Nucleic Acids 2: Videos & Practice Problems

Nucleic acids, such as DNA and RNA, are polymers of nucleotides linked by phosphodiester bonds. DNA strands are anti-parallel, with a 5' phosphate end and a 3' hydroxyl end. DNA is more stable than RNA due to the absence of a reactive 2' hydroxyl group. Base pairing rules dictate that adenine pairs with thymine (2 H bonds) and guanine pairs with cytosine (3 H bonds), leading to consistent DNA width. This complementary nature ensures that DNA is 50% purines and 50% pyrimidines, crucial for genetic information transmission.

Nucleic Acids 2

Nucleic acids, such as DNA and RNA, are polymers made up of nucleotide monomers linked by phosphodiester bonds. In DNA, the strands are anti-parallel, meaning they run in opposite directions. This is characterized by the 5' and 3' ends of the strands, where the 5' end has a phosphate group attached to the 5' carbon of the pentose sugar, and the 3' end has a hydroxyl group attached to the 3' carbon. The anti-parallel nature can be visualized as two arrows pointing in opposite directions, emphasizing the structural orientation of the strands.

RNA is generally less stable than DNA due to the presence of a reactive 2' hydroxyl group, which can lead to self-reactivity and strand breakage, making DNA the preferred genetic material for most life forms. While some viruses utilize RNA for genetic information, DNA's stability is a significant evolutionary advantage. The absorption of light by nucleotides occurs maximally at 260 nanometers, which is crucial for distinguishing between nucleic acids and proteins, as proteins absorb light at 280 nanometers. This property allows biochemists to isolate DNA from cellular samples effectively.

The two strands of DNA are complementary, adhering to specific base pairing rules: adenine pairs with thymine (forming two hydrogen bonds), and guanine pairs with cytosine (forming three hydrogen bonds). This specificity results in DNA strands with higher guanine-cytosine (GC) content having higher melting temperatures due to the increased number of hydrogen bonds. While RNA is typically single-stranded, it can form double-stranded structures and base pair with DNA during transcription, where adenine pairs with uracil instead of thymine.

In terms of nucleotide composition, DNA consists of 50% purines (adenine and guanine) and 50% pyrimidines (thymine and cytosine), ensuring a consistent width of the double helix. For example, if a double-stranded DNA molecule contains 35% adenine, it will also contain 35% thymine, while 15% cytosine will correspond to 15% guanine. This complementary nature of base pairing is fundamental to the transmission of genetic information within cells.

Here’s what students ask on this topic:

What are phosphodiester bonds and how do they function in nucleic acids?

Phosphodiester bonds are the linkages between nucleotide monomers in nucleic acid polymers like DNA and RNA. These bonds form between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next nucleotide. This creates a sugar-phosphate backbone that is essential for the structure of nucleic acids. In DNA, these bonds contribute to the stability and integrity of the double helix, while in RNA, they are part of the single-stranded structure. The formation of phosphodiester bonds is catalyzed by enzymes like DNA polymerase during DNA replication and RNA polymerase during transcription.

Why are DNA strands described as anti-parallel?

DNA strands are described as anti-parallel because they run in opposite directions. One strand runs from the 5' to 3' direction, while the complementary strand runs from 3' to 5'. This orientation is crucial for the proper base pairing and the overall stability of the DNA double helix. The 5' end of a DNA strand has a phosphate group attached to the 5' carbon of the sugar, while the 3' end has a hydroxyl group attached to the 3' carbon. This anti-parallel arrangement allows for the complementary base pairing of adenine with thymine and guanine with cytosine.

How does the stability of DNA compare to RNA, and why?

DNA is more stable than RNA primarily due to the absence of a 2' hydroxyl group in its sugar component. In RNA, the presence of the 2' hydroxyl group makes it more reactive and susceptible to hydrolysis, especially under alkaline conditions. This increased reactivity can lead to strand breakage. DNA's stability is further enhanced by its double-stranded structure, which provides additional protection against chemical and enzymatic degradation. This stability is one reason why DNA is the preferred molecule for long-term genetic information storage in most organisms.

What is the significance of base pairing rules in DNA?

Base pairing rules in DNA are crucial for maintaining the structure and function of the molecule. Adenine (A) pairs with thymine (T) via two hydrogen bonds, and guanine (G) pairs with cytosine (C) via three hydrogen bonds. These specific pairings ensure that the DNA double helix has a consistent width and that genetic information can be accurately copied during DNA replication. The complementary nature of base pairing also allows for the accurate transcription of DNA into RNA, which is essential for protein synthesis. These rules are fundamental to the fidelity of genetic information transmission.

How can you determine the presence of DNA versus protein using spectrophotometry?

To determine the presence of DNA versus protein using spectrophotometry, you measure the absorbance of your sample at specific wavelengths. DNA absorbs light maximally at 260 nm, while proteins absorb maximally at 280 nm, primarily due to the amino acids tryptophan and tyrosine. By running your sample through a spectrophotometer and observing the absorbance peaks, you can distinguish between DNA and protein. If the sample shows a peak at 260 nm and not at 280 nm, it indicates the presence of DNA with minimal protein contamination. This method is widely used in molecular biology for nucleic acid purification and quantification.