Past exam of the biochemistry and Molecular Biology course of the University of Cambridge / 2024 / Paper 1 / Section E

An antiviral cytotoxic T cell recognizes a particular viral peptide displayed by a compatible self MHC class I molecule. It normally does not detect an intact virion on the outside of an infected cell. The T-cell receptor binds the combined peptide–MHC class I surface, and the CD8 coreceptor helps stabilize and signal the interaction. Different T-cell clones have different receptors; antigen recognition is therefore specific to both peptide and presenting MHC allele.

Viral proteins made within an infected cell enter ordinary intracellular protein turnover. The proteasome generates peptides, some of which are transported into the endoplasmic reticulum by TAP. Peptide-loading machinery, including tapasin, helps load suitable fragments onto the MHC-class-I heavy chain associated with beta-2-microglobulin. Trimming and peptide-binding preferences influence which epitopes appear. Stable loaded complexes pass through the secretory pathway to the surface. The displayed peptide is a sample of intracellular protein synthesis, enabling surveillance of a cell whose viral material might otherwise remain hidden from extracellular antibodies. Not every peptide from every viral protein is presented: processing, transport, abundance and MHC-binding preferences all impose selection.

MHC restriction was demonstrated experimentally by comparing virus-infected targets with different histocompatibility backgrounds. Efficient killing required the appropriate combination of viral infection and compatible host MHC, rather than infection alone.^[ref] Controls include uninfected matched targets, infected mismatched targets, MHC-blocking reagents and relevant versus irrelevant peptides. Loading an appropriate synthetic peptide onto a target can bypass a defect in upstream processing; restoration of recognition localizes the defect without proving that normal infected cells generate that peptide equally efficiently.

Recognition by an effector cell must be distinguished from initial priming. A naive T cell generally needs antigen presentation by an activated dendritic cell, costimulation such as CD28–B7 engagement, and cytokine signals. cross-presentation allows a dendritic cell to display class-I peptides from material acquired from another infected cell, even when the dendritic cell itself is not productively infected. Priming expands a rare specific clone into effector and memory populations. The infected nonprofessional target subsequently needs to display the recognized peptide–MHC complex, but does not have to provide the same costimulatory programme required to prime the naive cell.

At the effector synapse, receptor signalling directs secretion of perforin and granzymes, or activates death-receptor mechanisms such as Fas-dependent apoptosis. Cytokines also restrict infection. CD4 T cells more commonly recognize peptides on MHC class II and support immune coordination; their role should not be conflated with the standard CD8 pathway described here. Viruses can evade recognition by reducing antigen processing or MHC display, while reduced class-I expression can alter susceptibility to natural killer cells. Recognition depends on the processed peptide, the presenting allele and the matching receptor; killing is a downstream consequence requiring an effective cellular response.

The proton current supplies energy, while a conformational switch changes how that current is coupled to rotor motion. Reversing torque therefore does not require reversing the electrochemical gradient. In the proton-driven bacterial flagellar motor of Escherichia coli, the cell maintains a proton-motive force that favours proton entry. MotA and MotB form stator units anchored to the cell envelope. Proton-dependent conformational cycles of those units exert force on the rotor, including interactions with FliG.

The rotor's switch complex includes FliG, FliM and FliN. Cooperative changes in its organization alter the relative geometry of rotor and stator contacts and hence the direction in which the energy-driven cycle produces angular displacement. Structural work on the torque ring supported a mechanism in which reorientation of interacting regions changes the sign of torque.^[ref] Such structural models constrain the explanation, but should not be treated as a complete direct movie of every proton-transfer and mechanical step. The central distinction is robust: the sign of mechanical rotation changes through the motor's coupling state, while the thermodynamically favourable direction of proton flow remains inward.

This is consistent with energy conservation. With a fixed electrochemical difference, inward proton movement has a negative free-energy change. In either rotational state, the magnitude of that input can supply positive work against a resisting load. Both torque and angular displacement reverse when the motor reverses, leaving their product, the work delivered during motion against that load, positive. No principle requires a given sign of proton flow to correspond to one immutable sign of angular displacement when the protein coupling apparatus can change conformation.

