Specific Heat

The specific heat is the amount of heat per unit mass required to raise thetemperature by one degree Celsius. The relationship between heat and temperature change is usually expressed in the form shown below where c is the specific heat. The relationship does not apply if a phase change is encountered, because the heat added or removed during a phase change does not change the temperature.

The specific heat of water is 1 calorie/gram °C = 4.186 joule/gram °C which is higher than any other common substance. As a result, water plays a very important role in temperature regulation. The specific heat per gram for water is much higher than that for a metal, as described in the water-metal example. For most purposes, it is more meaningful to compare the molar specific heats of substances.
The molar specific heats of most solids at room temperature and above are nearly constant, in agreement with the Law of Dulong and Petit. At lower temperatures the specific heats drop as quantum processes become significant. The low temperature behavior is described by the Einstein-Debye model of specific heat.

The specific heat (also called specific heat capacity) is the amount of heat required to change a unit mass (or unit quantity, such as mole) of a substance by one degree in temperature. Therefore, unlike the extensive variable heat capacity, which depends on the quantity of material, specific heat is an intensive variable and has units of energy per mass per degree (or energy per number of moles per degree).

The heat capacity of a substance can differ depending on what extensive variables are held constant, with the quantity being held constant usually being denoted with a subscript. For example, the specific heat at constant pressure is commonly denoted , while the specific heat at constant volume is commonly denoted . The specific heat of water at constant atmospheric pressure is

(1)

i.e., 1 calorie is needed per degree Kelvin (or Celsius) of temperature change for 1 gram of liquid water. In fact, the definition of (one of the several types of) the calorie is the amount of heat needed to change thetemperature of 1 g of water by 1  at its temperature of maximum density (roughly 3.98° C).

The heat capacity ratio is defined as the ratio of specific heats of a substance at constant pressure and constant volume,

Specific heat is another physical property of matter. All matter has a temperature associated with it. The temperature of matter is a direct measure of the motion of the molecules: The greater the motion the higher the temperature: Motion requires energy: The more energy matter has the higher temperature it will also have. Typicall this energy is supplied by heat. Heat loss or gain by matter is equivalent energy loss or gain. With the observation above understood we con now ask the following question: by how much will the temperature of an object increase or decrease by the gain or loss of heat energy? The answer is given by the specific heat (S) of the object. The specific heat of an object is defined in the following way: Take an object of mass m, put in x amount of heat and carefully note the temperature rise, then S is given by In this definition mass is usually in either grams or kilograms and temperatture is either in kelvin or degres Celcius. Note that the specific heat is "per unit mass". Thus, the specific heat of a gallon of milk is equal to the specific heat of a quart of milk. A related quantity is called the heat capacity (C). of an object. The relation between S and C is C = (mass of obect) x (specific heat of object). A table of some common specific heats and heat capacities is given below: Some common specific heats and heat capacities:  Substance  S (J/g0C)  C (J/0C) for 100 g  Air  1.01  101  Aluminum  0.902  90.2  Copper  0.385  38.5  Gold  0.129  12.9  Iron  0.450  45.0  Mercury  0.140  14.0  NaCl  0.864  86.4  Ice  2..03  203  Water  4.179  41.79       Consider the specific heat of copper , 0.385 J/g 0C. What this means is that it takes 0.385 Joules of heat to raise 1 gram of copper 1 degree celcius. Thus, if we take 1 gram of copper at 25 0C and add 1 Joule of heat to it, we will find that the temperature of the copper will have risen to 26 0C. We can then ask: How much heat wil it take to raise by 1 0C 2g of copper?. Clearly the answer is 0.385 J for each gram or 2x0.385 J = 0.770 J. What about a pound of copper? A simple way of dealing with different masses of matter is to dtermine the heat capacity C as defined above. Note that C depends upon the size of the object as opposed to S that does not. We are not in position to do some calculations with S and C. Example 1: How much energy does it take to raise the temperature of 50 g of copper by 10 0C? Example 2: If we add 30 J of heat to 10 g of aluminum, by how much will its temperature increase?   Thus, if the initial temperture of the aluminum was 20 0C then after the heat is added the temperature will be 28.3 0C. Converting between Common Units 1 Btu/lbmoF = 4186.8 J/kg K = 1 kcal/kgoC Example - Heating Aluminum 2 kg of aluminum is heated from 20 oC to 100 oC. Specific heat of aluminum is 0.91 kJ/kg0C and the heat required can be calculated as dQ = (2 kg) (0.91 kJ/kg0C) ((100 oC) - (20 oC))       = 145.6 (kJ) Example - Heating Water One litre of water is heated from 0 oC to boiling 100 oC. Specific heat of water is 4.19 kJ/kg0C and the heat required can be calculated as dQ = (1 litre) (1 kg/litre) (4.19 kJ/kg0C) ((100 oC) - (0 oC))       = 419 (kJ) Specific Heat Gases There are two definitions of Specific Heat for vapors and gases: cp = (δh / δT)p - Specific Heat at constant pressure (kJ/kgoC) cv = ( δh / δT)v - Specific Heat at constant volume (kJ/kgoC) Gas Constant  The gas constant can be expressed as R = cp - cv         (2) where R = Gas Constant Ratio of Specific Heat The Ratio of Specific Heat is expressed k = cp / cv         (3) Shailesh  kr shukla directoratace@gmail.com

WHALES: Everything about aquatic Hunk.

