Outline 1 What is an amino acid protein

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

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.

Amino Acids - peptide bond N-terminal C-terminal

Examples of protein 3 D-structure 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) Asp (D) Asn (N) Ile (I) Glu (E) Met (M) Lys (K) Trp (W) Gln (Q) Tyr (Y) Pro (P) Gly (G)

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

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

t. RNA – amino acids and codons Anti-codon Codon for Phenylalanine is TTC

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

DNA - a double helix 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 -CH 3 group in Thymine replaced with an -H in Uracil

Genes, chromosomes and base pairs • Genes are located at the chromosomes • 3. 000 bp in human genome - diploid => 6. 000 bp

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 => m. RNA Transcript – piece of DNA that is transcribed into RNA i. e. introns are spliced out m. RNA with UTR-regions

ARTN_HUMAN chr 1: 4440132944402434

Single Nucleotide Polymorphism SNP • SNPs can be located anywere in the genome • non synomous (ns. SNP) i. e. amino acid is changed • Synomous SNP does not affect the protein An amino acid is coded by 3 nucleotides Leu: TTG

RNA/DNA translation table - codon

Identify possible start codons how many ? GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG

Identify possible start codons how many ? GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCATGGGTAATGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG

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 TTCGATCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG Does the gene stop at that TAG ? 123 123 123. . . ATG CCA TGC ATA GCC CCT GCC ATA TCT. . . GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG

Reding frame - II GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTA GGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG 123 123 123. . . ATG CCA TGC ATA GCC CCT GCC ATA TCT. . . What is the result of translating the m. RNA into protein ? (only first 9 codons – use handout) 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 TTCGATCATTGTCATGGTAAGTGCCATGGTATAGCA TGATAATGGGGCATTCAGTACAAAAATCCCGTAGCT GGTAGCCCGATGCCATGCATAGCCCCTGCCATATCT TTCGATCATTGTCAGTGGGTAAGTGCCATGGTATAG 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 complement strings & reading frames -1: TCTATACCGTCCCCGATACGTACCGT -2: CTATACCGTCCCCGATACGTACCGT -3: TATACCGTCCCCGATACGTACCGT

Summary - protein 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

Summary – DNA/RNA translation transcription DNA -> m. RNA 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 -> Protein

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