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17 - From Gene to Protein

This document provides an overview of the process by which DNA directs protein synthesis through transcription and translation. It discusses the flow of genetic information from DNA to mRNA to protein. Key points include: transcription produces messenger RNA from DNA templates in the nucleus; eukaryotic pre-mRNA is processed before translation; translation occurs in the cytoplasm using tRNA to add amino acids to growing polypeptide chains on ribosomes according to mRNA codons. The genetic code is nearly universal and specifies 20 amino acids using triplets of nucleotides.

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LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson © 2011 Pearson Education, Inc. Lectures by Erin Barley Kathleen Fitzpatrick From Gene to Protein Chapter 17
Overview: The Flow of Genetic Information • The information content of DNA is in the form of specific sequences of nucleotides • The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins • Proteins are the links between genotype and phenotype • Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation © 2011 Pearson Education, Inc.
Basic Principles of Transcription and Translation • RNA is the bridge between genes and the proteins for which they code • Transcription is the synthesis of RNA under the direction of DNA • Transcription produces messenger RNA (mRNA) • Translation is the synthesis of a polypeptide, using information in the mRNA • Ribosomes are the sites of translation © 2011 Pearson Education, Inc.
• In prokaryotes, translation of mRNA can begin before transcription has finished • In a eukaryotic cell, the nuclear envelope separates transcription from translation • Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA • A primary transcript is the initial RNA transcript from any gene prior to processing © 2011 Pearson Education, Inc.
Figure 17.3 DNA mRNA Ribosome Polypeptide TRANSCRIPTION TRANSLATION TRANSCRIPTION TRANSLATION Polypeptide Ribosome DNA mRNA Pre-mRNA RNA PROCESSING (a) Bacterial cell (b) Eukaryotic cell Nuclear envelope
The Genetic Code • How are the instructions for assembling amino acids into proteins encoded into DNA? • There are 20 amino acids, but there are only four nucleotide bases in DNA • How many nucleotides correspond to an amino acid? © 2011 Pearson Education, Inc.
Codons: Triplets of Nucleotides • The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words • The words of a gene are transcribed into complementary nonoverlaping three-nucleotide words of mRNA • These words are then translated into a chain of amino acids, forming a polypeptide © 2011 Pearson Education, Inc.
Figure 17.4 DNA template strand TRANSCRIPTION mRNA TRANSLATION Protein Amino acid Codon Trp Phe Gly 5′ 5′ Ser U U U U U 3′ 3′ 5′3′ G G G G C C T C A A AAAAA T T T T T G G G G C C C G G DNA molecule Gene 1 Gene 2 Gene 3 C C
• During transcription, one of the two DNA strands, called the template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript • The template strand is always the same strand for a given gene • During translation, the mRNA base triplets, called codons, are read in the 5′ to 3′ direction • Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide © 2011 Pearson Education, Inc.
Cracking the Code • All 64 codons were deciphered by the mid-1960s • Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation • The genetic code is redundant (more than one codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acid • Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced © 2011 Pearson Education, Inc.
Figure 17.5 Second mRNA base FirstmRNAbase(5′endofcodon) ThirdmRNAbase(3′endofcodon) UUU UUC UUA CUU CUC CUA CUG Phe Leu Leu Ile UCU UCC UCA UCG Ser CCU CCC CCA CCG UAU UAC Tyr Pro Thr UAA Stop UAG Stop UGA Stop UGU UGC Cys UGG Trp GC U U C A U U C C C A U A A A G G His Gln Asn Lys Asp CAU CGU CAC CAA CAG CGC CGA CGG G AUU AUC AUA ACU ACC ACA AAU AAC AAA AGU AGC AGA Arg Ser Arg Gly ACGAUG AAG AGG GUU GUC GUA GUG GCU GCC GCA GCG GAU GAC GAA GAG Val Ala GGU GGC GGA GGG Glu Gly G U C A Met or start UUG G
Evolution of the Genetic Code • The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals • Genes can be transcribed and translated after being transplanted from one species to another © 2011 Pearson Education, Inc.
Figure 17.6 (a) Tobacco plant expressing a firefly gene gene (b) Pig expressing a jellyfish
13-15
Molecular Components of Transcription • RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides • The RNA is complementary to the DNA template strand • RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine © 2011 Pearson Education, Inc.
• The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator • The stretch of DNA that is transcribed is called a transcription unit © 2011 Pearson Education, Inc.
Figure 17.7-4 Promoter RNA polymerase Start point DNA 5′ 3′ Transcription unit 3′ 5′ Elongation 5′ 3′ 3′ 5′ Nontemplate strand of DNA Template strand of DNA RNA transcript Unwound DNA 2 3′ 5′3′ 5′ 3′ Rewound DNA RNA transcript 5′ Termination3 3′ 5′ 5′ Completed RNA transcript Direction of transcription (“downstream”) 5′ 3′ 3′ Initiation1
Synthesis of an RNA Transcript • The three stages of transcription – Initiation – Elongation – Termination © 2011 Pearson Education, Inc.
RNA Polymerase Binding and Initiation of Transcription • Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point • Transcription factors mediate the binding of RNA polymerase and the initiation of transcription • The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex • A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes © 2011 Pearson Education, Inc.
