Chapter 4: DNA, RNA, and the Flow of Genetic Information

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Chapter 4: DNA, RNA, and the Flow of Genetic Information

Overview

This chapter explores the molecular mechanisms by which genetic information is stored, transmitted, and expressed in living organisms. The focus is on the central dogma of molecular biology, the genetic code, and the processes of transcription and translation.

The Central Dogma of Molecular Biology

Definition and Flow of Genetic Information

The central dogma of molecular biology describes the directional flow of genetic information within a biological system:

DNA serves as the genetic blueprint.
Transcription is the process by which DNA is copied into RNA.
Translation is the process by which RNA is used to synthesize proteins.

The general scheme is:

DNA → RNA → Protein

Reverse transcription (RNA to DNA) and replication (DNA to DNA) are also possible in some biological contexts.

Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point

Translation and the Genetic Code

Protein synthesis is a process called translation, where the sequence information in nucleic acids (mRNA) is converted into the sequence of amino acids in a protein. The genetic code is the set of rules by which the nucleotide sequence of mRNA is translated into the amino acid sequence of proteins.

Codon: A sequence of three nucleotides in mRNA that specifies a particular amino acid.
The genetic code links nucleic acid information to amino acid information.

Characteristics of the Genetic Code

Key Properties

Triplet Code: Each amino acid is encoded by a group of three nucleotides (codon).
Non-overlapping: Codons are read one after another, without overlap.
No Punctuation: The code is continuous, with no spaces or punctuation between codons.
Directionality: The code is read from the 5' end to the 3' end of the mRNA.
Degeneracy: Most amino acids are encoded by more than one codon, which helps minimize the effects of mutations.

Example: The amino acid leucine is encoded by six different codons: UUA, UUG, CUU, CUC, CUA, and CUG.

The Genetic Code

Codon Table

The genetic code is summarized in a codon table, which shows the correspondence between mRNA codons and amino acids. The table is read by selecting the first base (5' end) from the left, the second base from the top, and the third base (3' end) from the right.

First Position (5')	Second Position	Third Position (3')	Amino Acid
U	U	U	Phe
U	U	C	Phe
U	U	A	Leu
U	U	G	Leu
C	G	G	Arg
A	U	G	Met (Start)
G	G	G	Gly

Stop codons: UAA, UAG, and UGA signal termination of translation.

Messenger RNA Contains Start and Stop Signals for Protein Synthesis

Initiation and Termination

mRNA is translated on ribosomes.
The first codon is almost always AUG, which codes for methionine (Met).
In prokaryotes, the AUG is preceded by a purine-rich sequence called the Shine-Dalgarno sequence, which helps position the ribosome. The initiator tRNA carries formylmethionine (fMet).
In eukaryotes, the AUG nearest the 5' end is the initiator codon, and the initiator tRNA carries methionine (Met).
The location of the initiator codon establishes the reading frame for translation.

Stop codons (UAA, UAG, UGA) signal the end of protein synthesis.

Initiation of Protein Synthesis

Start Signals in Prokaryotes and Eukaryotes

Prokaryotic mRNA: Contains a purine-rich Shine-Dalgarno sequence upstream of the start codon (AUG), which base-pairs with ribosomal RNA to position the ribosome. The initiator tRNA carries formylmethionine (fMet).
Eukaryotic mRNA: Has a 5' cap structure; the ribosome scans from the 5' end to the first AUG, which is the start codon. The initiator tRNA carries methionine (Met).

Start signals are essential for the correct initiation of protein synthesis and for establishing the correct reading frame.

The Genetic Code is Nearly Universal

Universality and Exceptions

Most organisms use the same genetic code, reflecting a common evolutionary origin.
Some organisms and organelles (such as mitochondria) have slight variations in their genetic code.
Example: In ciliated protozoa, some codons that are stop signals in most organisms encode amino acids.
Mitochondria also use variations of the genetic code.

Distinctive Codons of Human Mitochondria

Codon	Standard Code	Mitochondrial Code
UGA	Stop	Trp
UGG	Trp	Trp
AUA	Ile	Met
AUG	Met	Met
AGA	Arg	Stop
AGG	Arg	Stop

Additional info: These variations are important in understanding mitochondrial genetics and diseases.