Chapter 17 From Gene to Protein

What Is a Gene? The idea of the gene has evolved through the history of genetics We have considered a gene as A discrete unit of inheritance A region of specific nucleotide sequence in a chromosome A DNA sequence that codes for a specific polypeptide chain 2

Proteins= link between genotype and phenotype

Flow of Genetic Information DNA= “directions” are encoded in nucleotide sequences Sequences provide information for protein synthesis Gene expression= process by which DNA directs protein synthesis 2 stages: transcription and translation

Flow of Genetic Information Central Dogma Concept that cells are governed by a cellular chain of command: DNA RNA protein RNA= link between genes and the proteins Transcription= synthesis of RNA under the direction of DNA messenger RNA (mRNA) Translation= synthesis of a polypeptide, using information in the mRNA

Flow of Genetic Information DNA RNA Protein

Bacteria Translation can begin before transcription finishes mRNA molecule Eukaryotes Transcription occurs in nucleus Translation occurs in cytoplasm Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA DNA TRANSCRIPTION mRNA Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information. Ribosome TRANSLATION Ribosome TRANSLATION Polypeptide Polypeptide (a) Bacterial cell (b) Eukaryotic cell

Variation in Transcription and Translation Bacteria and eukaryotes differ in.. RNA polymerases Termination of transcription Ribosomes Archaea are prokaryotes, but share many features of gene expression with eukaryotes

Form = Function High diversity of molecules due to arrangement of monomers DNA composed of 4 nucleotides RNA composed of 4 nucleotides 20 amino acids (monomers of proteins)

Form = Function The flow of information from gene to protein is based on a triplet code Nonoverlapping, three-nucleotide codon Codons of a gene are… Transcribed into complementary codons of mRNA Translated into amino acids

First mRNA base (5 end of codon) Third mRNA base (3 end of codon) Second mRNA base U C A G UUU UCU UAU UGU U Phe Tyr Cys UUC UCC UAC UGC C U Ser UUA UCA UAA Stop UGA Stop A Leu UUG UCG UAG Stop UGG Trp G CUU CCU CAU CGU U His CUC CCC CAC CGC C C Leu Pro Arg CUA CCA CAA CGA A Gln CUG CCG CAG CGG G First mRNA base (5 end of codon) Third mRNA base (3 end of codon) AUU ACU AAU AGU U Asn Ser AUC Ile ACC AAC AGC C A Thr Figure 17.5 The codon table for mRNA. AUA ACA AAA AGA A Lys Arg AUG Met or start ACG AAG AGG G GUU GCU GAU GGU U Asp GUC GCC GAC GGC C G Val Ala Gly Gly GUA GCA GAA GGA A Glu GUG GCG GAG GGG G

Cracking the Code All 64 codons were deciphered by the mid-1960s Of the 64 triplets 61 codons represent amino acids 3 codons are “stop” signals Genetic code Redundant 1 amino acid coded by multiple codons Not Ambiguous 1 codon = 1 amino acid 12

Cracking the Code Codons must be read in the correct reading frame 5’ to 3’ direction 5’-AUGCUGGAACCGACCUGA-3’

Evolution of the Genetic Code Genetic code is nearly universal… From unicellular organisms…. ..to multicellular animals 14

Evolution of the Genetic Code Genes can be transcribed and translated after being transplanted from one species to another Tobacco plant expressing firefly gene Pig expressing jellyfish gene 15

Green sea slug expresses algal DNA Green sea slugs (Elysia chlorotica) have functional chloroplasts that carry out photosynthesis Chloroplasts are taken up from food source= algae Algae DNA incorporated into slug DNA

Transcription DNA Occurs in Nucleus RNA made from DNA directions RNA Messenger RNA (mRNA) Only one strand of DNA transcribed Template strand= 3’ to 5’ RNA made in 5’ to 3’ direction RNA

Transcription Enzyme= RNA polymerase DNA Purpose of RNA polymerase RNA Separates DNA strands Links RNA nucleotides together Several dozen nucleotide pairs in length Section of DNA transcribed = transcription unit RNA

