ULTRACENTRIFUGATION

CENTRAL UNIVERSITY OF KERALA

BCMB, ROLL NO.14

VIKKY KUMAR MAHTO

Centrifuge

A centrifuge is a device for separating particles from a solution according to their size, shape, density, viscosity of the medium and rotor speed.

HISTORY Swedish Biochemist Theoder

Svedberg invented the Ultracentrifuge in 1923.

And he won the Novel Prize in chemistry in 1926 for his research on colloids and protein using the ultracentrifuge.

Ultracentrifugation Machine

ULTRACENTRIFUGATION

It is an important tool in biochemical research. Which through rapid spinning imposes high centrifugal forces on suspended particles, or even molecules in solution, and causes separations of such matter on the basis of differences in weight.

Example;

Red cells separated from plasma of blood, nuclei from mitochondria in cell homogenates, one protein from another in complex mixtures. And also isolation of macromolecules such as DNA, RNA, Lipids etc.

Its rotational speed up to 150,000 rpm.

It is creating a centrifugal force up to 900,000 x g.

TYPES

1. Analytical ultracentrifugation:- The aim of Analytical ultracentrifugation is use to study molecular interactions between macromolecules or to analyse the properties of sedimenting particles such as their apparent molecular weight.

2. Preparative ultracentrifugation:- The aim of Preparative ultracentrifugation to isolate and purify specific particles such as subcellular organells.

There are two types of ultracentrifugation:

Analytical ultracentrifugation

Two kinds of experiments are commonly performedon these instruments:

1. Sedimentation velocity experiments:- Aim of SVEs to interpret the entire time-course of sedimentation, and report on the shape and molar mass of the dissolved macromolecules, as well as their size distribution.

2. Sedimentation equilibrium experiments:- SEEs are concerned only with the final steady-state of the experiment, where sedimentation is balanced by diffusion opposing the concentration gradients, resulting in a time-independent concentration profile.

Preparative ultracentrifugation

It is to isolate specific particles which can be reused

1. Differential ultracentrifugation:- Differential centrifugation is a common procedure in microbiology and cytology used to separate certain organelles from whole cells for further analysis of specific parts of cells.

2. Density gradient ultracentrifugation:- Based on denstiydifference. There are two types of density gradient ultracentrifugations under preparative ultracentrifugation such as.

1.ZONAL or RATE & 2.ISOPYCNIC

1} ZONAL or RATE Centrifugation:Mixture to be separated is layered on top of a

gradient (increasing concentration down the tube).Provides gravitational stability as different species.Move down tube at different rates.

2} ISOPYCNIC Centrifugation: Isopycnic means “of the same density”. Molecules separated on equilibrium position. Each molecule floats or sinks to position where

density.

Schematic presentation of a Ultracentrifuge:

Fig; A Beckman Ultracentrifugation.

Functions of analytical and preparative ultracentrifugation:Analytical Uses small sample size (less than 1 ml). Built in optical system to analyze progress of molecules during

centrifugation. Uses relatively pure sample. Used to precisely determine sedimentation coefficient and MW of

molecules. Beckman Model E is an example of centrifuge used for these purposes.

Preparative Larger sample size can be used. No optical read-out collect fractions and analyze them after the run. Less pure sample can be used. Can be used to estimate sedimentation coefficient and MW. Generally used to separate organelles and molecules. Most centrifugation

work done using preparative ultracentrifuge.

Rotor Four types of rotors are available for ultracentrifugation,

1. Fixed-angle rotor,2. Swinging-bucket rotor,3. Vertical rotor and4. Near-vertical rotor.

Rotors are made from either aluminum or titanium, or fromfiber-reinforced composites.

A titanium rotor is designated by T or Ti, as in the Type 100 Ti,the SW 55 Ti, or the NVT 90 rotor.

A composite rotor (fiber) is designated by C, as in VC 53.

A aluminum rotor is designated by AC, as in VAC 50.

Rotors without the T, Ti, C, or AC designation (such as the Type25) are fabricated from an aluminum alloy.

Titanium rotors are stronger and more chemical resistant than the aluminum rotors.

Exterior surfaces of titanium and composite rotors are finished with black polyurethane paint.

Titanium buckets and lids of high-performance rotors are usually painted red for identification.

1.FIXED ANGLE ROTOR

Fixed-angle rotors are general-purpose rotors that are especially useful for pelleting subcellular particles and in short column banding of viruses and subcellular organelles.

Tubes are held at an angle (usually 20 to 45 degrees) to the axis of rotation in numbered tube cavities.

2.SWINGING BUCKET ROTOR

Swinging-bucket rotor are used for pelleting, isopycnicstudies and rate zonal studies.

Tubes are attached to the rotor body by hinge pins or a crossbar. The buckets swing out to a horizontal position.

Isopycnic studies (separation as a function of density).

Rate zonal studies (separation as a function of sedimentation coefficient).

3.VERTICAL ROTOR

Vertical rotors hold tubes parallel to the axis of rotation; therefore, bands separate across the diameter of the tube rather than down the length of the tube.

Vertical rotors are useful for isopycnic and, in some cases, rate zonal separations when run time reduction is important.

4.NEAR VERTICAL ROTOR

Near-vertical rotors are designed for gradientcentrifugation when there are components in a sample mixture that do not participate in the gradient.

Tubes are held at an angle (typically 7 to 10 degrees) to the axis of rotation in numbered tube cavities.

