Ch. 17: Gene Expression: From DNA to Protein

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CH. 17: Gene Expression

Learning Objectives

Describe the overall location of transcription and translation in bacteria vs. eukaryotes
Explain the genetic code, including codons and reading frames
Outline the key components and steps of transcription and translation
Compare transcription and translation in bacteria and eukaryotes
Describe RNA processing in eukaryotes
Discuss mutations, their types, and effects

Gene Expression

Genes Specify Proteins

Gene expression is the process by which information from DNA directs the synthesis of proteins. This involves two major steps: transcription and translation.

Transcription: Synthesis of RNA using DNA as a template.
Translation: Synthesis of a polypeptide (protein) using information in mRNA.
Proteins are the link between genotype (genetic makeup) and phenotype (observable traits).

Bacteria vs. Eukaryotes

Cellular Location of Gene Expression

The major difference between bacteria and eukaryotes in gene expression is the presence of a nucleus in eukaryotes.

Bacteria: Transcription and translation both occur in the cytoplasm, often simultaneously.
Eukaryotes: Transcription occurs in the nucleus, producing pre-mRNA, which undergoes RNA processing before being exported to the cytoplasm for translation.

The Genetic Code

Codons and Reading Frame

The genetic code is the set of rules by which information encoded in DNA is translated into proteins.

DNA contains only four nucleotide bases, but these specify 20 amino acids.
Each amino acid is encoded by a codon, a sequence of three nucleotides.
The reading frame refers to how the sequence of nucleotides is divided into codons; shifting the frame changes the resulting protein.
The genetic code is nearly universal among all organisms.

Properties of the Genetic Code

There are 64 possible codons (43 combinations).
61 codons code for amino acids; 1 is a start codon (AUG), and 3 are stop codons (UAA, UAG, UGA).
Degenerate code: More than one codon may code for the same amino acid.
Nonsense codons: Stop signals to end translation.

Example: Reading Frame

"The dog can eat" (correct reading frame) vs. "hed ogc ane at" (shifted frame).

Genetic Code Table

The table below summarizes the codons and their corresponding amino acids:

Codon	Amino Acid	Function
AUG	Met	Start
UAA	-	Stop
UAG	-	Stop
UGA	-	Stop
UUU, UUC	Phe	-
UUA, UUG, CUU, CUC, CUA, CUG	Leu	-
... (other codons)	...	-

Additional info: The full codon table includes all 64 codons; only a subset is shown above for brevity.

Transcription

Key Components

RNA polymerase: Enzyme that synthesizes RNA from DNA template.
Promoter: DNA region where RNA polymerase binds to initiate transcription.
Terminator: DNA sequence signaling the end of transcription (in bacteria).
Transcription unit: Section of DNA transcribed into RNA.

Steps of Transcription

Initiation: RNA polymerase binds to promoter; in eukaryotes, transcription factors help RNA polymerase II bind to the TATA box (AT-rich sequence).
Elongation: RNA polymerase moves along DNA, unwinding it and synthesizing RNA in the 5' to 3' direction.
Termination: In bacteria, RNA polymerase stops at terminator sequence; in eukaryotes, a polyadenylation signal (AAUAAA) leads to release of pre-mRNA.

Differences: Bacteria vs. Eukaryotes

Bacteria: RNA polymerase recognizes promoter directly; mRNA is ready for translation immediately.
Eukaryotes: RNA polymerase II requires transcription factors; pre-mRNA undergoes processing before translation.

RNA Processing (Eukaryotes Only)

Major Steps and Functions

5' Cap: Modified guanine added to 5' end for stability and ribosome recognition.
Poly-A Tail: 50-250 adenine nucleotides added to 3' end for stability and export from nucleus.
Splicing: Removal of noncoding introns and joining of coding exons via the spliceosome (complex of proteins and small RNAs).

Translation

Key Components

Transfer RNA (tRNA): Carries specific amino acids and matches them to codons in mRNA via its anticodon.
Ribosome: Made of proteins and rRNA; facilitates coupling of tRNA anticodons with mRNA codons.
Aminoacyl-tRNA synthetase: Enzyme that attaches the correct amino acid to its tRNA using ATP.

Steps of Translation

Initiation: mRNA, initiator tRNA (carrying methionine), and ribosomal subunits assemble; requires initiation factors and GTP.
Elongation: Amino acids are added one by one to the growing polypeptide chain. Steps include codon recognition, peptide bond formation, and translocation. Ribosome moves 5' to 3' along mRNA.
Termination: When a stop codon enters the A site, a release factor binds, hydrolyzing the bond and releasing the polypeptide. The ribosome disassembles.

Differences: Bacteria vs. Eukaryotes

Bacteria: Translation can begin before transcription is finished; faster rate of amino acid addition.
Eukaryotes: Translation occurs after RNA processing and export from nucleus; slower rate of amino acid addition.

Mutations

Characteristics and Types

Mutation: Change in DNA sequence; source of new genes; can be large-scale or small-scale.
Point mutations: Change in a single nucleotide pair; includes substitutions, insertions, and deletions.
Can be beneficial, neutral, or harmful; may result from errors in replication, cell division, mutagens, or viral infection.
Not all mutations affect phenotype; only those in gametes are heritable.

Types of Point Mutations

Type	Description	Effect
Silent	No effect on amino acid produced	No effect on protein
Missense	Changes one amino acid to another	May have little or large effect
Nonsense	Produces a stop codon	Premature termination; nonfunctional protein
Insertions/Deletions	Add or remove nucleotides	May alter reading frame (frameshift); usually severe effects

Additional info: Insertions/deletions not in multiples of three change the reading frame, affecting all downstream codons.

Summary Equations

Transcription:
Translation: