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
Concept 17.1: 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 1909, 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
Nutritional Mutants in Neurospora: Scientific Inquiry
George Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants that were unable to survive on minimal medium as a result of inability to synthesize certain molecules
Using crosses, they identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for synthesizing arginine
They developed a one gene–one enzyme hypothesis, which states that each gene dictates production of a specific enzyme
The Products of Gene Expression: A Developing Story
Some proteins aren’t enzymes, so researchers later revised the hypothesis: one gene–one protein
Many proteins are composed of several polypeptides, each of which has its own gene
Therefore, Beadle and Tatum’s hypothesis is now restated as the one gene–one polypeptide hypothesis
Note that it is common to refer to gene products as proteins rather than polypeptides
Basic Principles of Transcription and Translation
RNA is the intermediate 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, which occurs under the direction of mRNA
Ribosomes are the sites of translation
In prokaryotes, mRNA produced by transcription is immediately translated without more processing
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
The central dogma is the concept that cells are governed by a cellular chain of command: DNA RNA protein
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 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, three-nucleotide words
These triplets are the smallest units of uniform length that can code for all the amino acids
Example: AGT at a particular position on a DNA strand results in the placement of the amino acid serine at the corresponding position of the polypeptide to be produced
During transcription, one of the two DNA strands called the template strand provides a template for ordering the sequence of nucleotides in an RNA transcript
During translation, the mRNA base triplets, called codons, are read in the 5 to 3 direction
Each codon specifies the amino acid to be placed at the corresponding position along a polypeptide
Codons along an mRNA molecule are read by translation machinery in the 5 to 3 direction
Each codon specifies the addition of one of 20 amino acids
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 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
Concept 17.2: Transcription is the DNA-directed synthesis of RNA: a closer look
Transcription, the first stage of gene expression, can be examined in more detail
Molecular Components of Transcription
RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides
RNA synthesis follows the same base-pairing rules as DNA, except uracil substitutes for thymine
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 initiation of RNA synthesis
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
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
In eukaryotes, the polymerase continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA
Concept 17.3: Eukaryotic cells modify RNA after transcription
Enzymes in the eukaryotic nucleus modify pre-mRNA 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
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
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
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
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
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
RNA may hydrogen-bond with other nucleic acid molecules
The Functional and Evolutionary Importance of Introns
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing
Such variations are called alternative RNA splicing
Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes
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
Concept 17.4: Translation is the RNA-directed synthesis of a polypeptide: a closer look
The translation of mRNA to protein can be examined in more detail
Molecular Components of Translation
A cell translates an mRNA message into protein with the help of transfer RNA (tRNA)
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
Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule
tRNA is roughly L-shaped
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
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)
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
Elongation of the Polypeptide Chain
During the elongation stage, amino acids are added one by one to the preceding amino acid
Each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation
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
Completing and Targeting the Functional Protein
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
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
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
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
Concept 17.5: 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 DNA template strand can lead to the production of an abnormal protein
Types of Point Mutations
Point mutations within a gene can be divided into two general categories
Base-pair substitutions
Base-pair insertions or deletions
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 DNA replication, recombination, or repair
Mutagens are physical or chemical agents that can cause mutations
Concept 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
Comparing Gene Expression in Bacteria, Archaea, and Eukarya
Bacteria and eukarya differ in their RNA polymerases, termination of transcription and ribosomes; archaea tend to resemble eukarya in these respects
Bacteria can simultaneously transcribe and translate the same gene
In eukarya, transcription and translation are separated by the nuclear envelope
In archaea, transcription and translation are likely coupled
What Is a Gene? Revisiting the Question
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 DNA sequence that codes for a specific polypeptide chain
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
You should now be able to:
Describe the contributions made by Garrod, Beadle, and Tatum to our understanding of the relationship between genes and enzymes
Briefly explain how information flows from gene to protein
Compare transcription and translation in bacteria and eukaryotes
Explain what it means to say that the genetic code is redundant and unambiguous
Include the following terms in a description of transcription: mRNA, RNA polymerase, the promoter, the terminator, the transcription unit, initiation, elongation, termination, and introns
Include the following terms in a description of translation: tRNA, wobble, ribosomes, initiation, elongation, and termination
