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1) Briefly explain molecular motion.
a. Molecular motors operate by small increments, converting changes in protein conformation into directed motion. This requires a track that steers the motion of the motor assembly. The motor proteins that are involved have high or low affinity for the filament tracks in response to ATP binding and hydrolysis, enabling a bind, pull, and release mechanism that generates motion.
1) Compare myosin and kinesin and contrast dynein.
a. Both contain P-loop NTPase cores homologous to those found in G proteins. Dynein is a member of the AAA subfamily of P-loop NTPases
1) What is the structure of myosin?
- a. It is a two-headed structure linked to a long stalk. The head domains contain the ATPases.
- b. Cleavage reveals four fragments: two S1 (which are the globular heads); heavy meromyosin, which includes S1 fragment and S2; and a fragment called light meromyosin.
- c. Extending away from the S1 fragments (globular heads) is a long alpha helix from the heavy chain, which binds the two light chains. Proteins wrap around an alpha helix to thick and stiffen it. The remaining fragments—S2 and light meromyosin—are largely alpha helical, forming two-stranded coiled coils wrapping around each other
1) What is the structure of kinesin?
- a. It is a dimeric protein with two heads connected by an extended structure. The head domain is 1/3 the size of myosin.
- b. The head domain is also built around a P-loop NTPase core. A region of about 500 amino acids extends from the head domain. This extended part forms an alpha-helical coiled coil.
- c. It also has light chains that bind near the carboxyl terminus and link the motor to intracellular cargo
1) What is the structure of dynein?
a. It has six regions that are homologous to the AAA subfamily of ATPase domains. The head domain is appended to a region of about 1300 amino acids that form an extended structure that links dynein units together to form oligomers and interacts with other proteins
1) What are the similarities among the three proteins?
a. Each structure is dimeric with two head domains (act as engines), has regions of extended but quite rigid structures (the levers that promote larger-scale motion), and has regions for interacting with other proteins (act as grasping hands).
1) Explain the conformational changes that myosin undergoes when bound to ATP. How would kinesin differ?
- a. The long helix that binds the light chain (the lever arm) protrudes outward from the head domain. The lever arm rotates by nearly 90o when bound to ATP than when it is nucleotide-free. The species in the nucleotide binding site (switch I and switch II) tightly conform to the shape of the gamma-phosphoryl group of ATP and adopt a looser conformation when it is absent. This change allows the alpha helix (termed the relay helix) to adjust its position. Since the carboxyl-terminal end of the relay helix interacts with structures at the base of the lever arm, a change in the position of the relay helix leads to a reorientation of the lever arm.
- b. Though kinesin has a relay helix that can adopt different configurations when nucleotides bind, since it lacks an alpha-helical lever arm, a short segment termed the neck linker changes conformation in response to nucleotide binding, binding to the head domain when ATP is bound and releasing when the site is vacant or occupied by ADP.
a. Each actin monomer comprises four domains, which come together to surround a bound nucleotide, either ATP or ADP. Actin monomers (G-actin) come together to form actin filaments (F-actin), which has a helical structure. The filament is polar since the actin monomers are oriented in the same direction. Actin filaments self-assemble. Though the aggregation of the first two or three monomers is unfavorable, after specialized protein complexes, Arp2/3, act as nuclei for actin assembly, the polymerization is favorable.
1) Why is actin considered dynamic?
a. It is continually gaining and losing monomers. Nucleation by complexes like Arp2/3 initiate the polymerization of actin-ATP. But, hydrolysis of ATP to ADP causes depolymerization; polymerization reactions can exert force as well. Regulated actin polymerization is central to the changes in cell shape associated with cell motility
1) How does ATP hydrolysis drive the power stroke?
- a. The binding of ATP to actin results in the dissociation of myosin from actin.
- b. With ATP bound and free of actin, the myosin domain can undergo the conformational change associated with the formation of the transition state for ATP hydrolysis.
- c. This conformational change results in the reorientation of the lever arm.
- d. In this form, the myosin head can dock onto the actin filament; phosphate is released with concomitant motion of the lever arm.
- e. This power stroke moves the body of the myosin molecule relative to the actin filament.
- f. The release of ADP completes the cycle.
