All living things require energy to perform the cellular processes which are essential for life.



     How did the ancestors of modern cells obtain energy?

     Most modern organisms depend on the metabolism of organic carbon compounds to obtain ATP and virtually all these carbon compounds are ultimately derived from photosynthesis.   There were other sources of energy in the primitive earth, however.  Organic molecules had accumulated in the oceans, creating the proverbial “primordial soup”.  While it was once thought that organic molecules could only come from living things (and it was even thought that they had a mysterious “vitalism” that separated them from inorganic molecules), it is now known that a variety of organic molecules are produced readily from inorganic substrates and a source of energy.  In the absence of bacteria and atmospheric oxygen, these organic molecules would have slowly accumulated in the earth’s oceans over millions of years.   In addition to organic molecules, inorganic molecules can be used as sources of energy.  In the thermal oceanic vents today, living things can survive by utilizing the potential energy in the inorganic compounds resulting from volcanic activity.  

     ATP might not have been the first energy carrier.  Iron-sulfur compounds, thioester compounds, and pyrophosphate might have served the first organisms.  Acetyl phosphate and thio acids may have served as intermediates linking thioester metabolism and iron-sulfur metabolism to that of pyrophosphate.  Pyrophosphate, unlike ATP, is produced through volcanic activity.  Today, the bacteria Rhodospirillum rubrum have a membrane bound enzyme, pyrophosphate synthase, and Rhodospirillum can use light energy to make either ATP or pyrophosphate as energy carriers.  When the ATP-generating mechanisms are inhibited, Rhodospirillum continues storing light energy in the form of pyrophosphate—perhaps this is a remnant of earlier mechanisms which were centered around pyrophosphate rather than ATP.

     Some living cells today continue to make use of pyrophosphate, even as an alternative to ATP.  Polyphosphate could have replenished ATP stores by reacting with ADP (enzymes polyphosphate kinase and exopolyphosphatase perform such reactions).  Some bacterial enzymes conserve the ability to use both ATP and pyrophosphate (such as fructo-1-kinase).  It is possible that ATP synthase evolved from pyrophosphate synthase (Baltscheffsky, ).


Why ATP and RNA?

    Before there was sufficient atmospheric oxygen to form an ozone layer, ultraviolet light would have been a significant feature of the early earth.  There is a group of ultraviolet wavelengths (240 to 290 nm) which are not absorbed by gases of the atmosphere but which are absorbed by purines and pyrimidines.  Adenine is the nitrogenous base which forms most readily in abiotic conditions (it is also the most abundant base in modern organisms), it is the most stable, and it offers the highest absorption ultraviolet light.  Ultraviolet light can cause the formation of adenosine from adenine and ribose and it can cause the formation of ADP and ATP from a solution of adenosine and ethyl methaphosphate (Baltscheffsky, p. 12).  Not only are many coenzymes (e.g. NAD, NADP, FAD, coenzymeA) derivatives of RNA nucleotides, they can interact with adenine and might have originally been involved in reactions of adenine with ultraviolet light.  RNA might have helped to harvest ultraviolet light for the production of ATP (which is itself, an RNA nucleotide).

     When carbohydrates were involved in the storage of energy and the production of ATP, lactate and hydrogen ions would have been produced.  The accumulation of hydrogen ions is a problem for living things, given the effect of pH on hydrogen bonds and thus the shapes of complex biomolecules.  Hydrogen ion pumps would have been needed.  Interestingly, the ATP synthase used in respiration and photosynthesis has two subunits; the Fo subunit pumps H+ across the membrane and is capable of functioning alone.  Such a mechanism would be limited by the accumulation of charge outside the cell—eventually the charge gradient would inhibit further pumping of hydrogen ions—unless an exchange of positive ions occurred, allowing positive ions (such as sodium or potassium) to enter in exchange for hydrogen.  The Fo subunits of some bacteria can transport sodium as well as hydrogen and gap junctions also possess the ability to transport positive charges in a nonspecific way  (Baltscheffsky, p. 18).


      RNA does not absorb the energy of visible light as well as ultraviolet light energy.  Bacteriorhodopsin is a relatively simple pigment (simpler than chlorophyll) which pumps one hydrogen ion per photon absorbed (chlorophyll results in multiple hydrogen ions pumped).   Bacteriorhodopsin is a G-protein coupled receptor, one of the largest known gene superfamilies.  Although the photosynthesis performed by cyanobacteria (and the chloroplasts that evolved from them) involves both cyclic and noncyclic pathways for electron flow, each of these pathways could have evolved separately.  Green sulfur bacteria perform photosynthesis using a noncyclic flow pathway that resembles that of cyanobacteria; purple bacteria perform photosynthesis using a cyclic flow which is almost identical to that of cyanobacteria  (Baltscheffsky, p. 20-5).  Once photosynthesis was performed by primitive cyanobacteria, oxygen would have slowly begun to accumulate in the atmosphere.  As the ozone layer formed, ultraviolet light would have become less and less a factor in the biology of organisms.  Cyanobacteria are depicted below.


