A. The Connection Between Genes and Proteins
1. The information content of DNA is in the form of specific sequences of nucleotides along the DNA strands.
a. The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins.
b. Proteins are the links between genotype and phenotype.
1. For example, Mendel�s dwarf pea plants lack a functioning copy of the gene that specifies the synthesis of a key protein, gibberellins.
2. Gibberellins stimulate the normal growth of stems.
c. Research has demonstrated that many proteins are composed of several polypeptides, each of which has its own gene.
d. This is the "one gene - one polypeptide" hypothesis.
2. Transcription and translation are the two main processes linking gene to protein.
a. Genes only provide the instructions for making specific proteins.
b. The bridge between the instructions in DNA and protein synthesis is RNA.
c. The specific sequence of hundreds or thousands of nucleotides in each gene carries the information for the primary structure of a protein, the order of amino acids in the polypeptide.
d. To get from DNA, written in one chemical language (nucleotides), to protein, written in another (amino acids), requires two major stages, transcription and translation.
1. During transcription, a DNA strand provides a template for the synthesis of a complementary RNA strand.
a. Transcription of a gene produces a messenger RNA (mRNA) molecule. The mRNA carries the code to the ribosome so the protein can be synthesized.
2. During translation, the information contained in the mRNA is used to determine the amino acid sequence of a polypeptide.
a. Translation occurs at ribosomes.
e. The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes. (Fig. 17.2)
1. Because bacteria lack nuclei, transcription and translation are located near each other.
2. In a eukaryotic cell, transcription occurs in the nucleus and translation occurs at ribosomes in the cytoplasm.
a. In addition, before the primary transcript can leave the nucleus it is modified in various ways during RNA processing before the finished mRNA is exported to the cytoplasm.
f. To summarize, genes program protein synthesis via messenger RNA.
1. The molecular chain of command in a cell is:
DNA -> RNA -> protein.
3. In the genetic code, nucleotide triplets specify amino acids.
a. If the genetic code consisted of a single nucleotide or even pairs of nucleotides per amino acid, there would not be enough combinations (4 and 16, respectively) to code for all 20 amino acids.
1. Triplets of nucleotide bases are the smallest units of length that can code for all the amino acids.
2. In the triplet code, three consecutive nucleotide bases specify an amino acid, creating 43 (64) possible code words.
3. The genetic instructions for a polypeptide chain are written in DNA as a series of three-nucleotide words.
b. During transcription, one DNA strand, the template strand, provides a template for ordering the sequence of nucleotides in an RNA transcript. (Fig. 17.3)
1. The complementary RNA molecule is synthesized according to base-pairing rules, except that uracil is the complementary base to adenine.
c. During translation, blocks of three nucleotides, codons, are decoded into a sequence of amino acids.
1. The codons are read in the 5�->3� direction along the mRNA.
2. Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide.
3. Because codons are base triplets, the number of nucleotides making up a genetic message must be three times the number of amino acids making up the protein product.
d. By the mid-1960s the entire genetic code was deciphered. (Fig. 17.4)
1. Most triplets code for amino acids.
2. The codon AUG not only codes for the amino acid methionine but also indicates the start of translation.
3. Three codons (stop codons) do not indicate amino acids but signal the termination of translation.
e. The genetic code is redundant but not ambiguous.
1. For most amino acids there is more than one different codon that indicates a specific amino acid.
2. However, any one codon indicates only one amino acid.
3. If you have a specific codon, you can be sure of the corresponding amino acid, but if you know only the amino acid, there may be several possible codons.
4. Codons synonymous for the same amino acid often differ only in the third codon position.
f. Extracting the message from the genetic code requires specifying the correct starting point.
1. The first AUG in the mRNA is the start codon.
2. This establishes the reading frame and subsequent codons are read in groups of three nucleotides.
3. Any subsequent AUG codons specify a methionine amino acid in the polypeptide chain.
4. The cell�s protein-synthesizing machinery reads the message as a series of nonoverlapping three-letter words.
4. The genetic code must have evolved very early in the history of life
a. The genetic code is nearly universal, shared by organisms from the simplest bacteria to the most complex plants and animals.
b. Exceptions to the universality of the genetic code exist in translation systems where a few codons differ from standard ones.
