From Gene to Protein. Chapter 17

Transcription

1 Chapter 17 From Gene to Overview: The Flow of Genetic Information The information content of is in the form of specific sequences of nucleotides The inherited by an organism leads to specific traits by dictating the synthesis of proteins s are the links between genotype and phenotype Gene expression, the process by which directs protein synthesis, includes two stages: ion and translation Fig : Basic Principles of Transcription and Translation is the intermediate between genes and the proteins for which they code Transcription is the synthesis of under the direction of Transcription produces messenger () Translation is the synthesis of a polypeptide, which occurs under the direction of Ribosomes are the sites of translation In prokaryotes, produced by ion is immediately translated without more processing In a eukaryotic cell, the nuclear envelope separates ion from translation ukaryotic s are modified through processing to yield finished A primary is the initial from any gene The central dogma is the concept that cells are governed by a cellular chain of command: protein 1

2 Fig. 17-a-2 Fig. 17-b-1 Nuclear envelope TRANSCRIPTION TRANSCRIPTION TRANSLATION Polypeptide Ribosome Pre- (a) Bacterial cell (b) ukaryotic cell Fig. 17-b-2 Fig. 17-b- Nuclear envelope Nuclear envelope TRANSCRIPTION TRANSCRIPTION PROCSSING Pre- PROCSSING Pre- TRANSLATION Ribosome Polypeptide (b) ukaryotic cell (b) ukaryotic cell The Genetic Code How are the instructions for assembling amino acids into proteins encoded into? There are 20 amino acids, but there are only four nucleotide bases in How many bases correspond to an amino acid? Codons: Triplets of Bases The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, threenucleotide words These triplets are the smallest units of uniform length that can code for all the amino acids 2

3 First base ( end of codon) Third base ( end of codon) During ion, one of the two strands called the template strand provides a template for ordering the sequence of nucleotides in an During translation, the base triplets, called codons, are read in the to direction ach codon specifies the amino acid to be placed at the corresponding position along a polypeptide Codons along an molecule are read by translation machinery in the to direction ach codon specifies the addition of one of 20 amino acids Fig molecule template strand Gene 1 TRANSCRIPTION Codon TRANSLATION Gene 2 Gene Cracking the Code All 64 codons were deciphered by the mid-1960s Of the 64 triplets, 61 code for amino acids; triplets are stop signals to end translation The genetic code is redundant 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 Amino acid Fig. 17- Second base volution 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 Copyright 2008 Pearson ducation Inc., publishing as Pearson Benjamin Cummings

4 Fig : Transcription is the -directed synthesis of : a closer look Transcription, the first stage of gene expression, can be examined in more detail Three types of : Ribosomal (r) Transfter (t) Messenger () (a) Tobacco plant expressing a firefly gene (b) Pig expressing a jellyfish gene Molecular Components of Transcription synthesis is catalyzed by polymerase, which pries the strands apart and hooks together the nucleotides synthesis follows the same base-pairing rules as, except uracil substitutes for thymine The sequence where polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of ion is called the terminator The stretch of that is transcribed is called a ion unit Go to the animation of Transciption (you can access this with the chapter materials on the website. The visual helps a great deal! Fig Promoter Transcription unit Fig. 17-7a-1 Promoter Transcription unit Start point polymerase 1 Initiation longation Nontemplate strand of Start point polymerase Unwound Template strand of 2 longation polymerase end nucleotides Rewound Termination Newly made Direction of ion ( downstream ) Template strand of Completed 4

5 Fig. 17-7a-2 Promoter Transcription unit Fig. 17-7a- Promoter Transcription unit Start point polymerase 1 Initiation Start point polymerase 1 Initiation Unwound Template strand of Unwound Template strand of 2 longation Rewound Fig. 17-7a-4 Promoter Transcription unit Start point polymerase 1 Initiation Fig. 17-7b longation Nontemplate strand of polymerase nucleotides Unwound Template strand of 2 longation end Rewound Termination Completed Newly made Direction of ion ( downstream ) Template strand of Synthesis of an Transcript The three stages of ion: Initiation longation Termination longation of the Strand As polymerase moves along the, 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 polymerases

6 Termination of Transcription The mechanisms of termination are different in bacteria and eukaryotes In bacteria, the polymerase stops ion at the end of the terminator In eukaryotes, the polymerase continues ion after the pre- is cleaved from the growing chain; the polymerase eventually falls off the 17.: ukaryotic cells modify after ion nzymes in the eukaryotic nucleus modify pre before the genetic messages are dispatched to the cytoplasm During processing, both ends of the primary are usually altered Also, usually some interior parts of the molecule are cut out, and the other parts spliced together Alteration of nds Fig ach end of a pre- molecule is modified in a particular way: The end receives a modified nucleotide cap The end gets a poly-a tail These modifications share several functions: They facilitate the export of They protect from hydrolytic enzymes They help ribosomes attach to the end -coding segment Polyadenylation signal G P P P AAUAAA AAA AAA Cap UTR Start codon codon UTR Poly-A tail Split Genes and Splicing Most eukaryotic genes and their s 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 splicing removes introns and joins exons, creating an molecule with a continuous coding sequence Fig xon Intron xon Intron xon Pre- Cap Poly-A tail Coding segment Introns cut out and exons spliced together Cap Poly-A tail UTR UTR 6

