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Campbell Biology: Molecular Diversity of Life (DNA) & Gene Expression

General Concepts: Life's Information System and Gene Expression

This chapter delves into the intricate molecular diversity of life, focusing specifically on deoxyribonucleic acid (DNA) as the central repository of genetic information and its crucial role in gene expression. It meticulously covers the fundamental structures of both DNA and ribonucleic acid (RNA), defines the concept of a gene as a functional unit, and details the complex processes of transcription and translation. A paramount theme explored is the direct mechanistic link between genetic variation (differences in DNA sequences) and phenotypic variation (observable traits), which serves as the foundational engine driving evolutionary change across all life forms.

Core Knowledge Requirements

  • General structure of DNA and RNA: A comprehensive understanding of the chemical building blocks (nucleotides) and their polymeric organization into strands, including the distinct sugar-phosphate backbones and differing nitrogenous bases, which dictate their unique roles.

  • The gene: Grasping the definition of a gene as a specific segment of DNA that encodes functional products, typically proteins or functional RNA molecules, thereby determining an organism's traits.

  • Transcription and translation: A thorough knowledge of the sequential steps involved in these two fundamental processes, from the DNA template to the final protein product, and their significance in the overall flow of genetic information (the Central Dogma).

Key Concepts to Consider

  • Genetic variation leads to phenotype variation: Understanding that alterations in the DNA sequence, such as mutations, epigenetic changes, or chromosomal rearrangements, directly result in changes in gene products (e.g., altered proteins), which in turn manifest as observable differences in an organism's characteristics.

Fundamental Understanding

  • Heritable phenotype variation drives evolution: Recognizing that these differences in traits, when heritable, provide the raw material upon which natural selection acts. Favorable variations enhance survival and reproduction, increasing their prevalence in subsequent generations and leading to the gradual adaptation and diversification of species over time.

Structure of DNA

  • Deoxyribonucleic acid (DNA): This remarkable polymeric molecule is universally recognized as the genetic material that carries all the hereditary instructions for the development, functioning, growth, and reproduction of all known living organisms and many viruses. It is composed of two polynucleotide strands entwined around each other to form a double helix.

  • Historical Data: The elucidation of DNA's double helix structure was a monumental scientific achievement. Rosalind Franklin, a brilliant X-ray crystallographer, played an indispensable role in this discovery. Her meticulous X-ray diffraction technique produced groundbreaking images of DNA fibers. Her most famous image, "Photograph 51," was particularly crucial. This photograph unequivocally showed the helical nature of DNA, its consistent width, and the repetitive distances between stacked bases, providing quantitative data that was essential for understanding its three-dimensional structure. This scientific evidence was instrumental for James Watson and Francis Crick in constructing their famous double helix model in 1953, integrating chemical data with physical structure. Without Franklin's expertise and experimental results, the accurate deduction of DNA's structure would have been significantly delayed.

    • A link to a video explaining this data is provided: https://youtu.be/JiME-W58KpU.

Components of Nucleic Acids

  • Polymers: Nucleic acids, both DNA and RNA, are long chain-like molecules classified as polymers. Specifically, they are known as polynucleotides because their monomeric units are nucleotides.

  • Monomers: Each long polynucleotide chain is constructed from individual repeating units called nucleotides.

  • Nucleotide Composition: Each nucleotide is a complex organic molecule fundamentally consisting of three key components:

    • A nitrogenous (nitrogen-containing) base: These are heterocyclic compounds that contain nitrogen atoms, and are responsible for encoding genetic information.

    • A pentose sugar: A five-carbon sugar that forms the backbone of the nucleic acid. In DNA, this is deoxyribose; in RNA, it is ribose. The carbons are numerically denoted as 1', 2', 3', 4', 5'.

    • One or more phosphate groups: Typically a negatively charged functional group attached to the 5' carbon of the pentose sugar via an ester bond, providing the linking unit in the polynucleotide chain.

  • Nucleoside: This term specifically refers to the combination of a nitrogenous base covalently linked to a pentose sugar (at the 1' carbon) but notably without the phosphate group(s). Examples include adenosine, guanosine, cytidine, uridine, and deoxythymidine.

