Biorhythms

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Questions received:

  1. How does water pass through the cell membrane?

  2. What are heat shock proteins? By contrast are there also cold shock proteins?

  3. Why does RNA contain uracil as a base rather than thymine as in DNA?

  4. Briefly discuss the significance of the Na+ - K+ - ATPase pump in maintaining homeostasis during nerve and muscle excitation.

  5. When proteins are synthesised in the cell, how do they know where to go?

  6. Can you give me a description of how patch clamp technique works?

  7. What is the job of cytoplasm?

Responses:

How does water pass through the cell membrane?

We take it almost for granted that water passes through the cell membrane in both directions - either entering the cell or leaving it. But then, the cell membrane is predominantly formed from a double layer of lipid (fat) molecules and it is therefore difficult to imagine how water molecules actually pass through - they will be repelled by the membrane.

As is so often the case with living systems, the answer is to do with proteins. Embedded in the cell membrane like currants in a Garibaldi biscuit are numerous proteins. These are large, complex, water-loving molecules with a range of functions: some are receptors waiting for incoming signals such as hormones and cytokines, while others provide channels through which smaller molecules can pass. The channel proteins are generally specific to a given substance, and there are indeed some which allow water molecules to pass through. The structure of aquaporin-1 has been described by Walz et al (1997) and Cheng et al (1997). This channel protein is a member of the major intrinsic protein (MIP) superfamily and it facilitates two-way exchanges of water between the inside of the cell and its surroundings. More recently, aquaporins have also been found on membranes within the cell - Yasui et al (1999) describe the possible role of aquaporin-6 in vesicle swelling and membrane fusion during exocytosis.

Above: structure of aquaporin

References

  1. Cheng, A., van Hoek, A.N., Yeager, M., Verkman, A.S., and Mitra, A.K .(1997) Three-dimensional organization of a human water channel. Nature, 387, 627-630.

  2. Walz,T., Hirai, T., Murata, K., Heymann, J.B., Mitsuoka, K., Fujiyoshi, Y., Smith, B., Agre, P., and Engel, A. (1997) The three-dimensional structure of aquaporin-1. Nature, 387, 624-627.

  3. Yasui, M., Hazama, A., Kwon, T-H., Nielsen, S., Guggino, W.B., and Agre, P. (1999) Rapid gating and anion permeability of an intracellular aquaporin. Nature, 402, 184-187.

What are heat shock proteins? By contrast are there also cold shock proteins?

15th July 1998; updated 7th August 1998

Heat-shock proteins are produced in more plentiful amounts in cells that experience a temperature above the normal range for that cell. They stabilise and repair other proteins that are much more sensitive to the temperature rise, and thereby help to protect the cell against irreversible damage. The temperature set-point for the release of heat-shock proteins is not the same for all cells within an organism. Think for example of the cells in the testis - they are accustomed to a lower temperature than cells forming internal organs, and they boost production of heat-shock proteins at a correspondingly lower temperature than say cells of the liver (Sarge, Bray, and Goodson, 1995. See also the answer to a previous question - not added yet). Heat-shock proteins are found throughout the living world - in micro-organisms and in our own cells. And yes, there are cold-shock proteins too, which as you may expect are produced in cells exposed to unusually low temperatures. In recent years, a broader understanding of these proteins has emerged and they are now known to play a more general role in protein folding and the transport of proteins across membranes within the cell. They tend to be known now as molecular chaperones.

The many functions of proteins in living systems are a result of their precise three-dimensional shapes. The shape of a protein molecule is determined mainly by the linear sequence of amino acids from which it is made - each protein has a built-in tendency to fold correctly. However, within the complex and bustling interior of a living cell the folding of a new protein molecule as it is being formed can be distorted and blocked by interactions with other nearby molecules. The molecular chaperones overcome this problem by stabilising the protein as it is synthesised and then they provide a sheltered environment in which the new protein can complete its folding before entering the turbulent activity within the cytoplasm.

chaprn3.jpg (14543 bytes)There are several families of chaperone proteins, the main ones being the heat-shock protein 70 (Hsp70) which stabilise new proteins as they are assembled, and the chaperonins which are hollow protein molecules inside which the completed proteins can fold safely. (For a review, see Hartl, 1996).

