclical Directed: Gene Ontology (1 or more parents)
  • Undirected: Metabolic network relationships

Other ontologies

Homology: Orthology, analogy, paralogy

  • Article in Wikipedia

  • Ortholog: Same ancestor origin. Speciation event
  • Analog: Not the same origin (despite having the same structure and/or function)
  • Paralog: Same former ancestor origin, but duplication event also involved

Gene phylogeny of histone H1 https://commons.wikimedia.org/wiki/File:Ortholog_paralog_analog_examples.svg

Moonlighting

  • Databases: MoonProt && MultiTaskDB
    • Example: P99999 - Cytochrome c
      • It transfers electrons between Complexes III (Coenzyme Q - Cyt C reductase)
      • Controlling apoptosis

Structure

  • Primary (sequence)

  • Secondary

    • Protein
    • RNA

Example of protein loop geometry with a loop, alpha-helix and a beta-sheet

  • Tertiary
    • Protein:
      • Domains
      • Binding site
      • Catalytic site.

Myoglobin and heme - https://commons.wikimedia.org/wiki/File:Myoglobin_and_heme.png

  • Quaternary
    • Protein:
      • Protein complexes
      • Protein-protein interaction
    • Protein-Nucleotide

Overview of the different levels of RNA structure https://commons.wikimedia.org/wiki/File:RNA_structure_(full).png

Warming up exercise

  • Find which is this protein and download as a FASTA file.
>protein S
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFR
SSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIR
GWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY
SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQ
GFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFL
LKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITN
LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCF
TNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN
YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPY
RVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFG
RDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAI
HADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPR
RARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTM
YICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFG
GFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFN
GLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQN
VLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGA
ISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMS
ECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAH
FPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD
SFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELG
KYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSE
PVLKGVKLHYT

  • Download the associated genome for this protein and save as FASTA.

  • Find a mRNA molecule related to this (check 1st session Entrez help reference)

Structural and functional annotation

PRINTS

  • PRINTS - Motifs/fingerprints

PROSITE

PATTERN (doc)

PA   P-x-[STA]-x-[LIV]-[IVT]-x-[GS]-G-Y-S-[QL]-G.

PROFILE (doc) Representation of a matrix…

MEME

  • For nucleotides: MEME suite

  • Exercise: Test our protein (our DNA and your RNA if possible) with the different tools above.

Databases

  • SMART
  • PFAM (and RNA equivalent: RFAM)
  • CATH

  • CDD

  • Exercise: try our protein in PFAM search, CATH and CDD and check results.
  • Exercise: try your mRNA in RFAM search.

Platforms that combine several tools

  • PSIPRED

  • Exercise: Test our protein with a few of the provided tools (only check a few options otherwise it will take too long)

InterPro

Families combined from different methods from databases described above.

KEGG