Genetic Code and Transcription: Structure, Function, and Regulation

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Genetic Code & Transcription

Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information in cells: DNA is transcribed into RNA, which is then translated into protein. This process is fundamental to gene expression and the synthesis of proteins necessary for life.

DNA stores genetic information.
Gene expression refers to accessing DNA to make proteins.
Structural genes code for proteins with various functions.
Proteins influence cellular traits and functions.

DNA molecule, chromosome, and human cell Overview of DNA replication, RNA transcription, RNA processing, mRNA transport, and protein translation

DNA Stores Information for Synthesis of Proteins and RNA

Humans possess between 20,000 and 30,000 genes, each coding for a unique protein. Not all proteins are produced in every cell; cell-specific proteins are synthesized as needed.

Proteins are made in the appropriate cell type (e.g., eye-specific proteins in eye cells).

Gene Expression: From DNA to Protein

Gene expression involves accessing genetic material in DNA to produce proteins or, in some cases, functional RNAs. The process includes transcription and translation.

Cell diagram showing protein transport and organelles

The Genetic Code

Properties of the Genetic Code

The genetic code is the set of rules by which information encoded in mRNA is translated into proteins. It is characterized by several key properties:

Unambiguous: Each codon specifies only one amino acid.
Degenerate: Multiple codons can code for the same amino acid.
Commales: Codons are read sequentially without gaps.
Nonoverlapping: Each nucleotide is part of only one codon.
Nearly universal: The code is conserved across most organisms.

Genetic code table

Exceptions to the Universal Genetic Code

Although the genetic code is nearly universal, some exceptions exist, particularly in mitochondria and certain protozoa.

Codon	Normal Code Word	Altered Code Word	Source
UGA	Termination	Trp	Human and yeast mitochondria; Mycoplasma
CUA	Leu	Thr	Yeast mitochondria
AUA	Ile	Met	Human mitochondria
AGA	Arg	Termination	Human mitochondria
AGG	Arg	Termination	Human mitochondria
UAA	Termination	Gln	Paramecium, Tetrahymena, and Stylonychia
UAG	Termination	Gln	Paramecium

Table of exceptions to the universal genetic code

Gene Expression: Transcription

Parts of a Bacterial Gene and Transcript

Bacterial genes contain specific sequences that regulate transcription and translation:

Promoter: Site for RNA polymerase binding; signals transcription start.
Regulatory sequences: Bind regulatory proteins to influence transcription rate.
Coding sequence (Open Reading Frame): Codes for the protein.
Terminator: Signals transcription end.

Bacterial mRNA may be polycistronic, encoding multiple polypeptides.

Transcription Process

Transcription is the process by which RNA polymerase synthesizes an RNA copy from the DNA template. The transcript is complementary to the template strand and similar to the coding strand (with U replacing T).

Transcription proceeds from the 5’ to 3’ end of the RNA.
The start codon sets the reading frame for translation.

Transcription from promoter to terminator RNA polymerase synthesizing mRNA from DNA template

Translation: Ribosome Reads mRNA

The ribosome reads the mRNA sequence in codons (three nucleotides at a time) to synthesize a polypeptide. The sequence of codons determines the sequence of amino acids in the protein.

DNA, mRNA, and tRNA translation process Protein structure: primary, secondary, tertiary, quaternary

Transcriptional Stages

Initiation, Elongation, and Termination

Transcription occurs in three main stages:

Initiation: RNA polymerase binds to the promoter, forming an open complex.
Elongation: RNA polymerase synthesizes RNA by moving along the DNA template.
Termination: A termination signal causes RNA polymerase and the transcript to dissociate.

Stages of transcription: initiation, elongation, termination

Functions of RNA Molecules

mRNA: Encodes protein sequence.
tRNA: Brings amino acids to the ribosome.
rRNA: Structural and functional component of ribosomes.
Other small RNAs: Various regulatory and processing functions.

Transcriptional Initiation in Prokaryotes

Promoter Structure and Sigma Factor

The promoter contains conserved sequences (e.g., -35 and -10 regions) recognized by the sigma factor, which directs RNA polymerase to the correct initiation site.

Promoter region with -35 and -10 sequences Sigma factor binding to DNA

RNA Polymerase Complexes

Core enzyme: Synthesizes RNA transcript.
Sigma factor: Directs core enzyme to promoter.
Holoenzyme: Core enzyme plus sigma factor.

