Life in the Universe: I. Background in Biology Part-2 - Remote Sensing Application - Completely Remote Sensing, GPS, and GPS Tutorial
Life in the Universe: I. Background in Biology Part-2

Proteins are the dominant molecular types in cells. Specific proteins (composition and/or structure) can specialize into Enzymes (that promote change and formation of new organic material by catalysis (bring about reactions without themselves being changed), Hormones (perform important physiological functions), Structural proteins (hair, skin, etc.), Transport proteins (carry material across membranes); Antibodies (involved in immune systems), and Muscle proteins (actin and myosin in fibrous forms). Enzymes are particularly important since they are involved in most biochemical reactions and can be very efficient; many enzymes work by attaching to the molecule they affect, which serves as the substrate responsive to their action. The list of important proteins is long and diverse. This table names many that are important:

Some of the most important proteins.

An example of how sequences of amino acids give rise to a specific protein molecule is given by insulin, used by mammals to extract energy from sugars:

The structure of insulin.

One of the most important proteins is hemoglobin, the main constituent of a red blood cell found in the circulatory systems of many mammals, including Man. As seen in the illustration below, hemoglobins consist of 4 folded units, 2 α-globin twisted chains and 2 β-globin chains, each harboring a heme (haem) group (blue disk) that contains Iron. The four hemes allow loose bonding of Oxygen to the Iron, which is carried in the blood and released where needed to promote oxidation reactions; this globular molecule also can carry CO2 for removal during lung exhalation:

Structure of the hemaglobin molecule.
From Farabee/Purves et al - see above citations

Proteins have many uses in animals. For the human body, these are some of the more common functions: 1) Enzymes - control metabolism; 2) Immuniglobulins - provide antibody defense against foreign cell invaders; 3) Globins - carry O2 and CO2 in blood and muscle; 4) Transporters - controls osmosis; 5) Fibers - affect cartilage, nails, hair; 6) Muscles - control movement of body parts; 7) Albumin - osmosis in the blood; 8) Hormones - affect blood glucose; water retention.

The topic of how new proteins are generated is a vital one in general Biology. We must defer an answer to this until you have grasped the basics of how Nucleic Acids function, after which we will return to the protein production topic near the bottom of this page.

The fourth group, Nucleic Acids, are of fundamental essence to life in that they contain the biochemical molecules that hold the blueprints for making and copying cells. RNA and DNA are called the information-bearing cells that determine the nature of any given organism, from simple bacteria to humans. DNA is found within all cells, both prokaryotic and eukaryotic. The basic unit is called a Nucleotide, consisting as shown below of a monosaccharide 5-Carbon sugar (pink), one of 5 Nitrogenous bases (purple), and a phosphate group (yellow).

Basic makeup of a nucleotide.
From Farabee/Purves et al - see above citations

The 5-carbon sugar molecule comes in two forms (ribose and dioxyribose). These are nearly identical, the only difference being that OH (hydroxyl)is the radical attached to Carbon-2 in the ribose and O (Oxygen) is attached to Carbon-2 in the dioxyribose molecule.

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The structure and composition of the five bases (usually identified by their first letters: Adenine; Cytosine; Guanine; Thymine, and Uracil) is given by this diagram; note that they are organized into two group - the single ring Pyrimidines and the double ring Purines.

The five Nitrogenous bases found in RNA and DNA.
From Raven and Johnson, Biology, 6th Ed., McGraw-Hill, Inc

The bases can be part of important organic molecules involved in various life-sustaining processes. For example, Adenine is a component of ATP (Adenosine Triphosphate) (see below) that has several crital functions including metabolism (energy-supplying reactions) and the formation of DNA. Here is the structural formula for ATP:

ATP structural formula.

However, the trilogy of the 5-carbon sugar molecule, a phosphate radical, and four of the five Nitrogenous bases organized together makes up the most fundamental organic units in all life forms. The two units are Ribonucleic acid (RNA) and Dioxyribonucleic acid (DNA). These are compared in this diagram:

DNA compared with RNA.

RNA occurs in single strands in which the sugars are linked by the phosphate (PO4) phosphodiester bond and the bases lie on the other side of the chain. The four bases present are A, C, G, and U. Multiple chains of nucleotides make up the nucleic acid.

Structural arrangement of RNA
From Farabee/Purves et al - see above citations

The main roles of RNA are in its intimate involvement in the production of proteins, and its intermediary action in duplicating DNA during cell division and growth.

DNA, arguably the most famous organic molecule of all, consists of two chains (sometimes called "backbones") side by side that are coiled into spiral shapes. This diagram shows the general pattern of their structure:

Schematic pattern of the paired and coiled chains in the DNA molecule.

The bases A, C, G, and T (note that T replaces the U present in RNA) produce a link (the straight lines in the above diagram) between the two chains that tie them together. Only certain pairings are allowed: A - T and G - C. These couple by Hydrogen bonds. Here is a schematic of this arrangement.