     As oxygen accumulated in the atmosphere, it also would have presented a selective pressure for organisms to detoxify its reactive by-products and eventually to exploit it in energy transactions.  Many bacteria which are obligate anaerobes would have become extinct although many survive in modern anoxic environments.  Today, there are bacteria which are strict anaerobes, aerotolerant, facultative aerobes, and obligate aerobes.  Eukaryotes evolved after oxygen had already become a significant component of the atmosphere and virtually all modern eukaryotes are obligate aerobes.  A few eukaryotes are facultative anaerobes such as yeast although they can exist without oxygen for some time (annelids and mollusks can often live for days without oxygen, Darnell, p. 588).  Virtually all eukaryotes involve their mitochondrial endosymbionts in their oxygen metabolism and cells may possess so many of these endosymbionts that they compose 25% of the cytosol (Darnell, p. 589).



    The glycolytic pathway is a set of metabolic reactions in which 6 carbon glucose molecules are split into 2 molecules of pyruvate, each with 3 atoms of carbon.  This set of reactions produces a little energy in the form of ATP (2 net molecules of ATP per glucose molecule) and does not require oxygen.  If oxygen is present, eukaryotic organisms transport pyruvate to the mitochondria to be broken down completely for more energy.  If oxygen is not present, pyruvate can be converted into other molecules such as lactic acid (as in humans) or ethanol (as in yeast).


Despite the fact that a microscopic bacteria may obtain its nutrition from decomposition in the soil and a human skeletal muscle cell from the digested products of lasagna brought to it by the bloodstream, they both begin to metabolize their food molecules through the same chemical reactions, catalyzed by the same enzymes.  The series of chemical reactions is referred to as glycolysis.  Glycolysis does not require any specialized part of the cell to occur nor does it require oxygen (neither of which would have been available to the most primitive cells).  The steps of the glycolytic pathway are given below followed by descriptions of the versions of these ubiquitous enzymes found in the human genome.

1)     HEXOKINASE converts Glucose to Glucose 6-phosphate

Humans have several hexokinase genes resulting from duplications of ancestral genes.  Some may be expressed preferentially in certain tissues: hexokinase 1 is the major isoform in red blood cells, hexokinase 2 in skeletal muscle, hexokinase 3 in white blood cells (such as human blood cells and skeletal muscle cells in the following images). 

There is a hexokinase gene which seems to produce an enzyme unique to mammalian sperm (such as that of humans, pictured below). 

Mutations in the hexokinase 1 can cause hemolytic anemia.  Insulin increases the transcription of hexokinase 2 and its expression is increased in many tumors. 

      Hexokinase 4 is only expressed in the liver and pancreatic islets where it has a role in regulating glucose metabolism, serving as a glucose sensor.  Mutations in hexokinase 4 can cause mature onset diabetes of the young type II, late onset non-insulin dependent diabetes mellitus, gestational diabetes mellitus, autosomal dominant hyperinsulinism, and neonatal onset diabetes mellitus.

     The hexokinase family can be divided into the eukaryotic hexokinases, eubacterial glucokinases and fructokinases, and additional eubacterial sugar kinases (Wu, 2001).  Although eukaryotes all use the same glycolytic pathway for glucose degradation, nonhomologous enzymes may catalyze the same step in different organisms.  For example, several of the most primitive amitochondrate eukaryotes use glucokinase and glucosephosphate isomerase enzymes in the early steps of glycolysis similar to some bacteria rather than the hexokinase typical of higher eukaryotes (Henze, 2001; Wu, 2001).  The ATP binding region of hexokinase is homologous to that found in several protein kinases (such as the proto-oncogenes src and myc).  At least 1 of the yeast and rat hexokinases can also act as a protein kinase (Griffin, 1991).


     In the mammalian enzyme hexokinase, the carboxy half of the protein is a duplication of the amino half and each half is homologous to the hexokinase of yeast which is half the size.  Although mammalian glucokinase is homologous to, and about the same size as, yeast hexokinase, it seems to have resulted from the mammalian hexokinase being split in half rather than a direct ancestry from yeast hexokinase (Griffin, 1991).


2)     PHOSPHOGLUCOISOMERASE converts glucose 6-phosphate to fructose 6-phosphate

Mutations in human phosphoglucoisomerase can cause hemolytic anemia and some neurological abnormalities.