Transcription mRNA= complementary to DNA template strand DNA RNA same base-pairing rules as DNA, with one exception Uracil substitutes for thymine Uracil-Adenine Eukaryotes Primary transcript= Initial RNA molecule produced by transcription Additional processing needed to make final mRNA RNA

Transcription: Initiation Promoter= nucleotide sequence signals binding site for RNA polymerase Transcription initiation complex= RNA polymerase II + transcription factors Transcription factors= proteins control translation of a gene by activating or preventing binding of RNA polymerase to promoter site A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes

Several transcription factors bind to DNA Transcription factors Figure 17.8 1 A eukaryotic promoter Promoter Nontemplate strand DNA 5 T A T A A A A 3 3 A T A T T T T 5 TATA box Start point Template strand 2 Several transcription factors bind to DNA Transcription factors 5 3 3 5 3 Transcription initiation complex forms RNA polymerase II Figure 17.8 The initiation of transcription at a eukaryotic promoter. Transcription factors 5 3 3 3 5 5 RNA transcript Transcription initiation complex

Transcription: Elongation RNA polymerase untwists the double helix 10-20 bases at a time Eukaryotes Rate of Transcription= 40 nucleotides/second Nucleotides= added to the 3 end of the growing RNA molecule 22

Nontemplate strand of DNA Figure 17.9 Nontemplate strand of DNA RNA nucleotides RNA polymerase T C C A A A 3 T 5 U C T 3 end T G U A G A C A U C C A C C A 5 A 3 T Figure 17.9 Transcription elongation. A G G T T 5 Direction of transcription Template strand of DNA Newly made RNA

Transcription: Termination Prokaryotes Terminator= nucleotide sequence signaling end of gene, RNA polymerase separates from DNA mRNA does not need additional modification Translation can begin immediately Eukaryotes Polyadenylation signal sequence= RNA transcript released 10–35 nucleotides past this sequence Additional processing needed to convert transcript into functional mRNA molecule Processing occurs before leaves nucleus

Nontemplate strand of DNA 5 3 3 5 Template strand of DNA Figure 17.7-4 Promoter Transcription unit 5 3 3 5 DNA Start point RNA polymerase 1 Initiation Nontemplate strand of DNA 5 3 3 5 Template strand of DNA RNA transcript Unwound DNA 2 Elongation Rewound DNA 5 3 3 3 5 5 Figure 17.7 The stages of transcription: initiation, elongation, and termination. RNA transcript 3 Termination 5 3 3 5 5 3 Completed RNA transcript Direction of transcription (“downstream”)

RNA Processing Enzymes in the eukaryotic nucleus modify RNA transcript before released to cytoplasm Alteration of ends of the primary transcript RNA splicing of interior portions of molecule

RNA Processing Each end of a pre-mRNA molecule is modified in a particular way 5 end= modified nucleotide 5 cap 3 end= poly-A tail Reasons for modifications Facilitate export of mRNA from nucleus Protect mRNA from enzymes in cytoplasm Assist with ribosomal attachment to 5 end

RNA Processing Most eukaryotic genes have introns between coding regions Introns= series of nucleotides in noncoding regions of genes Included in RNA transcripts Exons= coding regions of genes Expressed when translated into amino acid sequences RNA splicing removes introns and joins exons Spliceosomes Ribozymes End product= mRNA molecule with continuous coding sequence

What is the purpose of introns? Sequences may regulate gene expression Genes can encode more than one kind of polypeptide Type of polypeptide depends on which segments are removed during splicing Alternative RNA splicing Advantage= Number of different proteins produced is much greater than its number of genes 29

RNA Processing Spliceosomes= proteins + small nuclear ribonucleoproteins (snRNPs) Recognize splice sites

RNA Processing Ribozymes= catalytic RNA molecules Function as enzymes Splice RNA Discovery changed long-held belief that all biological catalysts were proteins Three properties of RNA enable it to function as an enzyme Form a 3-D structure Base-pair with itself Bases contain functional groups that act as a catalyst Hydrogen-bond with other nucleic acid molecules 31

RNA Processing Final Product 5 Exon Intron Exon Intron Exon 3 Pre-mRNA Codon numbers 5 Cap Poly-A tail 130 31104 105 146 Introns cut out and exons spliced together Final Product mRNA 5 Cap Poly-A tail 1146 5 UTR 3 UTR Figure 17.11 RNA processing: RNA splicing. Coding segment

