Gene Expression: From DNA to Protein

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Gene Expression

Central Dogma of Molecular Biology

The central dogma of molecular biology describes the unidirectional flow of genetic information from DNA to RNA to protein. This process is fundamental to all living organisms and explains how genetic information is expressed as functional products.

Transcription: The process of synthesizing RNA from a DNA template.
Translation: The process of synthesizing proteins using the information encoded in mRNA.
Gene Expression: The full process by which genotype becomes expressed as phenotype, encompassing both transcription and translation.
DNA can be replicated, and in some cases, RNA can be reverse-transcribed into DNA, but the transfer of information from nucleic acid to protein is irreversible.

Central Dogma: DNA to RNA to Protein

Transcription

Introduction to Transcription

Transcription is the process by which an RNA molecule is synthesized from a DNA template within a gene. Genes are specific sequences of DNA that encode products such as proteins or functional RNAs.

Promoter: DNA sequence where transcription begins; site of RNA polymerase attachment.
Terminator: DNA sequence where transcription ends.
RNA Polymerase: Enzyme that synthesizes RNA from scratch, without a primer.
Upstream: DNA sequences in the opposite direction of transcription.
Downstream: DNA sequences in the direction of transcription.

Gene structure: promoter, coding sequence, terminator

DNA Strands in Transcription

Genes are located on double-stranded DNA, but only one strand serves as the template for RNA synthesis.

Coding Strand: Has the same sequence as the RNA transcript (except T is replaced by U in RNA).
Template Strand: Serves as the template for RNA synthesis; RNA is complementary to this strand.
RNA is synthesized in the 5' to 3' direction by pairing free RNA nucleotides with the DNA template strand.
Base-pairing rules: A-U (in RNA), T-A, C-G, G-C.

Transcription: coding and template strands

Steps of Transcription

Transcription occurs in three main steps: initiation, elongation, and termination.

Initiation: RNA polymerase binds to the promoter and unwinds the DNA. In prokaryotes, RNA polymerase binds directly; in eukaryotes, transcription factors are required.
Elongation: RNA polymerase synthesizes the RNA molecule by adding nucleotides in the 5' to 3' direction.
Termination: Transcription ends when RNA polymerase reaches the terminator sequence. In eukaryotes, the resulting pre-mRNA requires further processing.

Initiation: Prokaryotes vs. Eukaryotes Elongation of Transcription Termination of Transcription

Eukaryotic RNA Processing & Splicing

RNA Processing

In eukaryotes, the initial RNA transcript (pre-mRNA) undergoes several modifications before becoming mature mRNA.

5' Cap: Addition of a modified guanine nucleotide to the 5' end.
Poly-A Tail: Addition of a long sequence of adenine nucleotides to the 3' end.
Functions: Facilitate export from the nucleus, protect mRNA from degradation, and help ribosomes attach for translation.

Pre-mRNA to Modified mRNA RNA Processing: 5' cap and Poly-A tail

RNA Splicing

Genes contain coding (exons) and noncoding (introns) regions. Splicing removes introns and joins exons to produce mature mRNA.

Introns: Noncoding regions removed from pre-mRNA.
Exons: Coding regions that remain and are expressed.
Spliceosome: Complex responsible for removing introns.
Alternative Splicing: Allows a single gene to code for multiple proteins by varying the combination of exons included in the final mRNA.

RNA Splicing and Alternative Splicing

Types of RNA

Major Types of RNA

Cells use several types of RNA, each with distinct functions:

Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes; contains codons.
Ribosomal RNA (rRNA): Structural and catalytic component of ribosomes.
Transfer RNA (tRNA): Brings amino acids to the ribosome during translation; contains anticodons complementary to mRNA codons.

Types of RNA: mRNA, rRNA, tRNA

The Genetic Code

Structure and Use of the Genetic Code

The genetic code is a set of rules by which information encoded in mRNA is translated into proteins. It is nearly universal and redundant (multiple codons can code for the same amino acid).

Each codon (three nucleotides) specifies one amino acid.
Start codon: AUG (codes for Methionine).
Stop codons: UAA, UAG, UGA (signal termination of translation).
Redundancy: More codons than amino acids, so some amino acids are specified by more than one codon.

Genetic Code Table DNA to mRNA to Polypeptide Genetic Code Table (alternate view)

Translation

Introduction to Translation

Translation is the process by which ribosomes synthesize proteins using the sequence of codons in mRNA.

Ribosomes: Complexes of rRNA and proteins that facilitate the linking of amino acids.
tRNA: Carries specific amino acids and matches them to codons in mRNA via its anticodon.
Charged tRNA: tRNA attached to an amino acid.
Discharged tRNA: tRNA that has released its amino acid.

Translation: tRNA and protein synthesis tRNA structure

Ribosome Structure and tRNA Binding Sites

Ribosomes have two subunits and three tRNA binding sites:

Prokaryotic ribosomes: 70S (50S large + 30S small subunit).
Eukaryotic ribosomes: 80S (60S large + 40S small subunit).
A-site (Aminoacyl): Holds tRNA with the next amino acid.
P-site (Peptidyl): Holds tRNA with the growing polypeptide chain.
E-site (Exit): Where discharged tRNAs leave the ribosome.

Ribosome subunits and tRNA binding sites tRNA binding sites: A, P, E

Steps of Translation

Translation occurs in three main steps: initiation, elongation, and termination.

Initiation: Small ribosomal subunit binds mRNA and initiator tRNA (carrying Methionine) at the start codon (AUG); large subunit then binds.
Elongation: Amino acids are added one by one to the C-terminus of the growing chain. tRNAs move through the A, P, and E sites.
Termination: When a stop codon is reached, release factors bind, the polypeptide is released, and the ribosome disassembles.

Initiation of Translation Elongation of Translation Termination of Translation Termination of Translation (alternate view)

Post-Translational Modification

Types and Functions

After translation, proteins may undergo covalent modifications that regulate their activity, localization, or stability. These are called post-translational modifications (PTMs).

Methylation
Acetylation
Ubiquitination
Phosphorylation
Glycosylation: Addition of carbohydrates to proteins.
PTMs can be reversible and regulate protein function.

Post-Translational Modifications

Comparison: Transcription vs. Translation

Transcription and translation are distinct but related processes in gene expression.

	Transcription	Translation
Product Formed	RNA Molecule	Polypeptide (Protein)
Macromolecule Change?	Nucleic Acid → Nucleic Acid	Nucleic Acid → Protein
Major Enzyme/Structure	RNA Polymerase	Ribosome
Location	Nucleus (Eukaryotes)	Cytoplasm
Direction of Synthesis	5' → 3'	N-terminus to C-terminus

Transcription vs. Translation Table

Mutations

Definition and Types

Mutations are permanent changes in the DNA sequence. They can affect gene expression and protein function, and may be harmful, beneficial, or neutral. Mutations can occur spontaneously or be induced by environmental factors (mutagens).

Point Mutations: Single nucleotide changes (substitution, insertion, deletion).
Frameshift Mutations: Insertions or deletions that alter the reading frame.
Missense Mutation: Changes one amino acid in the protein.
Nonsense Mutation: Introduces a premature stop codon.
Silent Mutation: Does not change the amino acid sequence due to redundancy in the genetic code.

Types of Mutations