HUMPBACK WHALE FACTS

• Average Length: (Adult) 35-50 ft (Newborn) 13-16 ft
• Average Weight: (Adult) 23-30 tons (Birth) 1-2 tons
• Population: 18,000-20,000 (2002 figure)
• Lifespan: estimated to be around 40 years (1998 figure)
• Threats: Caught in fishing nets, human disturbance, and being tangled in marine pollution
• The flukes (tails) have a distinct pattern on the underside, much like our fingerprints
• The humpback whale breaches more frequently than other baleen whales
• The Pacific humpback's pectoral fins are white underneath & black on top..
• The Atlantic humpback's pectoral fins are white on both sides- which makes it easier for us to see them
• While in their breeding grounds- the whales do NOT eat!
• Some humpbacks feed in the Southern Ocean and go north to their reproductive areas!
• Can stay underwater for 30 minutes but often dives for much shorter periods of time, usually 5 to 10 minutes
• Humpbacks emit high frequency "clicks" reaching 30,000 Hz
• The males produce, in frequencies between 20 and 9,000 Hz, songs that are the longest and the most varied in all the animal kingdom, with repeated sequences about 15 minutes long
• When they are in cold waters, the humpback whale eats 2 tons of fish and planktonic crustaceans a day, in 2 to 4 meals.

ORCA FACTS

• Average Length: (Adult) 18-32 ft (Newborn) 7-8 ft
• Average Weight: (Adult) 2.6-9 tons (Birth) 395 lbs
• Nicknames: Killer whale, blackfish, grampus
• Diet: "opportunistic"- the orca is one of the ocean's top predators (see below)
• Range: All oceans of the world
• Threats: Capture for public display, hunting, pollution
• The largest member of the dolphin family
• There is no known case of a wild orca ever killing a human
• Orcas stay in long-term social groups, or pods, for life (group size: 3-25)
• Orcas can be reliably seen on tours around Vancouver Island, off Antarctica, Norway, and Iceland, and occasionally in many other areas
• Orcas can travel at up to 34 mph (55 km/h)
• There are 2 'genetically' distinct forms of orcas, known as "transients" and "residents"
• A versatile predator and has one of the most varied diets of all cetaceans. It is known to eat anything from squid, fish, and birds to sea turtles, seals, and dolphins; it will even tackle animals as large as Blue Whales!
• Gestation period is thought to be 12-16 months, with most calves born between October and March

GRAY WHALE FACTS

• Average Length: (Male) 43 ft (Female) 41 ft (Newborn) 15 ft
• Average Weight: (Adult) 26 tons (Birth) 1,500 lbs
• Nicknames: Mussel digger, hard head, devil fish, gray back
• Group size: Generally 1-3; traveling groups can contain up to 16; hundreds can gather in good feeding conditions
• Lifespan: between 30 and 40 years, but may even be up to 60 years
• Gray whales are messy eaters
• Only whale that is known to feed often in the sand and mud ("bottom feeder")... feeding on shellfish, crabs and worms
• Each year, gray whales (only found in the North Pacific ocean) make the 12,400 mile round trip between Mexico and Alaska
• The cruising speed during migration is about 1 to 3 miles per hour
• Eastern Pacific gray whales, nearly extinct in the late nineteenth century, are now thought to number more than 20,000 (1998 figure)
• Young gray whales are often 'friendly', coming to the side of boats and even lifting them out of the water
• Pregnant females give birth to single calves just before or soon after arriving at the breeding lagoons; beginning in late December
• Gestation period is about 13.5 months, with approximately 2 years between pregnancies

BLUE WHALE FACTS

• The largest living creature on Earth!
• The record appears to be at least 110 feet long and a weight of 209 tons (It was a female)
• Average Length: (Male) 82 ft (Female) 85 ft (Birth) 19 1/2 ft
• Average Weight: (Adult) 100-120 tons (Newborn) 2.5-4 tons
• Population: low thousands (2002 figure)
• Diet: Krill and Fish
• Range: All oceans of the world
• Lifespan: More than 80 years
• Threats: Loss of food, pollution
• A blue whale drinks 50-150 gallons of milk a day, adding about 8 pounds of weight per hour, or 200 pounds a day
• At about 8 months of age, when the calf is weened, it can measure close to 50 feet long and weigh about 50,000 pounds
• At sea, blue whales usually feed alone or in pairs, often widely spaced
• A blue whale's "blow" can reach as high as 30 feet!
• During the feeding period, a blue whale can ingest 4 tons of krill a day. They feed at the beginning and the end of the night at a depth of at least 130 feet (40 m).
• Pre-whaling population estimates were over 350,000 blue whales, but up to 99% of blue whales were killed during whaling efforts
• Blue whales have no known predators (other than humans during the whaling years)
• By the 1950s, blue whales were endangered

