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11 Metabolism: The Synthesis of Nucleic Acids and Proteins

 

CHAPTER OVERVIEW

This chapter presents an overview of the synthesis of two major classes of macromolecules: nucleic acids and proteins. Adequate knowledge of these processes is essential to the understanding of molecular biology and microbial genetics. The chapter begins with general information about nucleic acid structure to increase the comprehension of the processes of DNA replication, RNA transcription, and polypeptide (protein) translation.

 

CHAPTER OBJECTIVES

After reading this chapter you should be able to:

o discuss the structural and compositional differences between DNA and RNA

o discuss the association of proteins with DNA and describe the differences in the types of proteins associated with procaryotic and eucaryotic DNA

o discuss the flow of genetic information from DNA, to RNA, to protein, and discuss the relationship between the nucleotide sequences of DNA and RNA and the amino acid sequences of proteins

o describe the replication of DNA and the processes used to minimize errors and correct those errors which do occur

o discuss the transcription of RNA and describe the similarities and differences between eucaryotic and procaryotic RNA transcription

o discuss the translation of proteins and describe the role(s) of the various components required for this process

 

CHAPTER OUTLINE

I. Nucleic Acid Structure

A. DNA Structure

1. DNA is composed of purine and pyrimidine nucleosides that contain the sugar 2¢-deoxyribose and are joined by phosphodiester bridges

2. DNA is usually a double helix consisting of two chains of DNA coiled around each other

3. The purine adenine (A) on one strand of DNA is always paired with the pyrimidine thymine (T) on the other strand, while the purine guanine (G) is always paired with the pyrimidine cytosine (C); thus, the two strands are said to be complementary

4. The two polynucleotide chains are antiparallel (i.e., their sugar-phosphate backbones are oriented in opposite directions)

5. The two strands are not positioned directly opposite one another; therefore, a major groove and a smaller minor groove are formed by the double helix backbone

B. RNA structure

1. RNA differs from DNA in that it is composed of the sugar ribose rather than 2¢-deoxyribose

2. RNA differs from DNA in that it contains the pyrimidine uracil (U) instead of thymine

3. RNA differs from DNA in that it usually consists of a single strand that can coil back on itself, rather than two strands coiled around each other

4. Three different kinds of RNA exist-ribosomal (rRNA), transfer (tRNA), and messenger (mRNA)-and differ from one another in function, site of synthesis in eucaryotic cells, and structure

C. The organization of DNA in cells

1. In procaryotes, the DNA exists as a closed circular, supercoiled molecule associated with basic (histonelike) proteins

2. In eucaryotes, the DNA is more highly organized

a. It is associated with basic (histone) proteins

b. It is coiled into repeating units known as nucleosomes

II. DNA Replication

A. Pattern of DNA synthesis

1. DNA replication is semiconservative: each strand of DNA is conserved, but the two strands are separated from each other and serve as templates for the production of another strand (according to the base-pairing rules discussed earlier)

2. Replication forks are the areas of the DNA molecule where this strand separation occurs and the synthesis of new DNA takes place

3. A replicon consists of an origin of replication and all the DNA that is replicated as a unit from that origin

4. The bacterial chromosome is usually a single replicon

5. Closed circular DNA molecules replicate by means of a rolling-circle mechanism

6. The large linear DNA molecules of eucaryotes employ multiple simultaneous replicons to efficiently replicate the relatively large molecules within a reasonable time span

B. Mechanism of DNA replication

1. Helicases unwind the two strands of DNA

2. Single-stranded DNA binding proteins (SSBs) keep the single strands apart

3. Topoisomerases relieve the tension caused by the unwinding process; DNA gyrase is a topoisomerase that removes the supertwists produced during replication

4. Primases synthesize a small RNA molecule (approximately 10 nucleotides) that will act as a primer for DNA synthesis

5. DNA polymerase III synthesizes the complementary strand of DNA according to the base-pairing rules established; on one strand (the leading strand), synthesis is continuous, while on the other (the lagging strand), a series of fragments are generated by discontinuous synthesis; a multiprotein complex called a replisome organizes all of these processes

