BIO 414 — Molecular Biology: Lecture Note

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This is the complete lecture note for BIO 414 Molecular Biology. You can read it online below, open it in the full viewer, or download the PDF for offline study. It pairs with the course's video lectures, so you can read and watch together.

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BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS Course code: BIO 414 Course title: Molecular Biology Course credit load: 2 Units Series 1: DNA Structure and Roles • Part 1.1: The Chemical Nature of DNA o Sub Part 1.1.1: Nucleotides and nucleosides o Sub Part 1.1.2: Phosphodiester bonds and the sugar-phosphate backbone o Sub Part 1.1.3: Chargaff's rules • Part 1.2: The Double Helix o Sub Part 1.2.1: Watson and Crick's model o Sub Part 1.2.2: Base pairing and stabilising forces o Sub Part 1.2.3: Forms of DNA: B, A, and Z helices • Part 1.3: DNA Organisation in Cells o Sub Part 1.3.1: Prokaryotic DNA organisation o Sub Part 1.3.2: Eukaryotic chromatin structure o Sub Part 1.3.3: Levels of chromatin compaction • Part 1.4: Roles of DNA o Sub Part 1.4.1: DNA as the genetic material o Sub Part 1.4.2: The central dogma o Sub Part 1.4.3: DNA in evolution and heredity

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS Introduction Molecular biology is the study of biological processes at the molecular level, with particular emphasis on the structure and function of nucleic acids and proteins. DNA (deoxyribonucleic acid) is the molecular repository of genetic information in all living organisms and most viruses. Understanding the chemical structure of DNA, how it is packaged in cells, and the multiple roles it plays is fundamental to all of molecular biology. This opening Series covers the chemistry of the DNA molecule: the nucleotide building blocks, the phosphodiester backbone, Chargaff's base composition rules, the Watson-Crick double helix model, the forces that stabilise the helix, the alternative helical forms, the organisation of DNA in prokaryotic and eukaryotic cells, and the fundamental roles of DNA as the carrier of genetic information and the template for gene expression. All subsequent Series build directly on this foundation. Series Learning Outcomes Upon completing this Series, you should be able to: • SLO 1.1 describe the chemical composition of a nucleotide and distinguish between a nucleoside and a nucleotide (Linked to Part 1.1), • SLO 1.2 explain how nucleotides are joined by phosphodiester bonds to form a polynucleotide chain (Linked to Part 1.1), • SLO 1.3 state Chargaff's rules and explain their significance for DNA structure (Linked to Part 1.1), • SLO 1.4 describe the Watson-Crick double helix model and the forces that stabilise it (Linked to Part 1.2), • SLO 1.5 describe the organisation of DNA in prokaryotic and eukaryotic cells (Linked to Part 1.3), and • SLO 1.6 state the roles of DNA including its function in the central dogma of molecular biology (Linked to Part 1.4).

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS 1.1 The Chemical Nature of DNA 1.1.1 Nucleotides and nucleosides DNA is a polymer composed of monomeric units called deoxyribonucleotides. Each deoxyribonucleotide consists of three components: (1) a pentose sugar, specifically deoxyribose (2-deoxyribose), which lacks the hydroxyl group at the 2' carbon present in ribose; (2) a nitrogenous base, which may be a purine (adenine, A, or guanine, G) or a pyrimidine (cytosine, C, or thymine, T); (3) one to three phosphate groups attached to the 5' carbon of the sugar. A nucleoside is the combination of a nitrogenous base and a deoxyribose sugar without the phosphate group: the four DNA nucleosides are deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine. A nucleotide is a nucleoside with one or more phosphate groups: deoxyadenosine 5'-monophosphate (dAMP), deoxyguanosine 5'-monophosphate (dGMP), deoxycytidine 5'-monophosphate (dCMP), and thymidine 5'-monophosphate (dTMP). The triphosphate forms (dATP, dGTP, dCTP, dTTP) are the substrates used during DNA synthesis. Fill in the blank: A ________ is a nucleoside without a phosphate group; a nucleotide is a nucleoside with one or more phosphate groups; the four DNA nucleosides are deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine.