Figure 17.8 Transcription initiation complex forms 3 DNA Promoter Nontemplate strand 5′ 3′ 5′ 3′ 5′ 3′ Transcription factors RNA polymerase II Transcription factors 5′ 3′ 5′ 3′ 5′ 3′ RNA transcript Transcription initiation complex 5′ 3′ TATA box T T T T T T A AA AA A A T Several transcription factors bind to DNA 2 A eukaryotic promoter1 Start point Template strand
Elongation of the RNA Strand • As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time • Transcription progresses at a rate of 40 nucleotides per second in eukaryotes • A gene can be transcribed simultaneously by several RNA polymerases • Nucleotides are added to the 3′ end of the growing RNA molecule © 2011 Pearson Education, Inc.
Nontemplate strand of DNA RNA nucleotides RNA polymerase Template strand of DNA 3′ 3′5′ 5′ 5′ 3′ Newly made RNA Direction of transcription A A A A A A A T T T T TTT G G G C C C C C G C CC A A A U U U end Figure 17.9
Termination of Transcription • The mechanisms of termination are different in bacteria and eukaryotes • In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification • In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence that codes for a polyadenylation signal (AAUAAA); the RNA transcript is cut free by proteins about 10–35 nucleotides past this polyadenylation signal © 2011 Pearson Education, Inc.
Eukaryotic cells modify RNA after transcription • Enzymes in the eukaryotic nucleus modify pre- mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm • During RNA processing, both ends of the primary transcript are usually altered • Also, usually some interior parts of the molecule are cut out, and the other parts spliced together © 2011 Pearson Education, Inc.
Alteration of mRNA Ends • Each end of a pre-mRNA molecule is modified in a particular way – The 5′ end receives a modified nucleotide 5′ cap – The 3′ end gets a poly-A tail • These modifications share several functions – They seem to facilitate the export of mRNA – They protect mRNA from hydrolytic enzymes – They help ribosomes attach to the 5′ end © 2011 Pearson Education, Inc.
Figure 17.10 Protein-coding segment Polyadenylation signal 5′ 3′ 3′5′ 5′Cap UTR Start codon G P P P Stop codon UTR AAUAAA Poly-A tail AAA AAA…
Split Genes and RNA Splicing • Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions • These noncoding regions are called intervening sequences, or introns • The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences • RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence © 2011 Pearson Education, Inc.
Figure 17.11 5′ Exon Intron Exon 5′ CapPre-mRNA Codon numbers 1−30 31−104 mRNA 5′Cap 5′ Intron Exon 3′ UTR Introns cut out and exons spliced together 3′ 105− 146 Poly-A tail Coding segment Poly-A tail UTR 1−146
• In some cases, RNA splicing is carried out by spliceosomes • Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites © 2011 Pearson Education, Inc.
Figure 17.12-3 RNA transcript (pre-mRNA) 5′ Exon 1 Protein snRNA snRNPs Intron Exon 2 Other proteins Spliceosome 5′ Spliceosome components Cut-out intronmRNA 5′ Exon 1 Exon 2
Ribozymes • Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNA • The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins © 2011 Pearson Education, Inc.
• Three properties of RNA enable it to function as an enzyme – It can form a three-dimensional structure because of its ability to base-pair with itself – Some bases in RNA contain functional groups that may participate in catalysis – RNA may hydrogen-bond with other nucleic acid molecules © 2011 Pearson Education, Inc.
The Functional and Evolutionary Importance of Introns • Some introns contain sequences that may regulate gene expression • Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing • This is called alternative RNA splicing • Consequently, the number of different proteins an organism can produce is much greater than its number of genes © 2011 Pearson Education, Inc.
• Proteins often have a modular architecture consisting of discrete regions called domains • In many cases, different exons code for the different domains in a protein • Exon shuffling may result in the evolution of new proteins © 2011 Pearson Education, Inc.
Gene DNA Exon 1 Exon 2 Exon 3Intron Intron Transcription RNA processing Translation Domain 3 Domain 2 Domain 1 Polypeptide Figure 17.13
Concept 17.4: Translation is the RNA- directed synthesis of a polypeptide: a closer look • Genetic information flows from mRNA to protein through the process of translation © 2011 Pearson Education, Inc.
Molecular Components of Translation • A cell translates an mRNA message into protein with the help of transfer RNA (tRNA) • tRNAs transfer amino acids to the growing polypeptide in a ribosome • Translation is a complex process in terms of its biochemistry and mechanics © 2011 Pearson Education, Inc.
Figure 17.14 Polypeptide Ribosome Trp Phe Gly tRNA with amino acid attached Amino acids tRNA Anticodon Codons U U U UG G G G C A C C C C G A A A C G C G 5′ 3′ mRNA
The Structure and Function of Transfer RNA • Molecules of tRNA are not identical – Each carries a specific amino acid on one end – Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA © 2011 Pearson Education, Inc.
• A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long • Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf • Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule • tRNA is roughly L-shaped © 2011 Pearson Education, Inc.
Figure 17.15 Amino acid attachment site 3′ 5′ Hydrogen bonds Anticodon (a) Two-dimensional structure (b) Three-dimensional structure (c) Symbol used in this book Anticodon Anticodon 3′ 5′ Hydrogen bonds Amino acid attachment site5′ 3′ A A G
• Accurate translation requires two steps – First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase – Second: a correct match between the tRNA anticodon and an mRNA codon • Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon © 2011 Pearson Education, Inc.