FIN WHALE FACTS

• Average Length: (Adult) 59-72 ft (Newborn) 19-21 ft
• Average Weight: (Adult) 30-80 tons (Birth) 2 tons
• Population: 100,000+ (2002 figure)
• Diet: squid, fish, krill or other crustaceans
• Range: Widely distributed... but less common in tropical waters than temperate waters, and the arctic and Antarctic oceans
• Lifespan: 85 to 90 years
• Threats: Noise from vessels & other underwater noice (which may mask their social sounds) and Chemical Pollution
• Fin whales have been severely reduced by whaling, which continued in some places until as recently as the 1980s

MINKE WHALE FACTS

• Average Length: (Adult) 23-33 ft (Newborn) 8-9 ft
• Average Weight: (Adult) 5-15 tons (Birth) 770 lbs
• Population: 500,000-1 million (2002 figure)
• Diet: Fish, krill or other crustaceans
• Range: All oceans of the world
• Threats: Target of commercial whaling, accidental capture in fishing gear, pollution
• Lifespan: probably live for 40 - 50 years, but they are sometimes attacked by killer whales and can be at risk from collisions with boat traffic
• Minke whales are generally solitary, although they can sometimes be seen in groups of 2 or 3
• Minke whales are highly inquisitive and are likely to approach boats, especially younger animals
• The species is still threatened by whaling, which still continues in the N. Atlantic and Antarctic, with an annual take of 500 - 1000 by countries such as Norway, Japan, & Iceland

SPERM WHALE FACTS

• Average Length: (Adult) 36-59 ft (Newborn) 11-14 ft
• Average Weight: (Adult) 20-50 tons (Birth) 1 ton
• Population: Unknown
• Diet: Squid, giant squid, octopus and fish
• Group size: 1-50, hundreds may travel together
• Range: Tropical to sub-polar deep ocean waters worldwide
• Threats: Pollution, noise disturbance, caught in nets
• Sperm whales have the largest heads in the animal kingdom (for males- up to 35 % of the body length)
• Can dive to depths of 655-985 feet
• Sperm whales can remain submerged for over 2 hours, but typical dive time is less than 45 minutes
• Sperm whales have unique wrinkled, prunelike skin
• The lifespan of sperm whales are thought to be 75 years or more

BOTTLENOSE WHALE FACTS

• Average Length: (Adult) 23-29 ft (Newborn) 9- 11 ft
• Average Weight: (Adult) 5.8-7.5 tons (Birth) unknown
• Population: Unknown
• Diet: Mainly squid; also fish & other invertebrates

PILOT WHALE FACTS

• Average Length: 12.5 - 20 ft
• Average Weight: 1.8 - 3.5 tons
• Nicknames: long-finned pilot whale, Blackfish
• Diet:
• Range: cold temperate and subpolar waters of all oceans except the North Pacific
• Population: unknown
• Pilot whales are one of the most commonly mass-stranded whales
• Young whales may breach, but this is rare in adults
• Capable of diving to at least 1,965 ft, but most dives are 100-195 ft

NORTHERN RIGHT WHALE FACTS

• Average Length: (Adult) 36-59 ft (Newborn) 15-20 ft
• Average Weight: (Adult) 30-80 tons (Birth) 1 ton
• Population: Northern ~ 300 (2002 figure)
• Diet: Krill or other crustaceans
• Threats: Fishing gear entanglements and ship strikes
• Right whales were originally named by whalers because they were considered the "right" whales to hunt- full of oil and easy to catch
• Southern Right whales sometimes raise their flukes at right angles to the wind and use them as sails, allowing themselves to be blown along through the water
• Right whales often breach, sometimes up to 10 times or more in a row
• The Northern Right whale is the most endangered whale in the ocean; about 300 in the N.Atlantic and possibly a handful in the N. Pacific
• The Right whale's baleen is ~ 12 inches long!

Shailesh kr Shukla

directoratace@gmail.com

CERN discovers Higgs-like Boson

Physicists working at the Large Hadron Collider (LHC) have announced the discovery of the Higgs boson – or at least a particle that resembles the Higgs. In two special seminars this morning at the CERN particle-physics lab in Geneva, spokespeople for the LHC's two main experiments – ATLAS and CMS – both reported measurements of the Higgs' mass at confidence levels of 5σ. Any finding that passes this statistical threshold is generally, but not always, considered a "discovery" among the particle-physics community.

However, today's announcement of a discovery of a particle that looks like the Higgs is by no means the end of the story, as physicists have yet to understand its complete nature.

Physicists have had the Higgs boson in their sights for nearly 50 years because its discovery would complete the Standard Model of particle physics. The particle and its associated field explain how electroweak symmetry broke just after the Big Bang, which gave certain elementary particles the property of mass. The Standard Model does not, however, predict the mass of the Higgs, and successive experimental programmes at CERN's Large Electron–Positron Collider (LEP), Fermilab's Tevatron and now the LHC have tried to measure the particle's mass.

Presenting the latest results from the CMS experiment, spokesperson Joe Incandela announced that his experiment has discovered the Higgs boson at a mass of 125 GeV/c² and a statistical significance of 5σ.

Incandela described the result as "A phenomenal effort considering that we stopped taking data two weeks ago."

Incandela was followed by ATLAS spokesperson Fabiola Gianotti, who says that ATLAS has measured the mass of the Higgs as 126 GeV/c², which agrees with preliminary results released by CERN in December 2011. The statistical significance of the measurement is 5σ.

