Question

Make a concept map (see Bioskills 12 ) that relates DNA's primary structure to its secondary structure. Your diagram should include deoxyribonucleotides, hydrophobic interactions, purines, pyrimidines, phosphodiester linkages, DNA primary structure, DNA secondary structure, complementary base pairing, and antiparallel strands.

Short answer

To create a concept map that relates DNA's primary structure to its secondary structure, start with the central concept of DNA primary structure and connect it to the individual deoxyribonucleotides (A, T, C, G). Indicate that purines and pyrimidines are subcategories of these nucleotides, and show the phosphodiester linkages forming the DNA backbone. Next, create an arrow from the primary structure to the secondary structure, connecting complementary base pairing (A-T and G-C hydrogen bonds) and antiparallel strands (5' to 3' and 3' to 5' orientation) to the secondary structure. Finally, emphasize the stabilizing role of hydrophobic interactions in the secondary structure. This concept map will visually represent the relationship between the primary and secondary structures and the critical terms involved.

Step-by-step solution

Define key terms

Before creating the concept map, it's essential to have a clear understanding of each term: 1. DNA primary structure: The sequence of deoxyribonucleotides along a DNA strand. 2. DNA secondary structure: The three-dimensional arrangement of the DNA double helix formed by complementary base pairing and antiparallel strands. 3. Deoxyribonucleotides: The building blocks of DNA, consisting of a sugar (deoxyribose), a phosphate group, and a nitrogenous base (either purine or pyrimidine). 4. Hydrophobic interactions: Non-covalent interactions between the hydrophobic DNA bases that contribute to the stability of the secondary structure. 5. Purines: The two-ring nitrogenous bases adenine (A) and guanine (G). 6. Pyrimidines: The single-ring nitrogenous bases cytosine (C) and thymine (T). 7. Phosphodiester linkages: Covalent bonds between the phosphate groups and deoxyribose sugar in deoxyribonucleotides, forming the DNA backbone. 8. Complementary base pairing: The specificity of the hydrogen bonds between purines and pyrimidines: A pairs with T, and G pairs with C. 9. Antiparallel strands: The orientation of the two DNA strands in opposite directions (5' to 3' and 3' to 5') in the double helix.

Arrange key terms in a concept map

Now that we have defined the key terms, we can create a concept map representing their connections. The concept map may be drawn as follows: 1. Begin with the central concept: DNA primary structure. 2. Connect the individual deoxyribonucleotides (A, T, C, G) to the primary structure. 3. Show how purines and pyrimidines are subcategories of deoxyribonucleotides. 4. From DNA primary structure, create an arrow to the secondary structure, indicating the relationship between the two. 5. Connect complementary base pairing to the secondary structure, indicating the A-T and G-C hydrogen bonds. 6. Show the phosphodiester linkages as part of the primary structure, connecting the sugars and phosphate groups. 7. Connect antiparallel strands to the secondary structure, indicating the 5' to 3' and 3' to 5' orientation. 8. At last, mention the role of hydrophobic interactions in stabilizing the secondary structure. By following these steps, you will create a concept map that visually represents the relationship between DNA's primary structure and secondary structure, along with the roles of the critical terms involved.

Key concepts

DNA Primary Structure

DNA's primary structure refers to the linear sequence of nucleotides in a DNA strand. Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base. These bases can be either purines or pyrimidines, which are the actual carriers of genetic information. The phosphodiester linkage, a bond formed between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of another, is what allows the sequence to form a long polymer with a distinct directionality from 5' to 3'.

Understanding the primary structure is crucial because any change in the sequence could lead to mutations affecting the organism's phenotype. Hence, the sequence specificity is of utmost importance in DNA's functioning.

DNA Secondary Structure

The DNA secondary structure is what most people are familiar with – the iconic double helix. This is the structure DNA assumes as two strands twist around each other, stabilized by hydrogen bonds between complementary bases and hydrophobic interactions that help shelter the bases from water. Crucially, the strands are antiparallel; one runs 5' to 3' and the other 3' to 5'. This provides a very stable arrangement and forms the structural backdrop for critical biological processes like DNA replication and repair.

Nucleotides

Nucleotides are the building blocks of DNA, each composed of a sugar (deoxyribose), one of four nitrogenous bases (adenine, thymine, cytosine, or guanine), and a phosphate group. These individual components are assembled into a chain through phosphodiester linkages to form one strand of DNA. The order of these nucleotides constitutes the genetic code, which is interpreted by cellular machinery to produce proteins.

Purines and Pyrimidines

The nitrogenous bases come in two forms: purines (adenine and guanine) with a two-ring structure, and pyrimidines (cytosine and thymine) with a single-ring structure. Their particular shapes and sizes are key to the fitting puzzle of DNA structure.

Base Pairing

Base pairing is the specific hydrogen bonding between adenine with thymine and guanine with cytosine in DNA. This principle, known as complementary base pairing, is fundamental because it enables the DNA to copy itself accurately during replication. Every time a cell divides, the base pairing rules ensure that each new cell receives an exact copy of the DNA, without which growth, development, and maintenance of organisms would not be possible.

Phosphodiester Linkage

The phosphodiester linkage is a chemical bond integral to the structure of nucleic acids like DNA. It is the connection between the phosphate group of one nucleotide and the 3' hydroxyl group of the sugar in the next nucleotide, creating a backbone for the DNA strand. This linkage is also responsible for the polarity of DNA, hence dictating the 5' to 3' directionality crucial for DNA replication and transcription.

Antiparallel Strands

DNA strands are antiparallel, meaning they run in opposite directions. This orientation facilitates the base pairing and enables the myriad of enzymes involved in DNA processes, such as DNA polymerase, to function effectively. In the antiparallel structure, while one strand runs from 5' (phosphate-end) to 3' (hydroxyl-end), the other runs from 3' to 5', creating a structure conducive for biological functions like replication and repair.

Hydrophobic Interactions

Hydrophobic interactions play a pivotal role in stabilizing the DNA structure. In an aqueous environment, the water-repelling (hydrophobic) bases in the DNA strand cluster inside the helix, away from the water, while the hydrophilic sugar-phosphate backbone interacts with the aqueous environment. This naturally occurring tendency helps to maintain the integrity of the DNA structure and is a key factor in the formation of the secondary structure of DNA, the double helix.

Purines and Pyrimidines

The purines (adenine and guanine) and pyrimidines (cytosine and thymine) are types of nitrogenous bases found in nucleotides. The structure of these molecules allows them to pair specifically: purines always with pyrimidines. This pairing is facilitated by hydrogen bonding – A with T forming two hydrogen bonds and G with C forming three. Their specific pairing mechanism is crucial for the accuracy of DNA replication and the preservation of genetic information.

Understanding the differences between these two types of bases and their pairing rules is essential for grasping the bigger picture of DNA's role in heredity and genetic expression.