D1.2 Protein synthesis

Transcription uses one DNA strand as a template to make a complementary messenger-RNA strand.

RNA polymerase opens a local section, matches RNA nucleotides and joins them into a strand that can carry the gene sequence away from DNA.

Trace: promoter; template strand; complementary RNA; mRNA export for translation.

A gene's DNA sequence is copied into mRNA before a ribosome reads its codons. The RNA sequence preserves the information needed for a ribosome to assemble the same polypeptide.

Transcription is RNA synthesis, not DNA replication or protein assembly. RNA polymerase reads only the selected gene region, not the whole chromosome.

Hydrogen bonds between complementary DNA bases can separate locally during transcription and reform behind the polymerase.

The covalent backbone stays intact while temporary base-pair bonds open. This exposes one template strand without destroying the chromosome. Opening is local and temporary, so the rest of the chromosome remains paired and protected while the polymerase moves.

Identify: local opening; exposed template; new RNA pairing; re-formation behind the enzyme.

A short transcription bubble moves along a gene while the rest of the DNA remains double-stranded. The bubble closes behind polymerase, leaving the DNA double helix ready for later use.

Weak hydrogen bonds do not mean DNA is structurally unimportant; the backbone provides continuity.

DNA stability protects the information source while temporary local opening permits transcription or replication.

The backbone and most base pairs remain protected in the chromosome. Controlled unwinding exposes only the region needed, reducing damage and preserving sequence fidelity.

Separate global stability from local access: chromosome stays intact; one gene region opens; copying or reading proceeds.

A polymerase can transcribe one gene without unzipping the entire DNA molecule. A cell can transcribe one gene while unrelated genes remain closed and protected elsewhere on the same chromosome.

Stable does not mean permanently closed; regulated local opening is part of gene expression. Controlled access is a balance: excessive opening can increase damage, but no opening prevents gene expression.

Transcription converts stored DNA information into an mRNA message that can be translated.

Regulatory signals determine whether transcription starts and how much mRNA is made. The message links a gene's sequence to the amount and timing of protein production.

Follow the chain: regulatory control; mRNA abundance; ribosome access; protein output.

If transcription of an enzyme gene increases, more mRNA can support more translation when later steps are not limiting.

More mRNA does not guarantee proportionally more protein; later controls can limit expression.

Translation uses a ribosome to read mRNA codons and join amino acids in the encoded order.

tRNA molecules pair anticodons with codons and deliver specific amino acids. The ribosome forms peptide bonds as it moves from start toward stop.

Trace: start codon; tRNA matching; peptide bond; codon movement; stop codon.

A ribosome reading three codons adds three specified amino acids before a stop signal ends the chain.

Translation reads RNA; it does not copy mRNA back into DNA. The ribosome assembles the chain; later folding and modification determine whether the polypeptide becomes functional.

mRNA supplies codon order, tRNA matches codons and carries amino acids, and the ribosome positions molecules and catalyzes peptide bonds.

Translation is accurate because each component solves a different problem: information, matching and chemical assembly. Coordination converts nucleotide sequence into protein sequence.

For each step name: codon; anticodon; amino acid; ribosome site; peptide bond.

A matching tRNA enters, places its amino acid beside the growing chain and then leaves.

tRNA does not determine the whole protein alone; codon order and ribosome movement are also required.

Complementary base pairing allows DNA to specify an mRNA sequence and codons to be recognized by tRNA anticodons.

Hydrogen-bonding patterns and base size make particular pairs fit. The same principle connects template reading during transcription with codon decoding during translation.

Check strand direction and pair type before predicting the next nucleotide or amino acid. Check pairing; strand direction; codon reading frame; and the matching anticodon.

A DNA template produces complementary mRNA, whose codon pairs with a matching tRNA anticodon. A single template base determines its partner in mRNA, which then helps select the tRNA carrying the next amino acid.

Pairing is complementary, not identical: the message is related to the template rather than a literal copy.

The genetic code assigns each three-base mRNA codon to an amino acid or stop signal.

Triplets provide enough combinations for all amino acids. The code is degenerate because several codons can specify one amino acid, but each codon has a defined meaning.

Read codons in threes, using the correct reading frame and checking start and stop signals. Check triplet grouping; reading frame; codon meaning; and stop signals.

Changing UUU to UUC may still specify phenylalanine because the code is degenerate. A codon table can show that two different triplets encode the same amino acid, reducing the effect of some substitutions.

Degenerate does not mean ambiguous for one codon; it means multiple codons can share an amino acid.

A genetic-code table is used by reading mRNA codons 5' to 3' and matching each to its amino acid.

The first, second and third bases select positions in the table. Reading-frame errors shift every later codon, so strand labels and grouping matter.

Use: locate start; split triplets; read each codon; stop at a stop codon; report amino-acid order.

For 5'-AUG-GCU-UAA-3', AUG starts, GCU adds alanine and UAA terminates. If one base is omitted before AUG, every later triplet may be regrouped, so the table must be used from the correct start frame.

Do not use the DNA template directly as if it were mRNA; transcribe first.