Aminoacyl-tRNA synthetase (enzyme) Amino acid P P P Adenosine ATP P P P P Pi i i Adenosine tRNA AdenosineP tRNA AMP Computer model Amino acid Aminoacyl-tRNA synthetase Aminoacyl tRNA (“charged tRNA”) Figure 17.16-4
Ribosomes • Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis • The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA) • Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences: some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes © 2011 Pearson Education, Inc.
tRNA molecules Growing polypeptide Exit tunnel E P A Large subunit Small subunit mRNA 5′ 3′ (a) Computer model of functioning ribosome Exit tunnel Amino end A site (Aminoacyl- tRNA binding site) Small subunit Large subunit E P A mRNA E P site (Peptidyl-tRNA binding site) mRNA binding site (b) Schematic model showing binding sites E site (Exit site) (c) Schematic model with mRNA and tRNA 5′ Codons 3′ tRNA Growing polypeptide Next amino acid to be added to polypeptide chain Figure 17.17
• A ribosome has three binding sites for tRNA – The P site holds the tRNA that carries the growing polypeptide chain – The A site holds the tRNA that carries the next amino acid to be added to the chain – The E site is the exit site, where discharged tRNAs leave the ribosome © 2011 Pearson Education, Inc.
Building a Polypeptide • The three stages of translation – Initiation – Elongation – Termination • All three stages require protein “factors” that aid in the translation process © 2011 Pearson Education, Inc.
Ribosome Association and Initiation of Translation • The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits • First, a small ribosomal subunit binds with mRNA and a special initiator tRNA • Then the small subunit moves along the mRNA until it reaches the start codon (AUG) • Proteins called initiation factors bring in the large subunit that completes the translation initiation complex © 2011 Pearson Education, Inc.
Figure 17.18 Initiator tRNA mRNA 5′ 5′ 3′ Start codon Small ribosomal subunit mRNA binding site 3′ Translation initiation complex 5′ 3′ 3′ U U A A G C P P site i + GTP GDP Met Met Large ribosomal subunit E A 5′
Elongation of the Polypeptide Chain • During the elongation stage, amino acids are added one by one to the preceding amino acid at the C-terminus of the growing chain • Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation • Translation proceeds along the mRNA in a 5′ to 3′ direction © 2011 Pearson Education, Inc.
Amino end of polypeptide mRNA 5′ E A site 3′ E GTP GDP + P i P A E P A GTP GDP + P i P A E Ribosome ready for next aminoacyl tRNA P site Figure 17.19-4
Termination of Translation • Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome • The A site accepts a protein called a release factor • The release factor causes the addition of a water molecule instead of an amino acid • This reaction releases the polypeptide, and the translation assembly then comes apart © 2011 Pearson Education, Inc.
Figure 17.20-3 Release factor Stop codon (UAG, UAA, or UGA) 3′ 5′ 3′ 5′ Free polypeptide 2 GTP 5′ 3′ 2 GDP + 2 iP When a ribosome reaches a stop codon on mRNA, the A site of the ribosome accepts a protein called a release factor instead of tRNA. The release factor hydrolyzes the bond between the tRNA in the P site and the last amino acid of the polypeptide chain. The polypeptide is thus freed from the ribosome. The two ribosomal subunits and the other components of the assembly dissociate.
Polyribosomes • A number of ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome) • Polyribosomes enable a cell to make many copies of a polypeptide very quickly © 2011 Pearson Education, Inc.
Figure 17.21 Completed polypeptide Incoming ribosomal subunits Start of mRNA (5′ end) End of mRNA (3′ end)(a) Polyribosome Ribosomes mRNA (b) 0.1 µm Growing polypeptides
Completing and Targeting the Functional Protein • Often translation is not sufficient to make a functional protein • Polypeptide chains are modified after translation or targeted to specific sites in the cell © 2011 Pearson Education, Inc.
Protein Folding and Post-Translational Modifications • During and after synthesis, a polypeptide chain spontaneously coils and folds into its three- dimensional shape • Proteins may also require post-translational modifications before doing their job • Some polypeptides are activated by enzymes that cleave them • Other polypeptides come together to form the subunits of a protein © 2011 Pearson Education, Inc.
Targeting Polypeptides to Specific Locations • Two populations of ribosomes are evident in cells: free ribsomes (in the cytosol) and bound ribosomes (attached to the ER) • Free ribosomes mostly synthesize proteins that function in the cytosol • Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell • Ribosomes are identical and can switch from free to bound © 2011 Pearson Education, Inc.
• Polypeptide synthesis always begins in the cytosol • Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER • Polypeptides destined for the ER or for secretion are marked by a signal peptide • A signal-recognition particle (SRP) binds to the signal peptide • The SRP brings the signal peptide and its ribosome to the ER © 2011 Pearson Education, Inc.
Figure 17.22 Ribosome mRNA Signal peptide SRP 1 SRP receptor protein Translocation complex ER LUMEN 2 3 4 5 6 Signal peptide removed CYTOSOL Protein ER membrane
Mutations of one or a few nucleotides can affect protein structure and function • Mutations are changes in the genetic material of a cell or virus • Point mutations are chemical changes in just one base pair of a gene • The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein © 2011 Pearson Education, Inc.
