From Gene to Protein

From Gene to Protein
Overview: The Flow of Genetic Information
The information content of DNA
Is in the form of specific sequences of nucleotides along the DNA strands

The DNA inherited by an organism
Leads to specific traits by dictating the synthesis of proteins
The process by which DNA directs protein synthesis, gene expression
Includes two stages, called transcription and translation

The ribosome
Is part of the cellular machinery for translation, polypeptide synthesis
Figure 17.1
Concept 17.1: Genes specify proteins via transcription and translation

Evidence from the Study of Metabolic Defects
In 1909, British physician Archibald Garrod
Was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell
Nutritional Mutants in Neurospora: Scientific Inquiry
Beadle and Tatum causes bread mold to mutate with X-rays
Creating mutants that could not survive on minimal medium
Using genetic crosses
They determined that their mutants fell into three classes, each mutated in a different gene
Figure 17.2
Working with the mold Neurospora crassa, George Beadle and Edward Tatum had isolated mutants requiring arginine in their growth medium and had shown genetically that these mutants fell into three classes, each defective in a different gene. From other considerations, they suspected that the metabolic pathway of arginine biosynthesis included the precursors ornithine and citrulline. Their most famous experiment, shown here, tested both their one gene–one enzyme hypothesis and their postulated arginine pathway. In this experiment, they grew their three classes of mutants under the four different conditions shown in the Results section below.
The wild-type strain required only the minimal medium for growth. The three classes of mutants had different growth requirements
Beadle and Tatum developed the “one gene–one enzyme hypothesis”
Which states that the function of a gene is to dictate the production of a specific enzyme
The Products of Gene Expression: A Developing Story
As researchers learned more about proteins
The made minor revision to the one gene–one enzyme hypothesis
Genes code for polypeptide chains or for RNA molecules

Basic Principles of Transcription and Translation
Transcription
Is the synthesis of RNA under the direction of DNA
Produces messenger RNA (mRNA)
Translation
Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA
Occurs on ribosomes
In prokaryotes
Transcription and translation occur together
Figure 17.3a
In eukaryotes
RNA transcripts are modified before becoming true mRNA
Cells are governed by a cellular chain of command
DNA RNA protein

The Genetic Code
How many bases correspond to an amino acid?
Codons: Triplets of Bases
Genetic information
Is encoded as a sequence of nonoverlapping base triplets, or codons
During transcription
The gene determines the sequence of bases along the length of an mRNA molecule
Cracking the Code
A codon in messenger RNA
Is either translated into an amino acid or serves as a translational stop signal
Codons must be read in the correct reading frame
For the specified polypeptide to be produced

Evolution of the Genetic Code
The genetic code is nearly universal
Shared by organisms from the simplest bacteria to the most complex animals
In laboratory experiments
Genes can be transcribed and translated after being transplanted from one species to another
Figure 17.6
Concept 17.2: Transcription is the DNA-directed synthesis of RNA: a closer look
Molecular Components of Transcription
RNA synthesis
Is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides
Follows the same base-pairing rules as DNA, except that in RNA, uracil substitutes for thymine
Synthesis of an RNA Transcript
The stages of transcription are
Initiation
Elongation
Termination

