Outline 1.What is an amino acid / protein 2. 20 naturally occurring amino acids 3.Codon – triplet...
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Transcript of Outline 1.What is an amino acid / protein 2. 20 naturally occurring amino acids 3.Codon – triplet...
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.
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
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
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
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