3)     PHOSPHOFRUCTOKINASE converts fructose 6-kinase to fructose 1,6 biphosphate

There are 3 subunits of phosphofructokinase in mammals coded by phosphofructokinase, muscle (chromosome 1), phosphofructokinase , liver (chromosome 21), and phosphofructokinase, platelet (chromosome 10).  In muscle, the enzyme is composed of homotetratmers of the M form; the L form is the major component of the enzyme found in the liver and kidneys.  Deficiencies /mutations of phosphofructokinase cause muscle cramps which occur in muscle exertion, myoglobinuria, and Tarui disease (with its weakness and muscle stiffness after exertion) (OMIM).

     In glycolysis, phosphofuctokinase regulates the metabolism of glucose.  Two alternate pathways also exist, one in eubacteria (which does not utilize phosphofructokinase) and the second known in some archaea (which uses an enzyme of the glucokinase family instead of phosphofructokinase).  Although phosphofructokinase functions in glycolysis in all three domains, it varies more than might be expected.  A duplication of an ancestral phosphofructokinase gene produced two groups of enzymes which differ in their use of ATP and inorganic pyrophosphate as the phosphate donor (Baptese, 2003; Ronimus, 2001).


4)     ALDOLASE splits fructose 1,6 biphosphate into glyceraldehyde phosphate and dihydroxyacetone phosphate,

Aldolase can compose up to 5% of the protein in adult muscle and vertebrates have 3 aldolase genes (aldolase A, B, and C).  Mutations in aldolase A cause myopathy, hemolytic anemia, weakness and fatigue.  Mutations in aldolase B cause fructose intolerance, aversion to sweets, and severe illness in infants.


5)     TRIOSEPHOSPHATE ISOMERASE converts dihydroxyacetone phosphate into glyceraldehyde phosphate; these two sugars are isomers of each other

Humans have one triose phosphate isomerase gene and 2 pseudogenes.  Mutations can cause hemolytic anemia and neuromuscular abnormalities.


6)     GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE converts glyceraldehyde phosphate into 1,3 biphosphoglycerate

Humans have a pseudogene of this enzyme in addition to the functioning gene.


7)     PHOSPHOGLYCERATE KINASE converts 1,3 biphosphoglycerate into 3 phosphoglycerate

Humans have a pseudogene in addition to the two functioning genes, phosphoglycerate kinase I and II.  Mutations in the phosphoglycerate kinase I gene can cause hemolytic anemia, retardation, and convulsions.  Phosphoglycerate kinase II is only expressed in spermatozoa.


8)     PHOSPHOGLYCEROMUTASE converts 3 phosphoglycerate to 2 phosphoglycerate

Mutations in humans can cause hemolytic anemia.


9)     ENOLASE converts 2 phosphoglycerate to phosphoenolpyruvate


Enolase may have been one of the earliest proteins which evolved. It is present in all groups of life, it is essential in carbon metabolism, it also balances ATP, ADP, and AMP levels, and in archebacteria it is encoded in the same superoperon which encodes ribosomal proteins (Martin, 2002a).

Humans have at least 4 enolase genes whose duplication seems to be linked to genome duplications which occurred early in the vertebrate lineage.  Enolase 1 is expressed in most tissues.  Enolase 2 is only expressed in the nervous system,  Enolase 3 is expressed only in muscles and is responsible for 90% of the enolase activity in muscles.  Enolase 4 is expressed specifically in sperm.  Sperm in the epididymis are depicted in the following image.


10) PYRUVATE KINASE converts phosphoenolpyruvate to pyruvate

Pyruvate kinase is composed of several subunits which may be products of the same pyruvate kinase gene or of different pyruvate kinase genes.   Various tissues differ in the subunits which comprise the holoenzyme.


11) LACTATE DEHYDROGENASE converts pyruvate to lactate if the cell does not metabolize pyruvate aerobically

Humans have a number of lactate dehydrogenase genes.  Mutations in lactate dehydrogenase A can result in myoglobinuria, fatigue, muscle stiffness, and, in pregnant women, may result in Caesarian section due to problems with uterine muscle.  Lactate dehdrogenase C is expressed in the testes and the D form is expressed in the heart, muscle, liver, and kidney.  There are no clinical symptoms associated with mutations in lactate dehydrogenase B.

     Lactate dehydrogenase (LDH) is an ancient gene which is expressed in bacteria, plants, and animals. Lampreys have a single lactate dehydrogenase gene which has a mixture of characteristics of the two main LDH genes in higher vertebrates: LDH-A in white skeletal muscle and LDH-B in aerobic tissues such as the heart and brain.   The lamprey brain is depicted in the following image.


Some higher vertebrates have a third LDH gene such as that expressed in several tissues in actinopterygian fishes and in the sperm of mammals and certain birds.  This third locus may have arisen independently in separate lineages (Stock, year ?).