Flow of Genetic Information DNA RNA Protein Translation Transcription

Transcription Translation Flow of information from DNA to protein is the triplet code of bases mRNA moves out of nucleus and into cytoplasm Ribosomes attach to mRNA and translation begins

Translation Ribosomes “read” code on mRNA to build polypeptide chain Amino acids brought to ribosome by transfer RNA (tRNA) Single RNA strand ~80 nucleotides long RNA Ribosomes Protein

Translation Molecules of tRNA pair with a specific amino acid 3’ End= Amino acid attachment site Anticodon Base-pairs with complementary codon on mRNA Hydrogen bonds give tRNA its 3-D structure L-shaped

Translation Accurate translation requires 2 steps: Match between tRNA and an amino acid Enzyme aminoacyl-tRNA synthetase Match between tRNA anticodon and mRNA codon Wobble= flexible pairing at the third base of a codon Allows some tRNAs to bind to more than one codon

Aminoacyl-tRNA synthetase Figure 17.16-4 Aminoacyl-tRNA synthetase (enzyme) Amino acid P Adenosine P P P Adenosine P P i Aminoacyl-tRNA synthetase ATP P i P tRNA i tRNA Amino acid Figure 17.16 An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA. P Adenosine AMP Computer model Aminoacyl tRNA (“charged tRNA”)

Ribosomes Facilitate specific coupling of tRNA anticodons with mRNA codons Two ribosomal subunits- large and small Proteins and ribosomal RNA (rRNA) 39

Ribosomes Two types of ribosomes Free ribosomes= in the cytosol Bound ribosomes= attached to the endoplasmic reticulum (ER) Both types are identical Switch from free to bound Free ribosomes mostly synthesize proteins that function in the cytosol Bound ribosomes make proteins of the endomembrane system and proteins to be secreted from the cell

Ribosomes Polypeptide synthesis always begins in the cytosol Finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER

Ribosomes Three binding sites for tRNA P site= holds the tRNA with the growing polypeptide chain A site= holds the tRNA with next amino acid to be added E site= exit site

Next amino acid to be added to polypeptide chain Figure 17.17c Growing polypeptide Amino end Next amino acid to be added to polypeptide chain E tRNA mRNA 3 Figure 17.17 The anatomy of a functioning ribosome. Codons 5 (c) Schematic model with mRNA and tRNA

Translation: Initiation Brings together translation initiation complex: mRNA tRNA with first amino acid two ribosomal subunits Small ribosomal subunit binds with mRNA and initial tRNA Small subunit moves along the mRNA to start codon (AUG) Proteins called initiation factors bring in the large subunit 44

Translation: Initiation First tRNA attaches at P site All other tRNA enter at A site

Translation: Elongation Amino acids added one by one to the growing chain Proteins called elongation factors Occurs in three steps Codon recognition Peptide bond formation Translocation Translation proceeds along the mRNA in a 5′ to 3′ direction 46

Amino end of polypeptide Figure 17.19-4 Amino end of polypeptide E 3 mRNA Ribosome ready for next aminoacyl tRNA P site A site 5 GTP GDP  P i E E P A P A Figure 17.19 The elongation cycle of translation. GDP  P i GTP E P A

Translation: Termination Stop codon in the mRNA reaches the A site of the ribosome A site accepts a protein called a release factor Release factor causes the addition of a water molecule instead of amino acid Reaction releases polypeptide Translation assembly separates

Translation Polyribosome: multiple ribosomes translate a single mRNA simultaneously Enable cell to make many copies of a polypeptide very quickly 49

Completed polypeptide Growing polypeptides Incoming ribosomal subunits Polyribosome Start of mRNA (5 end) End of mRNA (3 end) (a) Ribosomes Figure 17.21 Polyribosomes. mRNA (b) 0.1 m

DNA template strand 5 DNA 3 molecule Gene 1 5 3 TRANSCRIPTION mRNA 5 3 Codon TRANSLATION Figure 17.4 The triplet code. Protein Trp Phe Gly Ser Gene 3 Amino acid