"The search is more advanced today than we imagined possible," says Gianotti. However, she cautioned that "a little more time is needed to finalize these results, and more data and more study will be needed to determine the new particle's properties".

Measurements with 5σ from both detectors – combined with previous searches by Tevatron and LEP – leave no doubt that a "Higgs-like" particle has been discovered by the LHC.

"We have reached a milestone in our understanding of nature," says CERN director general Rolf-Dieter Heuer, who described the new particle as being "consistent with the Higgs boson".

Speaking in the CERN auditorium immediately after the results had been presented, Edinburgh University particle theorist Peter Higgs congratulated researchers on their finding. "For me, it's a really incredible thing that it's happened in my lifetime," he said.

However, mass appeal is not why we chose the discovery as our breakthrough of the year. The July announcement was much anticipated because physicists have had the Higgs boson in their sights for nearly 50 years. Its discovery completes the Standard Model of particle physics – making it the most important physics breakthrough so far in the 21st century.

The Higgs boson and its associated field explain how electroweak symmetry was broken just after the Big Bang to give certain elementary particles the property of mass. The Standard Model does not, however, predict the mass of the Higgs, which had remained a mystery until July. That was when both CERN experiments announced that they had independently discovered a particle with a mass of about 125 GeV/c². Crucially, both experiments were able to claim this figure with confidence levels of 5σ. Any finding that passes this statistical threshold is generally considered a "discovery" in the particle-physics community.

And if that were not enough, the CMS and ATLAS collaborations stand out because of the sheer scale of what has been achieved by their thousands of members over the past two decades. Starting in the early 1990s, when plans were first hatched for the Large Hadron Collider (LHC), physicists began thinking about how they could build detectors the size of small office blocks to capture and measure the multitude of particles produced when two protons collide at TeV energies. Some focused on how vast quantities of collision data could be stored and distributed to physicists around the world. Yet more began developing methods for analysing this vast and bewildering amount of information.

If both the ATLAS and CMS experiments had simply functioned as expected, that alone would have been worthy of a Physics Worldaward. However, both have overachieved since they first started taking data in 2010. Indeed, current ATLAS spokesperson Fabiola Gianotti told us that the accelerator has produced 10 times more data than would have been expected by this time. "The experiments, the computing grid and the LHC accelerator are performing well beyond our expectations," she says.

These are just a few reasons why both experiments have been able to home in on the Higgs after just a shade over two years of data-taking. In fact, the precise nature of the new particle is revealed by how it decays into other particles, which are then detected by the ATLAS and CMS collaborations. And while Physics World has been careful to call the discovery a "Higgs-like particle" – just as the collaborations themselves have done – evidence is now growing that the particle is a Higgs boson as described by the Standard Model of particle physics.

shailesh shukla

directoratace@gmail.com

THERMODYNAMICS: Reaction Profiling

The free energy change (DG) of a reaction determines its spontaneity. The free energy change (DG), and its relation to equilibrium constant, are discussed on p. 57-59 of Biochemistry 3rd Edition by Voet & Voet. A reaction is spontaneous if DG is negative (if the free energy of the products is less than the free energy of the reactants).

DG = change in free energy, DGo' = standard free energy change (with 1 M reactants and products, at pH 7), R = gas constant, T = absolute temperature.

Note that the standard free energy change (DG^o') of a reaction may be positive, for example, and the actual free energy change (DG) negative, depending on cellular concentrations of reactants and products. Many reactions for which DG^o' is positive are spontaneous because other reactions cause depletion of products or maintenance of high substrate concentrations.

At equilibrium, DG equals zero. Solving for DGo' yields the relationship at left.K'eq, the ratio [C][D]/[A][B] at equilibrium, is called the equilibrium constant. An equilibrium constant greater than one (more products than reactants at equilibrium) indicates a spontaneous reaction (negative DG').

The variation of equilibrium constant with DG^o' is shown in the table below.

Keq	DGo' (kJ/mol)	Starting with 1 M reactants and products, the reaction:
104	– 23	proceeds forward (spontaneous)
102	– 11	proceeds forward (spontaneous)
100 = 1	0	is at equilibrium
10–2	+ 11	proceeds in reverse
10–4	+ 23	proceeds in reverse

Energy coupling is discussed on p. 59-60 & 566-567.

• A spontaneous reaction may drive a non-spontaneous reaction.
• Free energy changes of coupled reactions are additive.