RNA Polymerase Binding and Initiation of Transcription
Promoters signal the initiation of RNA synthesis
Transcription factors
Help eukaryotic RNA polymerase recognize promoter sequences
Figure 17.8
Elongation of the RNA Strand
As RNA polymerase moves along the DNA
It continues to untwist the double helix, exposing about 10 to 20 DNA bases at a time for pairing with RNA nucleotides
Termination of Transcription
The mechanisms of termination
Are different in prokaryotes and eukaryotes
Concept 17.3: Eukaryotic cells modify RNA after transcription
Enzymes in the eukaryotic nucleus
Modify pre-mRNA in specific ways before the genetic messages are dispatched to the cytoplasm
Alteration of mRNA Ends
Each end of a pre-mRNA molecule is modified in a particular way
The 5 end receives a modified nucleotide cap
The 3 end gets a poly-A tail
Figure 17.9
Split Genes and RNA Splicing
RNA splicing
Removes introns and joins exons
Figure 17.10
Is carried out by spliceosomes in some cases
Figure 17.11
Ribozymes
Ribozymes
Are catalytic RNA molecules that function as enzymes and can splice RNA
The Functional and Evolutionary Importance of Introns
The presence of introns
Allows for alternative RNA splicing
Proteins often have a modular architecture
Consisting of discrete structural and functional regions called domains
In many cases
Different exons code for the different domains in a protein
Figure 17.12
Concept 17.4: Translation is the RNA-directed synthesis of a polypeptide: a closer look
Molecular Components of Translation
A cell translates an mRNA message into protein
With the help of transfer RNA (tRNA)
Translation: the basic concept
Figure 17.13
Molecules of tRNA are not all identical
Each carries a specific amino acid on one end
Each has an anticodon on the other end
The Structure and Function of Transfer RNA
A
C
C
A tRNA molecule
Consists of a single RNA strand that is only about 80 nucleotides long
Is roughly L-shaped
Figure 17.14b
A specific enzyme called an aminoacyl-tRNA synthetase
Joins each amino acid to the correct tRNA
Figure 17.15
Amino acid
ATP
Adenosine
Pyrophosphate
Adenosine
Adenosine
Phosphates
tRNA
P
P
P
P
P
Pi
Pi
Pi
P
AMP
Aminoacyl tRNA
(an “activated
amino acid”)
Aminoacyl-tRNA
synthetase (enzyme)
Active site binds the
amino acid and ATP.
1
Ribosomes
Ribosomes
Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis
The ribosomal subunits
Are constructed of proteins and RNA molecules named ribosomal RNA or rRNA
Figure 17.16a
The ribosome has three binding sites for tRNA
The P site
The A site
The E site
Figure 17.16b
E
P
A
Figure 17.16c
Building a Polypeptide
We can divide translation into three stages
Initiation
Elongation
Termination

Ribosome Association and Initiation of Translation
The initiation stage of translation
Brings together mRNA, tRNA bearing the first amino acid of the polypeptide, and two subunits of a ribosome
Elongation of the Polypeptide Chain
In the elongation stage of translation
Amino acids are added one by one to the preceding amino acid
Termination of Translation
The final stage of translation is termination
When the ribosome reaches a stop codon in the mRNA
Polyribosomes
A number of ribosomes can translate a single mRNA molecule simultaneously
Forming a polyribosome
Completing and Targeting the Functional Protein
Polypeptide chains
Undergo modifications after the translation process
Protein Folding and Post-Translational Modifications
After translation
Proteins may be modified in ways that affect their three-dimensional shape
Targeting Polypeptides to Specific Locations
Two populations of ribosomes are evident in cells
Free and bound
Free ribosomes in the cytosol
Initiate the synthesis of all proteins
Proteins destined for the endomembrane system or for secretion
Must be transported into the ER
Have signal peptides to which a signal-recognition particle (SRP) binds, enabling the translation ribosome to bind to the ER
The signal mechanism for targeting proteins to the ER
Concept 17.5: RNA plays multiple roles in the cell: a review
RNA
Can hydrogen-bond to other nucleic acid molecules
Can assume a specific three-dimensional shape
Has functional groups that allow it to act as a catalyst
Types of RNA in a Eukaryotic Cell
Table 17.1
Concept 17.6: Comparing gene expression in prokaryotes and eukaryotes reveals key differences
Prokaryotic cells lack a nuclear envelope
Allowing translation to begin while transcription is still in progress
Figure 17.22
In a eukaryotic cell
The nuclear envelope separates transcription from translation
Extensive RNA processing occurs in the nucleus
Concept 17.7: Point mutations can affect protein structure and function
Mutations
Are changes in the genetic material of a cell
Point mutations
Are changes in just one base pair of a gene
The change of a single nucleotide in the DNA’s template strand
Leads to the production of an abnormal protein
Figure 17.23
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
Is the replacement of one nucleotide and its partner with another pair of nucleotides
Can cause missense or nonsense
Figure 17.24
Insertions and Deletions
Insertions and deletions
Are additions or losses of nucleotide pairs in a gene
May produce frameshift mutations
Figure 17.25
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
A gene
Is a region of DNA whose final product is either a polypeptide or an RNA molecule
A summary of transcription and translation in a eukaryotic cell
Figure 17.26