Why nucleic acids are acids

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Chapter 1: Scientific Inquiry. Chapter 2: Chemistry of Life. Chapter 4: Cell Structure and Function. Chapter 5: Membranes and Cellular Transport. Chapter 6: Cell Signaling. Chapter 7: Metabolism. Chapter 8: Cellular Respiration. Chapter 9: Photosynthesis. Chapter Cell Cycle and Division.

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You can reuse this answer Creative Commons License. The cell encodes information, much like you recorded on a tape, into nucleic acids. So the sequence of these molecules in the polymer can convey "make a protein", "please replicate me", "transfer me to the nucleus And so if you think about the need to convey genetic information from one cell to another, you would want a molecule that is very stable and doesn't fall apart on its own, and that's a major feature of nucleic acids.

The name "nucleic acid" comes from the fact that they were first described because they actually had acidic properties, much like the acids that you know. One end 5' is different from the other 3'. Molecular weights for the DNA from multicellular organisms are commonly 10 9 or greater. Information is stored or encoded in the DNA polymer by the pattern in which the four nucleotides are arranged.

To access this information the pattern must be "read" in a linear fashion, just as a bar code is read at a supermarket checkout. Because living organisms are extremely complex, a correspondingly large amount of information related to this complexity must be stored in the DNA.

Consequently, the DNA itself must be very large, as noted above. Even the single DNA molecule from an E. The nuclei of multicellular organisms incorporate chromosomes, which are composed of DNA combined with nuclear proteins called histones.

The fruit fly has 8 chromosomes, humans have 46 and dogs 78 note that the amount of DNA in a cell's nucleus does not correlate with the number of chromosomes.

The DNA from the smallest human chromosome is over ten times larger than E. In addition to its role as a stable informational library, chromosomal DNA must be structured or organized in such a way that the chemical machinery of the cell will have easy access to that information, in order to make important molecules such as polypeptides.

Furthermore, accurate copies of the DNA code must be created as cells divide, with the replicated DNA molecules passed on to subsequent cell generations, as well as to progeny of the organism. The nature of this DNA organization, or secondary structure, will be discussed in a later section. The high molecular weight nucleic acid, DNA, is found chiefly in the nuclei of complex cells, known as eucaryotic cells , or in the nucleoid regions of procaryotic cells , such as bacteria.

It is often associated with proteins that help to pack it in a usable fashion. In contrast, a lower molecular weight, but much more abundant nucleic acid, RNA , is distributed throughout the cell, most commonly in small numerous organelles called ribosomes. Both have a more transient existence and are smaller than rRNA. As shown in the following diagram, the sugar component of RNA is ribose, and the pyrimidine base uracil replaces the thymine base of DNA. The RNA's play a vital role in the transfer of information transcription from the DNA library to the protein factories called ribosomes, and in the interpretation of that information translation for the synthesis of specific polypeptides.

These functions will be described later. A complete structural representation of a segment of the RNA polymer formed from 5'-nucleotides may be viewed by clicking on the above diagram. In the early 's the primary structure of DNA was well established, but a firm understanding of its secondary structure was lacking.

Indeed, the situation was similar to that occupied by the proteins a decade earlier, before the alpha helix and pleated sheet structures were proposed by Linus Pauling.

Rosalind Franklin , working at King's College, London, obtained X-ray diffraction evidence that suggested a long helical structure of uniform thickness. Francis Crick and James Watson, at Cambridge University, considered hydrogen bonded base pairing interactions, and arrived at a double stranded helical model that satisfied most of the known facts, and has been confirmed by subsequent findings.

Base Pairing Careful examination of the purine and pyrimidine base components of the nucleotides reveals that three of them could exist as hydroxy pyrimidine or purine tautomers, having an aromatic heterocyclic ring. Despite the added stabilization of an aromatic ring , these compounds prefer to adopt amide-like structures.

These options are shown in the following diagram, with the more stable tautomer drawn in blue. A simple model for this tautomerism is provided by 2-hydroxypyridine. As shown on the left below, a compound having this structure might be expected to have phenol-like characteristics, such as an acidic hydroxyl group.