Examples of different types of coupling:
A. Some enzyme-catalyzed reactions are interpretable as two coupled half-reactions, one spontaneous and the other non-spontaneous. At the enzyme active site, the coupled reaction is kinetically facilitated, while the individual half-reactions are prevented. The free energy changes of the half-reactions may be summed, to yield the free energy of the coupled reaction.
For example, in the reaction catalyzed by the Glycolysis enzyme Hexokinase, the two half-reactions are:

• ATP + H₂O ADP + P_i .................. DG^o' = -31 kJoules/mol
• P_i + glucose  glucose-6-P + H₂O ... DG^o' = +14 kJoules/mol

Coupled reaction: ATP + glucose ADP + glucose-6-P .. DG^o' = -17 kJoules/mol
The structure of the enzyme active site, from which water is excluded, prevents the individual hydrolytic reactions, while favoring the coupled reaction. 
B. Two separate enzyme-catalyzed reactions occurring in the same cellular compartment, one spontaneous and the other non-spontaneous, may be coupled by a common intermediate(reactant or product).
A hypothetical, but typical, example involving pyrophosphate:

• enzyme 1: A + ATP  B + AMP + PP_i ....DG^o' = +15 kJ/mol
• enzyme 2: PP_i + H₂O  2 P_i ....................DG^o' = –33 kJ/mol

Overall: A + ATP + H₂O  B + AMP  +  2P_i ... DG^o' = –18 kJ/mol
Pyrophosphate (PP_i) is often the product of a reaction that needs a driving force. Its spontaneous hydrolysis, catalyzed by Pyrophosphatase enzyme, drives the reaction for which PP_i is a product. For an example of such a reaction, see the discussion of cAMP formation below.

C. Ion transport may be coupled to a chemical reaction, e.g., hydrolysis or synthesis of ATP.In the diagram at right and below, water is not shown. It should be recalled that the ATP hydrolysis/synthesis reaction is ATP + H2O  ADP + Pi. Equivalent to equation 20-3 on p. 727, the free energy change (electrochemical potential difference) associated with transport of an ion S across a membrane from side 1 to side 2 is represented below.

R = gas constant, T = temperature, Z = charge on the ion, F = Faraday constant, and DY = voltage across the membrane.

Since free energy changes are additive, the spontaneous direction for the coupled reaction will depend on the relative magnitudes of:

• DG for the ion flux (DG varies with the ion gradient and voltage.)
• DG for the chemical reaction (DG^o' is negative in the direction of ATP hydrolysis. The magnitude of DG depends also on concentrations of ATP, ADP, and P_i .)

Two examples of such coupling are:1. Active transport. Spontaneous ATP hydrolysis (negative DG) is coupled to (drives) ion flux against a gradient (positive DG). For an example, see the discussion of SERCA.
2. ATP synthesis in mitochondria. Spontaneous H+ flux across a membrane (negative DG) is coupled to (drives) ATP synthesis (positive DG). See the discussion of the ATP Synthase.

"High Energy" Bonds
The structure of ATP is shown below at right (see also p. 566). Anhydride bonds (in red) link the terminal phosphates.

Phosphoanhydride bonds (formed by splitting out water between two phosphoric acids or between a carboxylic acid and a phosphoric acid) tend to have a large negative DG of hydrolysis, and are thus said to be "high energy" bonds. It is important to realize that the bond energy is not necessarily high, just the free energy of hydrolysis.

"High energy" bonds are often represented by the "~" symbol (squiggle), with ~P representing a phosphate group with a high free energy of hydrolysis.
Compounds with "high energy" bonds are said to have high group transfer potential. For example, P_i may be spontaneously removed from ATP for transfer to another compound (e.g., to a hydroxyl group on glucose).
Potentially two "high energy" bonds can be cleaved, as two phosphates are released by hydrolysis from ATP (adenosine triphosphate), yielding ADP (adenosine diphosphate), and ultimately AMP (adenosine monophosphate). This may be represented as follows (omitting waters of hydrolysis):

• AMP~P~P  AMP~P + P_i   (ATP  ADP + P_i)
• AMP~P  AMP + P_i            (ADP   AMP + P_i)

Alternatively, as discussed above:

• AMP~P~P  AMP + P~P_i    (ATP  AMP + PP_i)
• P~P  2 P_i

ATP often serves as an energy source. Hydrolytic cleavage of one or both of the "high energy" bonds of ATP is coupled to an energy-requiring (non-spontaneous) reaction, as in the examples presented above.
AMP functions as an energy sensor and regulator of metabolism. When ATP production does not keep up with needs, a higher portion of a cell's adenine nucleotide pool is in the form of AMP. AMP then stimulates metabolic pathways that produce ATP.

• Some examples of this role involve direct allosteric activation of pathway enzymes by AMP. (E.g., activation of the Glycogen Phosphorylase enzyme by AMP will be discussed later.)
• Some regulatory effects of AMP are mediated by the enzyme AMP-Activated Protein Kinase. (For example the role of AMP-Activated Protein Kinase in stimulation of fatty acid catabolism by AMP will be discussed later.)

Artificial ATP analogs have been designed that are resistant to cleavage of the terminal phosphate by hydrolysis, e.g., AMPPNP, depicted at right.Such analogs have been used to study the dependence of coupled reactions on ATP hydrolysis. In addition, they have made it possible to crystallize an enzyme that catalyzes ATP hydrolysis with an ATP analog at the active site.

A reaction that is important for equilibrating ~P among adenine nucleotides within a cell is that catalyzed by Adenylate Kinase:

 ATP + AMP  2 ADP

The Adenylate Kinase reaction is also important because the substrate for ATP synthesis, e.g., by the mitochondrial ATP Synthase, is ADP, while some cellular reactions dephosphorylate ATP all the way to AMP.
The enzyme Nucleoside Diphosphate Kinase (NuDiKi) equilibrates ~P among the various nucleotides that are needed, e.g., for synthesis of DNA and RNA. NuDiKi catalyzes reversible reactions such as:

ATP + GDP  ADP + GTP  ,   ATP + UDP  ADP + UTP  , etc.

