Nucleic Acids: DNA and RNA - Biochemistry

Nucleotides are the macromolecular building blocks of DNA and RNA. They contain a sugar that is attached to a nitrogenous base and a phosphate group. The nitrogenous base that makes up the nucleotide can vary between adenine, guanine, cytosine, thymine (in DNA) and uracil (in RNA). Furthermore, the sugar can also vary between deoxyribose in DNA and ribose in RNA. As nucleotides are added to a growing DNA strand, the enzyme DNA polymerase synthesizes the strand in the 5' to 3' direction. That is to say, the 3' end of the growing strand must have a group in order for another nucleotide to be added onto it. Thus, the 3' carbon of a free nucleotide must contain a group. The 1' carbon of the sugar moiety will always be bound to a nitrogenous base. Thus, this position cannot have a group. The 5' carbon of the sugar moiety is occupied by a phosphate group. The 2' carbon of the sugar moiety can have a group. In fact, in RNA the 2' position of the sugar has a group. However, this position in DNA does not have a group, but instead has a hydrogen bound in this position, hence the name deoxyribose. Thus, the 2' position does not have to have a hydroxyl group.

The DNA structure consists of the nitrogenous bases on the inside of the helix, bound together by hydrogen bonds, and the sugar phosphate backbone outside of the helix, bound together by phosphodiester bonds. This arrangement allows the hydrogen bonding to stabilize the DNA molecule, while making it relatively easy to pull apart when it needs to be replicated/transcribed.

Helicase is used to separate annealed nitrogenous bases of double-stranded DNA in order to allow access by other fundamental enzymes such as DNA polymerase so that replication may proceed. Topoisomerase helps relieve tension of the double helix that arises as a result of separating the strands during replication and/or transcription. Aldolase catalyzes the conversion of fructose-1,6-bisphosphate into triose phosphates during glycolysis. DNA polymerase catalyzes the polymerization of deoxynucleoside triphosphates into deoxynucleoside monophosphates, known as DNA strands.

Only about 5% of a cell’s RNA consists of mRNA. The highest percentage by type of RNA actually turns out to be rRNA. mRNA strands have great variation in size, from about 100 to more than 20,000 nucleotides. This variation is a reflection of the sizes of the genes which produce the mRNA. mRNA strands stay intact for very different lengths of time; gene expression is regulated by these varying lengths of time. mRNA is indeed transcribed from functional genes, and goes on further to be translated into proteins (DNA RNA protein).

The 5' end has a phosphate group, while the 3' end has an . The two strands do, indeed, have opposing polarities; that is, the 5' end of one is positioned next to the 3' end of the other. The sugar-phosphate backbone is on the outside of the molecule, giving it a negative charge. DNA turns once typically every 10.4 pairs, and the distance between the center of nucleotide pairs is about 3.4nm. The adenine (A)-thymine (T) base pair is connected by two hydrogen bonds, and cytosine (C)-guanine (G), three.

Nucleosomes represent the first level of chromosome organization, and occur in the interphase of the cell cycle. The nucleosome core has an eight histone-DNA complex, called a histone octamer. The region between two cores includes DNA up to a length of 80 base pairs. This packs the DNA tightly, to about one-third its initial length (a decrease of two-thirds). Histones all have are folded in a manner containing three alpha-helices as two loops. The DNA wraps around the core in a left-handed coil.

Nucleic acids are made up of nucleotides that contain a pentose sugar, a phosphate group, and a nitrogenous base. There are two types of nucleic acids; DNA and RNA. The difference between these two nucleic acids is their pentose sugar. DNA has deoxyribose whereas RNA has ribose sugar residues. Note that both are types of pentose sugar; therefore, all types of nucleic acids have pentose sugars.

Nitrogenous bases found in nucleic acids are classified as either purines or pyrimidines. Free purines in the blood are broken down to uric acid in the liver. Recall that purines (guanine and adenine) are found in both RNA and DNA; therefore, breakdown of either type of nucleic acid will lead to release of purines and, subsequently, formation of uric acid in the liver.

As mentioned, nucleic acids are made up of monomers called nucleotides. Nucleosides, on the other hand, only have a pentose sugar and nitrogenous base (they lack the phosphate group); therefore, they are not the monomers of nucleic acids.

To answer this question we need to recall that the monomer of nucleic acids is a nucleotide. Nucleotides are made up of three molecules: pentose sugar, phosphate group and nitrogenous base. The question tells us that the monomer has a phosphate group and a guanine (nitrogenous base); however, we are not given any information regarding the pentose sugar. Recall that the two types of nucleic acids (DNA and RNA) are distinguished from each other by the pentose sugar. DNA has deoxyribose whereas RNA has ribose. Since we do not know the type of pentose sugar, we cannot determine the monomer’s identity.

