1. Outline 1.What is an amino acid / protein 2. 20 naturally occurring amino acids 3.Codon – triplet coding for an amino acid 1.How are proteins synthesized 1.Transcription & translation 2.DNA, chromosomes and base-pairing 3.Genes, intron and exons 4.Reading frames

2. Amino Acids Amine and carboxyl groups. Sidechain ‘R’ is attached to C-alpha carbon The amino acids found in Living organisms are L-amino acids.

3. Amino Acids - peptide bond N-terminalC-terminal

4. Examples of protein 3D-structure Small protein one domain Bigger protein two domains

5. The 20 amino acids Asn (N) Asp (D) Gln (Q) Glu (E) Arg (R) Tyr (Y) Trp (W) Phe (F) Gly (G) Pro (P) Ile (I) Met (M) Leu (L) Ala (A) Val (V) Ser (S) Cys (C) Thr (T) His (H) Lys (K)

6. Sidechain determines physical property Arg - R Lys - K Asp - D Glu - E His - H Positive charged (basic) amino acids are: R, K, H Negative (acidic): D and E

7. Amino Acids Livingstone & Barton, CABIOS, 9, 745-756, 1993 A – Ala C – Cys D – Asp E – Glu F – Phe G – Gly H – His I – Ile K – Lys L – Leu M – Met N – Asn P – Pro Q – Gln R – Arg S – Ser T – Thr V – Val W – Trp Y - Tyr Amino acid

8. DNA - a double helix 5’ - A T T G C C - 3’ 3’ - T A A C G G - 5’ James Watson and Francis Crick with their model of the structure of the DNA molecule, 1953

9. DNA - Base pairing of nucleotides T in DNA is replaced by U (Uracil) in RNA -CH3 group in Thymine replaced with an -H in Uracil

10. tRNA – amino acids and codons Anti-codon Codon for Phenylalanine is TTC tRNA molecules are used in the process where mRNA is translated Into a protein sequence. The anti-codon is matched to a codon on the mRNA molecule. mRNA | Translation Protein

11. Transcription & translation DNA |Transcription mRNA | Translation Protein In higher organisms the picture is a bit more complex. DNA -> pre-mRNA -> mRNA ->protein Protein might need a chaperone in order to fold correctly. movie

12. Genes, chromosomes and base pairs Genes are located at the chromosomes 3 billion bp in human genome – diploid (2 copies of each chromosome)

13. Gene structure - start stop and UTR A gene starts in 5’ end with ATG - stop in 3’ end with TAG stop codon Introns are spliced out from DNA transcript => mRNA Transcript – piece of DNA that is transcribed into RNA i.e. introns are spliced out mRNA with UTR-regions

14. ARTN_HUMAN chr1:44401329- 44402434

15. Single Nucleotide Polymorphism SNP SNPs can be located anywere in the genome non synomous (nsSNP) i.e. amino acid is changed (shown below ) Synomous SNP does not affect the the protein An amino acid is coded by 3 nucleotides Valine (V): GTC V I T P

16. RNA/DNA translation table - codon

17. Identify possible start codons how many ? GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

18. Identify possible start codons how many ? GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

19. Reding frame GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG An open reading frame (orf) is a piece of DNA from start to stop ATG (start codon) -> TAG or TGA or TAA (stop codons) Does the gene stop at that TAG ? 123 123 123 123 123 123 123 123 123... ATG CCA TGC ATA GCC CCT GCC ATA TCT... GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

20. Reding frame - II GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG What is the result of translating the mRNA into protein ? (only first 9 codons – use link from course page) 123 123 123 123 123 123 123 123 123... ATG CCA TGC ATA GCC CCT GCC ATA TCT... 123 123 123 123 123 123 123 123 123... ATG CCA TGC ATA GCC CCT GCC ATA TCT... M P S I A P A I S

21. Forward and reverse strand GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG 5’-ATGCCATGCATAGCCC-3’ (forward or plus strand) 3’-TACGGTACGTATCGGG-5’ (reverse or negative strand)