During elongation, a matching tRNA enters, a peptide bond forms and the ribosome moves to the next codon.

Repeating this cycle extends the chain in a fixed direction while mRNA advances through the ribosome. Energy from charged tRNAs and factors supports the process.

Track each cycle: codon recognition; chain transfer; translocation; empty tRNA exit.

After one cycle the chain has one additional amino acid and the next codon is exposed.

Elongation is not random amino-acid addition; codon recognition controls the order. The cycle stops at a termination signal rather than continuing until the physical end of the mRNA.

A DNA mutation can alter an mRNA codon, amino-acid sequence and ultimately protein folding or function, although some changes have little effect.

Outcome depends on mutation type, code degeneracy, location and the chemical difference between residues. Folding translates sequence change into structure change.

Assess: DNA change; codon consequence; amino-acid change; structural or functional effect.

Replacing a charged residue in an enzyme's active site can alter binding and reduce catalytic activity.

A mutation is not automatically harmful; synonymous or distant changes may leave function largely unchanged.

Polymerases extend nucleic acids 5' to 3', while ribosomes read mRNA codons 5' to 3'. Directionality fixes how information is copied and decoded.

The 3' hydroxyl chemistry fixes extension direction. Labels keep codons in a consistent reading frame and explain why template orientation matters.

Mark 5' and 3' ends first; then place extension or ribosome movement arrows.

A ribosome starts at the 5' side of mRNA and moves toward its 3' end while the polypeptide grows.

Saying left to right is meaningless without strand labels and diagram orientation.

A promoter is a DNA region where transcription machinery binds to position RNA polymerase and define where transcription begins.

Promoter sequence and associated factors determine strand choice, start site and transcription level. Opening and early RNA synthesis proceed from that positioned complex.

Name: promoter; binding factor; start site; direction of RNA synthesis.

A promoter mutation can reduce mRNA production without changing the protein-coding sequence. RNA polymerase begins at the promoter and then moves along the template, so promoter position fixes which downstream sequence is copied.

A promoter is regulatory DNA, not the entire gene or translated region.

Non-coding DNA does not translate into protein, but it can contain regulatory sequences, introns, structural regions or genes for functional RNAs.

Its role depends on sequence and location. Binding sites can control transcription, while introns are removed from pre-mRNA and other regions organize chromosomes.

Classify a region as regulatory; transcribed but removed; structural; or functional RNA.

An enhancer can influence transcription even though its sequence is not translated into amino acids.

Non-coding does not mean useless, and it does not identify one single function.

Eukaryotic pre-mRNA is processed by adding a 5' cap and poly-A tail and removing introns so mature mRNA can be exported and translated.

Processing protects RNA, supports export and helps ribosomes recognize the message. Exons are joined in the order defining the coding sequence.

Trace: pre-mRNA; cap and tail; intron removal; exon joining; mature mRNA export.

Removing an intron prevents its sequence from being read as part of the final translated message.

Processing changes RNA, not the original DNA sequence; different processing choices can alter the final protein.

Alternative splicing joins selected exons in different combinations, allowing one gene to produce different mature mRNAs and protein isoforms.

Tissue-specific splicing factors influence which exons remain. Different combinations change amino-acid sequence and can alter localization or function. Splicing factors recognize sequence features near splice sites and select an exon pattern appropriate to the cell type.

Compare isoforms by checking shared exons, included or skipped exon and resulting protein difference. Compare shared exons; skipped or included exon; reading frame; and resulting protein domain.

A neuron and muscle cell can splice the same pre-mRNA differently and produce proteins with distinct interaction domains. Including an exon that encodes a binding domain can let one isoform interact with a partner while another isoform cannot.

Alternative splicing increases output from a gene but does not create a new DNA gene for every isoform.

Translation initiation positions the ribosome at a start codon and establishes the reading frame for all later codons.

Initiation factors and initiator tRNA recognize the start region. Once the frame is fixed, triplets are read sequentially until a stop codon.

Check: start codon; initiator tRNA; ribosome position; frame; downstream triplets.

If one base is inserted before the frame, every later triplet can change even though the start codon remains.

A start codon can also encode an amino acid internally; context determines initiation.

New polypeptides can be folded, cleaved or chemically modified after translation before becoming functional proteins.

Processing can expose an active site, add a targeting group, join subunits or alter stability. The final protein depends on sequence and post-translational handling.

Name: initial chain; processing event; structural change; functional consequence.

A precursor protein can be cleaved to remove a signal segment and reveal the mature active form.

Translation ending does not guarantee a functional protein; folding and processing may still be required.

Proteasomes break selected proteins into peptides, allowing amino acids to be recycled for new protein synthesis or metabolism.

Damaged or short-lived proteins are tagged and fed into a proteasome, where peptide bonds are hydrolysed. Released amino acids return to the cellular pool.

Trace: protein tag; proteasome entry; peptide breakdown; amino-acid reuse or catabolism.

A misfolded protein can be removed and its amino acids reused to build a different protein.

Proteasomal degradation is controlled recycling, not random digestion of every protein. Proteasomes do not recycle every protein immediately; tagging and recognition determine which substrates are selected.