The difference between nucleotides and nucleosides is that nucleotides contain a phosphate group whereas nucleosides do not. This means that a nucleoside is made up of just a pentose sugar and a nitrogenous base. The DNA and RNA differ from each other based on their pentose sugars (DNA has deoxyribose and RNA has ribose). Another difference between RNA and DNA is that uracil nitrogenous base is only found in RNA whereas thymine nitrogenous base is only found in DNA.

Nucleic acids such as DNA and RNA contain a series of nucleotides, each of which contains a sugar, a nitrogenous base, and a phosphate group. The sugar and phosphate group form the backbone of the linear chain, while the nitrogenous bases are able to protrude out. When hydridizing with other nucleic acid strands, only certain nitrogenous bases can pair with others. This base pairing is due to hydrogen bonds that form between the two nitrogenous bases, and the number of hydrogen bonds differs depending on what bases are involved.

For both DNA and RNA strands, guanine and cytosine will pair with one another via three hydrogen bonds.

In RNA, the nucleotide thymine is absent, but in its place is the nucleotide uracil. Uracil is able to base pair with adenine via two hydrogen bonds, but this only happens in RNA, not DNA!

In DNA, thymine is present rather than uracil. The thymine found in DNA is also able to base pair with adenine via two hydrogen bonds. Thus, out of all the answer choices, this is the only correct one that can occur within DNA.

tRNA is synthesized by RNA polymerase III, mRNA is synthesized by RNA polymerase II, and rRNA is synthesized by RNA polymerase I. DNA polymerase I is involved in DNA synthesis, and specifically, has a 5' to 3' exonuclease functionality, which removes RNA primers laid down by primase and replaces them with DNA nucleotides.

Two orthophosphates are connected via anhydride linkage to form the high energy pyrophosphate. This is the "" bond. Glycosidic linkage describes a bond between two or more sugar molecules, not between orthophosphates. This anhydride linkage is made up of single bonds, and not double or triple bonds. An amide bond is the specific chemical name for a peptide bond.

The (melting temperature)of DNA is defined as the temperature at which half of the DNA strands would become denatured. It is known that GC base pairs are kept together via hydrogen bonding at three different locations, compared to hydrogen bonding at just two locations in AT base pairs. Because of this additional interaction, a DNA strand with a higher component of GC base pairs will have a higher than one with a higher component of AT base pairs.

Eukaryotes have so much DNA that it needs to be compacted to make it less bulky and more protected. The lowest level of organization is known as a coil. Predictably, multiple coils together form a super-coil. Next, the DNA is wrapped around proteins known as histones. 8 histones together form a nucleosome. Finally, fully packed and organized DNA is known as chromatin.

Heterochromatin is dark, dense, tightly packed, and rich in repeating segments. It is often in cells that are inactive or less active. As such, heterochromatin is sometimes referred to as "non-coding DNA". Euchromatin, on the other hand, is less tightly packed, and more readily coded. Centromeres are the part of the chromosome that attach to kinetochores during cellular division. Finally, The ends of chromosomes are known as telomeres. Of note, centromeres and telomeres are actually both composed of heterochromatin.

Guanine is a purine, not a pyrimidine. The purines are guanine and adenine, while the pyrimidines are cytosine, thymine, and uracil. Uracil is present only in RNA, and thymine only in DNA. The rest of the bases are present in both DNA and RNA.

It is true that DNA is more stable than RNA. While the exact chemical reasons for this are complex, it is useful to know RNA is readily hydrolyzed in basic conditions. In order to make sense of this, remember that DNA acts as the genetic code, and must hold that genetic information for relatively long periods of time. While there are several types of RNA, it typically acts as a messenger, and is degraded after completing its task. While DNA does contain the base thymine and RNA does contain uracil, this is unrelated to the relative stabilities of the two nucleic acids.

While it could be useful to know that the bases are at the core of the DNA while the sugar-phosphate chains are on the outside, it is possible to answer the question without having memorized that fact. The bases (thymine, cytosine, guanine, adenine) are non-polar, and will cluster in the middle of the chain, away from water. They also connect to each other via hydrogen bonding. On the other hand, the sugar-phosphate groups are hydrophilic, and will cluster towards the outside of the molecule.

All DNA contains 50% purines and 50% pyrimidines due to Watson-Crick base pairing.

However, doing the calculations based on the information given can also give the correct answer. Adenine (A) and guanine (G) are purines. Cytosine (C) and thymine (T) are pyrimidines. Chargaff's rules state that in DNA, G = C and A = T. If the sample is 15% G, then it must also be 15% C. This leaves 70% for A and T, or 35% each. 15% C + 35% T = 50% pyrimidines.