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS Figure 1.1: Structure of DNA nucleotides and nucleosides 1.1.2 Phosphodiester bonds and the sugar-phosphate backbone Nucleotides in a DNA strand are joined covalently by phosphodiester bonds. A phosphodiester bond forms when the phosphate group at the 5' position of one nucleotide is joined to the hydroxyl group at the 3' position of the preceding nucleotide, with elimination of pyrophosphate. The result is a linear polynucleotide chain with a repeating sugar-phosphate backbone and the nitrogenous bases extending as side groups from the 1' carbon of each sugar. The DNA chain has directionality: one end terminates with a free 5' phosphate (the 5' end) and the other with a free 3' hydroxyl (the 3' end). By convention, DNA sequences are written 5' to 3' (left to right). The backbone is negatively charged at physiological pH because the phosphate groups carry a negative charge; this charge is partly neutralised by positively charged proteins (histones in eukaryotes; histone-like proteins in prokaryotes) in chromatin.

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS Fill in the blank: A ________ bond links the 5' phosphate of one deoxyribonucleotide to the 3' hydroxyl of the preceding nucleotide; these bonds form the sugar-phosphate backbone of the DNA chain; DNA chains have a 5' end and a 3' end. 1.1.3 Chargaff's rules In the late 1940s, Erwin Chargaff analysed the base composition of DNA from many organisms using paper chromatography. His two fundamental observations, now known as Chargaff's rules, are: (1) The base composition of DNA varies between species (different organisms have different A+T:G+C ratios); (2) within any given organism or tissue, the molar amount of adenine always equals the molar amount of thymine (A = T), and the molar amount of guanine always equals the molar amount of cytosine (G = C), such that purines (A+G) equal pyrimidines (T+C). Significance of Chargaff's rules: (1) The 1:1 ratio of purines to pyrimidines (A+G = T+C) suggested a structural pairing of purines with pyrimidines in the DNA molecule; (2) the specific pairing A = T and G = C provided the key empirical evidence for the Watson-Crick model of complementary base pairing; (3) the variation in base composition between species demonstrates that the sequence of bases (rather than any fixed composition) carries biological information. Chargaff's rules apply to double-stranded DNA; they do not apply to single-stranded DNA, RNA, or the individual strands of a double helix. Fill in the blank: Chargaff's first rule states that A = T and G = C in double-stranded DNA; Chargaff's second rule states that the base composition of DNA ________ between species, demonstrating that base sequence carries biological information. Pilot questions 1.1 1. State the three components of a deoxyribonucleotide. 2. Distinguish between a nucleoside and a nucleotide. 3. Explain how phosphodiester bonds are formed and what they connect. 4. State Chargaff's two rules. 5. Explain the significance of Chargaff's rules for DNA structure.

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS 1.2 The Double Helix 1.2.1 Watson and Crick's model In 1953, James Watson and Francis Crick proposed the double helix model of DNA, building on X-ray crystallographic data produced by Rosalind Franklin and Maurice Wilkins. The key features of the Watson-Crick model are: (1) Two antiparallel polynucleotide strands wound around a common central axis in a right-handed helix; the strands are antiparallel (one runs 5' to 3', the other 3' to 5'); (2) The sugar-phosphate backbones are on the outside of the helix; (3) The nitrogenous bases are on the inside, stacked perpendicular to the helix axis. B-form DNA (the predominant form under physiological conditions) has the following dimensions: the helix makes one complete turn every 10 base pairs (34 angstroms or 3.4 nm); the diameter of the helix is 20 angstroms (2 nm); the rise per base pair is 3.4 angstroms; the helix contains two grooves of unequal width: the major groove (approximately 12 angstroms wide) and the minor groove (approximately 6 angstroms wide). Protein-DNA interactions, including those of transcription factors and restriction enzymes, occur predominantly through the major groove, where base-specific information is more accessible. Fill in the blank: In the Watson-Crick double helix, the two polynucleotide strands are ________ (running in opposite 5'-to-3' directions); the backbones are on the outside and the bases are stacked on the inside.

BIO la-NET | ONLINE LEARNING VIDEO PLATFORM FOR POST-SECONDARY & HIGHER INSTITUTION STUDENTS Figure 1.2: The Watson-Crick double helix model 1.2.2 Base pairing and stabilising forces Complementary base pairing is the specific, non-covalent hydrogen bonding between bases on opposite strands: adenine pairs with thymine (A-T) through two hydrogen bonds; guanine pairs with cytosine (G-C) through three hydrogen bonds. The specificity of A-T and G-C pairing (not A-C or G-T) arises from the geometric complementarity (the two bases fit precisely in the space between the backbones) and the correct donor-acceptor alignment of hydrogen bond groups. This pairing rule is responsible for the complementarity of the two strands. Forces stabilising the double helix: (1) Hydrogen bonds between complementary base pairs (A-T: 2; G-C: 3); (2)

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