From DNA to Protein DNA 2014 Pearson Education

From DNA to Protein DNA © 2014 Pearson Education, Inc. RNA Protein

Protein Synthesis Pro vs. Eukaryotic Cells Nuclear envelope TRANSCRIPTION RNA PROCESSING DNA Pre-m. RNA DNA TRANSCRIPTION m. RNA Ribosome TRANSLATION Polypeptide (a) Bacterial cell © 2014 Pearson Education, Inc. Ribosome (b) Eukaryotic cell

DNA TRANSCRIPTION m. RNA (a) Bacterial cell © 2014 Pearson Education, Inc.

DNA TRANSCRIPTION m. RNA TRANSLATION Polypeptide (a) Bacterial cell © 2014 Pearson Education, Inc. Ribosome

Nuclear envelope TRANSCRIPTION DNA Pre-m. RNA (b) Eukaryotic cell © 2014 Pearson Education, Inc.

Nuclear envelope TRANSCRIPTION RNA PROCESSING m. RNA (b) Eukaryotic cell © 2014 Pearson Education, Inc. DNA Pre-m. RNA

Nuclear envelope TRANSCRIPTION RNA PROCESSING DNA Pre-m. RNA TRANSLATION Ribosome Polypeptide (b) Eukaryotic cell © 2014 Pearson Education, Inc.

DNA template strand 3 A C C A A A C C G A G T T G G T T T G G C T C A 5 5 3 TRANSCRIPTION U G m. RNA G U U U G G C U C 3 5 Codon TRANSLATION Protein Trp Amino acid © 2014 Pearson Education, Inc. A Phe Gly Ser

Second m. RNA base A C UUU U UUC First m. RNA base (5 end of codon) UUA UUG Leu CUU C A CUC CUA Leu UCU UAU UCC UAC UCA Ser CCC CCA Pro CAC CAA AAU AUC IIe ACC AUA ACA GUG C CAU ACU Val Cys CCU AUU GUC UGC U UAG Stop UGG Trp G CAG GUU UGU UCG CCG Met or start Tyr UAA Stop UGA Stop A CUG AUG G © 2014 Pearson Education, Inc. Phe G Thr AAC AAA ACG AAG GCU GAU GCC GCA GCG Ala GAC GAA GAG His Gln Asn Lys Asp Glu CGU CGC CGA U Arg CGG AGU AGC AGA AGG GGA GGG A G Ser Arg GGU GGC C U C A G U Gly C A G Third m. RNA base (3 end of codon) U

Promoter Transcription unit 5 3 1 Initiation Start point RNA polymerase 5 3 Unwound DNA © 2014 Pearson Education, Inc. 3 5 Template strand of DNA RNA transcript

Transcription unit Promoter 5 3 1 Initiation 3 5 Start point RNA polymerase 5 3 3 5 Template strand of DNA RNA transcript Unwound DNA 2 Elongation Rewound DNA 5 3 3 5 RNA transcript © 2014 Pearson Education, Inc. 3 5 Direction of transcription (“downstream”)

Transcription unit Promoter 5 3 1 Initiation 3 5 Start point RNA polymerase 5 3 3 5 Template strand of DNA RNA transcript Unwound DNA 2 Elongation Rewound DNA 5 3 5 RNA transcript 3 Termination 3 5 3 Direction of transcription (“downstream”) 5 3 3 5 5 Completed RNA transcript © 2014 Pearson Education, Inc. 3

Promoter DNA 5 3 Nontemplate strand 3 5 TA T A A ATAT T TATA box Start point Transcription factors promoter Template strand 5 3 3 5 Transcription factors RNA polymerase II 5 3 5 3 © 2014 Pearson Education, Inc. 2 Several transcription factors bind to DNA. 3 Transcription 3 5 RNA transcript Transcription initiation complex 1 A eukaryotic initiation complex forms.

Nontemplate strand of DNA RNA nucleotides RNA polymerase A T 3 C C A T A G G T A T U A U T G 5 T 3 end C A U C 5 C A A A C C 3 Direction of transcription Template strand of DNA Newly made RNA © 2014 Pearson Education, Inc. 5 G A T C

A Typical pre-m. RNA Transcript A modified guanine nucleotide added to the 5 end 5 G P P Protein-coding segment AAUAAA P 5 Cap 5 UTR © 2014 Pearson Education, Inc. 50– 250 adenine nucleotides added to the 3 end Polyadenylation signal 3 Start codon Stop codon 3 UTR AAA…AAA Poly-A tail

Pre-m. RNA strand vs. m. RNA Strand Pre-m. RNA Intron Poly-A tail 5 Cap 1– 30 105– 146 31– 104 Introns cut out and exons spliced together m. RNA 5 Cap 5 UTR Poly-A tail 1– 146 Coding segment 3 UTR AAUAAA © 2014 Pearson Education, Inc.