22. Reading frame and reverse complement TGCCATGCATAGCCCCTGCCATATCT Having a piece of DNA like: Forward strings & reading frames 1 : TGCCATGCATAGCCCCTGCCATATCT 2 : GCCATGCATAGCCCCTGCCATATCT 3 : CCATGCATAGCCCCTGCCATATCT Reverse and complement strings -1: TCTATACCGTCCCCGATACGTACCGT -> AGATATGGCAGGGGCTATGCATGGCT -2: CTATACCGTCCCCGATACGTACCGT -> GATATGGCAGGGGCTATGCATGGCT -3: TATACCGTCCCCGATACGTACCGT -> ATATGGCAGGGGCTATGCATGGCT

23. Summary – protein I o 20 naturally occurring amino acids  L-amino acids o Amino acid is defined by a codon o One and three letter codes (important) o Protein reads from N -> C terminal

24. Summary – protein II

25. Summary – DNA/RNA DNA -> mRNA -> Protein transcription translation o DNA: A-T, C-G o RNA: A-U, C-G o DNA/RNA strand reads from 5’ -> 3’ o Gene starts with ATG until stop codon o 64 codons, but only 20 amino acids o Reading frames 1,2,3,-1,-2,-3

26. Subcellular location An animal cell:

27. Proteins - where are they found 1.Proteins are found in all living organisms 2.In humans there are approx 25.000 proteins 3.Each protein has a specific function 1.Making up the human tissue - skin, hair, heart... 2.Degrading the food we eat 3.Immune system 4.Transportation of Oxygen in blood 5.Triggering the growth of cells 6.The brain - neural signalling 4.Typically a protein is approx 220 aa in human 5.Proteins talk, i.e. Protein-protein interactions 1.To relay a signal across the cell-membrane

28. 1 and 3-letter codes 1.There are 20 naturally occurring amino acids 2.Normally the one/three codes are used Ala - A Cys - C Asp - D Glu - E Phe - F Gly - G His - H Ile - I Lys - K Leu - L Met - M Asn - N Pro - P Gln - Q Arg - R Ser - S Thr - T Val - V Trp - W Tyr - Y

29. Graphic stick representation Different aa, different property Ile - Hydrophobic Phe - Hydrophobic & aromatic

30. The 20 amino acids

31. Charged amino acids (sidechain in red) Arg - R Lys - K Asp - D Glu - E His - H

32. Neutral amino acids Ile - I Leu - L Met - M Phe - F Pro - P

33. Property of amino acids (I) neutral, polar or charged ? Ala - A Asn - N Cys - C Gln - Q Gly - G

34. Property of amino acids (II) neutral, polar or charged ? Ser - S Thr - T Trp - W Tyr - Y Val - V

35. Protein structure Primary structure: Amino acids sequences Secondary structure: Helix/Beta sheet Tertiary structure: Fold, 3D cordinates

36. Protein structure  -helix    helix3 residues/turn - few, but not uncommon  - helix3.6 residues/turn - by far the most common helix Pi-helix4.1 residues/turn - very rare

37. Protein structure  strand/sheet

38. Protein structure Ribbon representation - easy to see the secondary structure elements

39. Protein structure

40. Protein structure Hydrophilic/hydrophobic & stacking

41. Protein folds Class 4’th is ‘few secondary structure Architecture Overall shape of a domain Topology Share secondary structure connectivity

42. Summary DNA -> mRNA -> Protein transcription translation 1.20 naturally occurring amino acids 2.Each amino acid has different properties, but can be grouped into: 1.Charged, neutral, polar (basic, acidic) 3.Secondary structure  -helix &  -strand/  -sheet 4.Protein hydrophobic inside, polar on the outside 5.Folds or classes: all , all ,  + , few secondar structure elements

43. Summary The amino acids A - Ala C -Cys D -Asp E -Glu F - Phe G -Gly H -His I -Ile K -Lys M -Met N -Asn P -Pro Q -Gln R -Arg S -Ser T -Thr V -Val W -Trp Y -TyrL -Leu