Molecular Biology of the Gene: DNA Replication, Transcription, and Translation

Molecular Biology of the Gene

Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information within a biological system. It explains how DNA is transcribed into RNA, which is then translated into protein, ultimately determining phenotype.

• DNA stores genetic information.

• Transcription is the process by which DNA is used to synthesize RNA.

• Translation is the process by which RNA is used to synthesize proteins (amino acid chains).

• Replication is the copying of DNA to produce identical DNA molecules.

• Reverse transcription (in some viruses) is the synthesis of DNA from an RNA template.

Equation:

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

DNA Structure and Complementarity

DNA Structure

DNA is a double helix composed of two antiparallel strands held together by hydrogen bonds between complementary nitrogenous bases.

• Nucleotides consist of a phosphate group, deoxyribose sugar, and a nitrogenous base.

• Bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

• Base Pairing: A pairs with T, C pairs with G

• Antiparallel orientation: One strand runs 5' to 3', the other 3' to 5'

Example: If one DNA strand reads GTACCCTA, the complementary strand reads CATGGGAT.

DNA Replication

Semi-Conservative Replication

DNA replication is the process by which DNA makes a copy of itself during cell division. It is termed "semi-conservative" because each new DNA molecule consists of one old (parental) strand and one newly synthesized strand.

• Origins of replication: Specific sequences where replication begins.

• Replication fork: The Y-shaped region where DNA is unwound and new strands are synthesized.

• Helicase: Enzyme that unwinds the DNA double helix.

• DNA polymerase: Enzyme that synthesizes new DNA strands by adding nucleotides to a primer.

• Leading strand: Synthesized continuously in the 5' to 3' direction.

• Lagging strand: Synthesized discontinuously as Okazaki fragments, later joined by DNA ligase.

• DNA ligase: Enzyme that joins Okazaki fragments on the lagging strand.

Replication accuracy: E. coli can replicate 4.6 million base pairs in under an hour; human cells replicate over 6 billion base pairs in a few hours. Error rate is about 1 in several billion base pairs.

RNA Structure and Types

RNA vs. DNA

RNA is typically single-stranded and contains ribose sugar instead of deoxyribose. Uracil (U) replaces thymine (T) as a base.

• Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes.

• Ribosomal RNA (rRNA): Forms the core of ribosome structure and catalyzes protein synthesis.

• Transfer RNA (tRNA): Brings amino acids to the ribosome during translation.

Base Pairing: G–C (DNA and RNA), A–T (DNA only), A–U (RNA only)

Transcription: DNA to mRNA

Gene Structure

• Gene: A unit of nucleotide sequences that encodes a functional product.

• Regulatory region: Sequences that control gene expression.

• Promoter: Sequence where RNA polymerase binds and transcription begins.

• Exons: Coding regions retained in mature mRNA.

• Introns: Non-coding regions removed during RNA processing.

Stages of Transcription

• Initiation: RNA polymerase binds to promoter; transcription factors assist in eukaryotes.

• Elongation: RNA polymerase synthesizes RNA by adding nucleotides complementary to the DNA template.

• Termination: RNA polymerase reaches a terminator sequence and releases the newly made RNA.

RNA Modifications in Eukaryotes

Before eukaryotic mRNA can be translated, it undergoes several modifications:

• Splicing: Removal of introns and joining of exons.

• Capping: Addition of a modified guanosine to the 5' end for stability and ribosome binding.

• Poly-A tail: Addition of 100–200 adenine nucleotides to the 3' end to increase stability and lifespan in cytosol.

Translation: mRNA to Protein

Genetic Code and Codons

The genetic code is read in triplets called codons, each specifying an amino acid or a stop signal.

• Start codon: AUG (codes for methionine)

• Stop codons: UAA, UAG, UGA

• Redundant: Multiple codons can code for the same amino acid.

• Unambiguous: Each codon codes for only one amino acid.

• Non-overlapping: Codons are read one after another.

• Conservative: First two bases of codon are usually identical for a given amino acid.

Property	Description
Redundant	All amino acids coded by more than one codon
Unambiguous	Single codon never codes for more than one amino acid
Non-overlapping	Reads each codon one after another
Conservative	First two bases usually identical for a given amino acid

Translation Process

• Initiation: Ribosome assembles at the start codon of mRNA; initiator tRNA binds.

• Elongation: tRNAs bring amino acids to the ribosome; peptide bonds form between amino acids.

• Termination: Release factor binds to stop codon; completed polypeptide is released.

tRNA Structure: Has a 3' single-stranded region for amino acid attachment and an anticodon that pairs with mRNA codon.

Polyribosome: Multiple ribosomes can translate a single mRNA simultaneously, producing many copies of a protein.

From Genotype to Phenotype

Gene Expression and Phenotype

Genetic information flows from DNA to RNA to protein, determining an organism's phenotype. Changes in genotype (DNA sequence) can lead to changes in phenotype (observable traits).

• Genotype: Genetic makeup of an organism.

• Phenotype: Physical traits resulting from gene expression.

• Example: Mice with different DNA sequences for fur color genes have different coat colors.

Summary Table: DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, C, G	A, U, C, G
Strands	Double	Single
Function	Genetic storage	Protein synthesis, regulation

Learning Objectives

• Understand the steps and processes involved in creating proteins

• Understand how DNA is replicated

• Compare and contrast mRNA and tRNA

• Know the general steps of transcription

• Know the general steps of translation

Additional info: These notes cover topics from General Biology chapters on the molecular basis of inheritance and gene expression, including DNA replication, transcription, translation, and the genetic code.