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Organic Chemistry
Table of Contents
Unit 28 Overview: Biomolecules
28.1 Nucleotides and Nucleic Acids
28.2 Base Pairing in DNA
28.3 Replication of DNA
28.4 Transcription of DNA
28.5 Translation of RNA: Protein Biosynthesis
28.6 DNA Sequencing
28.7 DNA Synthesis
28.8 The Polymerase Chain Reaction

DNA replication is a crucial process that ensures genetic information is accurately copied before cell division. This complex mechanism involves multiple enzymes and proteins working together to unwind, copy, and reassemble DNA strands.

The semiconservative nature of DNA replication means each new double helix contains one original strand and one newly synthesized strand. This process occurs differently on leading and lagging strands due to DNA's antiparallel structure and the directionality of DNA polymerase.

DNA Replication

Process of DNA replication

  • Begins at specific sites called origins of replication where the two strands of the DNA double helix separate
  • Helicase unwinds and separates the two strands by breaking the hydrogen bonds between complementary base pairs (adenine-thymine, guanine-cytosine)
    • Single-stranded binding proteins (SSBs) bind to the single-stranded DNA to prevent the strands from reannealing and maintain stability
    • Topoisomerase relieves the tension caused by unwinding of the DNA helix
  • DNA primase synthesizes short RNA primers complementary to the single-stranded DNA template which provide a starting point for DNA synthesis
  • DNA polymerase III is the main enzyme that synthesizes new DNA strands in the 5' to 3' direction by adding nucleotides complementary to the single-stranded DNA template
    • Requires a primer (RNA or DNA) to initiate synthesis
  • DNA polymerase I replaces the RNA primers with DNA nucleotides to create a continuous DNA strand
  • DNA ligase seals the nicks between the newly synthesized DNA fragments to create a continuous strand

Semiconservative nature of replication

  • Each newly synthesized DNA double helix contains one original (parental) strand and one newly synthesized (daughter) strand
  • During replication, the two parental DNA strands separate and each serves as a template for the synthesis of a new complementary strand
  • The newly synthesized daughter strands are complementary to their respective parental strands resulting in two DNA double helices that are identical to each other and to the original DNA molecule
  • Demonstrated by the Meselson-Stahl experiment using density labeling with heavy nitrogen ($^{15}N$) to distinguish between parental and newly synthesized DNA strands

Leading vs lagging strand synthesis

  • DNA replication is bidirectional with two replication forks moving away from the origin of replication
  • At each replication fork, the two DNA strands are synthesized differently due to the antiparallel nature of DNA and the 5' to 3' directionality of DNA polymerase
  • The leading strand is synthesized continuously in the 5' to 3' direction, in the same direction as the movement of the replication fork
    • DNA polymerase III can synthesize the leading strand continuously because it extends the primer in the same direction as the replication fork movement
  • The lagging strand is synthesized discontinuously in short fragments called Okazaki fragments
    • DNA polymerase III synthesizes the lagging strand in the 5' to 3' direction, but in the opposite direction of the replication fork movement
    • RNA primase lays down multiple RNA primers along the lagging strand template
    • DNA polymerase III extends these primers, forming Okazaki fragments which are typically 100-200 nucleotides long in eukaryotes and 1000-2000 nucleotides long in prokaryotes
  • DNA polymerase I removes the RNA primers and replaces them with DNA nucleotides
  • DNA ligase joins the Okazaki fragments together, creating a continuous lagging strand

DNA Structure and Replication Components

  • DNA is composed of nucleotides, which consist of a deoxyribose sugar, a phosphate group, and a nitrogenous base
  • Base pairing occurs between complementary bases (adenine with thymine, guanine with cytosine) through hydrogen bonding
  • The two strands of DNA are antiparallel, running in opposite directions (5' to 3' and 3' to 5')
  • Phosphodiester bonds connect adjacent nucleotides, forming the sugar-phosphate backbone of each DNA strand

Key Terms to Review (29)