Small RNAs Spliceosome 5 Pre-m. RNA Exon 2 Exon 1 Intron Spliceosome components m. RNA 5 © 2014 Pearson Education, Inc. Exon 1 Exon 2 Cut-out intron

t. RNA 3 A C C A C G C U U A A U C * C AG G G U * C * * C U * GA G G U * * A Amino acid attachment site 5 G C G G A U U A G * U A * C U C * G C G A G G * C C A G A A 5 3 Hydrogen bonds C U G Anticodon (a) Two-dimensional structure © 2014 Pearson Education, Inc. Amino acid attachment site A A G Anticodon (b) Three-dimensional structure 3 5 Anticodon (c) Symbol used in this book

Growing polypeptide t. RNA molecules r. RNA Exit tunnel Large subunit E P A Small subunit 5 m. RNA 3 (a) Computer model of functioning ribosome Growing polypeptide P site (Peptidyl-t. RNA binding site) Exit tunnel E P A E Large subunit m. RNA Small subunit 5 (b) Schematic model showing binding sites © 2014 Pearson Education, Inc. Next amino acid to be added to polypeptide chain A site (Aminoacylt. RNA binding site) E site (Exit site) m. RNA binding site Amino end t. RNA 3 Codons (c) Schematic model with m. RNA and t. RNA

Translation - Initiation Large ribosomal subunit Met 3 U A C 5 5 A U G 3 P site Met Pi Initiator t. RNA GTP GDP E m. RNA 5 Start codon 3 Small ribosomal m. RNA binding site subunit 1 Small ribosomal subunit binds to m. RNA. © 2014 Pearson Education, Inc. A 5 3 Translation initiation complex 2 Large ribosomal subunit completes the initiation complex.

Translation Elongation Amino end of polypeptide 1 Codon recognition E 3 m. RNA 5 P A site GTP GDP P i E P A © 2014 Pearson Education, Inc.

Translation Elongation Amino end of polypeptide 1 Codon recognition E 3 m. RNA 5 P A site GTP GDP P i E P A 2 Peptide bond formation E P A © 2014 Pearson Education, Inc.

Amino end of polypeptide Translation Elongation 1 Codon recognition E Ribosome ready for m. RNA next aminoacyl t. RNA 3 P A site 5 GTP GDP P i E E P A 2 Peptide bond GDP P i 3 Translocation formation GTP E P A © 2014 Pearson Education, Inc.

Translation - Termination Release factor 3 5 Stop codon (UAG, UAA, or UGA) 1 Ribosome reaches a stop codon on m. RNA. © 2014 Pearson Education, Inc.

Release factor Free polypeptide 3 5 Stop codon (UAG, UAA, or UGA) 1 Ribosome reaches a stop codon on m. RNA. © 2014 Pearson Education, Inc. 2 Release factor promotes hydrolysis.

Release factor Free polypeptide 5 3 5 2 Stop codon (UAG, UAA, or UGA) 1 Ribosome reaches a stop codon on m. RNA. © 2014 Pearson Education, Inc. 3 GTP 2 GDP 2 Release factor promotes hydrolysis. P i 3 Ribosomal subunits and other components dissociate.

Completed polypeptide Growing polypeptides Polyribosomes Incoming ribosomal subunits Start of m. RNA (5 end) Polyribosom e End of m. RNA (3 end) (a) Several ribosomes simultaneously translating one m. RNA molecule Ribosomes m. RNA (b) A large polyribosome in a bacterial cell (TEM) © 2014 Pearson Education, Inc. 0. 1 m

RNA polymerase Polyribosomes DNA m. RNA Polyribosome RNA polymerase Direction of transcription DNA Polyribosome Polypeptide (amino end) Ribosome m. RNA (5 end) © 2014 Pearson Education, Inc. 0. 25 m

DNA TRANSCRIPTION 3 5 RNA transcript RNA PROCESSING Exon A ly Po RNA polymerase RNA transcript (pre-m. RNA) Intron NUCLEUS Aminoacyl-t. RNA synthetase y-A Pol Amino acid AMINO ACID ACTIVATION t. RNA CYTOPLASM m. RNA 5 A E ap 3 C Aminoacyl (charged) t. RNA P Ribosomal subunits ap 5 C A C C U E TRANSLATION A A C A A A U G G U U U A U G Codon Ribosome © 2014 Pearson Education, Inc. Anticodon Po ly -A

DNA TRANSCRIPTION 3 5 RNA transcript RNA PROCESSING Exon A y- l Po RNA polymerase RNA transcript (pre-m. RNA) Intron NUCLEUS Aminoacyl-t. RNA synthetase y-A Pol Amino acid AMINO ACID ACTIVATION t. RNA CYTOPLASM m. RNA ap 5 © 2014 Pearson Education, Inc. C Aminoacyl (charged) t. RNA

m. RNA Growing polypeptide ap A E 3 C 5 Aminoacyl (charged) t. RNA P Ribosomal subunits p a 5 C A C TRANSLATION C U E A A C A A A U G G U U U A U G Codon Ribosome © 2014 Pearson Education, Inc. Anticodon A y- l Po