1) How is muscle contraction achieved?
a. It is achieved through the sliding of the think filaments along the length of the thick filaments, driven by the hydrolysis of ATP. The interaction of individual myosin heads with actin units creates the sliding force that gives rise to muscle contraction
1) How do tropomyosin and the troponin complex regulate the sliding?
a. They regulate it in response to nerve impulses. Under resting conditions, tropomyosin blocks the intimate interaction between myosin and actin. A nerve impulse leads to an increase in calcium ion concentration within the muscle cell. A component of the troponin complex senses the increases in Ca2+ and, in response, relieves the inhibition of myosin-actin interactions by tropomyosin
1) How does the myosin reaction cycle apply to muscle contraction?
a. Hundreds of head domains project form the ends of each thick filament. The head domains are paired in myosin dimers, but the two heads within each dimer act independently. Actin filaments associate with each head-rich region, with the barbed ends of actin toward the Z line. In the presence of normal levels of ATP, most of the myosin heads are detached from actin. Each head can act independently hydrolyze ATP, bind to actin, release Pi, and undergo its power stroke. Because few other heads are attached, the actin filament is relatively free to slide.
1) What is the effect of the lever arm on muscle contraction?
a. A shorter lever arm led to a decreased rate of activity. A longer lever arm led to an increased rate of activity.
- a. They are built from two kinds of subunits, alpha and beta subunits, which assemble in a helical array of alternating tubulin types to form the wall of a hollow cylinder. Alternatively, a microtubule can be regarded as 13 protofilaments that urn parallel to its long axis. They are polar structures, with a minus end anchored near the center of a cell, and the plus end extending toward the cell surface
- b. They are also key components of cilia and flagella
- c. They grow by adding tubulin to the ends of existing structures.
1) Explain microtubules in cilia and flagella.
a. A bundle of microtubules called an axoneme is surrounded by a membrane contiguous with the plasma membrane. It is composed of a peripheral group of nine microtubule pairs surrounding two singlet microtubules. It is a 9+2 array. Dynein drives the motion of one member of each outer pair relative to the other.
1) Explain tubulin and energy.
a. Tubulins bind and hydrolyze GTP. A newly formed microtubule consists primarily of GTP-tubulins. When GTP is hydrolyzed to GDP, the GDP-tubulin subunits remain polymerized, while those at the end dissociate. This is dynamic instability. Tubulins are members of the P-loop NTPase family.
1) Explain kinesin motion.
- a. When a kinesin molecule move along a microtubule, it does so in tandem; one binds, and then the next does. It is processive and can take many steps prior to releasing
- b. ATP strongly increases the affinity of kinesin for microtubules
- c. The steps are:
- i. The two headed kinesin molecules in ADP form are dissociated form a microtubule.
- ii. The initial interaction of one of the head domains with a tubulin dimer on a microtubule stimulates release of ADP and binding of ATP
- iii. The binding of ATP triggers a conformational change in the head domain that leads to two events
- 1. The affinity of the head domain for the microtubule increases, locking the head domain place
- 2. The neck linker binds to the head domain, throwing the second domain toward the plus end of the microtubule.
- iv. Meanwhile, ATP is hydrolyzed to ADP in the first head domain.
- v. When the second head domain binds to the microtubule, the first head releases ADP and binds ATP, which favors a conformational change that pulls the first domain forward
1) Why do kinesin and myosin function at different rates?
a. Myosin movement depends on the independent action of hundreds of different head domains working along the same actin filament, whereas the movement of kinesin is driven by the processive action of kinesin head groups working in pairs. Kinesin needs steady and slower transport, while myosin requires maximized speed
1) Explain bacterial flagella.
a. They are polymers made of flagellin, which associate into a helical structure with a hollow core. Flagella form not by growing at the base adjacent to the cell body but by the addition of new subunits that are added to the free end. Each flagellum is twisted in a left-hand sense
1) Explain the flagellar motor.
a. Five components crucial to motor function are MotA (membrane protein with four transmembrane helices and a cytoplasmic domain), MotB (another membrane protein with a single transmembrane helix and a large periplasmic domain), and FliG, FliM, and FliN (part of a disc-like structure called the MS (membrane and supramembrane) ring.
1) What is the mechanism of flagellar rotation?
a. The MotA-MotB pair and FliG combine to create a proton channel that drives rotation. Each MotA-MotB pair forms a structure that has two half-channels; FliG serves as the rotating proton carrier. A proton from the periplasmic space passes into the outer half-channel and is transferred to a FliG subunit. The MS ring rotates, rotating the flagellum with it and allowing the proton to pass into the inner half-channel and into the cell.
1) What is the pathway for chemotaxis?
- a. It begins with the binding of molecules to receptors. In their unoccupied forms, these receptors initiate a pathway leading to phosphorylation of a specific aspartate residue on a soluble protein called CheY, which binds to the base on the flagellar motor. When bound to phosphorylated CheY, the flagellar motor rotates clockwiseà tumbling.
- b. The binding of a chemoattractant to a surface receptor blocks the signaling pathway leading to CheY phosphorylation; and, other phosphorylated CheY hydrolyzes, causing a drop in concentration. Flagella are less likely to rotate clockwise and swim