Modern Inheritance, DNA, and Gene Expression

This is Unit Six of Biology, Part Three: reading the code. Part Two copied D N A. This part reads it — into R N A first, then into protein — and the whole run rests on a code with a specific shape. Sixty-four codons map onto twenty amino acids plus a stop signal, so most amino acids have more than one codon. The relationship runs many-to-one and never one-to-many. Reading frame is the other thing to fix early. A codon is three nucleotides, and an mRNA has three possible ways to group them. The start codon picks one, and shifting by a single base changes every codon after it. Then transcription twice over. Prokaryotes use one polymerase, guided by one helper subunit, and release a finished R N A directly. Eukaryotes use three polymerases, only one of which makes protein-coding transcripts, and that one cannot even find its promoter without an assembled complex of factors. Then three separate processing events — a cap, a tail, and splicing — and finally translation, which ends in an unusual way. No transfer R N A matches a stop codon, so it is that absence, filled by a release factor, that ends the chain. By the end you will be able to do five things. One: say what degeneracy means. Two: say what fixes the reading frame. Three: say what a eukaryotic polymerase needs. Four: name the three processing events. Five: say why a release factor ends translation.

Six entries fixing how a sequence gets read, before anything reads it. Two warnings here are the ones that keep coming back: degeneracy runs in one direction only, and wobble pairing is restricted to one position.

The direction.

Bio 1247 The Central Dogma

The central dogma states that genetic information flows from D N A to R N A by transcription, then from R N A to protein by translation. It names the ordinary direction of information flow — it does not claim every process runs this way without exception.

Three at a time.

Bio 1249 The Genetic Code's Triplet Codons

The genetic code reads messenger R N A in three-nucleotide units called codons, and each of the sixty-four codons specifies one amino acid or a stop signal. Because a codon is three bases, shifting the reading frame by even one changes every codon that follows.

Sixty-one onto twenty.

Bio 1251 Codon Degeneracy

Codon degeneracy means most amino acids are specified by more than one codon, so sixty-one sense codons map onto only twenty amino acids — leucine has six codons, methionine one. Degeneracy runs one way: several codons can mean one amino acid, and no codon means more than one.

Fewer transfer R N As.

Bio 1253 The Wobble Hypothesis

The wobble hypothesis holds that a transfer R N A's third anticodon position can pair loosely with more than one codon base, letting fewer transfer R N As read a degenerate code. Wobble is restricted to the third position — the first two must still pair exactly.

Where to start counting.

Bio 1255 The Reading Frame

The reading frame is the specific grouping of an mRNA sequence into consecutive, non-overlapping codons, fixed by where translation begins. An mRNA has three possible frames, and the start codon determines which one is actually translated.

Start, and stop.

Bio 1257 Start and Stop Codons

The start codon sets an mRNA's reading frame and specifies methionine; three stop codons end translation without specifying any amino acid. A stop codon has no matching transfer R N A — that absence, rather than any special pairing event, is what ends translation.

Three entries, and they are the simpler of the two systems. One polymerase does every gene, a detachable subunit finds each promoter, and the R N A comes off ready to use.

One enzyme.

Bio 1259 Prokaryotic RNA Polymerase and the Promoter

Prokaryotic R N A polymerase binds a promoter — a D N A sequence upstream of a gene — to begin transcribing it, and a single polymerase transcribes every gene in a bacterium. The promoter's sequence sets how often a gene is transcribed; the polymerase itself does not vary between genes.

Finding it.

Bio 1261 Sigma Factor

Sigma factor is a subunit joining prokaryotic R N A polymerase and directing it to recognise a promoter's consensus sequence, positioning the enzyme at the correct start site. It is needed for promoter recognition only, detaching once transcription is underway and leaving the core polymerase to continue alone.

Building and stopping.