Many organisms store energy as inorganic polyphosphate, a chain of many phosphate residues linked by phosphoanhydride bonds. It may be represented as: P~P~P~P~P... Hydrolysis of P_i residues from polyphosphate may be coupled to energy-dependent reactions. Depending on the organism or cell type, inorganic polyphosphate may have additional functions. For example, it may serve as a reservoir for P_i, a chelator of metal ions, a buffer, or a regulator.
Why do phosphoanhydride linkages have a high free energy of hydrolysis? Contributing factors for ATP and PP_i are thought to include:

• Resonance stabilization of the products of hydrolysis exceeds resonance stabilization of the compound itself. See Fig. 16-22 p. 568.
• Electrostatic repulsion between negatively charged phosphate oxygens favors separation of the phosphates.

Phosphocreatine (also called creatine phosphate), another compound with a "high energy" phosphate linkage, is used in nerve and muscle cells forstorage of ~P bonds.Creatine Kinase catalyzes:   phosphocreatine + ADP  ATP + creatine This is a reversible reaction, though the equilibrium constant slightly favors phosphocreatine formation. Phosphocreatine is produced when ATP levels are high. When ATP is depleted during exercise in muscle, phosphate is transferred from phosphocreatine to ADP, to replenish ATP.

Phosphoenolpyruvate (PEP), involved in production of ATP in Glycolysis, has a larger negative DG of phosphate hydrolysis than ATP.Removal of phosphate from the ester linkage in PEP is spontaneous because the enol product spontaneously converts to a ketone.

The ester linkage in PEP is an exception. Generally phosphate esters, formed by splitting out water between a phosphoric acid and a hydroxyl group, have a low but negative DG of hydrolysis. Examples, shown below, include:

the linkage between the first phosphate and the ribose hydroxyl of ATP. the linkage between phosphate and a hydroxyl group in glucose-6-phosphate or glycerol-3-phosphate. the linkage between phosphate and the hydroxyl group of an amino acid residue in a protein (serine, threonine or tyrosine). Regulation of proteins by phosphorylation and dephosphorylation will be discussed later. An example mentioned above is AMP-Activated Protein Kinase.

ATP has special roles in energy coupling and phosphate transfer. The free energy of hydrolysis of phosphate from ATP is intermediate among the examples listed in the table below (more complete table p. 566). ATP can thus act as a phosphate donor, and ATP can be synthesized by transfer of phosphate from other compounds, such as phosphoenolpyruvate (PEP).

Compound	DGo' of phosphate hydrolysis (kJ/mol)
Phosphoenolpyruvate (PEP)	- 61.9
Phosphocreatine	- 43.1
Pyrophosphate	- 33.5
ATP (to ADP)	- 30.5
Glucose-6-phosphate	- 13.8
Glycerol-3-phosphate	- 9.2

Some other "high energy" bonds:A thioester forms between a carboxylic acid and a thiol (SH) group, e.g., the thiol of coenzyme A (abbreviated CoA-SH). Thioesters are "high energy" linkages. In contrast to phosphate esters, thioesters have a large negative DG of hydrolysis.

The thiol of coenzyme A can react with a carboxyl group of acetic acid (yielding acetyl-CoA) or a fatty acid (yielding fatty acyl-CoA). The spontaneity of thioester cleavage is essential to the role of coenzyme A as an acyl group carrier. Like ATP, acyl-coenzyme A has a high group transfer potential.

Coenzyme A includes b-mercaptoethylamine, in amide linkage to the carboxyl group of the B vitamin pantothenate. The hydroxyl of pantothenate is in ester linkage to a phosphate of ADP-3'-phosphate.  The functional group is the thiol (SH) of b-mercaptoethylamine.

3',5'-Cyclic AMP (abbreviated cAMP), shown at right and below, is used by cells as a transient signal.Adenylate Cyclase (Adenylyl Cyclase) catalyzes cAMP synthesis: ATP cAMP + PPi. The reaction is highly spontaneous due to the production of PPi, which spontaneously hydrolyzes. Phosphodiesterase catalyzes catalyzes hydrolytic cleavage of one of the phosphate ester linkages (in red), converting cAMP  5'-AMP. This is a highly spontaneous reaction, because cAMP is sterically constrained by having a phosphate with ester linkages to two hydroxyls of the same ribose. The lability of cAMP to hydrolysis makes it an excellent transient signal.  Signal roles of cAMP will be discussed separately.

Explore at right the structure of cAMP. The coordinate file for this display was obtained using CHEM 3D with MM2 energy minimization.Right click to change the display to sticks or ball & stick. Drag the image to view the molecular conformation, and compare to the structure diagram above. Identify the bond that is cleaved when cAMP is hydrolyzed to AMP. Why is the cleavage of this bond by hydrolysis spontaneous?

