analyses of biological macromolecules
Biological macromolecules are polar
The main point of the first segment of this material is this: THE MONOMER UNITS OF BIOLOGICAL MACROMOLECULES HAVE HEADS AND TAILS. WHEN THEY POLYMERIZE IN A HEAD-TO-TAIL FASHION, THE RESULTING POLYMERS ALSO HAVE HEADS AND TAILS.
These macromolecules are polar [polar: having different ends] because they are formed by head to tail condensation of polar monomers. Let's look at the three major classes of macromolecules to see how this works, and let's begin with carbohydrates.
Monosaccharides polymerize to yield polysaccharides.
Glucose is a typical monosaccharide. It has two important types of functional group: a carbonyl group (an aldehyde in glucose, some other sugars have a ketone group instead.) hydroxyl groups on the other carbons. This is what you need to know about glucose, not its detailed structure.
Glucose exists mostly in ring structures. ( 5-OH adds across the carbonyl oxygen double bond.) This is a so-called internal hemiacetal. The ring can close in either of two ways, giving rise to anomeric forms, -OH down (the alpha-form) and -OH up (the beta-form)
The anomeric carbon (the carbon to which this -OH is attached) differs significantly from the other carbons. (note: it's easy to pick out because it is the only carbon with TWO oxygens -- ring and hydroxyl -- attached.)
Free anomeric carbons have the chemical reactivity of carbonyl carbons because they spend part of their time in the open chain form. They can reduce alkaline solutions of cupric salts. Sugars with free anomeric carbons are therefore called reducing sugars. The rest of the carbohydrate consists of ordinary carbons and ordinary -OH groups. The point is, a monosaccharide can therefore be thought of as having polarity, with one end consisting of the anomeric carbon, and the other end consisting of the rest of the molecule.
Monosaccharides can polymerize by elimination of the elements of water between the anomeric hydroxyl and a hydroxyl of another sugar. This is called a glycosidic bond.
If two anomeric hydroxyl groups react (head to head condensation) the product has no reducing end (no free anomeric carbon). This is the case with sucrose
If the anomeric hydroxyl reacts with a non-anomeric hydroxyl of another sugar, the product has ends with different properties. A reducing end (with a free anomeric carbon). A nonreducing end. This is the case with maltose.
Since most monosaccharides have more than one hydroxyl, branches are possible, and are common. Branches result in a more compact molecule. If the branch ends are the reactive sites, more branches provide more reactive sites per molecule.
Let's now turn to nucleotides and nucleic acids.
Nucleotides polymerize to yield nucleic acids.
Nucleotides consist of three parts.
Phosphate.
Monosaccharide.
Ribose (in ribonucleotides)
Deoxyribose, which lacks a 2' -OH (in deoxyribonucleotides)
The presence or absence of the 2' -OH has structural significance that will be discussed later.
There are four dominant bases; here are three of them: adenine (purine) cytosine (pyrimidine) guanine (purine)
The fourth base is (a pyrimidine) uracil (in ribonucleotides) or thymine (in deoxyribonucleotides)
Be aware that uracil and thymine are very similar; they differ only by a methyl group. You need to know which are purines and which are pyrimidines, and whether it is the purines or the pyrimidines that have one ring. The reasons for knowing these points relate to the way purines and pyrimidines interact in nucleic acids, which we'll cover shortly.
Nucleotides polymerize by eliminating the elements of water to form esters between the 5'-phosphate and the 3' -OH of another nucleotide.
A 3'->5' phosphodiester bond is thereby formed. The product has ends with different properties. An end with a free 5' group (likely with phosphate attached); this is called the 5' end. An end with a free 3' group; this is called the 3' end.
Let's look at the conventions for writing sequences of nucleotides in nucleic acids. Bases are abbreviated by their initials: A, C, G and U or T. U is normally found only in RNA, and T is normally found only in DNA. So the presence of U vs. T distinguishes between RNA and DNA in a written sequence.
