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 synthesized1. 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 3D-structure

Small proteinone domain Bigger protein

two domains

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)

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 Acids

Livingstone & Barton, CABIOS, 9, 745-756, 1993

A – AlaC – CysD – AspE – GluF – PheG – GlyH – HisI – Ile

K – LysL – Leu

M – MetN – AsnP – ProQ – GlnR – ArgS – SerT – ThrV – ValW – TrpY - Tyr

Amino acid

tRNA – amino acids and codons

Anti-codon

Codon for Phenylalanine is TTC

Transcription & translation

DNA | TranscriptionmRNA

| TranslationProtein

In higher organisms thepicture is a bit more complex.DNA -> pre-mRNA -> mRNA->protein

Protein might need a chaperonein order to fold correctly.

movie

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 modelof the structure of the DNA molecule, 1953

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

Genes, chromosomes and base pairs

• Genes are located at the chromosomes• 3.000.000 bp in human genome - diploid => 6.000.000 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 => mRNA

Transcript – pieceof DNA that is

transcribed into RNA i.e.introns are spliced out

mRNA withUTR-regions

ARTN_HUMAN chr1:44401329-44402434

Single Nucleotide PolymorphismSNP

• SNPs can be located anywere in the genome• non synomous (nsSNP) i.e. amino acid is changed• Synomous SNP does not affect the the protein

An amino acid is coded by 3 nucleotidesLeu: TTG

RNA/DNA translation table - codon

Identify possible start codonshow many ?

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

Identify possible start codonshow many ?

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGGTAATGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

Reding frame

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

An open reading frame (orf) is a piece of DNA from start to stopATG (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 ...

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

Reding frame - II

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

What is the result of translating the mRNAinto protein ? (only first 9 codons – use handout)

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

Forward and reverse strand

GATAATGGGGCATTCAGTACAAAAATCCCGTACGGAGCTAGGCAGCTAACCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCATGGTAAGTGCCATGGTATAGCATGATAATGGGGCATTCAGTACAAAAATCCCGTACGTAGCTGGTAGCTAGCCCGATGCCATGCATAGCCCCTGCCATATCTTTCGATCATTCATTGTCAGTGGGTAAGTGCCATGGTATAG

5’-ATGCCATGCATAGCCC-3’ (forward or plus strand)3’-TACGGTACGTATCGGG-5’ (reverse or negative strand)

Reading frame andreverse complement

TGCCATGCATAGCCCCTGCCATATCT

Having a piece of DNA like:

Forward strings & reading frames1 : TGCCATGCATAGCCCCTGCCATATCT2 : GCCATGCATAGCCCCTGCCATATCT3 : 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

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

Charged amino acids(sidechain in red)

Arg - R

Lys - K

Asp - D

Glu - E

His - H