Chemotaxis controls the switch bias. Receptor complexes regulate CheA, which transfers phosphoryl groups to CheY. Phosphorylated CheY binds the switch, particularly FliM-associated sites, increasing clockwise bias in the familiar E. coli swimming system. Counterclockwise rotation promotes a coherent flagellar bundle and a run; clockwise episodes disrupt the bundle and permit reorientation. An attractant response commonly reduces CheA activity and CheY phosphorylation, extending runs, while adaptation restores sensitivity. CheY phosphorylation is a regulatory signal; it does not provide the motor's main mechanical energy or reverse the proton gradient. Other bacteria can use different motor arrangements or sodium-driven stators, so this account should not be universalized to all species.

Experimentally, a tethered-cell or attached-bead assay resolves individual motor direction changes while external pH and membrane potential are controlled. Reversal without a measured reversal of the gradient supports switching of coupling. A protonophore should suppress energy supply and rotation, rather than reliably command the opposite direction. CheY perturbations and switch mutations can alter directional bias while leaving ion-driven torque generation intact. Simultaneous gradient measurements, motor speed and direction distinguish an energy deficit from a switch defect; a population swimming assay alone cannot do so. Directional control and energetic drive are separable functions of the same molecular machine.

In ciliates, sex often renews and reorganizes nuclei without immediately increasing cell number, and its outcomes depend on both germline DNA and the old somatic nucleus. nuclear dimorphism is central. A usually diploid micronucleus preserves the germline genome, while a transcriptionally active, often highly polyploid macronucleus controls vegetative cell function. Repeated binary fission can increase cell number without a sexual event; mitotic micronuclear inheritance and often amitotic macronuclear division maintain the two nuclear systems differently. Sex is therefore separable from routine population growth, although some species or strains undergo clonal ageing and benefit from, or eventually require, nuclear renewal for continued vigorous growth.

In the standard conjugation sequence of Tetrahymena thermophila, appropriately mature, compatible cells pair under suitable conditions, often starvation. The micronucleus undergoes meiosis; selected haploid products give stationary and migratory pronuclei after an additional division. Partners exchange migratory pronuclei, and each fuses its incoming and stationary pronucleus to establish a diploid zygotic nucleus. Postzygotic divisions generate new micronuclear and macronuclear lineages, while the old macronucleus is eliminated. The immediate products are two reorganized exconjugant cells, rather than a new single cell created by fusion of the entire parents. Details and product numbers vary across ciliates, so this sequence should not be imposed unchanged on every species.

Compatibility is also more varied than a male/female distinction. Tetrahymena thermophila has seven mating types, with compatibility between different types rather than differentiated sperm and eggs. Mating type is established during formation of the new somatic genome by gene-segment joining and deletion at the mating-type locus; the germline retains genetic potential not all expressed together in the macronucleus. The available outcomes are constrained by the inherited mating-type allele. Primary experiments connecting somatic rearrangements to mating-type expression demonstrate why a simple two-sex Mendelian account is inadequate.^[ref]

Some Paramecium undergo autogamy, in which meiosis and fusion of pronuclei derived from one cell renew the nuclear apparatus without a partner. This can generate pronounced homozygosity rather than introduce new alleles through outcrossing. The potential benefits of recombination and nuclear renewal must therefore be distinguished from the acquisition of genetic diversity from another individual. Sex is not invariably equivalent to outbreeding.

Formation of the new macronucleus also involves DNA elimination, amplification and extensive genome reorganization. Maternal somatic information can influence which sequences survive. In Paramecium tetraurelia, small-RNA-guided excision of the mtA promoter contributes to mating-type inheritance: the old macronuclear state can guide development of the new one.^[ref] This is an experimentally defined epigenetic pathway, not evidence that all acquired traits become heritable. After conjugation, exconjugants can share a newly combined micronuclear genotype yet develop distinct somatic states; later macronuclear assortment can further alter phenotype. Ciliate sex combines meiotic inheritance with somatic-genome reconstruction, and can serve nuclear renewal without immediate numerical reproduction or obligatory outcrossing.