Molecular Biology Overview and the Central Dogma

Molecular Biology Overview and the Central Dogma

• The lecture focuses on the fundamental aspects of molecular biology, particularly in relation to genetic information storage and transfer in living cells.

• Understanding the central dogma framework prepares us for further study of genetic information transfer stages.

DNA Structure and Replication

• DNA Replication: Semiconservative Model

  • Each daughter DNA molecule consists of one parental strand and one new strand.

  • Replication necessitates unwinding the helical structure and breaking hydrogen bonds between base pairs.

DNA Features

• DNA consists of four bases: adenine (A), thymine (T), guanine (G), and cytosine (C).

• Nucleotides link via 3’-5’ phosphodiester bonds, forming a double helix structure with antiparallel strands.

Base Pairing

• Nucleotides interact through hydrogen bonds:

  • In DNA, A pairs with T (2 hydrogen bonds) and G pairs with C (3 hydrogen bonds).

  • In RNA, A pairs with U (instead of T).

DNA Base Pair Distances

• AT Base Pair: Distance of 1.11 nm.

• GC Base Pair: Distance of 1.08 nm.

• GC pairs are more stable due to their three hydrogen bonds compared to two in AT pairs.

Features of Base Pairing

• Base pairing is vital for replication, transcription, and translation processes.

• Plans for base pairing and stability ensure constant distances within the double helix.

Central Dogma of Molecular Biology

• The central dogma illustrates the flow of genetic information:

  • From DNA to RNA to Protein.

• DNA templates its own replication and the synthesis of RNA, which in turn dictates protein formation.

Semiconservative Replication Mechanism

• After one generation, progeny DNA strands consist of one parental and one new strand.

• The pattern continues through subsequent generations, illustrating the semiconservative DNA replication model.

Melting Temperature (Tm)

• The melting temperature is the point at which double-stranded DNA separates to single-stranded DNA when subjected to heat.

• Melting Curve Analysis:

  • Shows lower absorbance in double-stranded DNA compared to single-stranded DNA; Tm defined where strands are 50% separated.

RNA and its Functions

• Three Types of RNA in Gene Expression:

  1. Messenger RNA (mRNA): Template for protein synthesis; varies in length—average around 1.2 kb in E. coli.

  2. Transfer RNA (tRNA): Carries activated amino acids for protein synthesis; typically about 75 nucleotides long.

  3. Ribosomal RNA (rRNA): Major component of ribosomes, playing both structural and catalytic roles—three types in E. coli (23S, 16S, and 5S).

RNA Characteristics in E. coli

• rRNA constitutes about 80% of cellular RNA, followed by tRNA (15%) and mRNA (5% average size around 1200 bases).

• Efficiency in gene structure is higher in prokaryotes than eukaryotes.

Transcription Overview

• RNA Polymerase Reaction: Requires template DNA, activated precursors, and a metal ion (Mg2+/Mn2+).

• Synthesized RNA strand follows the 5’ to 3’ direction.

• Unlike DNA polymerase, RNA polymerase does not need a primer and does not possess nuclease activity for mismatch correction.

Splicing in Eukaryotes

• Initial transcription produces a pre-mRNA which undergoes modifications:

  • Addition of a 5’ cap and 3’ poly(A) tail.

  • Removal of introns through splicing to form mature mRNA for translation.

Genetic Code and Protein Synthesis

• Codons: Groups of three nucleotides in mRNA encode amino acids; the code is non-overlapping and degenerate.

• Start and Stop Codons: AUG signals the start; UAA, UAG, UGA are stop signals for termination of translation.

Aminoacyl-tRNA and Protein Assembly

• Amino acids are connected to tRNAs at their 3' ends, linking codons in mRNA to corresponding amino acids during translation.

• The Shine-Dalgarno sequence in prokaryotes, and the presence of a 5’ cap in eukaryotes assists in the initiation of translation.

The Role of Introns and Exons

• Introns: Non-coding sequences removed during splicing.

• Exons: Coding regions that remain and define the functional domains in proteins.

Understanding Genomes

• A genome encompasses the complete genetic sequence of an organism, e.g., human genome has around 3 billion base pairs.

• Prokaryotic genomes are densely packed with genes, whereas eukaryotic genomes contain substantial non-coding DNA, including repetitive elements.

• Non-functional DNA may represent remnants of gene duplication events or provide material for new gene evolution.