The double chain DNA pattern.
From Farabee/Purves et al - see above citations

A DNA molecule is very long (a few meters) but extremely thin (narrow; measured in nanometers). Here is an electron microscope photo of a DNA strand:

A DNA strand.

In 1953 Francis Crick and James Watson discovered through analysis of X-ray crystallography photos (done earlier by Rosalind Franklin and Maurice Wilkins - all four living in England) that the double-chained DNA was composed of two spiraling chains arranged in the famed appellation "Double Helix"; this discovery won Crick Watson, and Wilkins the Nobel Prize in Biology - Franklin unfortunately was dead by then). Here is how it looks as rendered by colored balls representing the sugar, phosphate, and base components:

A segment of the DNA molecule showing the helical winding of the two chains, each bonded by photsphate unit and both linked by allowable base pairings; only a few nucleotides are shown.
From Farabee/Purves et al - see above citations

A process called "replication" involves duplicating specific DNA molecules. Rather than a lengthy discussion of this topic here, we refer you to the relevant Wikipedia web site. However, you should look at this next diagram (found commonly on the Internet) to gain a quick overview:

The DNA replication process.

During replication mistakes in reproducing a gene pairing constitute the biochemical explanation for the mutations that Charles Darwin and his compatriot Alfred Wallace cited as the basic cause for natural selection. That is the cornerstone of the Theory of Evolution - this holds that individuals in a species that have the best adapted means for survival in their envIronment(s) will live longer and therefore have the better likelihood of passing their specific gene makeup to offspring in the gene pool ("Survival of the fittest"). These "good" genes thus persist in the population, and enrich it. Occasional mutations over thousands of generations in an organism's reproductive history lead to gradual changes until differences are great enough to warrant designation as new species. More fundamental and long-ranging changes lead to generic, familial, and higher level variants that become new types of animals or plants.

The importance of RNA and DNA reside in their roles in making new cells and in determining the nature/function of a cell by imparting correct instructions for that in the process. DNA codes the hereditary information needed to reproduce an organism and also is involved with RNA in producing new protein cells. This subject, at the heart of concepts of genetics (genes, chromosomes, and genomes), is far too voluminous (knowledge-intensive) to cover on this page (see the Biology Tutorial Internet sites for the details). Suffice to say that the RNA and DNA strands may be very long (macromolecules consisting of 1000s of nucleotides). For DNA, the sequence of A-T amd G-C, arranged in groups of 3 (codons), can, at such lengths, encode a huge number of combinations. These lead to differences in a cell's nature (for example, different proteins are produced by RNA groupings that in turn are produced from DNA control), and when they are set in some fixed pattern of the sequenced pairings, a specific gene is determined. A gene is the fundamental unit of a (usually very long) sequence of nucleotides involved in DNA and RNA molecules. A string of varying genes make up a linear or circular chain of DNA and proteins that comprise chromosomes, the organic molecule that determine sex, heredity and the production of proteins. The full complement of various genes in some particular pattern establishes the genome that uniquely specifies a given organism.

A whole Tutorial could be devoted to describing and explaining genes and chromosomes. Worthy as these subjects are, we will divert you to these two Wikipedia sites, the first on genes and the second on chromosomes. Here we will make a few comments using illustrations with brief write-ups.

First, this general diagram which shows a paired set of individual chromosomes, with black and white bands representing genes, each of which contains thousands of DNA strands (one being shown as expanded) each one of which can consist of a base pair CG or AT.

A simplified example of a chromosome and its component genes.

The number of pairs of chromosomes differs for different living organisms.

The number of chromosomes in different plant and animal species.

The genes contain the basic information that defines the species and characterizes its individual traits. Note the number of genes estimated for the 46 chromosomes of the human species.

The number of genes in the total number of chromosomes in different living creatures.

The human chromosome assemblage is shown in this general diagram; the black and white markings are meant only to convey the idea that various genes of differing makeup are present in each chromosome:

Diagram showing a generalized pattern of genes in the 23 human chromosomes.

In the human gene assemblage there are 46 (23 times 2) chromosomes (long strands of DNA containing all the genetic information [the number varies among species]). Two of these are the sex chromosomes; the remainder are "autosomes" in which each chromosome has its own individual assemblage of genes that controls some aspect of the genetic makeup (other than the sex) of the organism (22 on the haploid strand of a human). The female human has two X chromosomes; the male has a paired X and Y chromosome. Here is a photo of X and Y chromosomes as imaged in an electron microscope:

The human X and Y  chromosomes.

The number of genes varies from one numbered chromosome to the next (left side of the next diagram). The total number of bases is shown on ther right (unfortunately, the numbers have been cropped off, but each horizontal black line is a jump of 50000 from the preceding line [starting at 0 at the bottom and ending at 450000 at the top]); most but not all the bases have a specific sequence (the coding in the DNA that determines the characteristics of the species). Some of the genes are dedicated to producing proteins instead of species traits.