Diagram showing the role of heat-shock proteins and a chaperonin in protein folding. As the ribosome moves along the molecule of messenger RNA, a chain of amino acids is built up to form a new protein molecule. The chain is protected against unwanted interactions with other cytoplasmic molecules by heat-shock proteins and a chaperonin molecule until it has successfully completed its folding.

Cold-shock proteins have also been conserved throughout evolution. They appear in larger quantities in cells exposed to a lower-than-usual temperature, and at least one type can exert a direct transcriptional effect on DNA in the nucleus of the affected cell (Schindelin, Marahiel, and Heinemann, 1993).

 

 

 

 

Just a thought - some micro-organisms are adapted to living at very high temperatures. For example, there are some that live at 95°C in the hot springs of the Yellowstone National Park (Deckert et al, 1998), and others have been found in the proximity of 'black smokers' on the ocean floor. Quite how they manage to survive in such hostile conditions is unknown, but heat-shock proteins are probably involved (Gross, 1998). It has even been suggested that life originally emerged under such conditions, and then radiated out into other, more moderate locations (Nisbet and Fowler, 1996). As a consequence the protective role of the heat-shock proteins became adapted to take on new functions.

References

Why does RNA contain uracil as a base rather than thymine as in DNA?

1st August 1998

Presumably the answer must be linked with the earliest stages in the evolution of life on this planet - the so-called ‘RNA-world’ which it is proposed preceded life as we know it - and also the chemical nature of single-stranded RNA compared with double-stranded DNA.

Both DNA and RNA are threadlike molecules constructed from building blocks called nucleotides. Each nucleotide consists of a base, a sugar, and a phosphate group. In DNA, the sugar is deoxyribose, while in RNA it is ribose. In both molecules there are 4 possible bases, and three of these are identical in DNA and RNA. However, the fourth is different: uracil is found only in RNA and thymine is found only in DNA. The structure of these two bases is quite similar and they are both able to form base pairs by linking with adenine.

Diagram showing structure of uracil and thymine

 

 

 

Molecules of RNA are believed to have been the first carriers of ‘genetic’ information in the period before living micro-organisms emerged some 4 billion years ago (Eigen et al). In most lifeforms that exist today, genetic information is carried by DNA, although some micro-organisms and viruses still use RNA for this purpose. Since DNA is more difficult to synthesise than RNA, and requires the help of ribose intermediates and RNA primers, it has been suggested that RNA must have emerged first in order to allow the subsequent construction of DNA molecules that could code for proteins. It is thought that RNA molecules acted both as enzymes and substrates for their own replication. Transcription and translation of DNA genes require the involvement of various types of RNA before protein molecules can be synthesised. The high degree of conservation of the sequence structure of ribosomal RNA adds further weight to the suggestion that RNA appeared first (Ferris, 1994; Robertson and Ellington, 1998).

References

Briefly discuss the significance of the Na+ - K+ - ATPase pump in maintaining homeostasis during nerve and muscle excitation.

1st July 1999

When nerve and muscle cells are at rest, there are differences in the concentration of certain ions between the inside of the cell and the outside. For example, sodium ions (Na+) are more concentrated in the fluid surrounding the cell compared with the inside of the cell, while potassium ions (K+) are more concentrated inside the cell than outside. These differences contribute to the resting membrane potential - there is an electrical difference of about 70 mV between the more negatively-charged inside of the cell and the surrounding medium. It is this resting potential that makes nerve and muscle cells so sensitive to stimulation. If the electical difference is reduced below a particular threshold, the cell reacts. In the case of a nerve cell, it reacts to depolarisation by generating a nerve impulse (action potential) that passes rapidly along the axon to its termination, which might be adjacent to another nerve cell or perhaps a muscle or gland cell. Here the action potential causes the release of a chemical signal called a neurotransmitter which will impinge on the next cell and cause it to change its behaviour. In the case of a muscle cell, depolarisation triggers muscle contraction. After excitation, the nerve cell or muscle cell has to restore the electrical difference between inside and outside (resting membrane potential) before it will be able to respond again.