Transcriptional Elongation

RNA polymerase synthesizes RNA in the 5’ to 3’ direction, using ribonucleoside triphosphates. The template strand is used for complementary base pairing, with U replacing T in RNA.

RNA polymerase elongation and DNA unwinding Structure of RNA polymerase

Transcriptional Termination

Rho-Dependent and Rho-Independent Termination

Termination occurs when the RNA-DNA hybrid is destabilized, either by the action of the Rho protein (Rho-dependent) or by the formation of a hairpin loop and U-rich sequence (Rho-independent).

Rho protein: Functions as an RNA-DNA helicase.
Rho-dependent: Requires Rho and a hairpin loop.
Rho-independent: Requires a hairpin loop and poly-U sequence; NusA stabilizes the pause.

Transcription in Eukaryotes

RNA Polymerases

Eukaryotes have three main RNA polymerases:

RNA polymerase I: Synthesizes rRNA (except 5s).
RNA polymerase II: Synthesizes mRNA and some snRNA.
RNA polymerase III: Synthesizes tRNA and 5s rRNA.

Eukaryotic Promoters and Transcription Initiation

Promoters in eukaryotes contain elements such as the TATA box. General transcription factors (GTFs) assemble at the promoter to recruit RNA polymerase II and initiate transcription.

Eukaryotic promoter structure Assembly of transcription factors at the TATA box TFIIH and transcription initiation complex

Chromatin Structure and Transcription

Nucleosome Modification and Remodeling

Chromatin structure can inhibit transcription by restricting access to DNA. Nucleosomes can be covalently modified (e.g., acetylation, methylation) or remodeled (e.g., moved or loosened) to enhance transcription.

Acetylation: Loosens histone-DNA interaction.
ATP-dependent remodeling: Uses energy to alter nucleosome structure.

Covalent modification of histones ATP-dependent chromatin remodeling

RNA Modification in Eukaryotes

Common RNA Modifications

Eukaryotic RNA undergoes several modifications to become functional:

Modification	Description
Trimming/Processing	Removal of part of 5’ and/or 3’ end; cleavage of long transcript
Splicing	Cleavage and rejoining of RNA molecules
5’ capping	Cap added to 5’ end for ribosome recognition and protection
3’ tailing	Poly A added to 3’ end for protection
RNA editing	Bases changed, added, or deleted
Base modification	Covalent modifications, often in tRNAs

Table of RNA modifications

RNA Splicing

Splicing removes introns from pre-mRNA and covalently joins exons. There are three main types:

Group I: Self-splicing ribozymes (e.g., rRNA in Tetrahymena).
Group II: Self-splicing ribozymes (found in organelles and some bacteria).
Group III: Requires spliceosome (multiunit complex in eukaryotic nuclear genes).

RNA splicing mechanism Group II self-splicing Spliceosome mechanism Spliceosome structure and function

Alternative Splicing

Alternative splicing allows different exons to be used in various tissues, producing multiple proteins from a single gene. This increases genetic diversity and protein complexity.

Alternative splicing concept

5’ Capping and 3’ Tailing

A 7-methylguanosine cap is added to the 5’ end of mRNA for protection and ribosome recognition. Poly-A tailing at the 3’ end increases stability and translation efficiency.

5' capping mechanism RNA editing mechanism

RNA Editing

RNA editing changes the nucleotide sequence of RNA, affecting the protein produced. For example, Apolipoprotein B mRNA is edited in the intestine, resulting in a shorter protein due to a C-to-U change (CAA to UAA stop codon).

RNA editing in Apolipoprotein B

Base Modification

Covalent modifications to RNA bases, especially in tRNAs, enhance their function and stability.

Types of RNA modifications

Summary Table: Modifications to Eukaryotic RNA

Type	Description
Trimming/Processing	Large becomes smaller
5’ Capping	Protects, tells ribosome where to begin translation
3’ Tailing	Protection
Splicing	Removes introns
Editing	Changes sequence of base(s)
Base Modification	Covalent changes, for tRNA function

Summary table of RNA modifications

Key Equations and Concepts

Transcription direction: RNA is synthesized 5’ to 3’.
Complementarity rule: AT/GC rule, with U replacing T in RNA.
Reading frame: Set by the start codon (AUG).

Example: The mRNA sequence 5’-AUG-GCU-AAA-3’ codes for the amino acids Met-Ala-Lys.

Formula:

Additional info: Alternative splicing and RNA editing significantly increase the diversity of proteins produced from a single gene, contributing to cellular complexity and adaptability.