7 The Functional and volutionary Importance of Introns Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing Such variations are called alternative splicing Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes s often have a modular architecture consisting of discrete regions called domains In many cases, different exons code for the different domains in a protein xon shuffling may result in the evolution of new proteins Fig Gene xon 1 Intron xon 2 Intron xon Transcription processing 17.4: Translation is the -directed synthesis of a polypeptide: a closer look Translation Domain Once the strand undergoes editing and modification of the ends cap and poly-a tail, the leaves the nucleus and translation can begin. Domain 2 Domain 1 Polypeptide Molecular Components of Translation Fig A cell translates an strand into protein with the help of transfer (t) Molecules of t are not identical: ach carries a specific amino acid on one end ach has an anticodon on the other end; the anticodon base-pairs with a complementary codon on Watch the Bioflix animation of protein synthesis. The file will be included in the post for chapter 17. Polypeptide Amino acids t with amino acid attached Ribosome t Anticodon Codons 7

8 The Structure and Function of Transfer A t molecule consists of a single strand that is only about 80 nucleotides long Flattened into one plane to reveal its base pairing, a t molecule looks like a cloverleaf Because of hydrogen bonds, t actually twists and folds into a three-dimensional molecule t is roughly L-shaped A C C Fig Amino acid attachment site Hydrogen bonds Anticodon (a) Two-dimensional structure Amino acid attachment site Hydrogen bonds Anticodon Anticodon (c) Symbol used (b) Three-dimensional structure in this book Fig b Anticodon Hydrogen bonds (b) Three-dimensional structure Amino acid attachment site Anticodon (c) Symbol used in this book Accurate translation requires two steps: First: a correct match between a t and an amino acid, done by the enzyme aminoacyl-t synthetase Second: a correct match between the t anticodon and an codon Flexible pairing at the third base of a codon is called wobble and allows some ts to bind to more than one codon Ribosomes Fig t molecules Growing polypeptide xit tunnel Ribosomes facilitate specific coupling of t anticodons with codons in protein synthesis The two ribosomal subunits (large and small) are made of proteins and ribosomal (r) Large subunit P A Small subunit (a) Computer model of functioning ribosome P site (Peptidyl-t binding site) A site (Aminoacyl- site t binding site) (xit site) P A Large subunit Small binding site subunit (b) Schematic model showing binding sites Growing polypeptide Next amino acid to be added to polypeptide chain t Codons (c) Schematic model with and t 8

9 Fig b P site (Peptidyl-t binding site) site (xit site) binding site A site (Aminoacylt binding site) Large subunit Small subunit (b) Schematic model showing binding sites P A Growing polypeptide Next amino acid to be added to polypeptide chain A ribosome has three binding sites for t: The P site holds the t that carries the growing polypeptide chain The A site holds the t that carries the next amino acid to be added to the chain The site is the exit site, where discharged ts leave the ribosome t Codons (c) Schematic model with and t Building a Polypeptide The three stages of translation: Initiation longation Termination All three stages require protein factors that aid in the translation process Ribosome Association and Initiation of Translation The initiation stage of translation brings together, a t with the first amino acid, and the two ribosomal subunits First, a small ribosomal subunit binds with and a special initiator t Then the small subunit moves along the until it reaches the start codon (AUG) s called initiation factors bring in the large subunit that completes the translation initiation complex Fig longation of the Polypeptide Chain Initiator t Start codon binding site U A C A U G Small ribosomal subunit GTP GDP P site A Large ribosomal subunit Translation initiation complex During the elongation stage, amino acids are added one by one to the preceding amino acid ach addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation 9

10 Fig Fig of polypeptide of polypeptide P site A site P site A site GTP GDP P A Fig Fig of polypeptide of polypeptide P site A site GTP Ribosome ready for next aminoacyl t P site A site GTP GDP GDP P A P A P A GDP GTP P A P A Termination of Translation Fig Termination occurs when a stop codon in the 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 Watch the Translation animation. On the website with the C17 materials. Release factor codon (UAG, UAA, or UGA) 10

