Unit 8 follows a gene from DNA to finished protein and explains how cells decide which genes to use. By the end, you should be able to transcribe and translate a short sequence by hand, describe how eukaryotes process mRNA, and explain how the lac operon and transcription factors control gene expression.
Read the overview first, then work through each topic's notes and answer the checkpoint before you look at the answer.
Earlier units showed that DNA stores genetic information. This unit shows how a cell actually uses that information to make proteins. It also shows how the cell controls which proteins it makes at any moment.
Honors Biology Unit 8 covers gene expression in three parts. First is transcription, where RNA polymerase copies a gene into mRNA and eukaryotic cells add a 5' cap and poly(A) tail and splice out introns. Second is translation, where ribosomes and tRNAs read mRNA codons and link amino acids into a polypeptide using the genetic code. Third is gene regulation, where prokaryotes use operons like the lac operon and eukaryotes use transcription factors, enhancers, silencers, alternative splicing and other controls to adjust how much of each protein a cell makes. Exact content and order vary by school, but these topics are commonly covered in honors biology.
RNA polymerase binds at a promoter, reads the template strand 3' to 5', and builds RNA 5' to 3' using A, U, G and C. In eukaryotes this happens in the nucleus, and the pre-mRNA is capped, given a poly(A) tail and spliced before it leaves.
A ribosome reads mRNA one three-base codon at a time, starting at AUG. Each tRNA has an anticodon that pairs with a codon and delivers the matching amino acid, and the ribosome joins those amino acids with peptide bonds until it hits a stop codon.
Bacteria often switch whole groups of genes on or off together using operons. Eukaryotes control expression at many points, from how tightly DNA is packed to how long an mRNA survives, which lets one genome produce hundreds of cell types.
Most nucleated cells in your body carry nearly the same DNA, but they differ in which genes they express. A protein-coding gene's base sequence provides the information for its protein's amino acid sequence. RNA processing and other forms of regulation affect which protein is made and how much is produced.
Transcription is the first step of gene expression, where a gene's DNA is copied into RNA.
Translation is the process where a ribosome reads mRNA and builds a polypeptide.
Gene regulation means controlling whether a gene is expressed and how much.
Transcription is the first step of gene expression, where a gene's DNA is copied into RNA. It happens in three stages. In eukaryotic initiation, transcription factors help recruit RNA polymerase to a promoter, which may contain a TATA box. In bacteria, a sigma factor helps RNA polymerase recognize the promoter. The polymerase unwinds a short stretch of DNA. In elongation, RNA polymerase reads the template strand 3' to 5' and builds RNA 5' to 3', pairing A with U, T with A, G with C and C with G. In termination, transcription stops and RNA polymerase leaves the DNA. For eukaryotic protein-coding genes, the RNA is cleaved before the polymerase stops.
In eukaryotes, the first transcript is pre-mRNA, and it gets processed in the nucleus. A 5' cap protects the mRNA and helps the ribosome attach. A poly(A) tail of many adenines on the 3' end slows breakdown. The spliceosome cuts out introns and joins exons. Through alternative splicing, one gene can produce several different proteins. Prokaryotic mRNAs usually do not undergo the same processing as eukaryotic mRNAs. In bacteria, translation can begin while an mRNA is still being transcribed.
Worked example. The template strand reads 3'-TACGGCATT-5'. Pair each base, using U instead of T. That gives an mRNA of 5'-AUGCCGUAA-3'. Now compare it with the coding strand, which is 5'-ATGCCGTAA-3'. The mRNA matches the coding strand except that U replaces T.
Check yourself: A template strand reads 3'-TTACGA-5'. What mRNA is made, and how does it compare to the coding strand? (Answer: The mRNA is 5'-AAUGCU-3'. The coding strand is 5'-AATGCT-3', so the mRNA matches it with U in place of T.)
| RNA type | Job | Where it works |
|---|---|---|
| mRNA | Carries a gene's coded instructions as a series of codons | Made in the nucleus (eukaryotes), read at ribosomes in the cytoplasm |
| tRNA | Brings a specific amino acid and matches it to a codon using its anticodon | Cytoplasm, at the ribosome |
| rRNA | Forms most of the ribosome and catalyzes peptide bond formation | Ribosome |
Translation is the process where a ribosome reads mRNA and builds a polypeptide. The genetic code has 64 codons. Of these, 61 code for amino acids and 3 (UAA, UAG, UGA) are stop codons. AUG codes for methionine and also marks the start. Most amino acids have more than one codon, but each codon names only one amino acid.
