What is next for Lecture 5

1
What is next for Lecture 5 ?

• Why is pairwise sequence alignment different
• for proteins and for nucleic acids ?
• General protein introduction.
• Scoring systems and matrices for protein data.
• 3. Wet experience for pairwise sequence
  alignment
• (for proteins, more options).
• 4. Special Blast pages.
• 5. Why is multiple alignment better ?
• 6. Wet experience for MSA (for proteins).

2
The Genetic Code

• The genetic code - Each amino acid is coded by
  3 nucleotides, named codon.
• Code redundancy - Most amino acids are coded
  by more than one codon.
• - 64 triplets code for 20
  amino acids 3 stop codons.

3
Reading Frames
http//cbms.st-and.ac.uk/academics/ryan/Teaching/m
edsci/Medsci3.htm
4
6 Possible Reading Frames
http//www.uni-paderborn.de/lst/pics/readframe.gi
f
5
DNA or Protein

• DNA query can be translated and searched against
  protein databases.
• Translate all reading frames (3 3).
• Find long ORF (open reading frames).

• Protein query can be back-translated and searched
  
• against DNA databases.
• A protein sequence can be back translated to many
  
• possible DNA sequences, based on the codon
  table.
• During translation (DNA to protein) we loose
  information.

6
Proteins - Biological Function

• 1. Enzymes - Biological catalysts, examples
• Read genetic information stored in DNA, make
  mRNA.
• Involved in protein synthesis .
• Synthesize non-protein components of cells.
• Storage - Various ions and small molecules
• are stored as complexes with proteins
• Example iron is stored with ferritin
• in the liver.
• Transport - Hemoglobin delivers oxygen from the
  lungs to other tissues, and carbon dioxide back
  to the lungs. Proteins form ion channels in
  cellular membranes
• (for ions passage).

7

• Proteins Biological Function (cont.)
• 4. Messengers - Transmission of nervous
  impulses.
• Signaling molecules (hormones).
• Hormone receptors.
• Antibodies -
• Form the immune system.
• Regulation - Protein production is promoted or
  
• repressed by other proteins, in
  complex
• feedback mechanisms.
• 7. Structural proteins -

8
Jellyfish green fluorescent protein
Spider webs, silk
Fireflies light
Rhino horn
Cobras venom
Also feathers, porcupine quills, fingernails,
wool, scales, tortoise shells, etc.
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Amino Acids - the Building Blocks of Proteins
From The structure of life. (NIH and National
Institute of General Medical Sciences)
www.nigms.nih.gov
RSide chains
Glycine (hydrophilic)
Asparagine (amides)
Phenylalanine (aromatic)
Methionine (hydrophobic)