Figure 17.23 Wild-type hemoglobin Wild-type hemoglobin DNA 3′ 3′ 3′5′ 5′ 3′ 3′5′ 5′ 5′5′3′ mRNA A AG C T T A AG mRNA Normal hemoglobin Glu Sickle-cell hemoglobin Val A A AUG G T T Sickle-cell hemoglobin Mutant hemoglobin DNA C
Types of Small-Scale Mutations • Point mutations within a gene can be divided into two general categories – Nucleotide-pair substitutions – One or more nucleotide-pair insertions or deletions © 2011 Pearson Education, Inc.
Substitutions • A nucleotide-pair substitution replaces one nucleotide and its partner with another pair of nucleotides • Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code • Missense mutations still code for an amino acid, but not the correct amino acid • Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein © 2011 Pearson Education, Inc.
Insertions and Deletions • Insertions and deletions are additions or losses of nucleotide pairs in a gene • These mutations have a disastrous effect on the resulting protein more often than substitutions do • Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation © 2011 Pearson Education, Inc.
Wild type DNA template strand mRNA5′ 5′ 3′ Protein Amino end A instead of G (a) Nucleotide-pair substitution 3′ 3′ 5′ Met Lys Phe Gly Stop Carboxyl end T T T T T TTTTTA A A A A AAAACC C C A A A A A A G G G G GC C G GGU U U U UG (b) Nucleotide-pair insertion or deletion Extra A 3′ 5′ 5′ 3′ Extra U 5′ 3′ T T T T T T T T A A A A A AT G G G G GAAA AC CCCC A T3′5′ 5′ 3′ 5′T T T T TAAAACCA AC C TTTTTA A A A ATG G G G U instead of C Stop UA A A A AG GGU U U U UG MetLys Phe Gly Silent (no effect on amino acid sequence) T instead of C T T T T TAAAACCA GT C T A T T TAAAACCA GC C A instead of G CA A A A AG AGU U U U UG UA A A AG GGU U U G AC AA U U A AU UGU G G C UA GA U A U AA UGU G U U CG Met Lys Phe Ser Stop Stop Met Lys missing missing Frameshift causing immediate nonsense (1 nucleotide-pair insertion) Frameshift causing extensive missense (1 nucleotide-pair deletion) missing T T T T TTCAACCA AC G AGTTTA A A A ATG G G C Leu Ala Missense A instead of T TTTTTA A A A ACG G A G A CA U A A AG GGU U U U UG TTTTTA T A A ACG G G G Met Nonsense Stop U instead of A 3′ 5′ 3′5′ 5′ 3′ 3′ 5′ 5′ 3′ 3′5′ 3′ Met Phe Gly No frameshift, but one amino acid missing (3 nucleotide-pair deletion) missing 3′ 5′ 5′ 3′ 5′ 3′ U T CA AA CA TTAC G TA G T T T G G A ATC T T C A A G Met 3′ T A Stop 3′ 5′ 5′ 3′ 5′ 3′ Figure 17.24
Mutagens • Spontaneous mutations can occur during DNA replication, recombination, or repair • Mutagens are physical or chemical agents that can cause mutations © 2011 Pearson Education, Inc.
What Is a Gene? Revisiting the Question • 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 © 2011 Pearson Education, Inc.
Figure 17.26 TRANSCRIPTION DNA RNA polymerase Exon RNA transcript RNA PROCESSING NUCLEUS Intron RNA transcript (pre-mRNA) Poly-A Poly-A Aminoacyl- tRNA synthetase AMINO ACID ACTIVATION Amino acid tRNA 5′C ap Poly-A 3′ Growing polypeptidemRNA Aminoacyl (charged) tRNA Anticodon Ribosomal subunits A AE TRANSLATION 5′ Cap CYTOPLASM P E Codon Ribosome 5′ 3′
• In summary, a gene can be defined as a region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule © 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.

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17 - From Gene to Protein

  • 1.
    LECTURE PRESENTATIONS For CAMPBELLBIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson © 2011 Pearson Education, Inc. Lectures by Erin Barley Kathleen Fitzpatrick From Gene to Protein Chapter 17
  • 2.
    Overview: The Flowof Genetic Information • The information content of DNA is in the form of specific sequences of nucleotides • The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins • Proteins are the links between genotype and phenotype • Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation © 2011 Pearson Education, Inc.
  • 3.
    Basic Principles ofTranscription and Translation • RNA is the bridge between genes and the proteins for which they code • Transcription is the synthesis of RNA under the direction of DNA • Transcription produces messenger RNA (mRNA) • Translation is the synthesis of a polypeptide, using information in the mRNA • Ribosomes are the sites of translation © 2011 Pearson Education, Inc.
  • 4.
    • In prokaryotes,translation of mRNA can begin before transcription has finished • In a eukaryotic cell, the nuclear envelope separates transcription from translation • Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA • A primary transcript is the initial RNA transcript from any gene prior to processing © 2011 Pearson Education, Inc.
  • 5.
  • 6.