Mutations Sickle-cell hemoglobin Wild-type hemoglobin DNA C T C 5 3 G A G 3 5 Mutant hemoglobin DNA C 3 G T G 5 m. RNA G A G 5 Normal hemoglobin Glu © 2014 Pearson Education, Inc. 5 3 3 5 G U G Sickle-cell hemoglobin Val 3

Silent Subsititution Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end 5 3 A 3 T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A Met Lys Phe Gly Stop Carboxyl end Nucleotide-pair substitution: silent A instead of G 3 5 T A C T T C A A A C C A A T T A T G A A G T T T G G T T A A 5 3 U instead of C 5 A U G A A G U U U G G U U A A Met © 2014 Pearson Education, Inc. Lys Phe Gly Stop 3

Missense Subsititution Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A Met Lys Phe Gly 5 3 A 3 Stop Carboxyl end Nucleotide-pair substitution: missense T instead of C 3 5 T A C T T C A A A T C G A T T A T G A A G T T T A G C T A A 5 3 A instead of G 5 A U G A A G U U U A G C U A A Met © 2014 Pearson Education, Inc. Lys Phe Ser Stop 3

Nonsense Subsititution Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A Met Lys Nucleotide-pair substitution: nonsense A instead of T 3 T A C A T C A 5 A T G T A G T U instead of A 5 A U G U A G U Met © 2014 Pearson Education, Inc. Stop Phe Gly 5 3 A 3 Stop Carboxyl end A A C C G A T T G G C T A A 5 3 U U G G C U A A 3

Nonsense Insertion Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end 5 3 A 3 T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A Met Lys Phe Gly Stop Carboxyl end Nucleotide-pair insertion: frameshift causing immediate nonsense Extra A 3 5 T A C A T T C A A A C C G A T T A T G T A A G T T T G G C T A A 5 3 Extra U 5 A U G U A A G U U U G G C U A A Met © 2014 Pearson Education, Inc. Stop 3

Missense Deletion – Frameshift Mutation Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A A Met Lys Phe Gly 5 3 3 Stop Carboxyl end Nucleotide-pair deletion: frameshift causing extensive missense A 3 5 T A C T T C A A C C G A T T A T G A A G T T G G C T A A U 5 Lys Leu 5 3 missing A U G A A G U U G G C U A A Met © 2014 Pearson Education, Inc. missing Ala 3

Deletion of 3 nucleotides Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A Met Lys Phe Gly Stop Carboxyl end 3 nucleotide-pair deletion: no frameshift, but one amino acid missing T T C missing 3 T A C A A A C C G A T T 5 5 A T G T T T G G C T A A 3 A A G missing 5 A U G U U U G G C U A A 3 Met © 2014 Pearson Education, Inc. Phe Gly Stop 5 3 A 3

Wild type DNA template strand 3 5 m. RNA 5 Protein Amino end T A C T T C A A A C C G A T T A T G A A G T T T G G C T A A A U G A A G U U U G G C U A Met Lys (a) Nucleotide-pair substitution A instead of G 3 5 T A C T T C A A A C C A A T T A T G A A G T T T G G T T A A Gly Phe Stop Carboxyl end (b) Nucleotide-pair insertion or deletion Extra A 5 3 3 5 A U G A A G U U U G G U U A A 3 5 Met Lys Phe T A C A T T C A A A C C G A T T A T G T A A G T T T G G C T A A A U G U A A G U U U G G U U A A Met Gly Stop Frameshift causing immediate nonsense (1 nucleotide-pair insertion) Stop Silent (no effect on amino acid sequence) T instead of C 3 5 A T A C T T C A A A T C G A T T A T G A A G T T T A G C T A A 5 3 3 5 U A U G A A G U U U A G C U A A Met Lys Phe Ser 3 5 Missense T A C A T C A A A C C G A T T A T G T A G T T T G G C T A A T T C A U G U A G U U U G G U U A A Met Nonsense © 2014 Pearson Education, Inc. Ala Stop missing 5 3 3 5 A T G 3 5 A U G U U U G G C U A A U instead of A 5 Leu 3 Frameshift causing extensive missense (1 nucleotide-pair deletion) A instead of T 3 5 Lys 5 3 missing A U G A A G U U G G G U A A Met Stop missing T A C T T C A A C C G A T T A T G A A G T T G G C T A A A instead of G 5 5 3 Extra U U instead of C 5 5 3 A 3 T A C A A A C C G A T T T G G C T A A G Met 5 3 missing Phe Gly 3 Stop No frameshift, but one amino acid missing (3 nucleotide-pair deletion) 3