In-Depth Notes on DNA Structure, Replication, and Gene Expression

Overview of DNA Structure and Function

• Complementarity of Bases

  • Adenine (A) forms 2 hydrogen bonds with Thymine (T)

  • Guanine (G) forms 3 hydrogen bonds with Cytosine (C)

  • This interaction maintains a consistent diameter across the DNA helix.

• Nucleotide Structure

  • Nucleotide consists of a sugar, phosphate group, and nitrogenous base.

  • Phosphodiester bonds link adjacent nucleotides, forming long strands with 5’ to 3’ orientation.

DNA Replication Process

• Three Requirements for Replication:

  • Parental DNA molecule (template)

  • Enzymes (e.g., DNA polymerases)

  • Nucleotide triphosphates (dATP, dGTP, dCTP, and dTTP)

• Stages of Replication:

  • Initiation: Begins at origins of replication, creating replication bubbles. In eukaryotes, multiple origins exist.

  • Elongation: Catalyzed by DNA polymerases, which only add nucleotides to the 3’ end of a growing strand. RNA primers, synthesized by primase, start the process.

  • Termination: Ends when replication is complete.

• Semiconservative Nature:

  • Each parental strand serves as a template for a new strand, conserving one original strand in each new DNA molecule.

• Leading vs. Lagging Strands:

  • Leading strand synthesizes continuously towards the replication fork.

  • Lagging strand synthesizes discontinuously in segments called Okazaki fragments, later joined by DNA ligase.

Gene Expression: Transcription and Translation

• Central Dogma: Genes (DNA) are transcribed to produce RNA, which is then translated into proteins.

  • Transcription:

  • Involves synthesis of mRNA from a DNA template.

  • Stages: Initiation (RNA polymerase binds to promoter), Elongation (RNA strand lengthens), Termination (ends transcription).

  • RNA Modifications in Eukaryotes:

  • 5’ cap added for protection and signaling.

  • Polyadenylation at the 3’ end improves stability.

  • Introns (non-coding regions) are removed via splicing.

• Translation:

  • Occurs on ribosomes, involving tRNA as an adapter molecule.

  • Stages:

  • Initiation: Binding of mRNA and tRNA to ribosome.

  • Elongation: Peptide bonds are formed between amino acids, facilitated by ribosomal action.

  • Termination: Occurs when ribosome encounters a stop codon, releasing completed polypeptide.

• Amino Acid Coding:

  • The genetic code consists of triplets (codons) where 61 code for amino acids, and 3 are stop signals. The code is redundant but unambiguous.

Significance of Splicing and Processing

• Exons vs. Introns:

  • Exons are coding sequences, whereas introns are noncoding sequences removed during RNA processing.

  • The process of splicing allows for alternative splicing, creating multiple protein variants from a single gene.

• Disease Example: Sickle-cell disease, caused by a mutation that alters the amino acid sequence of hemoglobin, illustrating the impact of genetic information on phenotype.

DNA Replication Basics:

• DNA Polymerase: Enzymes (e.g., DNA polymerases) that add nucleotides to the growing DNA strand during replication, specifically adding nucleotides to the 3’ end of a growing strand.

• Antiparallel: Refers to the orientation of the two strands of DNA, where one strand runs 5’ to 3’ and the other runs 3’ to 5’, allowing for complementary base pairing.

• Directionality in Replication: DNA replication occurs in the 5’ to 3’ direction. This means that nucleotides are added to the 3’ end of the new strand being synthesized.

• Base Pairing and Replication: The specific base pairing (A with T and G with C) ensures that each new strand is complementary to the template strand, allowing faithful copying of the genetic information.

• Leading vs. Lagging Strands:

  • Leading Strand: Synthesized continuously towards the replication fork.

  • Lagging Strand: Synthesized discontinuously in segments called Okazaki fragments, which are later joined together by DNA ligase. This difference arises because DNA polymerases can only add nucleotides at the 3’ end, necessitating a different approach for synthesizing the lagging strand.

Transcription Basics:

• mRNA Function: mRNA (messenger RNA) is synthesized from the DNA template during transcription and carries the genetic information from the DNA to the ribosome, where it serves as a template for protein synthesis.

Translation Basics:

• Ribosome Function: The ribosome's job is to facilitate the translation process by decoding the mRNA sequence and synthesizing proteins by forming peptide bonds between amino acids, as specified by the mRNA codons.

• Using the Codon Table: The genetic code consists of triplets (codons) that translate into amino acids. Each codon can be looked up using an amino acid codon table to determine which amino acid is specified by the mRNA sequence.

Chromosomal Ends and Telomeres:

• Problems with Chromosome Ends: During DNA replication, the ends of linear chromosomes (telomeres) present problems because DNA polymerase cannot fully replicate the 3’ ends of linear DNA molecules, leading to potential loss of genetic information.

• Telomeres: Repetitive nucleotide sequences at the ends of chromosomes protect them from degradation and prevent the loss of essential