    The Genetic Code •How are the instructions for assembling amino acids into proteins encoded into DNA? • There are 20 amino acids, but there are only four nucleotide bases in DNA • How many nucleotides correspond to an amino acid? © 2011 Pearson Education, Inc.
  • 7.
    Codons: Triplets ofNucleotides • The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words • The words of a gene are transcribed into complementary nonoverlaping three-nucleotide words of mRNA • These words are then translated into a chain of amino acids, forming a polypeptide © 2011 Pearson Education, Inc.
  • 8.
    Figure 17.4 DNA template strand TRANSCRIPTION mRNA TRANSLATION Protein Amino acid Codon TrpPhe Gly 5′ 5′ Ser U U U U U 3′ 3′ 5′3′ G G G G C C T C A A AAAAA T T T T T G G G G C C C G G DNA molecule Gene 1 Gene 2 Gene 3 C C
  • 9.
    • During transcription,one of the two DNA strands, called the template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript • The template strand is always the same strand for a given gene • During translation, the mRNA base triplets, called codons, are read in the 5′ to 3′ direction • Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide © 2011 Pearson Education, Inc.
  • 10.
    Cracking the Code •All 64 codons were deciphered by the mid-1960s • Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation • The genetic code is redundant (more than one codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acid • Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced © 2011 Pearson Education, Inc.
  • 11.
    Figure 17.5 Second mRNAbase FirstmRNAbase(5′endofcodon) ThirdmRNAbase(3′endofcodon) UUU UUC UUA CUU CUC CUA CUG Phe Leu Leu Ile UCU UCC UCA UCG Ser CCU CCC CCA CCG UAU UAC Tyr Pro Thr UAA Stop UAG Stop UGA Stop UGU UGC Cys UGG Trp GC U U C A U U C C C A U A A A G G His Gln Asn Lys Asp CAU CGU CAC CAA CAG CGC CGA CGG G AUU AUC AUA ACU ACC ACA AAU AAC AAA AGU AGC AGA Arg Ser Arg Gly ACGAUG AAG AGG GUU GUC GUA GUG GCU GCC GCA GCG GAU GAC GAA GAG Val Ala GGU GGC GGA GGG Glu Gly G U C A Met or start UUG G
  • 12.
    Evolution of theGenetic Code • The genetic code is nearly universal, shared by the simplest bacteria to the most complex animals • Genes can be transcribed and translated after being transplanted from one species to another © 2011 Pearson Education, Inc.
  • 13.
    Figure 17.6 (a) Tobaccoplant expressing a firefly gene gene (b) Pig expressing a jellyfish
  • 14.
  • 15.
    Molecular Components ofTranscription • RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides • The RNA is complementary to the DNA template strand • RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine © 2011 Pearson Education, Inc.
  • 16.
    • The DNAsequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator • The stretch of DNA that is transcribed is called a transcription unit © 2011 Pearson Education, Inc.
  • 17.
    Figure 17.7-4 Promoter RNApolymerase Start point DNA 5′ 3′ Transcription unit 3′ 5′ Elongation 5′ 3′ 3′ 5′ Nontemplate strand of DNA Template strand of DNA RNA transcript Unwound DNA 2 3′ 5′3′ 5′ 3′ Rewound DNA RNA transcript 5′ Termination3 3′ 5′ 5′ Completed RNA transcript Direction of transcription (“downstream”) 5′ 3′ 3′ Initiation1
  • 18.
    Synthesis of anRNA Transcript • The three stages of transcription – Initiation – Elongation – Termination © 2011 Pearson Education, Inc.
  • 19.
    RNA Polymerase Bindingand Initiation of Transcription • Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point • Transcription factors mediate the binding of RNA polymerase and the initiation of transcription • The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex • A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes © 2011 Pearson Education, Inc.
  • 20.
    Figure 17.8 Transcription initiation complexforms 3 DNA Promoter Nontemplate strand 5′ 3′ 5′ 3′ 5′ 3′ Transcription factors RNA polymerase II Transcription factors 5′ 3′ 5′ 3′ 5′ 3′ RNA transcript Transcription initiation complex 5′ 3′ TATA box T T T T T T A AA AA A A T Several transcription factors bind to DNA 2 A eukaryotic promoter1 Start point Template strand
  • 21.
    Elongation of theRNA Strand • As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time • Transcription progresses at a rate of 40 nucleotides per second in eukaryotes • A gene can be transcribed simultaneously by several RNA polymerases • Nucleotides are added to the 3′ end of the growing RNA molecule © 2011 Pearson Education, Inc.
  • 22.
    Nontemplate strand of DNA RNAnucleotides RNA polymerase Template strand of DNA 3′ 3′5′ 5′ 5′ 3′ Newly made RNA Direction of transcription A A A A A A A T T T T TTT G G G C C C C C G C CC A A A U U U end Figure 17.9
  • 23.
    Termination of Transcription •The mechanisms of termination are different in bacteria and eukaryotes • In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification • In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence that codes for a polyadenylation signal (AAUAAA); the RNA transcript is cut free by proteins about 10–35 nucleotides past this polyadenylation signal © 2011 Pearson Education, Inc.
  • 24.
    Eukaryotic cells modifyRNA after transcription • Enzymes in the eukaryotic nucleus modify pre- mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm • During RNA processing, both ends of the primary transcript are usually altered • Also, usually some interior parts of the molecule are cut out, and the other parts spliced together © 2011 Pearson Education, Inc.