6. DNA polymerase I removes the primers and fills the gaps that result from the RNA deletion

7. DNA ligases join the discontinuous fragments to form a complete strand of DNA

8. DNA replication is extraordinarily complex; at least 30 proteins are required to replicate the E. coli chromosome

9. The rate of DNA synthesis is 750 to 1,000 base pairs per second in procaryotes, and 50 to 100 base pairs per second in eucaryotes

III. DNA Transcription or RNA Synthesis

A. Three types of RNA are produced by transcription

1. tRNA carries amino acids during protein synthesis

2. rRNA molecules are components of the ribosomes

3. mRNA carries the message that directs the synthesis of proteins; in addition to the translated regions of the mRNA, there are several untranslated regions that serve particular purposes

a. Leader sequences consist of 25 to 150 bases at the 5¢ end of the mRNA, and precede the initiation codon

b. Spacer regions separate the segments that code for individual polypeptides in polygenic mRNAs (i.e., those RNAs that encode more than one polypeptide chain)

c. Trailer regions are found at the 3¢ end of the mRNA after the last termination codon

B. RNA polymerase (a large multi-subunit enzyme) is the enzyme responsible for the synthesis of RNA

C. A gene is a DNA segment or sequence that codes for a polypeptide, rRNA, or tRNA

D. In a given segment, only one strand (sense or template strand) is copied

E. A promoter is the region of the DNA to which RNA polymerase binds in order to initiate transcription

F. Terminators are regions of the DNA that, when transcribed, result in the termination of the transcription process

G. In eucaryotes, transcription yields large RNA precursors (heterogeneous nuclear RNA; hnRNA) that must be processed by posttranscriptional modification to produce mRNA

H. hnRNA is modified by the addition of adenylic acid to the 3¢ end to produce a polyA sequence about 200 nucleotides long

I. hnRNA is also modified by the addition of 7-methylguanosine to the 5¢ end by a tri-phosphate linkage

J. These two modifications are believed to protect the mRNA from exonuclease digestion

K. Eucaryotic genes are split or interrupted such that the expressed sequences (exons) are separated from one another by intervening sequences (introns); the introns are represented in the primary transcript but are subsequently removed by a process called RNA splicing; some splicing is self-catalyzed by RNA molecules called ribozymes

L. Interrupted genes have been found in cyanobacteria and archaeobacteria, but not in other procaryotes

IV. Protein Synthesis-translation

A. Ribosomes complex with mRNA and, using the information contained within the mRNA, combine the appropriate amino acids one at a time to form the complete polypeptide chain

B. The first stage of protein synthesis is the attachment of amino acids to tRNA molecules; this process is referred to as amino acid activation

C. Each tRNA can only carry a specific amino acid

D. Ribosomes are complex organelles constructed from several rRNA molecules and many polypeptides

E. Protein synthesis is divided into three phases:

1. Initiation takes place at a special initiator codon (AUG)

a. The two subunits of the ribosome complex with the mRNA

b. Three protein initiation factors are also required in procaryotes

2. Elongation involves the sequential addition of amino acids to the growing polypeptide chain

a. Each amino acid is positioned when the anticodon region of its tRNA approaches its complementary codon on the mRNA molecule

b. A ribosomal enzyme peptidyl transferase catalyzes the formation of the peptide bonds between adjacent amino acids; the 23S rRNA is a major component of this enzyme

c. After each amino acid is added to the chain, translocation occurs and thereby moves the ribosome to position the next codon appropriately

d. Several polypeptide elongation factors are required for this process

e. Hydrolysis of ATP and GTP provide the energy needed for this process

3. Termination takes place at any one of three special codons (UAA, UAG, or UGA)

a. Three polypeptide release factors aid in the recognition of these codons

b. No amino acids are incorporated into the growing polypeptide chain at these positions

c. The ribosome hydrolyzes the bond between the completed protein and the final tRNA, and the protein is released from the ribosome, which then dissociates into its two component subunits

d. As the protein leaves the ribosome it folds into its proper shape aided by molecular chaperones

F. Eucaryotic protein synthesis is similar, but may require more protein factors to mediate various parts of the process; and usually is less dependent on molecular chaperones for proper folding of the newly synthesized protein

G. Procaryotic proteins may undergo splicing after translation; such splicing removes intervening sequences (inteins) from the sequences (exteins) that remain in the final product

 

 

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