DNA Replication

DNA replication is more complex than simply unzipping the double helix and making new complementary strands. Replication starts from the origin of replication—the point at which the DNA unzips.

DNA replication

DNA is made up of two polynucleotide strands that form a double helix.
During DNA replication, each of the two strands are used as a template from which new strands are copied.
DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available.
- A lot of our understanding of DNA replication has come from studying the process in E. coli.

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Semi-conservative model

After replication, the new DNA is made up of one original polynucleotide strand and a new, complementary strand.
This explains why DNA replication is described as semi-conservative because one original strand is conserved.

The process of replication (1)

How does the replication machinery know where to begin?
It turns out that there are specific nucleotide sequences called origins of replication where replication begins.
- In E. coli, which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences.
The origin of replication is recognized by certain proteins that bind to this site.

The process of replication (2)

An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs.
- ATP hydrolysis is required for this process.
As the DNA opens up, Y-shaped structures called replication forks are formed.
Two replication forks are formed at the origin of replication and these get extended bi-directionally as replication proceeds.
Single-strand binding proteins coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix.

The process of replication (3)

DNA polymerase is able to add nucleotides only in the 5' to 3' direction (a new DNA strand can be only extended in this direction).
It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide.
This essentially means that it cannot add nucleotides if a free 3'-OH group is not available.
- How does it add the first nucleotide? The problem is solved with the help of a primer.

The process of replication (4)

Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA.
Because this sequence primes the DNA synthesis, it is appropriately called the primer.
DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand.

DNA Replication - Continued

Once the replication fork has been formed, the DNA is divided into the "leading" and "lagging" strands. These require different approaches for replication.

The process of replication (5)

DNA polymerase can only extend in the 5' to 3' direction, which poses a slight problem at the replication fork.
- As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction.
- The leading strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in the 5'-3' direction.

The process of replication (5)

The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments.
These fragments are known as Okazaki fragments, each requiring a primer to start the synthesis.
- The leading strand by comparison only requires one primer. -Okazaki fragments are named after the Japanese scientist who first discovered them.
The strand with the Okazaki fragments is known as the lagging strand.

The process of replication (6)

The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'.
A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides.
The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place.
Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it.

The process of replication (7)

As synthesis proceeds, the RNA primers are replaced by DNA.
The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides.
The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA ligase.
- Ligase catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment.