Sequences are written with the 5' end to the left and the 3' end to the right unless specifically designated otherwise.
Phosphate groups are usually not shown unless the writer wants to draw attention to them. The following representations are all equivalent. uracil adenine cytosine guanine | | | | P-ribose-P-ribose-P-ribose-P-ribose-OH 5' 3' 5' 3' 5' 3' 5' 3' pUpApCpG UACG 3' GCAU 5'
(Note that in the last line the sequence is written in reverse order , but the ends are appropriately designated.)
Branches are possible in RNA but not in DNA. RNA has a 2' -OH, at which branching could occur, while DNA does not. Branching is very unusual; it is known to occur only during RNA modification [the "lariat"], but not in any finished RNA species. Amino acids polymerize to form polypeptides or proteins. Amino acids contain a carboxylic acid (-COOH) group and an amino (-NH2) group. The amino groups are usually attached to the carbons which are alpha to the carboxyl carbons, so they are called alpha-amino acids.
The naturally occurring amino acids are optically active, as they have four different groups attached to one carbon, (Glycine is an exception, having two hydrogens) and have the L-configuration.
The R-groups of the amino acids provide a basis for classifying amino acids. There are many ways of classifying amino acids, but one very useful way is on the basis of how well or poorly the R-group interacts with water
The first class is the hydrophobic R-groups which can be aliphatic (such as the methyl group of alanine) or aromatic (such as the phenyl group of phenylalanine). The second class is the hydrophilic R-groups which can contain neutral polar (such as the -OH of serine) or ionizable (such as the -COOH of aspartate) functional groups.
My father, Herbert Bennett Fenn, the eldest of three children was born and raised on a farm in northern Delaware which his father operated but did not own. I never saw that farm but I vividly remember my Grandmother's frequent reference to a single chestnut tree in the front yard, so large and prolific that the nuts from that one tree paid the taxes on the farm every year!My mother was the sixth of ten children in the family of John Clarence Dingman, a country doctor in Spring Valley, N.Y. whose three surviving sons also became physicians. Dad worked his way through college, graduating in Electrical Engineering from Rutgers in 1910, the same year that mother received a degree in Home Economics and Nutrition from Columbia. They were both hired by the Presbyterian Mission Board to teach at the Sheldon Jackson Mission School in Sitka, originally settled by the Russians and sometime capital (until replaced by Juneau in 1900). The Chairman of that Board told each one about the other and warned them both not to fall in love, but if they did and got married he would provide them with a house for as long as they stayed in Sitka! They did and he did, so after mother's death in 1990 (Dad had died in 1944) we found in her papers a clipping from the Sitka paper with a photograph of the "Honeymoon Cottage".
During a cruise in 1996 I spent a day in Sitka. The Mission School is now Sheldon-Jackson University. I visited the library, discovered a complete file of student newspapers, and found several articles about my parents! Moreover, the present Librarian was then living in the "Honeymoon Cottage" and gave me a tour so I was actually able to look out through its front windows and see the magnificent view of Sitka Bay that my parents used to rave about.
The newlyweds were very happy in Alaska and no doubt would have remained there indefinitely had it not emerged that mother would be unable to bear children except by Caesarian Section, a procedure not then available in Sitka. Determined to have a family she persuaded Dad to move back to the States where he became manager of the Metacloth Company, a small enterprise in Lodi, N.J. whose main product was cotton duck treated by immersion in a concentrated ammoniacal solution of copper hydroxide followed by a wash in acid. The deep blue "cuprammonium" solution dissolved some of the cellulose which reprecipitated during passage through the succeeding acid bath, filling the pores of the cloth enough to make it "water resistant" but not "water-proof". Residual copper provided a characteristic blue-green color along with a high resistance to attack by micro-organisms and white ants. For these reasons, "Metacloth" was in fairly steady demand for tents and tarpaulins in tropical latitudes. My abrupt introduction to "chemistry" occurred on one of the treasured Saturdays when Dad took me to the plant. Nosing around outside I lifted a small flap on the cover of a large tank half full of cuprammonium solution. I still recoil at the memory of that ammoniacal, and demoniacal, assault on my eyes and nose. It was a startling revelation on how and why a whiff of smelling salts can often revive people from a dead faint!