Nitrogenous Bases

  • Types: The five primary nitrogenous bases found in nucleic acids are Cytosine (C), Thymine (T), Uracil (U), Adenine (A), and Guanine (G).

  • DNA Specific: Thymine (T) is a unique pyrimidine base almost exclusively found in DNA, where it pairs with adenine.

  • RNA Specific: Uracil (U) is a pyrimidine base found exclusively in RNA, where it replaces thymine and pairs with adenine.

  • Both DNA and RNA: Cytosine (C), Adenine (A), and Guanine (G) are purine and pyrimidine bases that are integral components of both DNA and RNA molecules.

  • Categories: Based on their chemical structure, nitrogenous bases are classified into two main groups:

    • Pyrimidines: Characterized by a single six-membered ring structure. These include Cytosine (C), Thymine (T, found in DNA), and Uracil (U, found in RNA).

    • Purines: Distinguished by a double-ring structure, consisting of a six-membered ring fused to a five-membered ring. These include Adenine (A) and Guanine (G).

Pentose Sugars

  • DNA Sugar: The sugar component in DNA is deoxyribose. Its distinguishing feature from ribose is the presence of a hydrogen atom (H) at the 2' carbon position, rather than a hydroxyl group (OH).

  • RNA Sugar: The sugar component in RNA is ribose. It has a hydroxyl group (OH) attached to the 2' carbon, making it more reactive and less stable than deoxyribose.

Nucleotide Polymers

  • Covalent Bonds: Individual nucleotides are linked together in a specific orientation to form a polynucleotide chain. This linkage occurs via phosphodiester bonds, which are covalent bonds formed between the phosphate group of one nucleotide (attached to its 5' carbon) and the hydroxyl group of the 3' carbon of the next nucleotide. This repeating sugar-phosphate-sugar-phosphate chain forms the strong sugar-phosphate backbone of the nucleic acid, from which the nitrogenous bases project laterally.

    • A polynucleotide strand is directional, possessing a distinct 5' end (where a phosphate group is typically attached to the 5' carbon of the terminal sugar) and a 3' end (where an unlinked hydroxyl group is present on the 3' carbon of the terminal sugar). This directionality is crucial for DNA replication and transcription.

  • DNA Double Helix: The functional form of DNA typically consists of two such polynucleotide strands wound around a common axis, forming the iconic double helix structure. These two strands are held together by relatively weak hydrogen bonds that form specifically between complementary nitrogenous bases residing on opposite strands.

    • Complementary Base Pairing: This is a fundamental rule in DNA structure and function:

      • Adenine (A) always forms two hydrogen bonds with Thymine (T).

      • Guanine (G) always forms three hydrogen bonds with Cytosine (C). This stronger pairing (three H-bonds) contributes to the stability of G-C rich regions.

    • Structural Dimensions: The physical characteristics of the DNA double helix are remarkably consistent:

      • The overall width (diameter) of the DNA double helix is approximately 2 \text{ nm}.

      • Each base pair (A-T or G-C) is stacked relatively flat, with a vertical separation of approximately 0.34 \text{ nm} between adjacent base pairs.

      • One complete helical turn of the DNA molecule spans approximately 3.4 \text{ nm} along its axis, which typically encompasses about 10 base pairs per turn. This helical arrangement creates major and minor grooves on the surface of the molecule, which are important for protein binding.

Example Problem: Complementary Strand

Given a DNA strand sequence: 5'-TAGGCCT-3'. The complementary strand would be:

  1. Determine the complementary sequence: Based on base pairing rules (A with T, G with C), the complementary bases are A T C C G G A.

  2. Orient the complementary strand: Due to the antiparallel nature of the DNA double helix (where one strand runs 5' to 3' and the other runs 3' to 5'), if the given strand is 5'-TAGGCCT-3', its complementary strand must be oriented 3'-ATCCGGA-5'. To express this in the standard 5' to 3' direction, we read it from right to left, resulting in 5'-AGGCCAT-3'.

  3. Are these two strands the same?: No. They are complementary (meaning their bases pair up according to the rules) but are not identical. This is due to the specific base pairing rules (A with T, G with C) and their antiparallel orientation, where one strand is essentially a