Bio 1263 Prokaryotic Transcription Elongation and Termination

Prokaryotic R N A polymerase elongates an R N A strand five prime to three prime until it reaches a terminator sequence signalling it to stop and release. Termination in prokaryotes releases a finished R N A directly — prokaryotic R N A generally needs none of the processing eukaryotic R N A requires.

Three entries covering the same job under a different architecture. Three polymerases instead of one, a promoter far larger than a bacterial one, and an enzyme that cannot reach it without help.

Three enzymes.

Bio 1265 Eukaryotic RNA Polymerases I, II, and III

Eukaryotes use three distinct R N A polymerases: the first transcribes most ribosomal R N A, the second the messenger R N A for nearly all protein-coding genes, and the third transfer R N A. Only the second makes protein-coding transcripts; the other two serve structural and catalytic roles.

The landmark.

Bio 1267 The Eukaryotic Promoter: the TATA Box

A eukaryotic promoter for the messenger-R N A polymerase contains a TATA box, an adenine-and-thymine-rich sequence twenty-five to thirty-five base pairs upstream of the start site, marking where the initiation complex assembles. A eukaryotic promoter is far larger than a prokaryotic one — the TATA box is one element within it, not the whole.

Assembling help.

Bio 1269 Eukaryotic Transcription Factors Assembling the Initiation Complex

Eukaryotic transcription factors bind a gene's promoter and assemble a complex that recruits the polymerase, which cannot bind the promoter unassisted — several basal factors bind in sequence, each stabilising the complex before the polymerase joins. A prokaryotic polymerase needs only sigma factor; this one needs a whole assembly.

Six entries. A eukaryotic transcript is not usable as it comes off the polymerase — three separate modifications have to happen first, and the walkthrough at the end insists they are three events rather than three stages of one.

The front.

Bio 1271 The 5' Cap

A eukaryotic pre-messenger R N A's five prime end is capped with a modified guanine shortly after transcription begins, protecting the R N A from degradation — the cap is added while the polymerase is still transcribing, not after it finishes. The other end is protected by a separate modification.

The back.

Bio 1273 The Poly-A Tail

A eukaryotic pre-messenger R N A's three prime end receives a poly-A tail — roughly two hundred adenine nucleotides — added after the R N A is cleaved at a specific site. The tail comes after transcription and cleavage, distinct from the cap added near transcription's start.

What has to go.

Bio 1275 Introns and Exons

A eukaryotic gene's transcript contains exons, the sequences appearing in mature messenger R N A, interrupted by introns that must be removed before translation. The two names describe a transcript rather than a protein — an intron never appears in a translated amino acid sequence.

Removing it.

Bio 1277 Splicing and the Spliceosome

Splicing removes a transcript's introns and joins its exons together, carried out by a large R N A-and-protein complex called the spliceosome, which recognises each intron's boundary sequences, cuts it out, and joins the flanking exons directly. It acts on introns identified by those boundaries and removes no exon sequence.

Kept but unread.

Bio 1279 The 5' and 3' Untranslated Regions

A mature messenger R N A's untranslated regions flank the coding sequence — one between cap and start codon, the other between stop codon and poly-A tail. An untranslated region is still transcribed and spliced along with the rest; what it lacks is translation into protein.

Transcript to finished message.

Bio 1281 Tracing Pre-mRNA Processing from Transcription to a Mature mRNA

The walkthrough runs one transcript from the polymerase to a translatable message. The cap goes on while transcription is still underway. At the gene's end the transcript is cleaved and tailed. The spliceosome then removes every intron and joins the exons, leaving only exon sequence between cap and tail — including the two untranslated regions, which survive every step without being translated. Capping, tailing and splicing are three separate events, not stages of one reaction; a transcript missing any of the three is not yet mature.

Three entries on what does the reading. A structure that exists in two pieces most of the time, three working positions inside it, and the molecule that delivers amino acids — which never touches D N A at any point.

Two pieces.