  • 25.
    Alteration of mRNAEnds • Each end of a pre-mRNA molecule is modified in a particular way – The 5′ end receives a modified nucleotide 5′ cap – The 3′ end gets a poly-A tail • These modifications share several functions – They seem to facilitate the export of mRNA – They protect mRNA from hydrolytic enzymes – They help ribosomes attach to the 5′ end © 2011 Pearson Education, Inc.
  • 26.
    Figure 17.10 Protein-coding segment Polyadenylation signal 5′ 3′ 3′5′5′Cap UTR Start codon G P P P Stop codon UTR AAUAAA Poly-A tail AAA AAA…
  • 27.
    Split Genes andRNA Splicing • Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions • These noncoding regions are called intervening sequences, or introns • The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences • RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence © 2011 Pearson Education, Inc.
  • 28.
    Figure 17.11 5′ ExonIntron Exon 5′ CapPre-mRNA Codon numbers 1−30 31−104 mRNA 5′Cap 5′ Intron Exon 3′ UTR Introns cut out and exons spliced together 3′ 105− 146 Poly-A tail Coding segment Poly-A tail UTR 1−146
  • 29.
    • In somecases, RNA splicing is carried out by spliceosomes • Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites © 2011 Pearson Education, Inc.
  • 30.
    Figure 17.12-3 RNA transcript(pre-mRNA) 5′ Exon 1 Protein snRNA snRNPs Intron Exon 2 Other proteins Spliceosome 5′ Spliceosome components Cut-out intronmRNA 5′ Exon 1 Exon 2
  • 31.
    Ribozymes • Ribozymes arecatalytic RNA molecules that function as enzymes and can splice RNA • The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins © 2011 Pearson Education, Inc.
  • 32.
    • Three propertiesof RNA enable it to function as an enzyme – It can form a three-dimensional structure because of its ability to base-pair with itself – Some bases in RNA contain functional groups that may participate in catalysis – RNA may hydrogen-bond with other nucleic acid molecules © 2011 Pearson Education, Inc.
  • 33.
    The Functional andEvolutionary Importance of Introns • Some introns contain sequences that may regulate gene expression • Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing • This is called alternative RNA splicing • Consequently, the number of different proteins an organism can produce is much greater than its number of genes © 2011 Pearson Education, Inc.
  • 34.
    • Proteins oftenhave a modular architecture consisting of discrete regions called domains • In many cases, different exons code for the different domains in a protein • Exon shuffling may result in the evolution of new proteins © 2011 Pearson Education, Inc.
  • 35.
    Gene DNA Exon 1 Exon2 Exon 3Intron Intron Transcription RNA processing Translation Domain 3 Domain 2 Domain 1 Polypeptide Figure 17.13
  • 36.
    Concept 17.4: Translationis the RNA- directed synthesis of a polypeptide: a closer look • Genetic information flows from mRNA to protein through the process of translation © 2011 Pearson Education, Inc.
  • 37.
    Molecular Components ofTranslation • A cell translates an mRNA message into protein with the help of transfer RNA (tRNA) • tRNAs transfer amino acids to the growing polypeptide in a ribosome • Translation is a complex process in terms of its biochemistry and mechanics © 2011 Pearson Education, Inc.
  • 38.
    Figure 17.14 Polypeptide Ribosome Trp Phe Gly tRNAwith amino acid attached Amino acids tRNA Anticodon Codons U U U UG G G G C A C C C C G A A A C G C G 5′ 3′ mRNA
  • 39.
    The Structure andFunction of Transfer RNA • Molecules of tRNA are not identical – Each carries a specific amino acid on one end – Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA © 2011 Pearson Education, Inc.
  • 40.
    • A tRNAmolecule consists of a single RNA strand that is only about 80 nucleotides long • Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf • Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule • tRNA is roughly L-shaped © 2011 Pearson Education, Inc.
  • 41.
    Figure 17.15 Amino acid attachment site 3′ 5′ Hydrogen bonds Anticodon (a)Two-dimensional structure (b) Three-dimensional structure (c) Symbol used in this book Anticodon Anticodon 3′ 5′ Hydrogen bonds Amino acid attachment site5′ 3′ A A G
  • 42.
    • Accurate translationrequires two steps – First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase – Second: a correct match between the tRNA anticodon and an mRNA codon • Flexible pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon © 2011 Pearson Education, Inc.
  • 43.
    Aminoacyl-tRNA synthetase (enzyme) Amino acid PP P Adenosine ATP P P P P Pi i i Adenosine tRNA AdenosineP tRNA AMP Computer model Amino acid Aminoacyl-tRNA synthetase Aminoacyl tRNA (“charged tRNA”) Figure 17.16-4
  • 44.
    Ribosomes • Ribosomes facilitatespecific coupling of tRNA anticodons with mRNA codons in protein synthesis • The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA) • Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences: some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes © 2011 Pearson Education, Inc.
