Biological Machines and Motors PDF

Biological Machines and Motors  What are Biological machines/motors? Key property: motion Motor protein (or protein complex) Able to generate force and therefore do work Molecular basis of biological motility ATP and other molecules Molecules at nanometer size-nanomachines In...

Biological Machines and Motors  What are Biological machines/motors? Key property: motion Motor protein (or protein complex) Able to generate force and therefore do work Molecular basis of biological motility ATP and other molecules Molecules at nanometer size-nanomachines Interactions include ionic and Vander Waals forces Natural (protein based)and synthetic (DNA based)machines Transfer of substances across the cell and catalytic functions –protein Why do we need them? Basis of biological motility Cell division Cell motion Transport within cells Growth Muscle contraction Types Protein based DNA based Chemical molecular motors ATP based molecular motors Examples include FOFI ATP synthase and bacteria flagellar motor, kinesin, myosin and dynein Depend on ATP directly or indirectly Disadvantage- ATP creating machinery are heavy ATP – energy currency of cell ADP + Pi -→ATP (F0FI ATP ase) Is present in mitochondria of animal cell and chloroplast of plant cell Consist of two portions:(smallest reversible natural motors) membrane spanning portion F0 Soluble portion F1 ATP synthase in action https://www.youtube.com/watch?v=kXpzp4RDGJI  Thus, the flagellar motor is the output organelle of a remarkable sensory system, the components of which have been honed to perfection by billions of years of evolution. A number of bacterial species in addition to E. coli depend on flagella motors for motility: e.g., Salmonella enterica serovar, Typhimurium (Salmonella), Streptococcus, Vibrio spp., Caulobacter, Leptospira, Aquaspirrilum serpens, and Bacillus. The rotation of flagella motors is stimulated by a flow of ions through them, which is a result of a build-up of a transmembrane ion gradient. There is no direct ATP-involvement; however, the proton gradient needed for the functioning of flagella motors can be produced by ATPase. https://www.youtube.com/watch?v= B7PMf7bBczQ&t=70s  The cytoskeleton is in constant state of change depending on the requirements of the cell. 3 major structural elements of the cytoskeleton Microtubules - hollow, rigid cylindrical tubes made from tubulin subunits Microfilaments - solid, thinner structures made of actin Intermediate filaments - tough, ropelike fibers made of a variety of related proteins Mitochondrion, Plasma membrane, Ribosomes, Rough Endoplasmic reticulum  Microtubules: hollow ,rigid cylindrical tubes made of tubulin 20-25nm in diameter Are scaffolds of cell gives shape Provides way through which organelles and vesicle move within the cell Form spindle fibre during mitosis Also seen in cilia and flagella  Microfilaments Solid thinner structure Made of actin 3-6 nm in diameter Work with myosin –muscle contraction Involved in gliding, contraction and cytokinesis  The kinesin and dynein families of proteins are involved in cellular cargo transport along microtubules, in contrast to myosin, which transports along actin. Microtubules have polarity; one end being the plus (fast-growing) end while the other end is the minus (slow-growing) end. Kinesins move from the minus end to the plus end of the microtubule, whereas dyneins move from the plus end to the minus end. Similar to myosin, kinesin is also an ATP-driven motor. One unique characteristic of the kinesin family proteins is their processivity; they bind to microtubules and literally walk on it for many enzymatic cycles before detaching. https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=-7AQVbrmzFw  Dyneins exist in two isoforms: cytoplasmic and axonemal.Cytoplasmic dyneins are involved in cargo movement,axonemal dyneins are involved in producing bendingmotions of cilia and flagella. DNA polymerase https://www.youtube.com/watch?v=sKe3UgH1AKg  DNA helicases https://evolutionnews.org/2013/02/unwinding_the_d_1/ A single strand of DNA passes through the central channel of the helicase hexamer, which contains DNA binding sites contributed by the helicase’s subunits. A cleft in each of the subunits binds ATP via side chains in conserved residues called Sensor 1, Sensor 2, Walker A and Walker B motifs. The wave of ATP binding, hydrolysis and release, shown in the animation above, results in the DNA being passed from one subunit to the next.  Together with the rotation between subunits induced by the ATP, this process causes the helicase to move forward at a rate of one nucleotide for each hydrolysis reaction. In T7 bacteriophage, binding of a subunit to ATP causes the subunit to rotate 15 degrees Since the genome of papillomavirus is circular, there are no ends available for loading of the helicase hexameric ring. Consequently, the E1 helicase has to initiate unwinding from double-stranded DNA. This is thought to be accomplished by melting the helix and loading the helicase onto a single-stranded region. The Beta-hairpins that are present in the motor domain of the E1 helicase (and which bind DNA) form a rising staircase around the helicase’s central channel. As the cycle of ATP binding, hydrolysis and release takes place, the Beta-hairpins descend the staircase. This enables the helicase to walk along the ssDNA. Ribosomes as motor proteins! https://www.youtube.com/watch?app=desktop&v=morl5e-jBNk