Chapter 4 : An Overview of Molecular Biology

The nucleotide. Carbon atoms of the deoxyribose sugar portion are numbered according to chemical convention.

A trinucleotide.

Complementary base pairs in DNA.

Ribbon model of DNA.

DNA replication. (A) Base pairing between an incoming nucleotide and the template strand of DNA guides the formation of a new daughter strand with a complementary base sequence. (B) In each round of DNA replication, each of the two DNA strands is used as a template for the synthesis of a new complementary strand, resulting in two daughter molecules, each with one “new” and one “old” strand.

A protein is a chain of amino acids (represented by beads) that folds into a specific three-dimensional shape. The three-letter abbreviations on the beads are standard for specific amino acids (see Figure 4.23 ).

The base sequence of DNA determines the amino acid sequence of proteins.

Chemical differences between DNA and RNA.

A single-stranded RNA molecule.

Transcription.(A) Base pairing between an incoming ribonucleotide and the DNA template guides the formation of a complementary mRNA molecule. The DNA template closes behind the RNA synthesis site, releasing the new RNA molecule.(B) In transcription, a single DNA strand is used as a template. The RNA transcript is released, leaving the DNA molecule intact.

A tRNA molecule. Complementary base pairing between different portions of the tRNA molecule maintains its shape.

Translation. Complementary base pairing between the anticodons of incoming tRNA molecules and the codons of the mRNA guides the formation of the amino acid chain.

Major genetic traffic signals in bacteria. These signals tell RNA polymerase where to begin and end transcription, enable the ribosome to recognize mRNA, and direct the ribosome to start and stop protein synthesis. RRE, ribosome recognition element.

Splicing of precursor RNA to create mRNA.

Transcriptional regulation of thelac operon. P is the promoter; O is the operator.

Transcriptional regulation of the trp operon. P is the promoter; O is the operator.

Activator proteins are needed for transcription in eukaryotic cells.

E. coli osmotically shocked to release DNA. (Photograph copyright K.G.Murti/Visuals Unlimited.)

Electron micrographs of various viruses. (A) Bacteriophage lambda (magnification, ×275,000). (Photograph copyright K. G. Murti/Visuals Unlimited.) (B) Purified bacteriophage T4. (Photograph courtesy of F. P. Booy; reprinted from J. D. Karam et al., ed., Molecular Biology of Bacteriophage T4, ASM Press, Washington, DC, 1994.) (C) Tobacco mosaic virus (magnification, ×144,000). (Photograph copyright K. G. Murti/ Visuals Unlimited.) (D) Vesicular stomatitis virus (rabies group) (magnification, ×100,000). (Photograph copyright K. G. Murti/Visuals Unlimited.)

General structure of an amino acid. R signifies one of the 20 different side chains shown in Figure 4.23 .

To form proteins, amino acids are joined by peptide bonds.

A polar covalent bond. Although the oxygen and hydrogen nuclei are sharing two electrons, the highly electronegative oxygen nucleus tends to draw them away from the weakly electronegative hydrogen nucleus. As a result, the oxygen end of the bond acquires a partial negative charge, while the hydrogen end is partially positive.

The amino acids commonly found in proteins. The three-letter abbreviation for each amino acid is shown beneath its full name.

Water is a very polar molecule. The strongly electronegative oxygen nucleus hogs the electrons it shares with the hydrogen nuclei.

A hydrogen bond (dotted line) is a weak electrostatic attraction between opposite partial charges.

Common hydrogen bonds in biological systems.

The alpha helix. Cα indicates the carbon atoms with side chains, which are not shown.

A beta sheet. Cα indicates the carbon atoms with side chains, which are not shown.

In this drawing of the replication termination protein of E. coli, each sphere represents an atom. Even though this protein is small, its structure is complex.(Drawing courtesy of Stephen White, in whose laboratory the structure was determined.)

Ribbon drawings of protein structures. The beta strands in panels A and B are numbered in order from the N terminus to the C terminus of the amino acid chain. (Drawings courtesy of Jane Richardson.)

Some protein structure motifs. (Panels A and C are from C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991; panels B and D are from A. Lehninger, D. Nelson, and M. Cox, Principles of Biochemistry, 2nd ed., Worth Publishers, Inc., New York, NY, 1993.)

Domain structure of the bacteriophage lambda repressor protein. (A) The N-terminal domain consists of amino acids 1 through 92, and the C terminal domain consists of residues 132 through 236. (B) The repressor forms dimers through the interaction of the C-terminal domains. The N-terminal domains bind to a specific DNA sequence. (From M. Ptashne, A Genetic Switch, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2004.)

Disulfide bridges stabilize protein structure. (Panel B is from C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991.)

Domain structures of some modular proteins. Epidermal growth factor (EGF) is a protein that signals several cell types to divide. The other four proteins are protein-cleaving enzymes with a variety of physiological roles. (From C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991.)

Keratin, a structural protein. (A) A single keratin molecule forms a long alpha helix. (B) Two keratin alpha helices then wrap around each other. (From J. D. Watson et al., Molecular Biology of the Gene, 4th ed., vol. 1, Benjamin/Cummings, Menlo Park, CA, 1987. Reprinted by permission of Addison Wesley Longman Publishers, Inc.) (C) Two-chain coils lie end to end and side by side, forming fibers. (From A. Lehninger, D. Nelson, and M. Cox, Principles of Biochemistry, 2nd ed., Worth Publishers, Inc., New York, NY, 1993.)

The biochemistry of a permanent hair wave.

Binding of lambda repressor protein to DNA. (From M. Ptashne, A Genetic Switch, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2004.)

Binding of the amino acid tryptophan to the trp repressor protein changes the conformation of the repressor so that it can bind to DNA. (Reprinted by permission from Nature 327:591–597, 1987.)

Mechanism of action of the proteinase chymotrypsin, an example of a serine protease. (Panel D is from C. Branden and J. Tooze, Introduction to Protein Structure, Garland Publishing, Inc., New York, NY, 1991.)

Representation of sickle-cell hemoglobin aggregation. (A) Normal hemoglobin molecules do not stick together. (B) The hydrophobic patch on the surface of sickle-cell hemoglobin caused by the glutamateto-valine substitution at position 6 (Val-6) fits neatly into a hydrophobic pocket on a second molecule. Thus, sickle-cell hemoglobin molecules can polymerize in a head-to-tail fashion.

Schematic representation of how the loss of 70 C-terminal amino acids from a receptor protein results in increased red blood cell (RBC) production.