The resting imbalance in sodium and potassium concentrations is generated by the action of special proteins in the cell membrane called sodium-potassium pumps. These proteins are able to pump sodium ions out of the cell and at the same time pump potassium ions into the cell. The energy required to achieve this is derived from ATP - adenosine triphosphate. ATP is an energy-rich molecule used throughout cells for a variety of processes, and is largely produced in mitochondria by the breakdown of energy-rich nutrients such as glucose. Each sodium-potassium pump can expel up to 300 sodium ions per second, and at the same time import about 200 ions of potassium. It does this by rapidly changing its shape (conformation), using the energy provided by ATP.

Diagram of sodium-potassium pump

The cell membranes of neurons and muscle cells contain other proteins called channels which open when the cell is depolarised to allow sodium ions to rush in and potassium ions to move out. They do this because of the concentration gradients between inside and outside that have been built up by the sodium-potassium pumps. These rapid ionic movements give rise to the action potential in neurons, and causes contraction in muscle cells.

So the sodium-potassium pumps enable normal functioning of neurons and muscle cells. They restore the resting ionic conditions that will be necessary for further responses to stimulation. In this way the pumps contribute to the complex web of processes within the body that are required for the maintenance of homeostasis.

Reading

Most contemporary biology textbooks contain a description of the sodium-potassium pump. See for example:

When proteins are synthesised in the cell, how do they know where to go?

24th October 1999

Günter Blobel was awarded this year’s Nobel Prize for Physiology or Medicine for his discovery that proteins incorporate an address label as they are synthesised. The various compartments of a cell where different activities occur are delineated by membranes that are generally impermeable to proteins. Blobel proposed that newly-synthesised proteins carry targeting signals that direct them to the appropriate membrane and across it by way of specific channels into the compartment where the new proteins are required. Subsequent work has shown that this process occurs in all living species so far studied.

Can you give me a description of how patch clamp technique works?

7th December 1999

This is a delicate technique that allows measurement of the flow of ions through a small sample of cell membrane. The flow of ions is regulated by specialised proteins known as channel proteins embedded in the cell membrane. If a small enough patch of membrane is studied, then the properties of a single channel protein can be investigated.

Diagram of the patch clamp technique.

A micropipette with a tip diameter of 1 or 2 micrometres is placed against the outside of the membrane enclosing a cell. To avoid damaging the cell, the instrument is guided by a micromanipulator. A gentle suction is then applied via the pipette to seal the membrane to the tip. This trapped membrane becomes the "patch" through which current flow can be recorded. If required, the patch can be separated from the rest of the cell and transferred to test solutions, perhaps to see the effects of changing the voltage difference between the two surfaces of the patch or the pharmacological effects of certain chemicals. The setting of voltage differences is referred to as "clamping" - hence the origin of the name of this technique.

 

 

 

What is the job of cytoplasm?

5th October 2000

Cytoplasm is the region of the cell between the nucleus and the plasma membrane (outer cell membrane). Its main job is to carry out many metabolic (chemical) processes that sustain the life of the cell and contribute to the welfare of the organism of which the cell is part. Cytoplasm consists mainly of water, electrolytes, carbohydrates, proteins, and lipids (fats), all beautifully arranged and organised. Organelles (‘tiny organs’) are suspended in the cytoplasm. These include ribosomes, endoplasmic reticulum, Golgi apparatus, mitochondria, lysosomes, centrioles, and the cytoskeleton. In specialised cells there are other structures (inclusions) such as melanin granules, fat stores and glycogen stores.

Materials continuously enter and leave the cytoplasm via the plasma and nuclear membranes. Water, electrolytes, energy-rich molecules, amino acids and vitamins enter the cell. Metabolic processes within the cytoplasm result in the formation of materials for export and waste products which are released from the cell. This dynamic balance between inputs and outputs contributes to cellular homeostasis.

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