Bio 1283 Ribosome Structure: Large and Small Subunits

A ribosome is built from a large and a small subunit, each made of ribosomal R N A and protein, joining only during translation — the small subunit binds messenger R N A first and the large one joins afterward. The two exist separately most of the time, assembling specifically to translate a message.

Three positions.

Bio 1285 The Ribosome's A, P, and E Sites

An assembled ribosome has three transfer-R N A sites: the first accepts an incoming transfer R N A, the second holds the growing peptide, and the third releases a used one. These are fixed positions within one ribosome, not three ribosomes acting on different transfer R N As.

The delivery.

Bio 1287 tRNA Structure and the Anticodon

A transfer R N A carries one specific amino acid at one end and displays a three-nucleotide anticodon at the other, pairing with a complementary codon. The anticodon pairs with a messenger R N A codon, not with a D N A sequence — transfer R N A never interacts with D N A directly.

Three entries. Assembly first, then a cycle repeating for every codon, and then an ending that works because something is missing rather than because something arrives.

Assembly.

Bio 1289 Translation Initiation

Initiation assembles the small ribosomal subunit, an initiator transfer R N A carrying methionine, and the messenger R N A's start codon, before the large subunit joins — in eukaryotes the small subunit scans from the five prime end until the initiator pairs with the start codon. Initiation ends once both subunits are assembled; no amino acid bond has formed yet.

The cycle.

Bio 1291 Translation Elongation

Elongation adds one amino acid at a time to the growing chain as the ribosome moves codon by codon — a charged transfer R N A enters the first site, its amino acid bonds to the chain at the second, and the ribosome shifts one codon. The cycle repeats for every codon between start and stop, skipping and reordering none.

The ending.

Bio 1293 Translation Termination

Termination occurs when a stop codon reaches the ribosome's accepting site, where a release factor rather than a transfer R N A binds and frees the protein. No transfer R N A carries an anticodon matching a stop codon — the release factor's shape mimics transfer R N A closely enough to bind in its place.

One capstone taking a single gene from D N A to a finished protein, and its warning is about sequence rather than mechanism: every processing step happens before translation starts, never during it.

The capstone. Gene to protein.

Bio 1295 Tracing One Gene from Transcription Through a Finished Protein

The capstone runs one eukaryotic gene the whole way. The polymerase transcribes it; the transcript is capped, cleaved, tailed and spliced into a mature message before reaching a ribosome. In the cytoplasm the small subunit finds the start codon, an initiator transfer R N A pairs with it, and the large subunit joins. Anticodons pair with successive codons, elongation adds amino acid after amino acid, and a stop codon brings a release factor instead of a transfer R N A. The finished protein's sequence was set entirely by the gene's original D N A, and capping, splicing and tailing all happened before any of the reading began.

Five things to carry out of Part Three. Degeneracy means most amino acids have more than one codon — sixty-one sense codons mapping onto twenty amino acids, leucine with six and methionine with one. It runs one way only: several codons can specify one amino acid, and no codon specifies more than one. Wobble pairing, restricted to a codon's third position, is what lets fewer transfer R N As read a code that degenerate. The start codon fixes the reading frame. A codon is three nucleotides, so any sequence can be grouped three different ways, and only the grouping that begins at the start codon is translated. Shift by one base and every codon after it changes. A eukaryotic polymerase needs an assembled complex of transcription factors to reach its promoter — it cannot bind unassisted. A prokaryotic polymerase needs only sigma factor, which detaches once transcription is underway. That is the sharpest difference between the two systems. Three processing events turn a transcript into a message, and they happen at different times. The cap goes on during transcription. The tail goes on after cleavage at the end. Splicing removes every intron and joins the exons. All three finish before translation begins. And a release factor ends translation because no transfer R N A carries an anticodon matching a stop codon. The ending works by absence — the release factor's shape mimics transfer R N A closely enough to bind the empty site and free the protein. Part Four turns to what happens when the sequence changes, and to how a cell controls which genes are read at all.