From Gene To Protein Chapter 17 Overview: The

From Gene To Protein Chapter 17 Overview: The

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 Genes specify proteins via transcription and translation How was the fundamental relationship between genes and proteins discovered?

Evidence from the Study of Metabolic Defects In 1902, British physician Archibald Garrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme

Linking genes to enzymes required understanding that cells synthesize and degrade molecules in a series of steps, a metabolic pathway 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 using information in DNA

Transcription produces messenger RNA (mRNA) Translation is the synthesis of a polypeptide, using information in the mRNA Ribosomes are the sites of translation Basic Principles of Transcription and Translation

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 the finished mRNA Basic Principles of Transcription and Translation

The central dogma is the concept that cells are governed by a cellular chain of command: DNA RNA protein central dogma DNA RNA Protein Basic Principles of Transcription and Translation

TRANSCRIPTION DNA RNA PROCESSING TRANSCRIPTION mRNA DNA mRNA TRANSLATION

TRANSLATION a) Bacterial cell b) Eukaryotic cell 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? Codons: Triplets of Nucleotides The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, threenucleotide words The words of a gene are transcribed into

complementary nonoverlapping three-nucleotide words of mRNA These words are then translated into a chain of amino acids, forming a polypeptide The Genetic Code DNA template strand Gene 1 TRANSCRIPTION Gene 2

mRNA Codon TRANSLATION Trp Amino acid Gene 3 The Genetic Code 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 The Genetic Code Codons along an mRNA molecule are read by

translation machinery 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 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 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 Expression of genes from different species. Tobacco plant expressing Pig expressing a jellyfish a firefly gene gene

Transcription is the DNA-directed synthesis of RNA: a closer look Transcription expression is the first stage of gene 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 Molecular Components of Transcription 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 Synthesis of an RNA Transcript The three stages of transcription Initiation Elongation Termination

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 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 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; the RNA transcript is released 1035 nucleotides past this polyadenylation

sequence Eukaryotic cells modify RNA after transcription Enzymes in the eukaryotic nucleus modify premRNA (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 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 Translation is the RNA-directed synthesis of a polypeptide: a closer look Genetic information flows from mRNA to protein through the process of translation

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

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 The Structure and Function of Transfer RNA 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 The Structure and Function of Transfer RNA Amino acid attachment site Anticodon

Anticodon Two-dimensional structure Three-dimensional structure Anticodon The Structure and Function of Transfer RNA Accurate translation requires two steps: First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyltRNA 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 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 Ribosomes 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 Building a Polypeptide The three stages of translation: Initiation Elongation 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 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 Ribosome Association and Initiation of Translation P site Met Large

ribosomal subunit Initiator tRNA mRNA binding site Small ribosomal subunit Translation initiation complex Elongation of the Polypeptide Chain

During the elongation stage, amino acids are added one by one to the preceding amino acid at the Cterminus 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

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 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 Polyribosomes

Ribosomes 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 Protein Folding and PostTranslational 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 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 Targeting Polypeptides to Specific Locations 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 Targeting Polypeptides to Specific Locations A signal-recognition particle (SRP) binds to

the signal peptide The SRP brings the signal peptide and its ribosome to the ER 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 Mutations Wild-type hemoglobin Wild-type hemoglobin DNA C TT mRNA

G A A Normal hemoglobin Glu Sickle-cell hemoglobin Mutant hemoglobin DNA C A T mRNA GU A Sickle-cell hemoglobin Val 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 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 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 DNA replication, recombination, or repair Mutagens are physical or chemical agents that can cause mutations 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 The End

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