These differences agree with the 2-pyridone tautomer, the stable form of the zwitterionic internal salt. Further evidence supporting this assignment will be displayed by clicking on the diagram. Note that this tautomerism reverses the hydrogen bonding behavior of the nitrogen and oxygen functions the N-H group of the pyridone becomes a hydrogen bond donor and the carbonyl oxygen an acceptor. The additional evidence for the pyridone tautomer, that appears above by clicking on the diagram, consists of infrared and carbon nmr absorptions associated with and characteristic of the amide group.

The data for 2-pyridone is given on the left. Similar data for the N-methyl derivative, which cannot tautomerize to a pyridine derivative, is presented on the right. Once they had identified the favored base tautomers in the nucleosides, Watson and Crick were able to propose a complementary pairing, via hydrogen bonding, of guanosine G with cytidine C and adenosine A with thymidine T. This pairing, which is shown in the following diagram, explained Chargaff's findings beautifully, and led them to suggest a double helix structure for DNA.

Before viewing this double helix structure itself, it is instructive to examine the base pairing interactions in greater detail. The G C association involves three hydrogen bonds colored pink , and is therefore stronger than the two-hydrogen bond association of A T.

These base pairings might appear to be arbitrary, but other possibilities suffer destabilizing steric or electronic interactions. By clicking on the diagram two such alternative couplings will be shown. The C T pairing on the left suffers from carbonyl dipole repulsion, as well as steric crowding of the oxygens.

The G A pairing on the right is also destabilized by steric crowding circled hydrogens. A simple mnemonic device for remembering which bases are paired comes from the line construction of the capital letters used to identify the bases. A and T are made up of intersecting straight lines. In contrast, C and G are largely composed of curved lines. After many trials and modifications, Watson and Crick conceived an ingenious double helix model for the secondary structure of DNA.

Two strands of DNA were aligned anti-parallel to each other, i. Complementary primary nucleotide structures for each strand allowed intra-strand hydrogen bonding between each pair of bases. These complementary strands are colored red and green in the diagram.

Coiling these coupled strands then leads to a double helix structure, shown as cross-linked ribbons in part b of the diagram. The double helix is further stabilized by hydrophobic attractions and pi-stacking of the bases. A space-filling molecular model of a short segment is displayed in part c on the right.

The helix shown here has ten base pairs per turn, and rises 3. This right-handed helix is the favored conformation in aqueous systems, and has been termed the B-helix. As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones. Two alternating grooves result, a wide and deep major groove ca.

Other molecules, including polypeptides, may insert into these grooves, and in so doing perturb the chemistry of DNA. Other helical structures of DNA have also been observed, and are designated by letters e. A and Z. A model of a short DNA segment may be examined by. Click Here. Frieda Reichsman, Univ.

In their announcement of a double helix structure for DNA, Watson and Crick stated, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.

The essence of this suggestion is that, if separated, each strand of the molecule might act as a template on which a new complementary strand might be assembled, leading finally to two identical DNA molecules. Indeed, replication does take place in this fashion when cells divide, but the events leading up to the actual synthesis of complementary DNA strands are sufficiently complex that they will not be described in any detail.

As depicted in the following drawing, the DNA of a cell is tightly packed into chromosomes. First, the DNA is wrapped around small proteins called histones colored pink below. These bead-like structures are then further organized and folded into chromatin aggregates that make up the chromosomes. An overall packing efficiency of 7, or more is thus achieved.

Clearly a sequence of unfolding events must take place before the information encoded in the DNA can be used or replicated. Once the double stranded DNA is exposed, a group of enzymes act to accomplish its replication. These are described briefly here:. Topoisomerase : This enzyme initiates unwinding of the double helix by cutting one of the strands. Helicase : This enzyme assists the unwinding.

Note that many hydrogen bonds must be broken if the strands are to be separated.. SSB : A single-strand binding-protein stabilizes the separated strands, and prevents them from recombining, so that the polymerization chemistry can function on the individual strands.

DNA Polymerase : This family of enzymes link together nucleotide triphosphate monomers as they hydrogen bond to complementary bases. These enzymes also check for errors roughly ten per billion , and make corrections.

Ligase : Small unattached DNA segments on a strand are united by this enzyme. Polymerization of nucleotides takes place by the phosphorylation reaction described by the following equation.

Di- and triphosphate esters have anhydride-like structures and are consequently reactive phosphorylating reagents, just as carboxylic anhydrides are acylating reagents. Since the pyrophosphate anion is a better leaving group than phosphate, triphosphates are more powerful phosphorylating agents than are diphosphates.