C   O   N   P   H

Distinction between thermodynamics and kinetics: A high activation energy barrier usually causes  hydrolysis of a "high energy bond" to be very slow in the absence of an enzyme catalyst. This "kinetic stability" is essential to the role of ATP and other compounds with ~ bonds. If ATP would rapidly hydrolyze in the absence of a catalyst, it could not serve its important roles in energy metabolism and phosphate transfer. Phosphate is removed from ATP only when the reaction is coupled via enzyme catalysis to some other reaction useful to the cell, such as transport of an ion, phosphorylation of glucose, or regulation of an enzyme by phosphorylation of a serine residue.

Shailesh shukla
directoratace@gmail.com

Bioplastics

Bioplastics are a “green” and sustainable alternative to traditional plastics, and are created using renewable resources like corn, tapioca, potatoes, sugar and algae.

Unlike traditional plastics, which are made using petroleum and other fossil fuels, bioplastics support the earth by offering a reduced carbon footprint, and a reduced use of fossil resources. Bioplastics are 100% biodegradable, compostable, or recyclable.
The cost of bioplastics is not dependent on the volatile and rising prices of crude oil, quickly making bioplastics a popular, cost-effective alternative to traditional plastics. 

Compostable Plastics Quick Facts

• Generally Freezer safe
• Depending on resin can handle hot food till 200F.
• Fully compostable in commercial composting operations
• Feel and look like plastics for the most part
• Est. Home Composting Time: Varies
• Est. Commercial Composting Time: Varies

Compostable Plastics
Compostable Plastics are a new generation of plastics which are biodegradable and compostable. They are derived generally from renewable raw materials like starch (e.g. corn, potato, tapioca etc), cellulose, soy protein, lactic acid etc., are not hazardous/toxic in production and decompose back into carbon dioxide, water, biomass etc. when composted.  Some compostable plastics may not be derived from renewable materials, but instead derived made from petroleum or made by bacteria through a process of microbial fermentation.

Currently, there are a number of different compostable plastics resins available in the market and the number is growing every day. The most commonly used raw material for making the compostable plastics is corn starch, which is converted into a polymer with similar properties as normal plastic products. Other compostable resins are available made from potato starch, soybean protein, cellulose and as well from petroleum and petroleum by products. It is counter intuitive to think that compostable resins could be derived from petroleum, when all normal plastic products are derived from petroleum and are non compostable. However, there are certified compostable resins available in the market, derived from petroleum and the field of compostable plastics is constantly evolving with new materials and technologies being worked on and being brought to market. There is even research underway to make compostable plastics from carbon dioxide.

Properties The compostable resins for the most part mimic plastic properties, and different resins have different properties related to heat resistance, tensile strength, impact resistance, MVTR, oxygen barrier etc. One of the main compostable resin PLA, for example has a heat resistance of only 110F, while other compostable resins can have a much higher heat resistance.

Biodegradability & Compostability
Bioplastics can take different length of times to totally compost, based on the material and are meant to be composted in a commercial composting facility, where higher composting temperatures can be reached and is between 90-180 days. Most existing international standards  require biodegradation of 60% within 180 days along with certain other criteria for the resin or product to be called compostable. It is important to make the distinction between degradable, biodegradable and compostable. These terms are often (incorrectly) used interchangeably.

Compostable Plastic is plastic which is "capable of undergoing biological decomposition in a compost site as part of an available program, such that the plastic is not visually distinguishable and breaks down to carbon dioxide, water, inorganic compounds, and biomass, at a rate consistent with known compostable materials (e.g. cellulose). and leaves no toxic residue."  American Society for Testing & Materials (ASTM).  In order for a plastic to be called compostable, three criteria need to be met:

1. Biodegrade - break down into carbon dioxide, water, biomass at the same rate as cellulose (paper).
2. Disintegrate - the material is indistinguishable in the compost, that it is not visible and needs to be screened out
3. Eco-toxicity - the biodegradation does not produce any toxic material and the compost can support plant growth.

Biodegradable Plastic is plastic which will degrade from the action of naturally occurring microorganism, such as bacteria,  fungi etc. over a period of time.  Note, that there is no requirement for leaving "no toxic residue", and as well as no requirement for the time it needs to take to biodegrade.
Degradable Plastic is plastic which will undergo a significant change in its chemical structure under specific environmental conditions resulting in a loss of some properties.  Please note that there is no requirement that the plastic has to be degrade from the action of "naturally occurring microorganism" or any of the other criteria required for compostable plastics.

A plastic therefore may be degradable but not biodegradable or it may be biodegradable but not compostable (that is, it breaks down too slowly to be called compostable or leaves toxic residue).  

Estimated Composting Times

Product	Home Composting	Commercial Composting
Wheat Straw or Sugarcane Fiber  Plates, Takeout Contianers, Bowls, Cups and Trays	Upto 6 months	1-3 Months
Ingeo Cold Cups, Clear Containers, Straws	Not recommended	3-6 Months
TPLA Heat Resistant & Non Heat Resistant Utensils	Not recommended	3-6 Months
Trash/Kitchen Bags	Upto 1 year	2-4 Months

The rate of biodegration for different biocompostables is dependent upon the composition and thickness of the material as well as composting conditions. Commercial composting facilities grind the materials, turn over the piles and reach high temperatures, thus reducing the amount of time it takes to compost and, is thus, the recommended method for composting these products. Home composting rates are slower and can vary, depending on how frequently the pile is turned over, the moisture and material content and the temperature.   Composting utensils at home is not recommeded, due to their thickness and they may not break down for few years.  Similarlry, Ingeo products are not recommended to be composted at home. 

