Gene Expression: From Gene to Protein (Campbell Biology, Ch. 17) – Study Notes

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Gene Expression: From Gene to Protein

Overview of Gene Expression

Gene expression is the process by which information encoded in DNA directs the synthesis of proteins, which are essential for cellular structure and function. This process involves two main stages: transcription (DNA to RNA) and translation (RNA to protein).

Central Dogma: The flow of genetic information is summarized as DNA → RNA → Protein.
Transcription: Synthesis of RNA using DNA as a template.
Translation: Synthesis of a polypeptide using the information in mRNA.
Ribosomes: Sites of protein synthesis.

Transcription and translation in a bacterial cell Transcription, RNA processing, and translation in a eukaryotic cell

Transcription: DNA to RNA

Basic Principles of Transcription

Transcription is the process by which a segment of DNA is used as a template to synthesize a complementary RNA strand. In eukaryotes, this occurs in the nucleus; in prokaryotes, it occurs in the cytoplasm.

RNA Polymerase: Enzyme that synthesizes RNA in the 5′ to 3′ direction, does not require a primer.
Template Strand: The DNA strand used as a template for RNA synthesis.
Promoter: DNA sequence where RNA polymerase attaches and initiates transcription.
Terminator: Sequence signaling the end of transcription (in prokaryotes).

RNA polymerase and sigma form a holoenzyme Promoter recognition by RNA polymerase and sigma factor

Stages of Transcription

Initiation: RNA polymerase binds to the promoter with the help of sigma factor (in bacteria) or transcription factors (in eukaryotes).
Elongation: RNA polymerase moves along the DNA, unwinding the helix and synthesizing RNA.
Termination: In bacteria, transcription ends at a terminator sequence; in eukaryotes, RNA polymerase II transcribes a polyadenylation signal, and the transcript is released.

Stages of transcription: initiation, elongation, and termination Initiation of transcription at a eukaryotic promoter Elongation of the RNA strand during transcription

RNA Processing in Eukaryotes

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

5′ Cap: Modified guanine nucleotide added to the 5′ end for stability and ribosome binding.
3′ Poly-A Tail: 50–250 adenine nucleotides added to the 3′ end for stability and export from the nucleus.
Splicing: Removal of noncoding regions (introns) and joining of coding regions (exons).

RNA processing: addition of the 5′ cap and poly-A tail Spliceosome splicing a pre-mRNA

Alternative Splicing and Exon Shuffling

Alternative splicing allows a single gene to code for multiple proteins by varying the combination of exons included in the final mRNA. Exon shuffling can create new proteins by mixing exons from different genes.

Alternative splicing of mRNA Correspondence between exons and protein domains

Translation: RNA to Protein

Genetic Code and Codons

The genetic code is a set of rules by which the nucleotide sequence of mRNA is translated into the amino acid sequence of a protein. Each group of three nucleotides (codon) specifies one amino acid.

Start Codon: AUG (methionine) signals the start of translation.
Stop Codons: UAA, UAG, UGA signal the end of translation.
Redundancy: Multiple codons can code for the same amino acid.

Codon table for mRNA

tRNA and Aminoacyl-tRNA Synthetases

Transfer RNA (tRNA) molecules bring amino acids to the ribosome and match them to the mRNA codons via their anticodon region. Aminoacyl-tRNA synthetases are enzymes that attach the correct amino acid to its corresponding tRNA.

Structure of transfer RNA (tRNA) Aminoacyl-tRNA synthetases provide specificity in joining amino acids to their tRNAs

Wobble Base Pairing

Wobble refers to the flexible pairing at the third base of a codon, allowing some tRNAs to recognize more than one codon, reducing the number of tRNAs needed.

Codon table highlighting wobble position

Ribosomes and Sites of Translation

Ribosomes are composed of large and small subunits, each made of rRNA and proteins. They have three binding sites for tRNA:

A site (Aminoacyl): Holds the tRNA carrying the next amino acid.
P site (Peptidyl): Holds the tRNA with the growing polypeptide chain.
E site (Exit): Where discharged tRNAs leave the ribosome.

Translation: the basic concept

Stages of Translation

Initiation: The small ribosomal subunit binds to mRNA, and the initiator tRNA binds to the start codon. The large subunit then joins to form the complete initiation complex.
Elongation: Amino acids are added one by one to the growing polypeptide chain as the ribosome moves along the mRNA.
Termination: When a stop codon is reached, a release factor binds, causing the polypeptide to be released and the ribosome to dissociate.

Post-Translational Modifications and Protein Targeting

Protein Folding and Modifications

After translation, polypeptides fold into their functional three-dimensional shapes. Some proteins undergo post-translational modifications, such as cleavage, phosphorylation, or glycosylation, to become fully functional.

Targeting Proteins to Specific Locations

Proteins may contain signal peptides that direct them to specific cellular locations, such as the endoplasmic reticulum (ER) for secretion or membrane insertion.

Polyribosomes

Multiple ribosomes can simultaneously translate a single mRNA, forming a polyribosome (polysome), which increases the efficiency of protein synthesis.

Mutations and Their Effects on Proteins

Types of Mutations

Point Mutations: Changes in a single nucleotide pair. Can be silent (no effect), missense (change one amino acid), or nonsense (introduce a stop codon).
Insertions and Deletions (Indels): Addition or loss of nucleotides, which may cause frameshift mutations, altering the reading frame and often resulting in nonfunctional proteins.

Molecular basis of sickle-cell disease: a point mutation Types of small-scale mutations that affect mRNA sequence

Consequences of Mutations

Mutations can lead to genetic disorders or hereditary diseases if they adversely affect phenotype.
Mutations in noncoding regions can affect gene expression and regulation.

Summary Table: Key Differences in Gene Expression

Feature	Prokaryotes	Eukaryotes
Location of Transcription	Cytoplasm	Nucleus
RNA Processing	Absent	Present (capping, poly-A tail, splicing)
Coupling of Transcription & Translation	Yes	No
Number of RNA Polymerases	1	3 (I, II, III)