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Outline What is an amino acid / protein

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

2 Amino Acids Functional group 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
Send around a model of a di-peptide N-terminal C-terminal

4 Examples of protein 3D-structure
Human proteins typically has a length of 220aa Small protein one domain Bigger protein two domains

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

6 Sidechain determines physical property
Positive charged (basic) amino acids are: R, K, H Negative (acidic): D and E Arg - R Lys - K Asp - D Glu - E What is the charge ? R,K (+) at physiological pH D,E (-) at physiological pH H sometimes (+) at physiological pH These amino acids are also polar His - H

7 Livingstone & Barton, CABIOS, 9, 745-756, 1993
Amino acid Amino Acids 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 What is the charge ? R,K (+) at physiological pH D,E (-) at physiological pH H sometimes (+) at physiological pH These amino acids are also polar Livingstone & Barton, CABIOS, 9, , 1993

8 DNA - a double helix 5’ - A T T G C C - 3’ 3’ - T A A C G G - 5’
Many organelles in a cell: Mention: Nucleus, cytoplasma, membrane, ER James Watson and Francis Crick with their model of the structure of the DNA molecule, 1953 5’ - A T T G C C - 3’ 3’ - T A A C G G - 5’

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
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 Anti-codon Codon for Phenylalanine is TTC

11 Transcription & translation
DNA | Transcription mRNA | Translation Protein movie 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.

12 Genes, chromosomes and base pairs
Genes are located at the chromosomes 3 billion bp in human genome – diploid (2 copies of each chromosome) Many organelles in a cell: Mention: Nucleus, cytoplasma, membrane, ER

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:

15 RNA/DNA translation table - codon

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

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

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

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

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

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

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

23 Summary – protein II

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

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