• Biodegradability is determined by measuring the amount of CO₂ produced over a certain time period by the biodegrading plastic.  The standards require 60% conversion of carbon into carbon dioxide within 180 days for resins made from single polymer and 90% conversion of carbon into carbon dioxide for co-polymers or polymer mixes.
• Disintegration is measured by sieving the material to determine the biodegraded size and less than 10% should remain on a 2mm screen within 120 days.
• Eco toxicity is measured by having concentrations of heavy metals below the limits set by the standards and by testing plant growth by mixing the compost with soil in different concentrations and comparing it with controlled compost.

Shailesh shukla

directoratace@gmail.com

AYURVEDA: A trusted an unbeatable therepy

Traditional medicine and modern medicine differ in many ways. Traditional medicine (or TM) is largely empirical while modern medicine (MM) is largely reductionist in approach. TM is old, dating back to millennia while MM is at best 300 years in the making. TM looks at results, not how the treatment works while MM advances by understanding the mechanism of action, and cause and effect. TM has been used directly on people while MM proceeds by testing first on cells and organs of animals and then on humans. TM uses material from local flora and fauna; MM isolates molecules, synthesises them in the lab and makes them available. TM invariably uses formulations, extracts and combinations, MM works by and large with single molecules and compounds. TM has a lot of home remedies while MM insists on prescription drugs. TM comes with a cultural baggage while MM does not. TM is cheap and easy on the purse while MM can be expensive. And TM is far more prevalent in rural areas for a variety of reasons. MM is more easily available in urban areas. Many modern hospitals and specialists consider TM as inexact, unproven and even useless. This has relegated TM to the back burners, to be used only as a backup or add-on.


"Traditional medicine looks at results, while modern medicine advances by understanding the mechanism of action, cause and effect "

 

Can the twain meet? Can we understand how TM works using the knowledge we have gained using the tools of modern chemistry, molecular and cell biology, genetics and pharmacology? This has been the goal of Professor M.S. Valiathan of Manipal University. Both an eminent cardiac surgeon, and scholar in the history of medicine, he has initiated a programme to understand and rationalise some ayurvedic medications using the tools of modern biology. In this he has partnered with Professor Subhash Lakhotia of Banaras Hindu university, who is an eminent molecular geneticist and cell biologist, to study the mechanisms of action of two well-known ayurvedic formulations – Amalaki Rasayana (or AR) and Rasa Sindoor (or RS).

Chromatography

To do so, they collaborated with the famous Kottakkal Arya Vaidya Sala and had the formulations made as per recorded practices, determined the components using modern methods of chromatography, ensured no lot-to-lot variations, and thus made certain of the quality, purity and identity of the test material.

Next, they decided to work not directly on human subjects, but animal models. Here, Prof Lakhotia brought his knowledge and experience on working with the fruit-fly (Drosphila) as the experimental animal. Fruit-flies have short lives (a month or so), come in huge varieties with genetic differences, can be genetically modified at their larval stage so that one can determine the effect of the loss of, or addition of, genes on their physiology and pathology. And we know a great lot about its anatomy, physiology and cell biology. Thus, we can create disease models of the fly with ease, using such genetic and physiological manipulations. Plus, they can be studied in large numbers at a time so that results are statistically significant. Drosophila is thus an excellent model to study the effect of TM (AR and RS).

Fruit-fly study

In the first set of experiments, the team fed the flies known portions (0 to 2 per cent) in the food as supplement of AR or RS and studied how the formulation affects their life span, ability to withstand stress (upon changing the surrounding temperature) and tolerance to starvation, They found that the two formulations affect the biology of the flies significantly, but with some differences in specific situations. AR increases the life span if given as 0.5 per cent supplement. Higher doses do not, and are indeed harmful. RS had no effect on longevity, but was again harmful at high concentrations. Both AR and RS increase the fecundity, but with some difference. Interestingly RS, which contains mercury (a known poison) as a component, was not harmful or poisonous. It turns out that the ayurvedic procedure of preparing RS generates nanoparticles of HgS (25-35 nm) and at such sizes mercury is not harmful! (Those interested may read the entire paper by accessing <PLOS ONE 7(5): e37113. doi.10.1371/journal. pone.0037113>)

A step further

Prof Lakhotia went one step further, and attempted to see how AR and RS affect flies genetically modified to display neuro-degeneration, and thus modelling Alzheimer’s and Huntington’s disorders. His team found that supplementation with AR or RS in the diet of the flies prevented the formation and accumulation of “inclusion bodies” and of amyloid plaques (associated with Alzheimer’s disease). These are insoluble particles that hinder the conduction of electrical signals in the nervous system. Supplementation was also seen to suppress cell death (apoptosis). AR and RS were seen to increase the levels of certain proteins known as hnRNPs, known to lead to more robust levels of gene expression. The Lakhotia group concludes in their latest paper (Current Science 105 (12), 1711, December 25, 2013) that AR and RS provide holistic relief from the increasingly common neurodegenerative disorders.

Shailesh shukla

directoratace@gmail.com