Numbers of genes and numbers of bases in the human chromosomes.

It is interesting to realize that many species share some of the same genes. The sequence may vary. In humans, almost 99% of the genes are the same in any two individuals that can be compared but small differences are distinctive (this fact allows DNA analysis to be used in tracking down an individual suspected of a crime).

The sequence of bases, which defines the genetic code, is divided into triplets called codons. The standard genetic code for RNA consists of 43 or 64 combinations. This is the resulting Codon Table:

The Codon Table for RNA.

Note how it is organized. The first letter in a Codon is taken from the left side. The second letter is selected according to the Column involved, as indicated in the top row. The third letter is chosen from the right side, in the sequence U, C, A, G. Observe that names have been given to different codons.

The same idea applies to this Codon Table set up for DNA. The difference is that U is now replaced by T:

The DNA Codon Table.

Thus, in a chromosome, the genes consist of various sequential combinations of codons that can number in the thousands

Working out the genomes of individual species and genera has proved a bonanza for reconstructing the patterns of evolution, both within and between species. This cladistic analysis has led to various "trees of life" that present the relationships among the animals or plants being compared. Here is an interesting one found on page 128 in "The Language of God" by Francis S. Collins:
Cladistic diagram for a group of seemingly diverse animals, including humans.

Another important topic that is just too involved to be treated on this review page is Mendelian genetics. Instead, we refer you to this Wikipedia web site. We also have omitted any discussion of cell division and organism reproduction, both sexual and asexual, two important but very involved topics. Again, we steer you to another Wikipedia web site for a general overview, which has links to other relevant terms such as gametes, alleles, mitosis, meiosis. You may also wish to learn these terms: haploid, diploid, genotype and phenotype, zygote, homozygous and heterozygous, blastula and gastrula (most of these can be looked up directly in an Internet Search engine).

Armed with this knowledge of DNA, RNA, and genetics, we are equipped to examine the roles they play in producing or synthesizing new organic molecules. To illustrate this, we will show how the most abundant and versatile molecules - the proteins - are generated. Start with this Overview diagram:

The protein production process.

Deceptively simple in this representation, the process is actually complex. In the first step, Transcription (TrScrip), the RNA complement in one strand is synthesized by enzymes into a messenger segment, m-RNA, that is a reversed copy of the original DNA strand, but with T (thymine) replaced by U (uracil).

The general process by which RNA is transcribed from DNA.

The m-RNA serves as a template for natural protein synthesis within a ribosome (see cell diagram below. which also contains r-RNA (ribosomal RBA) This ribosome assemblage participates in the manufacture of a protein by Translation) (TrLate) using t-RNA cells (transfer-RNA containing various amino acids that bind to the m-RNA by Hydrogen bonding. The process continues as the polypeptide protein builds until addition of a 'chain termination' group signals the particular protein with its diagnostic codification is completed. The specific protein composition depends on the sequences involved in the synthesis. The production of mRNA occurs within the nucleus; the mRNA migrates into the cytoplasm and seeks out ribosomes where the next step - Translation - takes place.

In the Transcription phase, segments, called Introns, of the first resulting RNA are not used in building the mRNA. Only the Exons are spliced together in sequence. Note that there are Promotor (initiator) and Terminator segments.

Some details of the Transcription-Translation process.

There is a key intermediate step in Translation. The cell in which the synthesis occurs contains various amino acids. The mRNA must be matched up and bound with its appropriate amino acid. That amino acid is specified by its codon. An enzyme molecule called aminoacyl-tRNA synthetase plays the critical role by serving as a template for preparing a paired tRNA-amino acid that will then be used in the final phase of protein synthesis. Check this figure:

The function of aminoacyl-tRNA synthetase

There are two sites on the molecule that are involved. One is so configured that it can accept (bind) only one specific amino acid. The other site accepts the tRNA. The two are brought together through the action of adenosine triphosphate (ATP) as a catalyst. The pair is then released. The same process takes place with other amino acids, each with their site specific aminoacyl-tRNA synthetase molecule. This diagram shows the steps involved in terms of structural formulae:

Steps involved in the intermediate stage of protein synthesis; AMP = Adenosine monophosphate.

The organic chemistry of the process is complicated and will not be further summarized here. Consult this NIH web site for more details.

The final phase of protein synthesis now enters the picture. This involves the interaction within a ribosome that uses the various tRNA-amino acid pairs to form a polypeptide protein molecule. The pairs are added sequentially according to the master template. The process is involved and will not be discussed here in any detail. Perhaps these two figures will help to visualize what happens.

First steps in protein construction within a ribosome.
Subsequent steps in the construction process.

Because of the importance of this topic - protein production - the writer has extracted excerpts from two web sites. The information is bounded by two green lines. Examine these paragraphs if you wish, otherwise skip to the final material below the second green line

Source: http://rst.gsfc.nasa.gov/