In this rotor used only Quick-Seal and Opti-Seal tubes.

Common Centrifuge Classes and Their Applications

( ) = can be done but not usually used for this purpose.

Tube Type and Rotor Compatibility

Rotor TypesTube Types Fixed-Angle Swinging-bucket VerticalThin wall open top No Yes NoThick wall open top Yes Yes NoThin wall sealed Yes Some tubes YesOak ridge Yes No No

Types of Rotors and Theirs ApplicationsRotor Types Pelleting R or Z-Sedimentation IsopycnicFixed-angle Excellent Limited VariableS-bucket Inefficient Good GoodVartical Not suitable Good ExcellentN-vertical Not suitable Excellent Good

Rotor Balance The mass of a properly loaded rotor will be evenly distributed on

the ultracentrifuge drive hub, causing the rotor to turn smoothly with the drive.

An improperly loaded rotor will be unbalanced; consistent running of unbalanced rotors will reduce ultracentrifuge drive life.

To balance the rotor load, fill all opposing tubes to the same level with liquid of the same density.

Weight of opposing tubes must be distributed equally.

Place tubes in the rotor symmetrically.

Start A Run

Set the RPMs, time, and the temperature of the run by

gently pressing the setup screen.

Never exceed the manufacturer’s stated maximum speed

for any rotor.

Press the run/start button when settings are correct.

Wait until reaching desired speed.

After the Spin

Once a run is complete, make sure the rotor has

completely stopped before opening the centrifuge door.

Never attempt to open the door of a centrifuge or slow the

rotor by hand while the rotor is in motion.

Please log in after every use which will provide info for

maintenance and repair.

Each centrifuge has a log book as the following.

Return the clean (have to clean if spillage has occurred)

rotors to their location.

Rotor Sterilization and Disinfection Autoclave the rotor (and/or buckets) upside-down for up

to an hour (O-ring and gaskets can be left in place on

the rotor) if necessary.

70% ethanol may be used on all rotor components.

If Spillage Has OccurredWash the rotor and rotor components

immediately with cleaning kit.

Beckman Solution 555

Plastic coated brushes

If radioactive, toxic or pathogenic

materials are involved, please contact

Tech Support Team.

Please never leave unclean rotor to dry out which will

damage the rotor

make it very difficult for subsequent users.

Operating Procedures Sign up for it on website and log in on the log book.

Turn on the centrifuge.

Set up the parameters, speed, time, temperature, accelerate and

decelerate speed.

Open the centrifuge door.

Install the rotors with O-ring that contain balanced bottles or tubes.

Make sure the rotor is properly seated to the drive hub.

Secure the rotor with lid, close the centrifuge door.

Press enter then run/start.

Wait until reaching desired speed.

After completely stopped, open the door and take out the sample

bottles or tubes, check whether spilling was happened or not, if

there is spill, take out the rotor, wash and dry it and return to its

storage place; never leave rotor inside the centrifuge; also clean the

chamber.

Leave the high speed centrifuge door open and ultra speed

centrifuge door close and turn off the machine.

Care of Centrifuges and Rotors Carefully read the operating manual or receive proper

instructions before use any centrifuge.

Select the proper operating conditions on the instrument.

Check the rotor chamber for cleanliness and for damage.

Select the proper rotor. Many sizes and types are available.

Be sure the rotor is clean and undamaged.

Filled centrifuge tubes or bottles should be weighed carefully andbalanced before centrifugation.

Rotor manufactures provide a max. allowable speed limit for eachrotor. Do nor exceed that limit.

Keep an accurate record of centrifuge and rotor use.

If an unusual noise or vibration develops during centrifugation,immediately turn the centrifuge off.

Carefully clean the rotor chamber and rotor after centrifugation.

What happens to a particle in a centrifugal field

The particle (m) is acted on by three forces:FC: the centrifugal forceFB: the buoyant forceFf: the frictional force between the particle and the liquid

Equation that describes the motion of this particle as follows:

F = mawhere m is the mass of the particle and a is the acceleration.

The Physics of UltraCentrifugation1.Centrifugal force:- The tube containing the suspension of particles isrotated at a high speed, which exerts a centrifugal force directed from the centerof the rotor towards the bottom of the tube.

Centrifugal Force:

Where,

M: mass of particle

r: radius of rotation (cm) (ie distance of particle from axis of rotation)

ω :Average angular velocity (radians/sec)

Centrifugal field :- Depends on the radical distance of

the particle from the rotation axis and the square of the

angular velocity.

OR

Angular Velocity:- Detect to revolution per minute (r.p.m)

2.Sedimentation rate:- This force acts on the suspendedparticles pushing them towards the bottom of the tube at a ratedetermined by the velocity of the spinning rotor.

Rate of Sedimentation:

Where,r = radius at which the organelle is locatedt = timeM = molecular weightν = partial specific volume of the molecule; inverse of thedensityρ = density of the solventf = translational frictional coefficientω = angular velocityNA = Avagadro’s number

3.Sedimentation coefficient:- Centrifugation separates particles in a suspension based on differences in size, shape and density that together define their sedimentation coefficient.

Sedimentation Coefficient:

This is know as the Svedberg equation and is usually expressed in Svedberg units,

S (= second).

This equation indicates that ‘S’ is dependent upon the molecular weight, the density and the frictional coefficient.

Some High Speed Centrifuges and Rotors

Some ultra Speed Centrifuges and Rotors

Thank you