3.5: How to Be the Cell

Most simple, prokaryotic cell should perform several essential duties in order to survive. These are:

1. Obtaining energy. In all living world, the energy is accumulated in the form of ATP molecules. To make ATP, there are three most common ways:

   Phototrophy

   Energy from the light of Sun.

   Organotrophy

   Energy from burning of organic molecules, either slow (fermentation), or fast (respiration).

   Lithotrophy

   Energy from inorganic chemical reactions (“rocks”).

2. Obtaining building blocks (monomers which are using to built polymers like nucleic acids, proteins and polysaccharides). The principal monomer in the living world is glucose. From glucose, it is possible to chemically create everything else (of course, one must add nitrogen and phosphorous when needed). There are two principal ways to obtain monomers:

   Autotrophy

   Make monomers from carbon dioxide.

   Heterotrophy

   Take monomers from somebody else’s organic molecules.

   There are six possible combinations of these above processes. For example, what we called “photosynthesis” is in fact photoautotrophy. Prokaryotes are famous because they have all six combinations at work.

3. Multiply. There are always three steps:
   1. Duplicate DNA. As it is a double spiral, one must unwind it, and then build the antisymmetric copy of each chain in accordance with a simple complement rule—each nucleotide make hydrogen bond only with one nucleotide of other type:

      A	T
      T	A
      G	C
      C	G

   2. Split duplicated DNA.
   3. Split the rest of the cell.

   Prokaryotic DNA is small and circular, optimized for the speedy duplication and division. Consequently, prokaryotes multiply with alarming speed.

4. Make proteins. This process involves transcription ans translation. As proteins are “working machines” of the cell and DNA is an “instruction book”, there must be the way to transfer this information from DNA to proteins. It usually involves RNA which serves as temporary “blueprints” for proteins:
   1. DNA and RNA each contains four types of nucleotides, this is an alphabet.
   2. With help of enzymes, pieces of DNA responsible for one protein (gene) copied into RNA. Rules are almost the same as for DNA duplication above, but T from DNA is replaced in RNA with U.
   3. The sequence of nucleotides is a language in which every tree nucleotides mean one amino acid.
   4. Ribosomes translate trios of nucleotides (triplets) into amino acids and make proteins. They do it in accordance with genetic code:

      Genetic code. All amino acids designated with shortcuts.

      	U	C	A	G
      U	UUU Phe UUC Phe UUA Leu UUG Leu	UCU Ser UCC Ser UCA Ser UCG Ser	UAU Tyr UAC Tyr UAA STOP UAG STOP	UGU Cys UGC Cys UGA STOP UGG Trp	U C A G
      C	CUU Leu CUC Leu CUA Leu CUG Leu	CCU Pro CCC Pro CCA Pro CCG Pro	CAU His CAC His CAA Gln CAG Gln	CGU Arg CGC Arg CGA Arg CGG Arg	U C A G
      A	AUU Ile AUC Ile AUA Ile AUG Met	ACU Thr ACC Thr ACA Thr ACG Thr	AAU Asn AAC Asn AAA Lys AAG Lys	AGU Ser AGC Ser AGA Arg AGG Arg	U C A G
      G	GUU Val GUC Val GUA Val GUG Val	GCU Ala GCC Ala GCA Ala GCG Ala	GAU Asp GAC Asp GAA Glu GAG Glu	GGU Gly GGC Gly GGA Gly GGG Gly	U C A G

5. Make sex. To evolve, organisms must diversify first, natural selection works only if there is an initial diversity. There are two ways to diversify:
   1. Mutations which are simply mistakes in DNA. Majority of mutations are bad, and many are lethal. The probability to obtain useful mutation is comparable with probability to mend your cell phone using hammer.
   2. Recombinations are much safer, they increase diversity but unable to create novelties. In addition, recombinations serve also as a way to discard bad genes from the “gene pool” of population because from time to time, two or more bad genes meet together in one genotype and this combination becomes lethal.

   Prokaryotes developed bacterial conjugation when two cell exchange parts of their DNA, this facilitates recombination. In bacterial world, recombination is possible not only within one population, but sometimes also between different species, this is called horizontal gene transfer.