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

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.

Amino Acids - peptide bond Send around a model of a di-peptide N-terminal C-terminal

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

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)

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

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, 745-756, 1993

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’

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

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

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.

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

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

ARTN_HUMAN chr1:44401329-44402434

RNA/DNA translation table - codon

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

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

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 ? 123 123 123 123 123 123 123 123 123 ... ATG CCA TGC ATA GCC CCT GCC ATA TCT ... GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

Reding frame - II GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCT GGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG 123 123 123 123 123 123 123 123 123 ... 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) 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

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

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

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

Summary – protein II

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