In this question, we're given the pKa of a peptide's functional group and we're told that the peptide is in a solution at a certain pH. We're asked to estimate the proportion of the functional group that we would expect to be protonated.

The first thing we can realize about this problem is that the peptide is in a solution that is far more acidic than the pKa of the functional group. Therefore, we would certainly expect a lot of it to be protonated. The question is, by how much?

We can make use of the Henderson-Hasselbalch equation to quantify the degree to which the functional group will become protonated.

In the equation above, we can take base to mean the deprotonated functional group, while acid we can take as the protonated functional group.

We can also rearrange the above expression in order to isolate the base to acid ratio.

Next, we can plug in the values given to us in the question stem.

We can rewrite this expression alternatively to make it more intuitive.

In other words, for every one equivalent of base, there are  equivalents of acid. To find the proportion of acid, we can take the number of acidic equivalents and divide that by the total number of acidic plus basic equivalents.

Thus,  of the functional group is expected to be in the protonated form. This makes sense, considering that the solution is significantly more acidic than this particular functional group's pKa.

Glutamate is the primary source of ammonia. Glutamine is similar however it is the amide free form of ammonia. Glutamate plays an important role in the urea cycle. The urea cycle serves to rid the body of ammonia, which can be toxic in high amounts.

Charged hydrophilic amino acids are polar and their side chains carry a net charge at or near a neutral pH. For instance, lysine has a positive charge at a pH of 7. Examples of essential amino acids that are in this group include arginine, histidine, and lysine.

RNA contains uracil, while DNA contains thymine. All of the other statements are true. Note that DNA is usually double-stranded and RNA is usually single-stranded, but both can exist in the opposite configuration under certain conditions.

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.