1. These occur in certain single-celled eukaryotes like Paramecium.
2. Other examples include translation in certain mitochondria and chloroplasts.
c. The near universality of the genetic code indicates it must have been operating very early in the history of life.
B. The Synthesis and Processing of RNA
1. Transcription is the DNA-directed synthesis of RNA.
a. Messenger RNA (mRNA) is transcribed as a complementary copy of the template strand of a gene.
b. The enzyme RNA polymerase separates the DNA strands at the appropriate point and bonds the RNA nucleotides as they base-pair along the DNA template.
1. Like DNA polymerases, RNA polymerases can add nucleotides only to the 3� end of the growing polymer.
c. Specific sequences of nucleotides along the DNA mark where gene transcription begins and ends.
1. RNA polymerase attaches and initiates transcription at the promotor, "upstream" of the information contained in the gene.
2. The terminator signals the end of transcription.
d. Transcription can be separated into three stages: initiation, elongation, and termination.
1. Stage 1: RNA polymerase binding and initiation of transcription
a. The presence of a promotor sequence determines which strand of the DNA helix is the template.
1. Within the promotor is the starting point for the transcription of a gene.
2. The promotor also includes a binding site for RNA polymerase several dozen nucleotides upstream of the start point.
b. In prokaryotes, RNA polymerase can recognize and bind directly to the promotor region.
c. In eukaryotes, proteins called transcription factors recognize the promotor region, especially the TATA box, and bind to the promotor. (Fig. 17.7)
1. After they have bound to the promotor, RNA polymerase binds to transcription factors to create a transcription initiation complex.
2. RNA polymerase then starts transcription.
2. Stage 2: Elongation of the RNA strand
a. As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at time. (Fig. 17.6)
b. The enzyme adds nucleotides to the 3� end of the growing strand.
c. Behind the point of RNA synthesis, the double helix re-forms and the RNA molecule peels away.
d. A single gene can be transcribed simultaneously by several RNA polymerases at a time.
e. Many polymerase molecules simultaneously transcribing a single gene increases the amount of mRNA transcribed from it.
3. Stage 3: Termination of transcription
a. Transcription proceeds until after the RNA polymerase transcribes a terminator sequence in the DNA.
b. In prokaryotes, RNA polymerase stops transcription right at the end of the terminator.
c. In eukaryotes, the polymerase continues past the terminator sequence, AAUAAA.
At a point about 10 to 35 nucleotides past this sequence, the mRNA is released from the enzyme. (Textbook Activity #17B)
2. At this point the mRNA is considered a pre-mRNA because it will need further processing before it can be used.
2. Eukaryotic cells modify RNA after transcription.
a. Alteration of mRNA ends
1. At the 5� end of the pre-mRNA molecule, a modified form of guanine nucleotide is added, the 5� cap.
a. This helps protect mRNA from enzymes that would degrade it.
b. It also functions as an "attach here" signal for ribosomes because the code now carried in the mRNA will be translated by the ribosome starting at the 5' end.
2. At the 3� end, an enzyme adds 50 to 250 adenine nucleotides, the poly(A) tail. (Fig. 17.8)
a. In addition to inhibiting degradation, the poly(A) tail also seems to facilitate the export of mRNA from the nucleus.
b. RNA splicing
1. RNA processing includes the removal of a large portion of the RNA molecule during RNA splicing.
2. Most eukaryotic genes and their RNA transcripts have long noncoding (do not code for amino acids) stretches of nucleotides.
a. Noncoding segments (introns) lie between coding regions (exons).
b. The final mRNA transcript includes coding regions, exons, which are translated into amino acid sequences, plus the leader and trailer sequences. The introns are discarded and degraded into single nucleotides which can be reused in DNA synthesis. (Fig. 17.9)
c. The importance of introns
1. Some introns contain sequences that control gene activity in some way.
2. In many cases 1 or more exons are also removed from the mRNA.
a. This is called alternative RNA splicing and enables one gene to code for more than one polypeptide.
b. Humans have approximately 30,000 genes but over 100,000 proteins and this is due, in part, to alternative splicing of mRNA. (Fig. 19.11)
C. The Synthesis of Protein
1. Translation is the RNA-directed synthesis of a polypeptide and involves tRNA (transfer RNA), rRNA (ribosomes) and mRNA.
a. In the process of translation, a cell interprets a series of codons along a mRNA molecule.