Before translation, enzymes called aminoacyl-tRNA synthetases load each tRNA with its correct amino acid. In eukaryotic initiation, the small ribosomal subunit attaches near the 5' end of the mRNA and usually finds an AUG start codon. In bacteria, it usually binds a ribosome-binding site near the start codon. The initiator tRNA sits in the P site, and the large subunit joins. It carries methionine in eukaryotes and a modified methionine in bacteria. In elongation, a matching tRNA enters the A site, and rRNA in the large subunit forms a peptide bond. The ribosome then shifts one codon toward the 3' end, and the empty tRNA leaves from the E site. In termination, a release factor binds the stop codon and the polypeptide is released. It then folds, and it may be modified before it works.
Worked example. Take the mRNA 5'-AUG UUU GGC UAA-3'. Read it in codons from AUG. AUG gives Met, UUU gives Phe, and GGC gives Gly. UAA is a stop codon, so translation ends. The product is Met-Phe-Gly, which has 3 amino acids and 2 peptide bonds. Now scale it up. A coding region of 303 nucleotides, including the stop, has codons. That gives 100 amino acids and peptide bonds.
Check yourself: What amino acid sequence does 5'-AUG GCU UGG UGA-3' code for? (Answer: Met-Ala-Trp. UGA is a stop codon, so the chain ends after tryptophan.)
Gene regulation means controlling whether a gene is expressed and how much. Bacteria often group related genes into an operon, which has one promoter, an operator and several structural genes that are transcribed together as one mRNA.
The lac operon is an inducible operon. When lactose is absent, a repressor protein sits on the operator and blocks RNA polymerase. When lactose is present, some of it becomes allolactose, which binds the repressor and changes its shape so it falls off the operator. The lac operon also has positive control. When glucose is low, the protein CAP binds near the promoter and boosts transcription. So the genes are transcribed strongly only when lactose is present and glucose is low. The trp operon works the opposite way. It is repressible, so when tryptophan is plentiful, tryptophan helps the repressor bind and shuts the genes off.
Most eukaryotic genes are transcribed separately, each with its own promoter, although some eukaryotes also have operons. Activators bind enhancers, which can be thousands of base pairs away, while repressors bind silencers. Control also happens at other levels. Tightly packed chromatin generally reduces gene expression. Alternative splicing can change which protein is made. mRNA lifespan and microRNAs can affect how much protein is produced, while protein modification can change a protein's activity or stability.
Check yourself: An E. coli cell has lactose and plenty of glucose. Is the lac operon strongly transcribed? (Answer: No. The repressor is removed because allolactose is present, but CAP is not active when glucose is high, so transcription stays low.)
| Feature | Prokaryotes | Eukaryotes |
|---|---|---|
| Gene organization | Related genes often grouped in operons | Most genes have their own promoters, though some eukaryotes have operons |
| Main control point | Transcription, using repressors, activators and the operator | Many levels, from chromatin packing to protein modification |
| Distant regulatory DNA | Rare | Enhancers and silencers, sometimes thousands of base pairs away |
| RNA processing | Some RNA processing occurs, but bacterial translation can start during transcription | Cap, poly(A) tail and splicing, including alternative splicing |
| Term | Definition |
|---|---|
| Gene expression | The process of using a gene's DNA sequence to make a functional RNA or protein. |
| Transcription | The synthesis of RNA from a DNA template by RNA polymerase. |
| RNA polymerase | The enzyme that reads a DNA template strand and builds a complementary RNA strand in the 5' to 3' direction. |
| Pre-mRNA | A eukaryotic protein-coding RNA transcript before processing is complete. Capping and splicing can begin while it is still being transcribed. |
| Alternative splicing | Joining different combinations of exons from the same pre-mRNA so one gene can code for more than one protein. |
| Translation | The process where a ribosome reads mRNA codons and links amino acids into a polypeptide. |
| Genetic code | The set of 64 codons that specify the 20 amino acids plus start and stop signals. |
| Ribosome | A two-part structure made of rRNA and protein that carries out translation. |
| Transcription factor | A protein that binds DNA near a gene and helps turn its transcription up or down. |
| Lac operon | A group of E. coli genes for using lactose that is switched on by allolactose and boosted by CAP when glucose is low. |
Two DNA strands make it easy to pair with the wrong one. The mRNA is complementary to the template strand, so it has the same sequence as the coding strand with U in place of T. Always check which strand you were given before you start pairing.
Codon charts are written for mRNA codons, not anticodons. If a question gives you a tRNA anticodon like UAC, first convert it to the mRNA codon (AUG), then look it up to get methionine.
Translation starts at a start codon, usually AUG, rather than automatically at the first nucleotide of the mRNA. The ribosome reads in groups of three from that start codon, so starting at the wrong spot can shift the reading frame and give the wrong protein.
Lactose removes the repressor, but strong transcription also needs CAP, which is only active when glucose is low. Cells prefer glucose, so they make lactose enzymes mainly when lactose is present and glucose is scarce.