  • 45.
    tRNA molecules Growing polypeptide Exit tunnel EP A Large subunit Small subunit mRNA 5′ 3′ (a) Computer model of functioning ribosome Exit tunnel Amino end A site (Aminoacyl- tRNA binding site) Small subunit Large subunit E P A mRNA E P site (Peptidyl-tRNA binding site) mRNA binding site (b) Schematic model showing binding sites E site (Exit site) (c) Schematic model with mRNA and tRNA 5′ Codons 3′ tRNA Growing polypeptide Next amino acid to be added to polypeptide chain Figure 17.17
  • 46.
    • A ribosomehas three binding sites for tRNA – The P site holds the tRNA that carries the growing polypeptide chain – The A site holds the tRNA that carries the next amino acid to be added to the chain – The E site is the exit site, where discharged tRNAs leave the ribosome © 2011 Pearson Education, Inc.
  • 47.
    Building a Polypeptide •The three stages of translation – Initiation – Elongation – Termination • All three stages require protein “factors” that aid in the translation process © 2011 Pearson Education, Inc.
  • 48.
    Ribosome Association andInitiation of Translation • The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits • First, a small ribosomal subunit binds with mRNA and a special initiator tRNA • Then the small subunit moves along the mRNA until it reaches the start codon (AUG) • Proteins called initiation factors bring in the large subunit that completes the translation initiation complex © 2011 Pearson Education, Inc.
  • 49.
    Figure 17.18 Initiator tRNA mRNA 5′ 5′ 3′ Start codon Small ribosomal subunit mRNAbinding site 3′ Translation initiation complex 5′ 3′ 3′ U U A A G C P P site i + GTP GDP Met Met Large ribosomal subunit E A 5′
  • 50.
    Elongation of thePolypeptide Chain • During the elongation stage, amino acids are added one by one to the preceding amino acid at the C-terminus of the growing chain • Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation • Translation proceeds along the mRNA in a 5′ to 3′ direction © 2011 Pearson Education, Inc.
  • 51.
    Amino end of polypeptide mRNA 5′ E A site 3′ E GTP GDP+ P i P A E P A GTP GDP + P i P A E Ribosome ready for next aminoacyl tRNA P site Figure 17.19-4
  • 52.
    Termination of Translation •Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome • The A site accepts a protein called a release factor • The release factor causes the addition of a water molecule instead of an amino acid • This reaction releases the polypeptide, and the translation assembly then comes apart © 2011 Pearson Education, Inc.
  • 53.
    Figure 17.20-3 Release factor Stop codon (UAG,UAA, or UGA) 3′ 5′ 3′ 5′ Free polypeptide 2 GTP 5′ 3′ 2 GDP + 2 iP When a ribosome reaches a stop codon on mRNA, the A site of the ribosome accepts a protein called a release factor instead of tRNA. The release factor hydrolyzes the bond between the tRNA in the P site and the last amino acid of the polypeptide chain. The polypeptide is thus freed from the ribosome. The two ribosomal subunits and the other components of the assembly dissociate.
  • 54.
    Polyribosomes • A numberof ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome) • Polyribosomes enable a cell to make many copies of a polypeptide very quickly © 2011 Pearson Education, Inc.
  • 55.
    Figure 17.21 Completed polypeptide Incoming ribosomal subunits Start of mRNA (5′end) End of mRNA (3′ end)(a) Polyribosome Ribosomes mRNA (b) 0.1 µm Growing polypeptides
  • 56.
    Completing and Targetingthe Functional Protein • Often translation is not sufficient to make a functional protein • Polypeptide chains are modified after translation or targeted to specific sites in the cell © 2011 Pearson Education, Inc.
  • 57.
    Protein Folding andPost-Translational Modifications • During and after synthesis, a polypeptide chain spontaneously coils and folds into its three- dimensional shape • Proteins may also require post-translational modifications before doing their job • Some polypeptides are activated by enzymes that cleave them • Other polypeptides come together to form the subunits of a protein © 2011 Pearson Education, Inc.
  • 58.
    Targeting Polypeptides toSpecific Locations • Two populations of ribosomes are evident in cells: free ribsomes (in the cytosol) and bound ribosomes (attached to the ER) • Free ribosomes mostly synthesize proteins that function in the cytosol • Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell • Ribosomes are identical and can switch from free to bound © 2011 Pearson Education, Inc.
  • 59.
    • Polypeptide synthesisalways begins in the cytosol • Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER • Polypeptides destined for the ER or for secretion are marked by a signal peptide • A signal-recognition particle (SRP) binds to the signal peptide • The SRP brings the signal peptide and its ribosome to the ER © 2011 Pearson Education, Inc.
  • 60.
  • 61.
    Mutations of oneor a few nucleotides can affect protein structure and function • Mutations are changes in the genetic material of a cell or virus • Point mutations are chemical changes in just one base pair of a gene • The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein © 2011 Pearson Education, Inc.
  • 62.
    Figure 17.23 Wild-type hemoglobin Wild-typehemoglobin DNA 3′ 3′ 3′5′ 5′ 3′ 3′5′ 5′ 5′5′3′ mRNA A AG C T T A AG mRNA Normal hemoglobin Glu Sickle-cell hemoglobin Val A A AUG G T T Sickle-cell hemoglobin Mutant hemoglobin DNA C
  • 63.
    Types of Small-ScaleMutations • Point mutations within a gene can be divided into two general categories – Nucleotide-pair substitutions – One or more nucleotide-pair insertions or deletions © 2011 Pearson Education, Inc.
