Biological background

From Protein Prediction 1 Summer Semester 2016 For Informaticians

This page is organized as follows:

Keywords are terms that you need to understand to follow the lecture. To test your knowledge, try to define and explain these keywords (in a few sentences). If you cannot think of anything to say about a keyword, read up on that topic.

Under Sources you find literature we suggest (textbooks, web pages, articles) that will help you to understand the topic. You can use this as a resource to complete your knowledge of the keywords and to help you answer the questions and solve the tasks. You are not required to read and study any of these, but they provide more detailed knowledge on the topic and are a good complement to the lecture. Of course you can feel free to use any other source you like.

In the section Exercise we provide Questions and Hands-on tasks that allow you to test and further your knowledge of the given topic. During the exercise session you can ask questions pertaining to the topic (keywords and exercises).


  • Archaea, bacteria, prokaryotes, eukaryotes, virus
  • Prokaryotic, eukaryotic cell
  • DNA, genes, RNA, genetic code
  • Proteins, soluble and (trans-)membrane
  • Protein sequence
  • UniProt, Swiss-Prot
  • Proteome, genome


Textbooks on (molecular) biology and biochemistry, introductory chapters

  • Lesk, Introduction to Bioinformatics
  • Campbell, Biology
  • Alberts, Molecular biology of the cell
  • Lehninger, Principles of biochemistry




  • What is the smallest unit of life?
  • How do prokaryotic cells differ from eukaryotic cells?
  • What are prokaryotes?
  • Is a virus alive?
  • Is a virus a cell?
  • What is a protein?
  • Where do you find proteins?
  • What is a gene?
  • How do cells proliferate?
  • What is the 'central dogma of molecular biology'
  • Explain replication, transcription and translation (1 or 2 sentences per term).
  • What are important chemical elements in biology/for life?
  • Define the term 'macromolecule' in one sentence.
  • List two biological macromolecules and their building blocks.
  • What is a proteome and a genome? Explain in 1 or 2 sentences.

Hands on tasks

  • Go to the UniProt website
    • Check the current release/date
    • How many protein sequences are stored in UniProt?
    • How many protein sequences are in Swiss-Prot?
    • How many human protein sequences are in UniProt? Try first searching for "human". If you look at the column "Organism", you will see that not all sequences are human. Searching UniProt for "human": Why do you find the protein "ZEP2_RAT" (UniProt AC)? Use now the advances search. Select the keyword "Organism" and search for "Homo sapiens". How many sequences do you find? How many are "Reviewed" (sequences in Swiss-Prot) and how many are "Unreviewed" (TrEMBL)?
    • Search in Swiss-Prot for the protein myoglobin from Homo sapiens. What is the UniProt entry (UniProt ID) and entry name (UniProt AC)? How long is the sequence? Download the protein sequence in FASTA format. What is the FASTA format? Open the UniProt entry for this protein and have a look at the information provided (for example the protein sequence).
  • Write a simple script to translate the genetic code (from DNA or RNA) into an amino acid sequence (1- or 3-letter code).
  • Given the sequence of the DNA template strand, write a small script that transcribes the DNA to RNA.