Our home was in Hackensack, N.J., next door to Lodi and County Seat of Bergen County. I was born in New York City in 1917 and three plus years later my brother Norman arrived in Paterson, N.J. where two of mother's brothers were surgeons. The Metacloth company was sold in 1926 and Dad was unceremoniously dumped by the new owners. He was not a vindictive man but he got no little satisfaction out of the several occasions in the next two years when his help was needed in overcoming mistakes made by the new management. Meanwhile, approaching fifty and finding equivalent jobs scarce, he was paying the bills by working as a draftsman at the Fokker Aircraft Company in Teterboro, N.J. The value of having a trade as back-up for a profession was an enduring object lesson for a youngster on the eve of the Great Depression but there was for him a far more exciting consequence of the Fokker connection. When Lindbergh's "Spirit of St. Louis" was shipped back from Paris after its famous flight across the Atlantic, it was parked for a time in a hangar at the Teterboro airport. The thrill of a lifetime for a ten year old boy was when his Dad took him into that hangar where he was allowed to sit in the cockpit and move the controls, pretending to be pilot of that famous plane!
Meanwhile the family fortunes were going down hill, much further than my brother and I were aware. Just before Dad lost his job, he and mother had invested their life savings in a new (for us) house that everyone insisted was worth "every nickel" of the $15,000 that it cost! Unfortunately, after we had to move and before the house could be sold the great depression had begun. No prospective buyers had enough nickels so those savings disappeared in the meltdown of foreclosure. Meanwhile, a door of opportunity had opened in Berea, Kentucky, a small community of 3500 or so inhabitants at the edge of bluegrass country some 40 miles south of Lexington and roughly halfway between Cincinnati, Ohio and Knoxville, Tennessee. The town of Berea was home for a remarkable institution known by the same name but officially entitled "Berea College and Allied Schools". Both the community and the school had their roots in a non-sectarian Union Church founded in 1848 by John G. Fee, on a ridge of land donated by Cassius Clay, a brother of Henry Clay, the famous orator and statesman from Lexington, Ky.
Fee was a Congregational Minister from Massachusetts and a fervent abolitionist determined to provide educational opportunities for needy students, regardless of their race or creed. After decades of effort by himself and his followers his dream grew into what in 1928 comprised a coeducational student body of about 1700 divided among four schools: (1) The Foundation-Junior-High School with an ungraded program into which students with as little as two years of formal schooling could enroll and progress at their own rate up through the equivalent of 8th grade into a standard and accredited 9th grade curriculum; (2) The Academy, with an accredited curriculum for grades 10 through 12, (3) the Normal School with a two year program leading to a Teaching Certificate, and (4) the College which offered accredited curricula leading to BA degrees in the liberal arts and sciences as well as BS degrees in Home Economics and Agriculture. Mother's sister was teaching in the College and knew that the Industrial Arts Department of the Foundation School and the Academy needed someone to teach Auto Mechanics and Practical Electricity. Dad was eminently qualified and got the job. We moved to Kentucky in time for me to enter the eighth grade in the "Training School" of Berea's Normal School in the fall of 1928. The next fall I entered ninth grade in the Foundation School and continued on through the Academy and College.
