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TDC - Topic 4

memorize.ai (lvl 286)

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What are the common features of motor proteins?

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6 years ago

Date created

Mar 1, 2020

Cards (29)

Section 1

(29 cards)

What are the common features of motor proteins?

Front

- hydrolyse ATP - Conformational change coupled to hydrolysis - Conformational change coupled to polymer

Back

How does PGK protect 1,3-PGA from water?

Front

As the enzyme closes, water is excluded and the two substrates become buried, avoiding the hydrolysis reaction.

Back

What else helps to reduce the energy humour that the reaction needs to overcome?

Front

- In the closed form, two positively charged side chains are found next to where the phosphate is transferred to reduce the high energy of all the negative charges that are coming together. - The Mg+ 2 on that is attached to the phosphate group

Back

what is PGK?

Front

phosphoglycerate kinase

Back

How can you show that there is an inversion in configuration when ADP binds to the phosphate group on 1,3-PGA?

Front

Can make all of the oxygens around the phosphate non-equivalent by using isotopes or replacing an oxygen with a sulphur atom.

Back

What is the motor protein evolved with actin?

Front

Myosin (a type of kinesin)

Back

What is the actin cytoskeleton?

Front

Dense weave of actin filaments

Back

What is PGK used for?

Front

To convert 1,3-bisphosphoglycertae to 3-phosphoglycerate ADP is converted into ATP (first time that ATP is made in glycolysis)

Back

How would you test that there are two active sites not just one which the two substrates bind to one after another?

Front

Saturate enzyme with one of the substrates e.g. ADP (could be the other way around) Experimentally, normal MM kinetics happens as if there is one binding site due to the ADP site being already filled and so the curve only showing results for [1,3, PGA]. Very high [ADP] bound would inhibit binding of 1,3, PGA if there was only one site.

Back

Why doesn't 1,3PGA get hydrolysed before it finds PGK?

Front

PGK and glycolytic enzymes are present at relatively very high concentrations high concentration of E vs S So, all substrate is enzyme bound (substrate saturated by enzyme) Substrates could be handed on from enzyme to enzyme if the enzymes form substrate-complexes = metabolon

Back

Why is ATP hydrolysis often needed for motor protein movement?

Front

if they are moving to where the concentration gradient is higher, there has to be energy to move it along the gradient

Back

What is the structure of a kinesin?

Front

Has globular N terminus which is mainly the motor domain - Motor domain is highly conserved - Different kinesins have different structures and placement of their motor domains C terminus attaches to vesicle

Back

What is the structure of actin filaments?

Front

- There are two different ends (associates in a polar way) - Barbed end and pointed end - Two filaments twist around each other to give higher strength - Barbed ends found closer to cell membrane - Pointed end point towards cell interior

Back

When do PGK and TIM work together?

Front

A hyperthermophile (Thermotoga maritima) has PGK and TIM (triose phosphate isomerase) in the same gene (fused together on the gene). They form the same polypeptide chain and work together.

Back

How are microtubules orientated?

Front

Orientated so that minus end is towards the cell centre/microtubule orientating centre Plus-end is orientated towards the cell periphery - Creates a star-like formation

Back

How does PGK help the reaction to occur?

Front

- it reduces the activation energy e.g. where the oxygens are too close during the bonding of ADP and 1,3 PGA and reaction to get to this is uphill (transition state). - it protects the molecules from water e.g. 1,3 PGA is unstable and can be hydrolysed meaning if it comes into contact with water, its high energy will be lost to water, producing heat.

Back

What is the structural mechanism of myosin?

Front

1. attached - myosin head it bound to an actin filament in a rigor conformation 2. Release - a molecule of ATP binds to the large clef on the 'back' of the head and causes a conformational change in the actin-binding site. This reduces the heads affinity for actin and allows it to move along the filament 3. cocked - the clef closes around the ATP molecule causing the head to be displaced along the filament. Hydrolysis of ATP occurs but the ADP and Pi remain bound 4. Force-generating - a weak binding of the myosin head to a new site casques the Pi to be released which allows it to bind more tightly. this release triggers the power stroke - the head returns to its original conformation. over the course of the power stroke, the lysin loses the ADP molecule

Back

What is the crystal structure of PGK?

Front

it has two lobes with a gap between them - two different domains, same polypeptide chain

Back

How are the products released from PGK?

Front

Energy is released when the products are released into solution as when the enzyme opens, the positive charges no longer compensate the negative charges. This repels the products into solution.

Back

What is the mechanism of PGK?

Front

ADP attacks the phosphate group on 1,3-PGA forming 3-PGA and ATP

Back

What is kinesin?

Front

A motor protein

Back

What are the rough steps for PGK action?

Front

1. Both of the substrates are bound at separate sites on the enzyme molecule 2. Transfer of phosphate occurs on the enzyme 3. Randomly, either ATP comes off first or 3PGA comes off first

Back

Where does PGK bind its substrates?

Front

PGK has 2 active sites - one for 1,3-PGA and one for ADP (the order of binding doesn't matter)

Back

Why is the release of products from PGK rate limiting?

Front

because it involves a conformational change in the enzyme - lobes will have to move apart again to be re-used.

Back

How does the bond made between ADP and the phosphate group have to be aligned for the reaction with to work?

Front

Has to be an in-line attack: The bond made between ADP and the phosphate group has to be in line with the angle that the phosphate group is attached to the 1,3, PGA. - The oxygens on the phosphate group of the 1,3, PGA are equally spread out - When the bond forms, they are no longer equally spread as there is an extra oxygen bonded to the phosphate = uphill reaction - When the bond to the 1,3 PGA breaks, the configuration is inverted back to a tetrahedral shape

Back

if the use of both PGK and TIM is useful, why hasn't it been used again in any other species?

Front

Running with the red queen

Back

At equilibrium, what is the approx. delta G value of the reaction? And why?

Front

0. Energy needed to get over the hump is released again to get back to the product.

Back

What is the structure of myosin?

Front

- Globular N terminus - Coiled coil of two alpha helices Myosin associates into arrays (e.g. in muscles) in two different directions forming a thick filament

Back

What happens to PGK when the substrates bind?

Front

ADP and 1,3 PGA found in different lobes (relatively far apart when attached singly). When both are bound at the same time, there is a conformational change meaning the two lobes come together.

Back