Chapter 10: Molecular Biology of the Gene

Deoxyribonucleotide Structure

Deoxyribonucleotides are the building blocks of DNA. Each consists of three components: a deoxyribose sugar, a phosphate group, and a nitrogenous base.

• Deoxyribose Sugar: A five-carbon sugar lacking an oxygen atom at the 2' position compared to ribose.

• Phosphate Group: Attached to the 5' carbon of the sugar; represented as an encircled "P" in diagrams.

• Nitrogenous Base: Attached to the 1' carbon; can be a purine (adenine or guanine) or pyrimidine (cytosine or thymine).

• Diagram Representation: Pentagon for sugar, encircled "P" for phosphate, and one or two pentagons for bases.

Example: A deoxyribonucleotide of adenine (dAMP) contains deoxyribose, a phosphate, and adenine.

Chargaff’s Rule and Nucleotide Percentages

Chargaff’s rule states that in DNA, the amount of adenine (A) equals thymine (T), and the amount of guanine (G) equals cytosine (C).

• Rule: %A = %T and %G = %C

• Application: If %A = 30%, then %T = 30%, and %G + %C = 40% (so %G = 20%, %C = 20%).

Example: Given 35% cytosine, then guanine is 35%, and adenine and thymine are each 15%.

Numbering of Carbons in Ribose and Deoxyribose

The carbons in the sugar are numbered 1' through 5'. This numbering is crucial for understanding DNA structure and replication.

• 1' Carbon: Attached to the nitrogenous base.

• 3' Carbon: Has a hydroxyl (-OH) group; site of new nucleotide addition during DNA synthesis.

• 5' Carbon: Attached to the phosphate group.

Significance: DNA strands have directionality, running from 5' to 3'.

Key Terms in DNA Structure

• Double Helix: The spiral structure formed by two complementary DNA strands.

• Double-Stranded: DNA consists of two strands held together by base pairing.

• Antiparallel: The two DNA strands run in opposite directions (one 5'→3', the other 3'→5').

• 5'-Phosphate: The end of a DNA strand with a free phosphate group on the 5' carbon.

• 3'-Hydroxyl: The end of a DNA strand with a free hydroxyl group on the 3' carbon.

• Hydrogen Bonding: Weak bonds between complementary bases (A-T: 2 bonds, G-C: 3 bonds).

• Base Pairing: Specific pairing: A with T, G with C.

DNA vs. RNA: Structure and Function

• DNA: Double-stranded, contains deoxyribose, bases are A, T, G, C; stores genetic information.

• RNA: Single-stranded, contains ribose, bases are A, U, G, C; functions in gene expression (mRNA, tRNA, rRNA).

Comparison Table:

Semiconservative Replication of DNA

DNA replication is semiconservative: each new DNA molecule consists of one parental and one new strand.

• Parental (Template) Strands: Serve as templates for new synthesis.

• Direction: New strands synthesized 5' to 3'.

• Origin of Replication: Specific sequence where replication begins.

• Replication Fork: Y-shaped region where DNA is unwound.

• DNA Polymerases: Enzymes that add nucleotides to the growing strand.

• Continuous Synthesis: Leading strand synthesized continuously.

• Synthesis in Pieces: Lagging strand synthesized in Okazaki fragments.

Equation:

Additional info: dNMP = deoxynucleoside monophosphate; dNTP = deoxynucleoside triphosphate; = pyrophosphate.

Transcription and Translation: Phases and Locations

Gene expression involves two main processes: transcription (DNA to RNA) and translation (RNA to protein).

• Transcription: Occurs in the nucleus; synthesizes RNA from DNA template.

• Translation: Occurs in the cytoplasm (on ribosomes); synthesizes protein from mRNA.

• Phases:

  • Initiation: RNA polymerase binds promoter (transcription); ribosome assembles at start codon (translation).

  • Elongation: RNA strand grows (transcription); polypeptide chain elongates (translation).

  • Termination: RNA polymerase releases RNA at terminator (transcription); ribosome releases polypeptide at stop codon (translation).

The Genetic Code: Redundancy and Universality

The genetic code translates nucleotide sequences into amino acids. It is redundant and nearly universal.

• Redundant: Multiple codons can specify the same amino acid.

• Nearly Universal: The same codons specify the same amino acids in almost all organisms.

Example: Both UUU and UUC code for phenylalanine.

tRNA Structure and Function

Transfer RNA (tRNA) molecules bring amino acids to the ribosome during translation.

• Anticodon Site: Triplet of bases that pairs with mRNA codon.

• Amino Acid Binding Site: At the 3' end; attaches specific amino acid.

• Structure: Cloverleaf shape with three loops; often drawn as a simplified diagram.

Example: tRNAPhe has anticodon AAA (pairs with UUU codon) and carries phenylalanine.

Ribosome Structure and Function

Ribosomes are the sites of protein synthesis, composed of small and large subunits.

• Small Subunit: Binds mRNA and initiates translation.

• Large Subunit: Contains sites for tRNA binding and peptide bond formation.

• A Site (Aminoacyl): Holds incoming tRNA with amino acid.

• P Site (Peptidyl): Holds tRNA with growing polypeptide chain.

• E Site (Exit): Where tRNA exits after amino acid delivery.

• Peptide Bond Formation: Catalyzed by rRNA in the large subunit.

Example: During elongation, the polypeptide is transferred from the tRNA in the P site to the amino acid on the tRNA in the A site.