Transcription, RNA Processing, and Translation: Central Dogma and Protein Synthesis

Central Dogma: Flow of Genetic Information

Overview of Genetic Information Transfer

The central dogma of molecular biology describes the flow of genetic information within a cell: DNA is transcribed into RNA, which is then translated into protein. This process is fundamental to gene expression and cellular function.

• DNA Replication: DNA is copied to produce identical molecules for cell division.

• Transcription: DNA is used as a template to synthesize RNA.

• Translation: RNA directs the synthesis of proteins.

Key Features:

• Semi-conservative replication: Each new DNA molecule contains one old and one new strand.

• Leading strand: Synthesized continuously; lagging strand: synthesized discontinuously.

• Transcription involves initiation, elongation, and termination.

• RNA processing (in eukaryotes): Includes splicing of introns, addition of 5' cap, and poly-A tail.

Protein Function

Roles of Proteins in Cells

Proteins are large molecules composed of amino acid subunits joined by peptide bonds and folded into specific three-dimensional shapes. Their diverse functions include:

• Structural support (e.g., keratin in skin)

• Enzymatic activity (speeding chemical reactions)

• Movement (muscle contraction)

• Immune response (antibodies binding foreign substances)

Transcription, RNA Processing, and Translation

Transcription

Transcription is the process by which RNA is synthesized from a DNA template. In eukaryotes, this occurs in the nucleus and involves several steps:

• Initiation: RNA polymerase binds to the promoter region of DNA.

• Elongation: RNA polymerase synthesizes the RNA strand by adding nucleotides.

• Termination: RNA polymerase releases the newly formed RNA molecule.

In eukaryotes, the initial RNA transcript (pre-mRNA) undergoes processing:

• Splicing removes introns and joins exons.

• 5' cap and poly-A tail are added for stability and export.

Translation

Translation is the process by which the sequence of bases in mRNA is converted into an amino acid sequence in a protein. This occurs in the cytoplasm at the ribosome.

• Initiation: Assembly of ribosome and initiator tRNA at the start codon.

• Elongation: Sequential addition of amino acids to the growing polypeptide chain.

• Termination: Release of the completed polypeptide when a stop codon is reached.

Translation in Bacteria and Eukaryotes

Key Differences

• In eukaryotes, transcription and translation are separated by the nuclear envelope.

• mRNAs are synthesized and processed in the nucleus, then transported to the cytoplasm for translation.

• In bacteria, transcription and translation are coupled; ribosomes begin translating mRNA before transcription is complete.

• Multiple ribosomes can translate a single mRNA simultaneously, forming a polyribosome.

How Does an mRNA Codon Specify an Amino Acid?

Codon-Anticodon Interaction

Genetic information in mRNA is read in sets of three nucleotides called codons, each specifying an amino acid. Two hypotheses were proposed:

• Direct interaction between mRNA codons and amino acids (not supported).

• Adapter hypothesis: Transfer RNA (tRNA) acts as an adapter, binding amino acids and interacting with mRNA codons.

tRNAs carry amino acids to the ribosome and match their anticodon sequence to the mRNA codon.

Structure and Function of tRNA

tRNA Characteristics

• Short molecules: 75–85 nucleotides long.

• Fold into stem-and-loop secondary structures.

• 3' end has a CCA sequence for amino acid attachment.

• Aminoacyl tRNA: tRNA linked to its specific amino acid.

• Anticodon loop base-pairs with mRNA codon.

Attachment of Amino Acids to tRNAs

Aminoacyl-tRNA Synthetases

• ATP is required to attach an amino acid to tRNA.

• Aminoacyl-tRNA synthetases are enzymes that catalyze this attachment.

• There is a specific synthetase for each of the 20 amino acids.

• One or more tRNAs exist for each amino acid.

How Many tRNAs Are There?

Wobble Hypothesis

• There are 61 codons for amino acids but only about 40 tRNAs in most cells.

• Wobble hypothesis: The anticodon of tRNA can base-pair with more than one codon, especially at the third position, allowing nonstandard base pairing.

Structure of Ribosomes and Their Function in Translation

Ribosome Composition and Activity

• Ribosomes are composed of many proteins and ribosomal RNA (rRNA).

• The active site is entirely rRNA, which catalyzes peptide bond formation.

• The ribosome is a ribozyme (an RNA molecule with catalytic activity).

• Ribosomes have two subunits: small (holds mRNA) and large (forms peptide bonds).

Ribosomal Sites

• During translation, three tRNAs line up within the ribosome:

• A site: Accepts aminoacyl tRNA.

• P site: Peptidyl site where peptide bond forms.

• E site: Exit site for tRNAs without amino acids.

Steps of Translation

Initiation

• Initiator tRNA binds to the start codon on mRNA.

• Small ribosomal subunit assembles with mRNA and initiator tRNA.

• Large subunit joins to complete the ribosome.

Elongation

• Incoming aminoacyl tRNA enters the A site.

• Peptide bond forms between amino acids in the P and A sites.

• Translocation moves the ribosome along the mRNA, shifting tRNAs through the sites.

Termination

• Release factor binds to stop codon in the A site.

• Polypeptide and uncharged tRNAs are released.

• Ribosome subunits separate.

Genetic Code Table

Codon-Amino Acid Assignments

The genetic code specifies which codons correspond to which amino acids. For example, a tRNA with the anticodon 3' UGG 5' would carry the amino acid threonine (Thr).

Codon	Amino Acid
ACU	Thr
ACC	Thr
ACA	Thr
ACG	Thr

Post-Translational Modifications

Protein Processing and Folding

• Most proteins undergo post-translational modifications before becoming fully functional.

• Folding determines protein shape and function; molecular chaperones assist in proper folding.

• Chemical modifications may include addition of sugar, lipid, or phosphate groups.

• Phosphorylation is catalyzed by enzymes called protein kinases.

Applications: mRNA Vaccines

Mechanism and Example

• mRNA vaccines introduce synthetic mRNA encoding viral proteins.

• Cells translate the mRNA to produce viral proteins, triggering an immune response.

• Example: COVID-19 vaccines (Pfizer-BioNTech and Moderna).

Summary Table: Key Differences Between Bacteria and Eukaryotes in Transcription and Translation

Feature	Bacteria	Eukaryotes
Location of Transcription	Cytoplasm	Nucleus
RNA Processing	Minimal	Extensive (splicing, capping, poly-A tail)
Coupling of Transcription and Translation	Yes	No
Polyribosome Formation	Yes	Yes

Learning Objectives

• Relate the structure of RNA polymerase to its function in transcription.

• Describe the steps in initiation, elongation, and termination of transcription and translation.

• List major differences between transcription and RNA processing in bacteria and eukaryotes.

• Explain how mRNA is processed in eukaryotes.

• Relate the structure of ribosomes and tRNA to their functions in translation.

Key Equations and Concepts

• Peptide Bond Formation:

$\text{Amino acid}_n + \text{Amino acid}_{n+1} \xrightarrow{\text{Ribosome}} \text{Peptide bond} + \text{Water}$

• Energy Requirement for tRNA Charging:

$\text{Amino acid} + \text{tRNA} + \text{ATP} \xrightarrow{\text{Aminoacyl-tRNA synthetase}} \text{Aminoacyl-tRNA} + \text{AMP} + \text{PP}_i$

• Central Dogma:

$\text{DNA} \xrightarrow{\text{Transcription}} \text{RNA} \xrightarrow{\text{Translation}} \text{Protein}$