Nucleic acids (article) | Khan Academy
The nucleic acids, which include deoxyribonucleic acid, or DNA, and to take up the building blocks of nucleic acids, called nucleotides, from the digestive tract. Question 1 Answer a) In a simple way, the relationship between the nucleotide, nucleic acid and DNA is as follows. The group or polymer of nucleotides is called . The particular name for the units of nucleic acids are called nucleotides and each contains three things: a phosphate group, a sugar.
Properties of DNA Deoxyribonucleic acid, or DNA, chains are typically found in a double helix, a structure in which two matching complementary chains are stuck together, as shown in the diagram at left. The sugars and phosphates lie on the outside of the helix, forming the backbone of the DNA; this portion of the molecule is sometimes called the sugar-phosphate backbone. The nitrogenous bases extend into the interior, like the steps of a staircase, in pairs; the bases of a pair are bound to each other by hydrogen bonds.
Structural model of a DNA double helix. This is referred to as antiparallel orientation and is important for the copying of DNA.
So, can any two bases decide to get together and form a pair in the double helix? The answer is a definite no. Because of the sizes and functional groups of the bases, base pairing is highly specific: A can only pair with T, and G can only pair with C, as shown below.
This means that the two strands of a DNA double helix have a very predictable relationship to each other. This allows each base to match up with its partner: The A-T pairs are connected by two hydrogen bonds, while the G-C pairs are connected by three hydrogen bonds.
When two DNA sequences match in this way, such that they can stick to each other in an antiparallel fashion and form a helix, they are said to be complementary. Hydrogen bonding between complementary bases holds DNA strands together in a double helix of antiparallel strands. Thymine forms two hydrogen bonds with adenine, and guanine forms three hydrogen bonds with cytosine. Image modified from OpenStax Biology.
A nucleotide in an RNA chain will contain ribose the five-carbon sugarone of the four nitrogenous bases A, U, G, or Cand a phosphate group. Here, we'll take a look at four major types of RNA: The transcript carries the same information as the DNA sequence of its gene. Once an mRNA has been produced, it will associate with a ribosome, a molecular machine that specializes in assembling proteins out of amino acids.
The tRNA that binds, and thus the amino acid that's added, at a given moment is determined by the sequence of the mRNA that is being "read" at that time. Some rRNAs also act as enzymes, meaning that they help accelerate catalyze chemical reactions — in this case, the formation of bonds that link amino acids to form a protein.
In this framework, binding specificity and an appreciable level of interaction appear primarily at the level of longer mRNA and protein stretches. Moreover, we have derived interaction preference scales for nucleobases and amino-acid sidechains by analyzing binding interfaces in a large set of 3D structures of RNA—protein complexes By comparing the nucleobase-content profiles of mRNA sequences with the nucleobase-preference-weighted profiles of their cognate protein sequences, we have found strong evidence for the complementarity hypothesis, but also demonstrated exceptions from it in some cases.
For example, we found that purine density in mRNA sequences correlates directly with guanine preference profiles of their cognate protein sequences, yet inversely with the equivalent adenine preference profiles. Sidechain analogs have been widely used instead of complete amino acids for testing the interaction specificity of amino-acid residues in different contexts 2026 There are several advantages to such a choice.
First, zwitterionic amino acids contain charged groups which, apart from the N- and C-terminal residues, are not present in proteins. Second, capping of amino acids necessarily introduces groups that do not represent the actual protein backbone.
What is the relationship between the nucleotides, nucleic acids, and DNA? | Socratic
Finally, sidechain analogs have been used to parameterize GROMOS 54a8, arguably the most accurate classical force field when it comes to capturing amino-acid hydrophobicity 40 On the other hand, a clear disadvantage of using sidechain analogs is that glycine and proline cannot be treated in the same way as other amino acids.
Moreover, it has been shown that the backbone contribution to amino-acid solvation free energies does vary between different amino acids because of self-solvation effects However, as self-solvation arises primarily in the gas phase 42this becomes less relevant in our context.
In order to study the effect of the environment on the binding preferences, our US simulations are performed in both water and methanol. The latter is chosen based on its lower dielectric constant, which is expected to capture the environment at nucleic acid-protein interfaces more accurately than pure water 43 Here, we apply the newly obtained binding preferences to study the putative physico-chemical foundation of the universal genetic code and critically examine the cognate mRNA—protein complementarity hypothesis 36 — In this manner, 18 out of the 20 natural occurring amino acids could be studied all except glycine and proline.
The amino acids arginine, aspartate, glutamate, lysine and histidine were represented in their charged forms at pH 7. Further details concerning MD are given in Supplementary Information. Umbrella sampling The reaction coordinate r for the potential of mean force was defined as the distance between the center of geometry cog of the nucleobase and the cog of the amino-acid sidechain analog.
The restraining simulations were performed sequentially, i.