a. Based on the DNA model, Francis Crick proposed two theses about the use of genetic information. These two ideas are known as Crick's Law:

b. RNA is an informational intermediate between DNA and protein.

c. RNA synthesis from DNA is called transcription, since RNA and DNA use the same "language."

d. Translation is the process whereby the "language" of RNA nucleic acids is changed into the "language" of protein (amino acids). (See Textbook Art on transcription and translation.)

e. RNA is similar to DNA, but contains ribose sugars, and the base uracil in place of thymine.

f. Uracil and thymine form identical hydrogen bonds with adenine, so that in RNA, G bonds with C and A bonds with U, as if it were T.

g. DNA and RNA can thus bind to each other via complementary base pairing.

h. DNA thus acts as a template for RNA synthesis, which is catalyzed by RNA polymerase (Figure 14.2), which opens the DNA helix to make a template strand available.

i. RNA polymerase (called a "transcriptase") moves along a DNA template in the 3' to 5' direction, and adds nucleotides to a new RNA molecule (the transcript) at the 3' end.

j. Crick hypothesized that the RNA transcribed from DNA, and the polypeptide translated from RNA are all colinear, and that the information is transferred by reading directly from one to the other (see Textbook Art).

k. Transcription does, in fact, occur directly, through Watson-Crick base pairing, but translation and the production of the protein product is more complex.

l. A codon is a group of three nucleotides that encodes for one amino acid (see Textbook Art).

m. A promoter is a DNA site near a gene, where RNA polymerases bind preferentially, and which determine where transcription begins.

n. A terminator is a DNA site where RNA polymerases stop transcription.

o. Only one strand in a DNA double-helix serves as a template for transcription; the other strand can serve as a template for DNA repair synthesis, or to help during transcription by keeping the template strand covered except when an RNA polymerase is present.

a. A ribosome is a protein-synthesizing complex composed of a ribosomal RNA (rRNA) subunit and a protein complex subunit (Figure 14.3).

b. Ribosomal RNA is about the same in every cell, in every species, and is very stable, thus it cannot be composed of the transcripts from genes, which are highly variable and unstable.

c. The actual messages for protein synthesis are carried on messenger RNA (mRNA), which are short-lived molecules that bind to ribosomes, where they are translated and then destroyed.

a. Crick postulated that a special adaptor molecule was needed as an intermediate between an RNA codon and an amino acid, since these two units did not have complementary shapes.

b. Transfer RNA (tRNA) was discovered in 1957 by Hoagland, Zamecnik, and associates, and fit the prediction of Crick (Figure 14.4).

c. For each type of amino acid, cells have at least one type of tRNA, each with an anticodon sequence of nucleotides that is complementary to the mRNA codon for that amino acid.

d. Amino-acyl tRNA synthetases are enzymes that recognize amino acids, activate them with ATP, and combine them with the proper tRNA (Figures 14.5, 14.6).

e. Pyrophosphate molecules, released during protein synthesis, are split in half by pyrophosphatases, effectively preventing the synthesis process from reversing.

f. An mRNA-ribosome complex binds amino-acyl tRNA molecules one at a time, and a nascent protein is sequenced, one amino acid at a time (Figure 14.6).

g. Ribosomes are recycled, forming polyribosomes when bound to mRNA, and dissociating upon reaching the end of a messenger (Figure 14.7).

a. Marshal Nirenberg identified the first genetic code word in 1961, and developed a system for cracking the rest of the code.

b. The entire code has been translated, and is illustrated in Table 14.1.

c. The code is redundant, in that several codons specify the same amino acid.

d. The first two bases of mRNA carry the most information, and the third base does not always matter; that is, the amino acid can be specified completely by the first two bases.

e. Crick termed this the wobble hypothesis, stating that the third base of the codon is not fixed in place, but can wobble slightly.

f. "Nonsense" triplets UAA, UAG, and UGA, are termination codons, which do not code for amino acids, but terminate protein synthesis.

g. The initiation codon AUG is the first codon in almost every gene.

h. E. coli and possibly other bacteria were found to encode a 21st amino acid; this has implications for the growth of HIV (see Chapter 48).

a. Crick's Law shows there is no mechanism for a reverse transfer of information, from protein to DNA, and further excludes Lamarckian theories of evolution (Chapter 2).

b. Offspring, therefore, inherit no more than the propensity to develop the same structures as their parents, and random mutations in DNA are what produce changes in protein structure.

a. Figure 14.8 compares transcription and translation in procaryotes and eucaryotes.

b. All cells synthesize messenger, transfer, and ribosomal RNA, two of which are stable components of the cell, thus the concept of a gene must include DNA sequences that specify stable RNAs.

c. In eucaryotes, transcription occurs on chromosomes in the nucleus, and mRNA and tRNA must be transported out of the nucleus to interact with ribosomes.

d. Figure 14.9 shows simultaneous transcription and translation, as ribosomes are in direct contact with DNA.