Replication forks: Replication forks are Y-shaped structures that form as the DNA double helix is separated into two single strands during DNA replication, allowing each strand to serve as a template for the synthesis of a new complementary strand. They are essential for the accurate and efficient copying of the entire genome before cell division.
Lagging strand: The lagging strand is one of the two strands of DNA at the replication fork that is synthesized discontinuously in short segments known as Okazaki fragments, opposite to the direction of the replication fork. This process occurs because DNA polymerase can only add nucleotides in a 5' to 3' direction, necessitating a more complex synthesis for the lagging strand.
Semiconservative replication: Semiconservative replication is the method by which DNA duplicates itself before cell division, ensuring each new cell receives an exact copy of the DNA. In this process, each original strand serves as a template for a new complementary strand, resulting in two DNA molecules that each contain one original and one newly synthesized strand.
Leading strand: The leading strand in DNA replication is the strand of new DNA which is synthesized continuously towards the replication fork. It is created by the enzyme DNA polymerase adding nucleotides in the direction of 5' to 3'.
Okazaki fragments: Okazaki fragments are short sequences of DNA nucleotides synthesized discontinuously and later joined together to form the lagging strand during DNA replication. They are essential for replicating the antiparallel strand of the double helix.
Deoxyribose: Deoxyribose is a monosaccharide, a type of simple sugar, that serves as the primary structural component of the backbone of deoxyribonucleic acid (DNA) molecules. It is an essential building block for the genetic material found in all living organisms.
DNA Ligase: DNA ligase is an enzyme that catalyzes the formation of phosphodiester bonds between adjacent DNA fragments, effectively sealing breaks in the DNA backbone. It is a crucial enzyme involved in various DNA repair and replication processes.
Single-Stranded Binding Proteins: Single-stranded binding proteins (SSBs) are a class of proteins that bind to and stabilize single-stranded DNA (ssDNA) molecules during key cellular processes such as DNA replication, repair, and recombination. These proteins play a crucial role in maintaining the integrity and functionality of the genetic material.
Semiconservative Replication: Semiconservative replication is the process by which DNA is replicated in a way that produces two new DNA molecules, each containing one original strand and one newly synthesized strand. This ensures the accurate transmission of genetic information to daughter cells during cell division.
Meselson-Stahl Experiment: The Meselson-Stahl experiment was a landmark study that provided experimental evidence for the semi-conservative replication of DNA, demonstrating that DNA replicates in a way where the two strands of the double helix separate and each serve as a template for the synthesis of a new complementary strand.
Origins of Replication: The origins of replication refer to the specific locations on a DNA molecule where DNA replication is initiated. These are the sites on the DNA where the replication process begins, allowing for the duplication of the genetic material during cell division.
Antiparallel Strands: Antiparallel strands refer to the orientation of the two complementary DNA strands that make up the DNA double helix. The two strands run in opposite directions, with one strand running in the 5' to 3' direction and the other running in the 3' to 5' direction, forming an antiparallel arrangement that is crucial for the replication and transcription of genetic information.
DNA primase: DNA primase is an enzyme responsible for synthesizing short RNA primers that are required to initiate DNA replication. It plays a crucial role in the replication of DNA, ensuring that the process can occur efficiently and accurately.
DNA Polymerase III: DNA polymerase III is the primary enzyme responsible for the replication of DNA during the process of cell division. It is a highly accurate and efficient enzyme that plays a crucial role in ensuring the faithful duplication of genetic information as cells divide and proliferate.
5' to 3' Directionality: 5' to 3' directionality refers to the orientation of DNA and RNA molecules, where the 5' (five prime) end of a nucleic acid strand is distinct from the 3' (three prime) end. This directionality is crucial for various biological processes, including DNA replication, transcription, and translation.
Leading Strand: The leading strand is the continuously synthesized DNA strand during DNA replication. It is the strand that is replicated in the 5' to 3' direction, moving along the DNA template as the replication fork progresses.
Nucleotides: Nucleotides are the basic structural units of nucleic acids, such as DNA and RNA. They consist of a nitrogenous base, a five-carbon sugar, and one to three phosphate groups. Nucleotides play crucial roles in various biological processes, including energy transfer, cell signaling, and the genetic storage and transmission of information.
Helicase: Helicase is a class of enzymes that play a crucial role in the replication of DNA by unwinding the double-stranded DNA molecule, separating the two strands to allow other enzymes to access and copy the genetic information.
Daughter Strand: The daughter strand refers to the newly synthesized strand of DNA that is produced during the process of DNA replication. It is the complementary copy of the original or parent DNA strand that serves as the template for the replication process.
Okazaki Fragments: Okazaki fragments are short, discontinuous DNA sequences that are synthesized during the lagging strand replication of DNA. They are named after the Japanese scientist Reiji Okazaki, who first described this process in the 1960s.
Topoisomerase: Topoisomerase is an essential enzyme involved in the replication and transcription of DNA. It functions by introducing temporary breaks in the DNA backbone, allowing the strands to unwind and relieve the torsional stress that builds up during these crucial cellular processes.
Parental Strand: The parental strand refers to the original DNA molecule that serves as the template for DNA replication during the process of DNA replication. It is one of the two strands that make up the double-helix structure of DNA and provides the blueprint for the synthesis of new, complementary DNA strands.
DNA Replication: DNA replication is the process by which a double-stranded DNA molecule is duplicated to produce two identical copies. It is a fundamental biological process that ensures the accurate transmission of genetic information from one generation to the next.
RNA Primers: RNA primers are short sequences of ribonucleic acid (RNA) that serve as starting points for DNA replication. They are synthesized by the enzyme primase and provide a free 3' hydroxyl group for DNA polymerase to begin the process of DNA synthesis.
Phosphodiester Bonds: Phosphodiester bonds are the covalent chemical bonds that link the sugar and phosphate groups together to form the backbone of nucleic acid molecules, such as DNA and RNA. These bonds are essential for the structural integrity and function of these biomolecules.
Base Pairing: Base pairing is the fundamental mechanism that allows for the accurate replication and transcription of genetic information in living organisms. It describes the specific interactions between the nitrogenous bases that make up the DNA and RNA molecules, which are essential for maintaining the double-helix structure of DNA and the proper coding of genetic information.
Lagging Strand: The lagging strand refers to the discontinuous synthesis of one of the two new DNA strands during DNA replication. It is the strand that is replicated in the opposite direction to the movement of the replication fork.
Replication Fork: The replication fork is a key structure that forms during the process of DNA replication, where the double-stranded DNA molecule is unwound and replicated to produce two identical copies of the genetic material. The replication fork is the point where the separation and duplication of the DNA strands occur.
DNA polymerase I: DNA polymerase I is an enzyme responsible for the replication and repair of DNA in prokaryotic organisms. It plays a crucial role in the process of DNA replication by synthesizing new DNA strands complementary to the original template.