11 Fig Fig Release factor Free polypeptide Release factor Free polypeptide codon (UAG, UAA, or UGA) 2 GTP 2 GDP codon (UAG, UAA, or UGA) 2 GTP 2 GDP Polyribosomes Fig Growing polypeptides Completed polypeptide A number of ribosomes can translate a single simultaneously, forming a polyribosome (or polysome) Polyribosomes enable a cell to make many copies of a polypeptide very quickly Incoming ribosomal subunits (a) Start of ( end) nd of ( end) Ribosomes (b) 0.1 µm Completing and Targeting the Functional Often translation is not sufficient to make a functional protein Polypeptide chains are modified after translation Completed proteins are targeted to specific sites in the cell Folding and Post- Translational Modifications During and after synthesis, a polypeptide chain spontaneously coils and folds into its threedimensional shape s 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 11

12 Targeting Polypeptides to Specific Locations Two populations of ribosomes are evident in cells: free ribosomes (in the cytosol) and bound ribosomes (attached to the R) 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 Polypeptide synthesis always begins in the cytosol Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the R Fig Ribosome Signal peptide Signalrecognition particle (SRP) CYTOSOL R LUMN Translocation complex SRP receptor protein Signal peptide removed R membrane 17.: Point mutations 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 template strand can lead to the production of an abnormal protein Copyright 2008 Pearson ducation Inc., publishing as Pearson Benjamin Cummings Fig Wild-type hemoglobin C T T G A A G A A Mutant hemoglobin C A T G T A G U A Types of Point Mutations Point mutations within a gene can be divided into two general categories Base-pair substitutions Base-pair insertions or deletions Normal hemoglobin Glu Sickle-cell hemoglobin Val 12

13 Fig template strand Wild-type Carboxyl end Fig. 17-2a template strand Wild type A instead of G U instead of C Silent (no effect on amino acid sequence) xtra A xtra U Frameshift causing immediate nonsense (1 base-pair insertion) Carboxyl end Missense A instead of T T instead of C A instead of G missing missing Frameshift causing extensive missense (1 base-pair deletion) missing A instead of G U instead of C U instead of A Nonsense missing No frameshift, but one amino acid missing ( base-pair deletion) Silent (no effect on amino acid sequence) (a) Base-pair substitution (b) Base-pair insertion or deletion Fig. 17-2b template strand Wild type Fig. 17-2c template strand Wild type Carboxyl end Carboxyl end Missense T instead of C A instead of G A instead of T U instead of A Nonsense Fig. 17-2d Wild type Fig. 17-2e Wild type template strand template strand Carboxyl end Carboxyl end xtra A xtra U missing missing Frameshift causing immediate nonsense (1 base-pair insertion) Frameshift causing extensive missense (1 base-pair deletion) 1

14 Fig. 17-2f template strand Wild type missing missing Carboxyl end No frameshift, but one amino acid missing ( base-pair deletion) Substitutions A base-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 necessarily the right amino acid Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein 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 Mutagens Spontaneous mutations can occur during replication, recombination, or repair Mutagens are physical or chemical agents that can cause mutations 17.6: While gene expression differs among the domains of life, the concept of a gene is universal Archaea are prokaryotes, but share many features of gene expression with eukaryotes These processes are very similar across all living organisms thus is the central dogma of Biology. Comparing Gene xpression in Bacteria, Archaea, and ukarya Bacteria can simultaneously transcribe and translate the same gene because both processes occur in the cytoplasm In eukarya (Animals, Plants, Fungi and Protists), ion and translation are separated by the nuclear envelope. There is pre- editing and post ional editing of the protein produced. In archaea, ion and translation are likely coupled 14

15 Fig polymerase What Is a Gene? Revisiting the Question polymerase Polyribosome Polypeptide (amino end) Polyribosome Direction of ion Ribosome ( end) 0.2 µm The idea of the gene itself is a unifying concept of life We have considered a gene as: A discrete unit of inheritance A region of specific nucleotide sequence in a chromosome A sequence that codes for a specific polypeptide chain Fig TRANSCRIPTION PROCSSING CYTOPLASM xon NUCLUS polymerase (pre-) Intron Amino acid t Aminoacyl-t synthetase AMINO ACID ACTIVATION In summary, a gene can be defined as a region of that can be expressed to produce a final functional product, either a polypeptide or an molecule P A Ribosomal subunits Growing polypeptide Activated amino acid TRANSLATION A Anticodon Codon Ribosome Fig. 17-UN1 Review Promoter Transcription unit Template strand of polymerase 1

16 Fig. 17-UN2 Fig. 17-UN Pre- Cap Poly-A tail Polypeptide Ribosome Fig. 17-UN Fig. 17-UN6 Fig. 17-UN7 You should now be able to: 1. Briefly explain how information flows from gene to protein 2. Compare ion and translation in bacteria and eukaryotes. xplain what it means to say that the genetic code is redundant and unambiguous 4. Include the following terms in a description of ion:, polymerase, the promoter, the terminator, the ion unit, initiation, elongation, termination, and introns 16

17 . Include the following terms in a description of translation: t, wobble, ribosomes, initiation, elongation, and termination 17