1. Transfer RNA (tRNA) transfers amino acids from the cytoplasm�s pool of amino acids to the ribosome.
2. The ribosome adds each amino acid carried by tRNA to the growing end of the polypeptide chain.
b. tRNA
1. tRNA molecules are not all identical.
a. A tRNA molecule consists of a strand of about 80 nucleotides that folds back on itself to form a three-dimensional structure.
b. Each tRNA arriving at the ribosome carries a specific amino acid at an attachment site on one end. (Fig. 17.13)
c. It also includes a loop containing the anticodon at the other end.
1. The anticodon is a specific nucleotide triplet that corresponds to the amino acid the tRNA carries.
2. The anticodon is complementary to the mRNA codon and base-pairs (hydrogen bonds) with the complementary codon on mRNA.
3. Example: if the codon on mRNA is UUU, a tRNA with an AAA anticodon and carrying the amino acid phenylalanine will bind to it. (Fig. 17.12)
d. Codon by codon, tRNAs deposit amino acids in the prescribed order and the ribosome joins them into a polypeptide chain.
e. Each tRNA is used repeatedly. After depositing its amino acid at the ribosome it returns to the cytosol to pick up another copy of that amino acid.
2. If each anticodon had to be a perfect match to each codon, we would expect to find 61 types of tRNA, but the actual number is about 45.
a. The anticodons of some tRNAs recognize more than one codon.
b. This is possible because the rules for base pairing between the third base of the codon and anticodon are relaxed (called wobble).
c. At the wobble position, U on the anticodon can bind with A or G in the third position of a codon.
d. Some tRNA anticodons include a modified form of adenine, inosine, which can hydrogen bond with U, C, or A on the codon.
3. Each amino acid is joined to the correct tRNA by aminoacyl-tRNA synthetase. (Fig. 17.14)
a. The 20 different synthetases match the 20 different amino acids.
b. Each has active sites for only a specific tRNA and amino acid combination.
c. The synthetase catalyzes a covalent bond between them, forming aminoacyl-tRNA or activated amino acid.
c. rRNA
1. Ribosomes facilitate the specific coupling of the tRNA anticodons with mRNA codons. (Fig. 17.15)
a. Each ribosome has a large and a small subunit.
b. These are composed of proteins and ribosomal RNA (rRNA).
2. Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.
a. The P site holds the tRNA carrying the growing polypeptide chain.
b. The A site holds the tRNA with the next amino acid.
c. Discharged tRNAs leave the ribosome at the E site.
d. Translation can be divided into three stages: initiation, elongation and termination.
1. All three phases require protein factors that aid in the translation process.
2. Initiation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits. (Fig. 17.17)
a. First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, which carries methionine and attaches to the start codon.
b. Initiation factors bring in the large subunit such that the initiator tRNA occupies the P site.
3. Elongation consists of a series of three-step cycles as each amino acid is added to the proceeding one. (Fig. 17.18)
a. During codon recognition, an elongation factor assists hydrogen bonding between the mRNA codon under the A site with the corresponding anticodon of tRNA carrying the appropriate amino acid.
b. During peptide bond formation, a peptide bond forms between the polypeptide in the P site with the new amino acid in the A site.
c. During translocation, the ribosome moves the tRNA with the attached polypeptide from the A site to the P site.
1. Because the anticodon remains bonded to the mRNA codon, the mRNA moves along with it.
2. The next codon is now available at the A site.
3. The tRNA that had been in the P site is moved to the E site and then leaves the ribosome.
4. Termination occurs when one of the three stop codons reaches the A site. (Fig. 17.19)
a. A release factor binds to the stop codon and breaks the bond between the polypeptide and its tRNA in the P site.
b. This frees the polypeptide and the translation complex disassembles. (Textbook Activity #17D)