a. The endoplasmic reticulum (ER) is a system of interconnected protein-sorting membranes in the eucaryotic cell cytoplasm.

b. ER membranes separate the cytosol from the lumen (Figure 14.10) inside the ER, which is continuous with the space between the membranes of the nuclear envelope.

c. Proteins may have one of three destinations: the cytosol, a membrane-bound organelle, or some place outside the cell.

d. Signal peptides, distinct sequences in the protein itself, or signal patches, formations that appear after the completed protein is folded, guide proteins to their proper destination (Figure 14.11) either during or after synthesis.

e. George Palade used the pulse—chase radioactive labeling technique to work out the pathway of protein secretion, using digestive enzymes in their inactive form, zymogen (see Section 47.6 for anatomy of the pancreas and intestine).

f. Palade labeled cells in pancreatic tissue and followed labeled zymogen (Figure 14.12), a common protein product of the tissue, which was found later in transitional vesicles at the edge of the ER.

g. Transitional vesicles were shown to pinch off from the ER and move toward the Golgi complex.

a. Figure 14.13 shows how transitional vesicles merge into the cis face of Golgi membranes, and other vesicles emerge from the trans face.

b. Vesicles leaving the trans face of the Golgi complex become tightly packed together, until a trigger signal releases them, at which point they fuse with the plasma membrane and are expelled from the cell by exocytosis.

c. In passing through the Golgi complex, proteins are changed by the addition of sugar chains, some of which "tag" the proteins for their final destinations; sugar receptors in the membranes of vesicles transport enzymes according to these tags (Figure 14.14).

d. Section 11.15 further addresses coated vesicles.

e. In addition to tagging proteins, Golgi enzymes sometimes change protein structures, especially for proproteins which enter the complex in unfinished form; see Figure 14.15 on proinsulin.

a. Figure 14.16 summarizes the entire secretion pathway.

b. Coated vesicles (Section 11.14) handle excess membrane material that would otherwise accumulate in the plasma membrane, as membrane material continually moves outward from the ER.

a. Larger initial RNA transcripts, known as pre-messenger RNA or heterogeneous nuclear RNA, are reduced to much smaller mRNA molecules (see Methods 14.1), which contain only the sequence that encodes the primary protein structure.

b. Eucaryotic gene sequences contain intervening sequences (introns) that do not encode proteins, among expressed sequences (exons) that do encode protein (see Figure 14.7).

c. A single protein transcription unit, consisting of introns plus exons, is typically more intron than exon.

d. An entire transcription unit is transcribed into a pre-mRNA transcript (Figure 14.7), which later has introns clipped out by special enzymes that produce the sequence encoding a protein.

e. Methods 14.1 and Figure 14.A cover DNA sequencing methods.

f. Eucaryotic intron-exon gene structure is probably preserved for development and evolutionary reasons, since combining exons in new ways rather quickly form new genes encoding for new proteins with novel functions.

a. Alternative splicing of exon sequences in eucaryotic cells produces more than one kind of protein (Figures 14.18 and 14.19).

b. The eucaryotic genome thus has increased efficiency, as different proteins are made in various cells of the organism from the same original genetic information.

c. Specific examples include starch-digesting enzymes and thyroid hormones, each made differently in different tissues after different mRNA sequences are produced from the same genes.

a. A nucleolus is an aggregate of protein and RNA around a central DNA molecule.

b. Nucleoli develop around the nucleolar organizer, which is located on one of the chromosomes.

c. Diploid organisms typically have two organizers in each cell nucleus, one on each of two homologous chromosomes, but may have up to thousands, depending on the cell type.

d. Figure 14.20 is an electron micrograph, taken by Miller and Beatty, of spread-out nucleolar-organizer DNA, showing several rRNA transcription units being transcribed simultaneously.

e. The nucleolus is thus the site of ribosome assembly.

a. Parts of the eucaryotic genome are contained outside the nucleus in mitochondria and chloroplasts.

b. This DNA is closed-circle with no histones, is comparable to the bacterial genome, and might be a remnant of larger genomes from symbiotic bacteria that lived inside ancient cells (see Chapter 30).

c. Frederick Sanger determined the sequence of human mitochondrial DNA.

d. Mitochondria encode a few of their own proteins, but use a different code and different rRNAs.

a. The genome specifies information for production of proteins, but cannot specify the correct orientation of different proteins in various structures.

b. For example, proteins and lipids in a functioning membrane are oriented properly only if they are produced in a functioning cell and put in place by other cell components such as ribosomes.

c. Biological structures thus conserve intrinsic patterns during growth by properly arranging new units as they are added.

d. Epigenetic information, essential for normal cell functions, resides in existing cell structures, not in the genome.

e. Tracy Sonneborn used protists to show that changing the orientation of existing cell structures caused new structures to be oriented according to the new, rather than the old, pattern (Figure 14.21).

f. Animal embryo development (Chapter 21), for example, depends greatly on epigenetic information, which is critical to the proper organization of the cytoplasm in the egg.