A lot of misgivings, pain and confusion attended our passage through the newly opened door, including an automobile accident on the way to Kentucky, but life on the other side turned out to be rich and rewarding beyond what any of us had dreamed. In later years Dad and Mother both said, time and again, that losing his "good" job in New Jersey turned out to be the greatest blessing that we could have received! To this day my brother and I share those sentiments and count ourselves especially privileged to have been reared in what was a truly remarkable community. Its soul was its President, William J. Hutchins, father of Robert Maynard Hutchins, the "boy wonder" of the American education scene who became Secretary of Yale at the age of 24, Dean of its Law School at 26 and President of the University of Chicago at 30! "William J", as the father was fondly known at his own institution, was truly one of nature's noblemen. A striking man of vision and patrician to the core, his Berea was a singular stage on which the play was always provocative and the message meaningful. Name an outstanding man or woman of letters, the arts, science, or religion, of those days and the odds are high that he or she came to Berea to talk at one of the thrice weekly "United Chapels" for students from all schools. Attendance was required of all, and resented by most, but at my 50th class reunion there was a remarkable consensus among my surviving classmates that the community experiences of those United Chapel services were by far the most memorable and valuable components of their educational. Alas, that tradition has long since disappeared, one more victim of "students' rights" and television. Moreover, as the public education system improved in surrounding "Appalachia", the need for Berea's Foundation School, Academy and Normal School faded over the years, so that the only survivor is a now a substantially larger Berea College.
A unique feature of Berea was and is a student labor program that provided much of the manpower required to run the institution. Under the supervision of permanent staff, the dining halls, dormitories, offices, and yard work were all maintained and operated by student labor. In addition were several "Industries" including a bakery, broom factory, dairy, large truck garden, sheep farm, piggery, a "woodwork department" that made fine furniture, and a weaving establishment. The normal work load was two hours a day by which a student could earn as much as half or two thirds of his or her out of pocket expenses that in the 1930's averaged only $250 to $300 per year because tuition was free! The system was very democratic because every student was required to work at least two hours a day. A fair fraction of the student body comprised so-called half-day students who worked four hours a day, earning enough to pay all expenses. I knew students who arrived at Berea with nothing but the clothes on their backs, having dropped out of school after the second grade, and worked their way through college! It is not surprising that competition to enter Berea, especially the college, was extremely keen. In order to avoid having to reject such a large fraction of applicants, the Trustees had established a policy requiring that 85 per cent of the student body come from a region of Appalachia comprising some 500 or so counties in Virginia, West Virginia, Kentucky, Tennessee, and North Carolina. The remaining 15 percent of the students came from the rest of the world. Today's Berea is quite a different place because the growth of alternative educational opportunities in Berea's "Territory", has decreased demand to the point that in 1987, at my 50th reunion, I learned there were only two applicants for every opening in the College compared to 20 or 30 in my day. Part of that decrease in demand is due to a higher level of average income in that "territory" so that fewer students can show that they cannot afford to go elsewhere, a requisite for admission.
When I graduated from the Academy in 1932 I was only 15, too young, my parents thought, to go to college, so I stayed in the Academy an extra year taking courses in mechanical drawing and shorthand. I also continued the piano lessons that I had started the year before and spent enough time practicing so that I actually gave a recital during my last year in college! Alas, whatever piano skills I had have faded until now I do well to play chopsticks with my grandchildren! When I entered College with the class of '38 I had not decided on a major but I leaned toward a science, probably because of my long affair with the Book of Knowledge, an encyclopedia for young people which my parents bought when I was around eight or nine. During the hours that I pored over them, its 20 volumes became a well worn magic carpet to new and fascinating worlds. I've often quipped that "I got through college on the Book of Knowledge", a bit of rhyming hyperbole that contains an appreciable kernel of truth.
The College required at least one course in science for all students no matter what their major. Having enjoyed my chemistry course in the Academy I enrolled in Introductory Chemistry during my freshman year. It was taught by Professor Julian Capps, the senior of the two member chemistry faculty. He was a wonderful teacher who made his subject live. I was so seduced that Chemistry became my major even though Gravimetric Analysis gave me fits in my sophomore year. I repeated the lengthy phosphorous determination on three samples each of ten unknowns before I got one set of three results with acceptable agreement! It seems ironic that mass spectrometry, the center of my scientific life for the last 20 years, is really just an exercise in gravimetric analysis!