DNA Structure and Antiparallel Configuration

• DNA is antiparallel, meaning one strand runs in the opposite direction to the other, similar to a two-way highway.

• One end is the three prime (3') end, signifying the third carbon atom, while the opposite end is the five prime (5') end, indicating the fifth carbon atom.

• New nucleotides are always added to the three prime (3') end, meaning DNA is synthesized in the five prime to three prime (5' to 3') direction.

• The five prime end of one strand aligns with and runs opposite to the five to three (5' to 3') orientation on the other side.

• If one end is given, all other ends can be determined based on the antiparallel configuration. For example, given a five prime end, the opposite end is the three prime end.

DNA Replication Process

• Origin of Replication: The specific location where DNA unwinds and separates, initiating the replication process. The DNA unwinds, exposing nucleotides.

• Thousands of these exist across the DNA.

• Helicase: The enzyme responsible for unwinding or unzipping the DNA double helix. It facilitates separation by breaking hydrogen bonds. At each replication fork, helicases unzip the DNA in opposite directions.

• Single-Stranded Binding Proteins: These proteins bind to and stabilize the separated DNA strands, preventing them from re-annealing or closing back up.

• RNA Primer: A short sequence of RNA nucleotides synthesized by primase. Serves as the starting point for DNA polymerase to initiate DNA synthesis.

• Primase: The enzyme that synthesizes the RNA primer. It adds the primer to the DNA template, providing a starting point for replication.

• The primer provides an attachment point for DNA polymerase to bind and begin synthesis.

• DNA Polymerase: The main enzyme responsible for synthesizing new DNA strands by adding nucleotides to the 3' end of the primer. It proofreads and corrects errors during replication.

• Nucleotides: Building blocks of DNA (A, T, C, G), which are added according to base pairing rules (A with T, and C with G).

DNA Polymerases

• DNA Polymerase III: The primary enzyme responsible for synthesizing most of the new DNA during replication.

• DNA Polymerase I: This enzyme removes RNA primers and replaces them with DNA nucleotides.

• G always pairs with C, and A always pairs with T.

• Gs are shaped like Cs, and As and Ts contain straight lines.

Leading and Lagging Strands

• Leading Strand: Synthesized continuously in the 5' to 3' direction towards the replication fork.

• Lagging Strand: Synthesized discontinuously in short fragments (Okazaki fragments) in the 5' to 3' direction away from the replication fork.

• Okazaki Fragments: Short DNA fragments synthesized on the lagging strand during DNA replication. These are later joined together by DNA ligase.

DNA Synthesis Steps

1.  Helicase unwinds the DNA at the origin of replication.
2.  Single-stranded binding proteins (SSBPs) bind to the DNA strands to keep them separated.
3.  Primase synthesizes RNA primers, providing a starting point.
4.  DNA polymerase III adds nucleotides to the 3' end of the primer, synthesizing a complementary strand of DNA.
5.  On the lagging strand, Okazaki fragments are synthesized discontinuously.
6.  DNA polymerase I removes the RNA primers and replaces them with DNA nucleotides.
7.  Ligase: joins Okazaki fragments together to create a continuous strand.

DNA Repair Mechanism

• Excision Repair: A process where damaged or incorrect DNA sequences are cut out by enzymes called nucleases, and the gap is filled in by DNA polymerase and sealed by DNA ligase.

• Excision repair involves cutting out flawed DNA and using DNA polymerase and ligase to repair the segment.

Telomeres and End Replication Problem

• Telomeres: Protect ive caps at the end of chromosomes, preventing DNA degradation and maintaining genomic stability. The ends of DNA where the sequence repeats multiple times.

• End Replication Problem: The inability of DNA polymerase to replicate the ends of linear chromosomes, leading to gradual shortening of telomeres with each cell division. This is because DNA polymerase can only add nucleotides to the 3' end of an existing strand and can't replicate the very end of a chromosome where the RNA primer was located.

• Each time DNA replicates, one primer's length of DNA is lost at the telomeres.

• Telomerase: An enzyme that elongates telomeres by adding repetitive nucleotide sequences to the ends of chromosomes, compensating for the shortening that occurs during replication. It's present in germ cells (sperm and egg) and cancer cells, allowing them to maintain telomere length and divide indefinitely.

Rosalind Franklin

• Rosalind Franklin discovered the structure of DNA - a double helix from an X-ray diffraction graph.

Homology and Phylogeny

• Homology: Similarity in structure, physiology, or development of different organisms based on their descent from a common evolutionary ancestor.

• Anatomical Homology: Similar anatomical structures in different species that indicate shared ancestry (e.g., bones in a bat's wing and bones in a human arm and hand).

• Embryological Homology: Similar patterns of embryological development in different species, suggesting common ancestry.

• Vestigial Organ: A structure in an organism that has lost all or most of its original function in the course of evolution (e.g., appendix in humans).

• Molecular Homology: Similarity in the DNA or RNA sequences of different organisms, indicating shared ancestry. Example is genetic similarity between chimpanzees and humans

• Phylogeny: The evolutionary history and relationships among individuals or groups of organisms.

Phylogeny and Cladograms

• Cladogram: A branching diagram that depicts the evolutionary relationships among groups of organisms.

• Species on the same branch have a recent common ancestor.

• The most recent split in a cladogram represents the closest relationship.

Microevolution and Hardy-Weinberg

• Microevolution: A change in gene frequency within a population over time.

• Population: A group of organisms of the same species that live in the same area and interbreed.

• Species: A group of organisms capable of interbreeding and producing viable, fertile offspring.

• Hardy-Weinberg Equilibrium: A principle that describes the conditions under which allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences.

• \p + q = 1

• \p^2 + 2pq + q^2 = 1

• p represents the frequency of the dominant allele.

• q represents the frequency of the recessive allele.

• p^2 represents the frequency of the homozygous dominant genotype.

• q^2 represents the frequency of the homozygous recessive genotype.

• 2pq represents the frequency of the heterozygous genotype.

  • The Hardy-Weinberg equation needs to be memorized.

• Hardy-Weinberg problem with example math problem to solve the allele and genotype frequencies in a population.