  • 64.
    Substitutions • A nucleotide-pairsubstitution replaces one nucleotide and its partner with another pair of nucleotides • Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code • Missense mutations still code for an amino acid, but not the correct amino acid • Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein © 2011 Pearson Education, Inc.
  • 65.
    Insertions and Deletions •Insertions and deletions are additions or losses of nucleotide pairs in a gene • These mutations have a disastrous effect on the resulting protein more often than substitutions do • Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation © 2011 Pearson Education, Inc.
  • 66.
    Wild type DNA templatestrand mRNA5′ 5′ 3′ Protein Amino end A instead of G (a) Nucleotide-pair substitution 3′ 3′ 5′ Met Lys Phe Gly Stop Carboxyl end T T T T T TTTTTA A A A A AAAACC C C A A A A A A G G G G GC C G GGU U U U UG (b) Nucleotide-pair insertion or deletion Extra A 3′ 5′ 5′ 3′ Extra U 5′ 3′ T T T T T T T T A A A A A AT G G G G GAAA AC CCCC A T3′5′ 5′ 3′ 5′T T T T TAAAACCA AC C TTTTTA A A A ATG G G G U instead of C Stop UA A A A AG GGU U U U UG MetLys Phe Gly Silent (no effect on amino acid sequence) T instead of C T T T T TAAAACCA GT C T A T T TAAAACCA GC C A instead of G CA A A A AG AGU U U U UG UA A A AG GGU U U G AC AA U U A AU UGU G G C UA GA U A U AA UGU G U U CG Met Lys Phe Ser Stop Stop Met Lys missing missing Frameshift causing immediate nonsense (1 nucleotide-pair insertion) Frameshift causing extensive missense (1 nucleotide-pair deletion) missing T T T T TTCAACCA AC G AGTTTA A A A ATG G G C Leu Ala Missense A instead of T TTTTTA A A A ACG G A G A CA U A A AG GGU U U U UG TTTTTA T A A ACG G G G Met Nonsense Stop U instead of A 3′ 5′ 3′5′ 5′ 3′ 3′ 5′ 5′ 3′ 3′5′ 3′ Met Phe Gly No frameshift, but one amino acid missing (3 nucleotide-pair deletion) missing 3′ 5′ 5′ 3′ 5′ 3′ U T CA AA CA TTAC G TA G T T T G G A ATC T T C A A G Met 3′ T A Stop 3′ 5′ 5′ 3′ 5′ 3′ Figure 17.24
  • 67.
    Mutagens • Spontaneous mutationscan occur during DNA replication, recombination, or repair • Mutagens are physical or chemical agents that can cause mutations © 2011 Pearson Education, Inc.
  • 68.
    What Is aGene? Revisiting the Question • 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 © 2011 Pearson Education, Inc.
  • 69.
    Figure 17.26 TRANSCRIPTION DNA RNA polymerase Exon RNA transcript RNA PROCESSING NUCLEUS Intron RNA transcript (pre-mRNA) Poly-A Poly-A Aminoacyl- tRNAsynthetase AMINO ACID ACTIVATION Amino acid tRNA 5′C ap Poly-A 3′ Growing polypeptidemRNA Aminoacyl (charged) tRNA Anticodon Ribosomal subunits A AE TRANSLATION 5′ Cap CYTOPLASM P E Codon Ribosome 5′ 3′
  • 70.
    • In summary,a gene can be defined as a region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule © 2011 Pearson Education, Inc.© 2011 Pearson Education, Inc.

Editor's Notes

  • #6 Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information.
  • #9 Figure 17.4 The triplet code.
  • #12 Figure 17.5 The codon table for mRNA.
  • #14 Figure 17.6 Expression of genes from different species.
  • #18 Figure 17.7 The stages of transcription: initiation, elongation, and termination.
  • #21 Figure 17.8 The initiation of transcription at a eukaryotic promoter.
  • #23 Figure 17.9 Transcription elongation.
  • #27 Figure 17.10 RNA processing: Addition of the 5  cap and poly-A tail.
  • #29 Figure 17.11 RNA processing: RNA splicing.
  • #31 Figure 17.12 The roles of snRNPs and spliceosomes in pre-mRNA splicing.
  • #36 Figure 17.13 Correspondence between exons and protein domains.
  • #39 Figure 17.14 Translation: the basic concept.
  • #41 For the Cell Biology Video A Stick and Ribbon Rendering of a tRNA, go to Animation and Video Files.
  • #42 Figure 17.15 The structure of transfer RNA (tRNA).
  • #44 Figure 17.16 An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA.
  • #46 Figure 17.17 The anatomy of a functioning ribosome.
  • #50 Figure 17.18 The initiation of translation.
  • #52 Figure 17.19 The elongation cycle of translation.
  • #54 Figure 17.20 The termination of translation.
  • #56 Figure 17.21 Polyribosomes.
  • #61 Figure 17.22 The signal mechanism for targeting proteins to the ER.
  • #63 Figure 17.23 The molecular basis of sickle-cell disease: a point mutation.
  • #67 Figure 17.24 Types of small-scale mutations that affect mRNA sequence.
  • #70 Figure 17.26 A summary of transcription and translation in a eukaryotic cell.