1Cell Biology

2Molecular Biology

2.1Water

2.1.1Water & Hydrogen Bonding

2.1.2IB Multiple Choice - Water & Hydrogen Bonding

2.1.3Extended Response - Water

2.2Carbohydrates & Lipids

2.2.1Monosaccharides

2.2.2Disaccharides & Polysaccharides

2.2.3Triglycerides & Phospholipids

2.2.4Cellulose

2.2.5Starch & Glycogen

2.3Proteins

2.3.1Structure & Functions of Proteins

2.4Enzymes

2.4.1Enzymes

2.4.2Factors Affecting Enzyme Activity

2.4.3Enzyme-Controlled Reactions

2.4.4End of Topic Test - Enzymes

2.5Structure of DNA & RNA

2.5.1DNA & RNA

2.6DNA Replication, Transcription & Translation

2.6.1Protein Synthesis

2.6.2Transcription & Translation

2.6.3End of Topic Test - DNA, Genes & Protein Synthesis

2.6.4Exam-Style Question - Protein Synthesis

2.6.5End of Topic Test - Coronavirus Translation

2.6.6IB Multiple Choice - Transcription

2.6.7IB Multiple Choice - Translation

2.7Cell Respiration

2.7.1Overview of Respiration

2.7.2Anaerobic Respiration

2.7.3End of Topic Test - Anaerobic Respiration

2.7.4Respiration Experiments

2.7.5End of Topic Test - Respiration

2.7.6IB Multiple Choice - Respiration

2.8Photosynthesis

2.8.1Overview of Photosynthesis

3Genetics

4Ecology

4.1Species, Communities & Ecosytems

4.1.1Population Dynamics

4.1.2Communities & Measuring Diversity

4.1.3Relationships Between Populations

4.1.4Overview of Ecosystems

4.1.5Nutrient Cycles

4.1.6Fertilisers

4.1.7Eutrophication

4.1.8Chi-Squared Test

4.2Energy Flow

4.2.1Energy

4.2.2Energy Flow

4.2.3Biomass & Food Chains

4.2.4Heterotrophs & Autotrophs

4.3Carbon Cycle

4.3.1Carbon Cycle

4.4Climate Change

4.4.1Carbon Dioxide

4.4.2The Greenhouse Effect

4.4.3Global Warming

4.4.4Maintaining Biodiversity

5Evolution & Biodiversity

5.1Evidence for Evolution

5.1.1Evidence for Evolution - Fossils & DNA

5.1.2Evidence for Evolution - Anatomy & Geography

5.1.3IB Multiple Choice - Evidence for Evolution

5.1.4Extended Response - DNA & Evolution

5.2Natural Selection

5.2.1Introduction

5.2.2Evolutionary Fitness

5.2.3Natural Selection & Variation

5.2.4End of Topic Quiz - Natural Selection

5.2.5IB Multiple Choice - Natural Selection

5.2.6Speciation

5.3Classification of Biodiversity

5.3.1Introduction to Biodiversity

5.3.2Keystone Species

5.3.3Courtship & Ancestry

5.3.4Classification

5.4Cladistics

5.4.1Evolutionary Relationships

5.4.2IB Multiple Choice - Species & Taxonomy

6Human Physiology

6.1Digestion & Absorption

6.1.1Overview of Digestion

6.1.2Digestion in Mammals

6.1.3Absorption

6.1.4End of Topic Test - Substance Exchange & Digestion

6.1.5End of Topic Test - Substance Ex & Digestion

6.2The Blood System

6.2.1The Circulatory System

6.2.2The Heart

6.2.3Blood Vessels

6.2.4Cardiovascular Disease

6.3Defence Against Infectious Disease

6.3.1Immune System

6.3.2The Immune Response

6.3.3Antibodies

6.3.4Primary & Secondary Response

6.3.5Vaccines

6.3.6HIV

6.3.7End of Topic Test - Immune System

6.3.8Exam-Style Question - Immune System

6.3.9End of Topic Test - Immune System

6.4Gas Exchange

6.4.1Lung Structure & Alveoli

6.4.2Ventilation

6.4.3Lung Disease

6.4.4Lung Disease Data

6.5Neurons & Synapses

6.5.1Neuron Structure

6.5.2Transmission of an Impulse

6.5.3Speed of Transmission

6.5.4End of Topic Test - Neurones & Action Potentials

6.5.5Synapses

6.5.6Types of Synapse

6.5.7Medical Application

6.5.8End of Topic Test - Synapses

6.5.9End of Topic Test - Nervous Comm&Coord

6.6Hormones, HomeoStasis & Reproduction

6.6.1Overview of Homeostasis

6.6.2Blood Glucose Concentration

6.6.3Controlling Blood Glucose Concentration

6.6.4End of Topic Test - Blood Glucose

6.6.5Type I & Type II Diabetes

6.6.6Human Reproductive Systems

6.6.7Hormonal Control of the Menstrual Cycle

7AHL: Nucleic Acids

7.1DNA Structure & Replication

7.1.1DNA

7.1.2RNA

7.1.3DNA Replication

7.1.4DNA Replication - Summary

7.1.5IB Multiple Choice - DNA Replication

7.2Transcription & Gene Expression

7.2.1Introduction to Transcription & Protein Synthesis

7.2.2Types of RNA

7.2.3Transcription

7.2.4RNA Processing in Eukaryotes

7.2.5IB Multiple Choice - Transcription

7.3Translation

7.3.1Translation

7.3.2Retroviruses

7.3.3Scientific Practices: Coronavirus

7.3.4IB Multiple Choice - Translation

8AHL: Metabolism, Cell Respiration & Photosynthesis

8.1Metabolism

8.1.1Molecules to Metabolism

8.2Cell Respiration

8.2.1Glycolysis

8.2.2Aerobic Respiration

8.3Photosynthesis

8.3.1Light-Dependent Reaction

8.3.2Light-Independent Reaction

8.3.3End of Topic Test - Photosynthesis Reactions

8.3.4Limiting Factors

8.3.5Photosynthesis Experiments

8.3.6End of Topic Test - Photosynthesis

8.3.7End of Topic Test - Photosynthesis

9AHL: Plant Biology

9.1Transport in the Xylem of Plants

9.1.1Structure

9.1.2Cohesion-Tension Theory

9.1.3Investigating Transpiration Rate

9.2Transport in the Phloem of Plants

9.2.1Structure

9.2.2Translocation

9.3Growth in Plants

9.3.1Plant Tropisms

10AHL: Genetics & Evolution

10.1Meiosis

10.1.1Stages of Meiosis

10.2Inheritance

10.2.1Linked Genes

10.2.2Sex-Linked Genes

10.2.3Non-Nuclear Inheritance

10.2.4Chi-Squared Test

10.2.5End of Topic Quiz - Inheritance

10.2.6IB Multiple Choice - Non-Mendelian Genetics

10.2.7Introduction to Non-Mendelian Inheritance

10.2.8Extended Response - Inheritance

10.2.9Grade 4-5 (Scientific Practices) - Inheritance

10.3Gene Pools & Speciation

10.3.1Populations

10.3.2Mutations, Genetic Drift, & Gene Flow

10.3.3Speciation

10.3.4Rate of Speciation

10.3.5Allopatric & Sympatric Speciation

11AHL: Animal Physiology

11.1Antibody Production & Vaccination

11.1.1Immune System

11.1.2The Immune Response

11.1.3Antibodies

11.1.4Primary & Secondary Response

11.1.5Vaccines

11.2Movement

11.2.1Skeletal Muscle

11.2.2Sliding Filament Theory

11.2.3Contraction

11.3The Kidney & Osmoregulation

11.3.1Kidneys & Osmoregulation

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