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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.

Central Dogma: DNA to RNA to Protein

Key Point: DNA is replicated, RNA can be reverse-transcribed into DNA, but information transfer from nucleic acid to protein is irreversible.

Transcription

Introduction to Transcription

Transcription is the process by which RNA 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/Downstream: 'Upstream' refers to sequences before (5' direction) the gene; 'downstream' refers to sequences after (3' direction) the gene.

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 (except T is replaced by U in RNA).

  • Template Strand: Serves as the template for RNA synthesis; RNA is complementary to this strand.

  • Base Pairing: A pairs with U (in RNA), T with A, C with G, and G with 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.

  • Elongation: RNA polymerase synthesizes RNA by adding nucleotides complementary to the DNA template strand in the 5' to 3' direction.

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

Initiation of transcription: prokaryotes vs. eukaryotes Elongation of transcription Termination of transcription

Comparison: In prokaryotes, RNA polymerase binds directly to the promoter. In eukaryotes, transcription factors are required for RNA polymerase to bind.

Eukaryotic RNA Processing & Splicing

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 ribosome attachment.

Pre-mRNA to modified mRNA RNA processing: 5' cap and poly-A tail

RNA Splicing

Pre-mRNA contains both coding (exons) and noncoding (introns) regions. Splicing removes introns and joins exons to produce mature mRNA.

  • Introns: Noncoding regions removed during splicing.

  • Exons: Coding regions that remain in the mature mRNA.

  • 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).

  • Codon: A sequence of three nucleotides in mRNA that specifies an amino acid.

  • Start Codon: AUG (codes for Methionine) signals the start of translation.

  • Stop Codons: UAA, UAG, UGA signal the end of translation.

Genetic code table DNA to mRNA to polypeptide Genetic code table (redundancy)

Translation

Introduction to Translation

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

  • Ribosome: Molecular machine composed of rRNA and proteins; catalyzes peptide bond formation.

  • tRNA: Delivers specific amino acids to the ribosome; each tRNA has an anticodon that pairs with an mRNA codon.

  • Charged tRNA: tRNA attached to its corresponding amino acid.

  • Discharged tRNA: tRNA that has released its amino acid.

Translation: tRNA and ribosome tRNA structure

Ribosome Structure and tRNA Binding Sites

Ribosomes have two subunits and three tRNA binding sites:

  • Prokaryotic Ribosome: 70S (50S large + 30S small subunit)

  • Eukaryotic Ribosome: 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: prokaryote vs. eukaryote Ribosome tRNA binding sites

Steps of Translation

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

  • Initiation: Small ribosomal subunit binds mRNA and initiator tRNA (carrying methionine), followed by the large subunit.

  • Elongation: Amino acids are added one by one to the C-terminus of the growing chain; ribosome moves 5' to 3' along mRNA.

  • Termination: A stop codon is reached, release factors bind, and the completed polypeptide is released.

Translation: tRNA binding sites and polypeptide synthesis Elongation of translation Initiation of translation Termination of translation

Post-Translational Modification

Types and Functions

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

  • Methylation

  • Acetylation

  • Ubiquitination

  • Phosphorylation

  • Glycosylation: Addition of carbohydrates to proteins.

Post-translational modifications

Comparison: Transcription vs. Translation

Transcription and translation are distinct but interconnected 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 → C-terminus

Transcription vs. Translation comparison 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.

  • Point Mutation: Change in a single nucleotide (can be silent, missense, or nonsense).

  • Frameshift Mutation: Insertion or deletion of nucleotides that alters the reading frame.

  • Causes: Spontaneous errors, environmental factors, or mutagens.

Impact: Mutations are a major source of genetic diversity among organisms.

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