Lecture Outline:

1. Central Dogma of Molecular Biology: genetic information flows unidirectly from DNA to RNA to make proteins. The discovery of retroviruses contradicted this view. Why?

2. Composition and Structure of Nucleic Acids: DNA and RNA

• building blocks of nucleic acids, nucleotides.
  • sugar- ribose in RNA and deoxyribose in DNA
  • phosphate- present in both DNA and RNA
  • nitrogen containing bases-
    • DNA- adenine, guanine, cytosine, and thymine
    • RNA- adenine, guanine, cytosine, and uracil.
  • nucleoside/nucleotide- the covalent bonding of a nitrogen containing base to the sugar forms a nucleoside. The convalent attachment of phosphate to the nucleoside forms a nucleotide.
  • nucleic acids are polymers of nucleotides-
    • the covalent linkage of two nucleotides is through a phosphodiester bond.
    • RNA consists of a "string" of nucleotides (single stranded).
    • DNA is a double stranded structure- base pairing between nitrogen containing bases holds strands together.
      • hydrogen bonds hold bases together
      • base-pairing rules- adenine hydrogen bonds with a thymine and cytosine base-pairs with a guanine.
      • to have proper alignment of bases, strands must be of opposite polarity. What does this mean?

3. Replication of the Bacterial Chromosome: replication occurs by the semi-conservative model of replication in which each strand of DNA serves as a template for the synthesis of the complementary strand. Figs. 7.4, 7.5, and 7.6

• origin of replication- replication begins at one site on the closed circular molecule called the origin of replication.
• strand seperation- at the origin of replication strands come apart, and each strand serves as a template.
• directionality of replication- synthesis of the new strand always proceeds in the 5' to 3' direction (strand that is being synthesized not template strand). Synthesis requires the enzyme DNA polymerase and ligase. One strand is synthesized in a continuous manner the other in a discontinuous manner. What does this mean? Replication is not an error free process. Make about1 incorrect base insertion for every 10¹⁰ bases added.
• takes 40 minutes to replicate chromosome (E. coli). How does DNA replication keep pace with cell division (E. coli can divide every 20 minutes!).

4. Gene Expression: How is the information encoded in the order of specific nucleotide sequence of DNA, that makes up a gene, used to synthesize a protein? Process requires two interrelated processes, transcription and translation.

• transcription- the copying of specific regions of DNA into specific RNA molecules. Figs. 7.7, .8, and 7.9
  • initiation- at a specific nucleotide sequences on DNA, called a promoter region, RNA polymerase binds and begins to transcribe a region of DNA (either a gene or a group of genes). Only one of two DNA strands is transcibed, and synthesis always proceeds in the 5' to 3' direction. Which promoters RNA polymerase binds to is determined by the sigma subunit of RNA polymerase. Not all genes get transcribed. If an adenine on DNA is serving as a template, the complementary base in RNA will be uracil.
  • termination- occurs at a specific nucleotide sequence.
  • products of transcription- ribosomal, r, RNA (5S, 16S, and 23S rRNA), transfer, t, RNA (50 different types, at least one for every amino acid), and messenger, m, RNA (many, mRNA may be a mono or polycistron message. In bacteria, most mRNA's are polycistronic).
    
• translation: the reading of mRNA into a polypeptide chain(s).
  • basic structure of amino acids. See Fig. 2.12
  • compostion and structure of proteins- a polypeptide chain is composed of amino acids held together by a covalent bond called a peptide bond (Figs. 2.15 ). Polypeptide chain folds to give rise to a protein with a specific function (structural or enzymatic). Fig. 2.16 and 2.17
  • rRNA's made combine with certain proteins to form the 50S and 30S subunits of the bacterial ribosome, designated a 70S ribosome.
  • tRNA's made are covalently linked to specific amino acids. These "charged" tRNA's can now participate in protein synthesis.
  • process- Fig. 7.14 and 7.15
    • the 70S ribosome binds to a mRNA (5' end). mRNA translated in the 5' to 3' direction. Base-pair rules are essential to process. More than one ribosome may be bound to an mRNA.
    • reading- the nucleotide sequence of mRNA is read in groups of 3 bases, called a codon. What is the genetic code?
    • on surface of ribosome 2 codons are present. charged tRNA's that are complimentary to these codons base-pair (the three complimentary tRNA nucleotides is called an anticodon).
    • a peptide bond is formed between two amino acids, and ribosome moves over one codon, releasing the uncharged tRNA. Steps are repeated. Fig. 7.15
    • termination- when ribosome reaches a nonsense codon, this is read as a stop signal, and polypeptide chain is released. What is a nonsense codon?
• eucaryotes- introns, exons. Fig. 7.16
• See Table 7.4 for major differences between prokaryotic and eukaryotic transcription and translation.
• Regulation at the level of transcription:
  • Lactose Operon- Under both positive and negative control. What does this mean?

Learning Objectives:

• How is information stored in a DNA molecule?
• What is meant by the Central Dogma of Molecular Biolgoy?
• How can you distinguish between DNA and RNA?
• Describe how the bacterial chromosome is replicated and the role DNA polymerase and ligase.
• How is the information encoded in a DNA molecule used to synthesize proteins?
• You should be familiar with the following terms: the genetic code, codons, anticodons, and nonsense codons, promoters, polycistronic messages.

 6/17/09