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Jul 31, 202412 min read

BI

Bioinformatics

Final Project

Perquisites:

Concepts

Original Slides

Questions

  • Why do we use just the final part of the cDNA for ESTs (Expressed Sequence Tags)?
    • Because the final part before the (AAA…A sequence) is usually unique (it’s also short so it’s more fast to search for it using algorithms)
  • Percentage of active genes in Prokaryotes and Humans:
    • - of the Prokaryotes DNA are active genes, coding DNA (the “DNA spam” is only at most), in the Human DNA the coding DNA is just .
  • Cos’è il “trasfermento orizzontale dei geni” negli eucarioti?
    • Si tratta di una mutazione del DNA di una creatura, per esempio mutato da un virus ad RNA, il trasferimento orizzontale è molto utile soprattutto per le creature che si riproducono in modo asesuato (il loro DNA non muta molto tra diverse generazioni)
  • Why does the DNA length keeps increasing over new generations?
    • Con l’andare del tempo il DNA di un organismo è destinato ad allungarsi, principalemente colpa dei trasposoni, specialmente il DNA degli eucarioti, anche se ci sono dei fenomeni di taglio (soprattutto in sequence ripetute, il DNA polimerasi “perde il filo”), ma in ogni caso in generale la lunghezza del DNA tenderà ad aumentare.
  • One DNA amminoacid sequnce does not produce always the same mRNA:NOT_SURE_ABOUT_THIS
    • Once the DNA is traduced in RNA, the RNA is then modified if needed, for example the intrones are removed, what we are left with is the mRNA that will be traduced into a protein.
  • Does the same mRNA produce the same protein in every species?NOT_SURE_ABOUT_THIS
    • In the eukaryotes the same mRNA does produce the same protein for every individual.
  • What is the purpose of the Lattice Model?NOT_SURE_ABOUT_THIS
    • It’s just to model the central carbon , it does not find anything else that is actually useful
  • What do tumors originate from?
    • Form a different transcription and/or post-transcription of proteins, we can see this from proteomics studies, and studying the RNA of the cancer cell, this is the most common type of cancer
    • From a mutation of the DNA, a cancer devoleped this way is way more rare than the previous case
  • What does an Enzyme do?
    • Enymes are Catalyst (speed up processes)
      • Enzymes form complex tissues (like blood, blood is a complex tissue)
      • Enxymes also breake up big proteins, into smaller ones know as products, which are more easly menaged.
    • Enzymes are not consumed once used
    • Enzymes are extreamely specific (they accept only one type of protein)
    • Proteins change their shape during their life, the enzymes need a particular active site to bind an work on their protein.
  • How are Cofactors and Coenzimes attached and deatached to an Enzyme?
    • A protein binds a Cofactor or Coenzyme to an Enzyme.
    • And another protein separeates them, when it is not needed anymore.
  • ?
  • ?

Questions

How Big is the Human DNA?
  • Total size of human genome: each cell carries 3.2 billion base pairs
What is the goal of Bioinformatics?
  1. To understand the basis of biological diversity and to trace the evolutionary history of the life on the Earth, which is written in our molecules
  2. To explain normal biological processes, to highlight malfunctions which lead to diseases, and to define approaches that can improve drug discovery and design
What does DNA stands for?
  • DeoxyriboNucleic Acid
What is DNA made of?
  • DNA molecules are made up of a few kinds of atoms ⎯ carbon, hydrogen, nitrogen, oxygen and phosphorus
  • DNA molecules use only four nucleo-bases, guanine, adenine, thymine and cytosine (G, A, T, C), which are attached to a phosphate group (PO ) and to a deoxyribose sugar (CHO), to form a nucleotide
  • The nucleotides are divided into 2 groups Purines and Pyrimidines, we make this distinction because in the double helix of the DNA Guanine binds only with Adenine (both Purines) and Thymine binds only with Cytosine (both Pyrimidines)
What is the difference between nucleo-bases and nucleotides?
  • Nucleo-Bases or Bases: Adenine Cytosine Thymine and Guanine (A, C, T, G)
  • Nucleotides: the Bases attached to a phosphate group (PO ) and to a deoxyribose sugar (CHO).
What is the “function” of DNA?
  • It is actually the information contained in the DNA that allows the organization of inanimate molecules in living cells and organisms, capable of regulating their internal chemical composition and their growth and reproduction
  • It is also the DNA that gives us the inheritance of our ancestors’ physical traits, through the transmission of genes
  • Genes contain the information, in the form of specific nucleotide sequences, which constitute the DNA molecules
What is a Gene?
  • A gene is a sequence of nucleotides along a strand of DNA that a cell nucleus uses to produce proteins. Genes determine the specific traits of an organism.
  • Complicated genes may be composed by hundreds of nucleotides
What is the Genome?
  • The genetic code “which describes” an organism, known as its genome, is conserved in millions/billions of nucleotides
What is a Chromosome?
What is the Phenotype?
  • The physical aspect of an individual (or animal, bacteria, …)
What are the Taxonomic Units?
What are the differences between Substitution and Indel Events?
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Project: [Velocit]

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