Draw the principal ionic species of \(5^{\prime}\) -GMP occurring at pH 2.

Short Answer

Expert verified
The principal ionic species of \(5^{\prime}\) -GMP at pH 2 includes the ribose sugar, guanine base, and phosphate group, all in their fully protonated states.

Step by step solution

01

Identify Functional Groups

The \(5^{\prime}\) -GMP molecule has several functional groups that can accept a proton: the phosphate group, the carboxyl group, and the amino group on the base. Each of these groups can accept a proton under acidic conditions such as at pH 2.
02

Sketch the Basic Structure

Sketch the basic structure of \(5^{\prime}\) -GMP. Include the ribose sugar, guanine base, and phosphate group.
03

Add Protons to Functional Groups

Considering the acidic environment, add protons to the functional groups identified in Step 1. The phosphate group will have all of its oxygens protonated, the carboxyl group on the base will also be protonated, and the amino group will have an extra proton.
04

Finalize the Structure

Finally add the protons to form the fully protonated structure of \(5^{\prime}\) -GMP at pH 2.

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Key Concepts

These are the key concepts you need to understand to accurately answer the question.

Functional Groups in Nucleotides
To understand the behavior of nucleotides like 5'-GMP under different pH conditions, it's essential to firstly know about the functional groups they contain.

5'-GMP, or guanosine monophosphate, contains a nucleobase (guanine), a sugar ring (ribose), and a phosphate group. Nucleobases have functional groups like amine (-NH2) and carbonyl (C=O) groups, which are critical for their interactions. The ribose sugar is also important, featuring hydroxyl (-OH) groups that affect the nucleotide's chemical properties. Finally, the phosphate group brings a high potential for protonation due to its oxygen atoms.

Key Functional Groups:

  • Amine group in the guanine base
  • Carbonyl group in the guanine base
  • Hydroxyl groups in the ribose sugar
  • Phosphate group with its oxygen atoms
These functional groups define the behavior and the ionic species formed when conditions change, such as variations in pH.
Protonation under Acidic Conditions
Under acidic conditions, protonation is the key chemical process affecting the structure of nucleotides like 5'-GMP.

Protonation occurs when a molecule gains a hydrogen ion (H+), typically sourced from an acid in the environment. The pH denotes how acidic or basic a solution is, and at a low pH, such as pH 2, there is a high concentration of hydrogen ions available to be added to nucleotide molecules. Each functional group in the nucleotide has a different propensity to attract and bind these protons.

Protonation Sites on 5'-GMP:

  • Phosphate oxygens
  • Oxygen of the carbonyl group
  • Nitrogen atoms in the amino group
Understanding where these protons are likely to attach is crucial for predicting the molecular charge at various pH levels.
Nucleotide Structure
The structure of a nucleotide is integral for its function in biological systems, and it consists of three main parts: a phosphate group, a sugar (ribose or deoxyribose), and a nitrogenous base (like guanine in the case of 5'-GMP).

The phosphate group is negatively charged and highly reactive, which allows it to form phosphodiester bonds that connect nucleotides together in the backbone of nucleic acids. The ribose sugar provides a scaffold for the entire nucleotide, holding the base and phosphate together. Lastly, the nitrogenous base, be it adenine, thymine, cytosine, guanine, or uracil, carries the genetic code in its sequence.

Each nucleotide's structure and the presence of specific functional groups dictate how it will behave when faced with changes in the environment, such as shifts in pH levels.
pH and Molecular Charge
The pH of a solution can considerably influence the molecular charge of nucleotides like 5'-GMP.

pH is a scale used to measure how acidic or basic a solution is, with lower pH values indicating higher acidity and higher concentration of hydrogen ions (H+). The dissociation of hydrogen ions from the functional groups of a nucleotide leads to changes in its overall charge. At lower pH, as we find more protonation, the molecule may become more positively charged because it has gained H+ ions.

Impact on 5'-GMP:

  • At pH 2, 5'-GMP becomes fully protonated, gaining a more positive charge at the nitrogenous base's amine and the phosphate group's oxygens.
  • This change affects its interactions with other molecules and its solubility in water.
Overall, understanding the relationship between pH and the charge of a molecule like 5'-GMP is critical in both biochemistry and pharmaceutical applications.

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Most popular questions from this chapter

A carbohydrate group is an integral part of a nucleoside. a. What advantage does the carbohydrate provide? Polynucleotides are formed through formation of a sugarphosphate backbone. b. Why might ribose be preferable for this backbone instead of glucose? c. Why might 2-deoxyribose be preferable to ribose in some situations?

Gene expression is controlled through the interaction of proteins with specific nucleotide sequences in double-stranded DNA. a. List the kinds of noncovalent interactions that might take place between a protein and DNA. b. How do you suppose a particular protein might specifically interact with a particular nucleotide sequence in DNA? That is, how might proteins recognize specific base sequences within the double helix?

Structural complementarity is the key to molecular recognition, a lesson learned in Chapter 1. The principle of structural complementarity is relevant to answering problems \(5,6,7,11,12,\) and 19 The quintessential example of structural complementarity in all of biology is the DNA double helix. What features of the DNA double helix exemplify structural complementarity?

Restriction endonucleases also recognize specific base sequences and then act to cleave the double-stranded DNA at a defined site. Speculate on the mechanisms by which this sequence recognition and cleavage reaction might occur by listing a set of requirements for the process to take place.

The bases of nucleotides and polynucleotides are "information symbols." Their central role in providing information content to DNA and RNA is clear. What advantages might bases as "information symbols" bring to the roles of nucleotides in metabolism?

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