Modifications of Proteins During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape After translation, many proteins must undergo modifications before becoming functional Activated by enzymes that cleave them Multiple polypeptide chains come together to form a larger protein

Modifications of Proteins Targeted to specific sites in cell Polypeptides destined for the ER or for secretion are marked by a signal peptide A signal-recognition particle (SRP) binds to the signal peptide Brings the signal peptide and its ribosome to the ER Signal peptide removed and protein enters ER for transport

Effect of Mutations on Proteins Mutations = changes in the genetic material of a cell Can occur during DNA replication, recombination, or repair Mutagens= physical or chemical agents that can cause mutations Point mutations= changes in one base pair of a gene Single change in a DNA template strand can lead to the production of an abnormal protein

Sickle-cell hemoglobin Wild-type hemoglobin Sickle-cell hemoglobin Wild-type hemoglobin DNA Mutant hemoglobin DNA 3 C T T 5 3 C A T 5 5 G A A 3 5 G T A 3 mRNA mRNA 5 G A A 3 5 G U A 3 Figure 17.23 The molecular basis of sickle-cell disease: a point mutation. Normal hemoglobin Sickle-cell hemoglobin Glu Val

Point Mutations Two general categories Nucleotide-pair substitutions One or more nucleotide-pair insertions or deletions

Nucleotide-Pair Substitution Replaces one nucleotide pair with another pair of nucleotides Silent mutations= no effect on the amino acid because of redundancy in the genetic code Missense mutations= codes for incorrect amino acid Nonsense mutations= change an amino acid codon into a stop codon Usually creates nonfunctional protein

(a) Nucleotide-pair substitution: silent Figure 17.24a Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end (a) Nucleotide-pair substitution: silent A instead of G 3 T A C T T C A A A C C A A T T 5 Figure 17.24 Types of small-scale mutations that affect mRNA sequence. 5 A T G A A G T T T G G T T A A 3 U instead of C 5 A U G A A G U U U G G U U A A 3 Met Lys Phe Gly Stop

(a) Nucleotide-pair substitution: missense Figure 17.24b Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end (a) Nucleotide-pair substitution: missense T instead of C 3 T A C T T C A A A T C G A T T 5 Figure 17.24 Types of small-scale mutations that affect mRNA sequence. 5 A T G A A G T T T A G C T A A 3 A instead of G 5 A U G A A G U U U A G C U A A 3 Met Lys Phe Ser Stop

(a) Nucleotide-pair substitution: nonsense Figure 17.24c Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end (a) Nucleotide-pair substitution: nonsense A instead of T T instead of C 3 T A C A T C A A A C C G A T T 5 Figure 17.24 Types of small-scale mutations that affect mRNA sequence. 5 A T G T A G T T T G G C T A A 3 U instead of A 5 A U G U A G U U U G G C U A A 3 Met Stop

Insertions and Deletions Additions or losses of nucleotide pairs in a gene Often has greater negative effect than substitutions Frameshift mutation Missing amino acid (loss of 3 nucleotides) 61

Figure 17.24d Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end (b) Nucleotide-pair insertion or deletion: frameshift causing immediate nonsense Extra A 3 T A C A T T C A A A C G G A T T 5 Figure 17.24 Types of small-scale mutations that affect mRNA sequence. 5 A T G T A A G T T T G G C T A A 3 Extra U 5 A U G U A A G U U U G G C U A A 3 Met Stop 1 nucleotide-pair insertion

Figure 17.24e Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end (b) Nucleotide-pair insertion or deletion: frameshift causing extensive missense A missing 3 T A C T T C A A C C G A T T 5 Figure 17.24 Types of small-scale mutations that affect mRNA sequence. 5 A T G A A G T T G G C T A A 3 U missing 5 A U G A A G U U G G C U A A 3 Met Lys Leu Ala 1 nucleotide-pair deletion

Figure 17.24f Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end (b) Nucleotide-pair insertion or 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 Figure 17.24 Types of small-scale mutations that affect mRNA sequence. 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 Phe Gly Stop 3 nucleotide-pair deletion

Accuracy Transcription less accurate than replication Errors occur 1 in 10000 nucleotides Protein synthesis more tolerant of errors than replication Redundancy of codons for amino acids