DNA Structure, Replication, and Repair: Study Notes

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Chargaff's rules describe the proportion of nucleotide bases in DNA and are foundational for understanding DNA structure.

Chargaff's Rules: In any double-stranded DNA, the amount of adenine (A) equals thymine (T), and the amount of guanine (G) equals cytosine (C).
Base Pair Proportions:
- A = T
- G = C
- Total purines (A + G) = Total pyrimidines (T + C)
Application: If an organism's DNA contains 30% adenine, it will also have 30% thymine, and the remaining 40% will be split equally between guanine and cytosine (20% each).

DNA is a double helix composed of nucleotides, with specific structural features that enable its function and replication.

Nucleotide Structure: Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (A, T, G, or C).
Antiparallel Orientation: The two DNA strands run in opposite directions: one 5’ to 3’, the other 3’ to 5’.
5’ to 3’ Directionality: DNA synthesis and reading occur from the 5’ end (phosphate group) to the 3’ end (hydroxyl group).
Base Pairing Rules: Adenine pairs with thymine via two hydrogen bonds; guanine pairs with cytosine via three hydrogen bonds.
Support for Replication: Complementary base pairing allows each strand to serve as a template during DNA replication.

Example: The sequence 5’-ATCG-3’ pairs with 3’-TAGC-5’.

DNA replication begins at specific sites called origins of replication, with differences between prokaryotes and eukaryotes.

Origin of Replication: A specific DNA sequence where replication starts.
Bacteria (Prokaryotes): Typically have a single origin of replication on their circular chromosome.
Eukaryotes: Have multiple origins of replication on each linear chromosome, allowing for faster replication of large genomes.

DNA polymerase is the enzyme responsible for synthesizing new DNA strands.

Requirements: DNA polymerase needs a template strand, a primer with a free 3’ OH group, and deoxynucleoside triphosphates (dNTPs).
Directionality: DNA polymerase adds nucleotides only in the 5’ to 3’ direction.
Energy Source: The energy for DNA synthesis comes from the hydrolysis of the high-energy phosphate bonds in dNTPs. The reaction is: (where is pyrophosphate, which is further hydrolyzed to drive the reaction forward)

DNA replication is continuous on one strand (leading) and discontinuous on the other (lagging) due to the antiparallel structure of DNA.

Leading Strand: Synthesized continuously in the 5’ to 3’ direction, following the replication fork.
Lagging Strand: Synthesized discontinuously as short fragments (Okazaki fragments), each initiated by a primer, moving away from the replication fork.
Reason for Difference: DNA polymerase can only add nucleotides to the 3’ end, so the lagging strand must be synthesized in pieces as the fork opens.

Example: Okazaki fragments are later joined by DNA ligase to form a continuous strand.

Cells have multiple mechanisms to ensure DNA replication fidelity and to repair errors.

Proofreading: DNA polymerase has 3’ to 5’ exonuclease activity to remove incorrectly paired nucleotides during replication.
Mismatch Repair: Specialized enzymes recognize and correct mismatched bases missed by DNA polymerase.
Excision Repair: Damaged DNA is cut out by nucleases, and the gap is filled by DNA polymerase and sealed by DNA ligase.

Basic Steps in DNA Repair:

Mismatches that escape repair can lead to permanent changes in the DNA sequence of daughter cells.

Mutation: If a mismatch is not corrected, one daughter cell will inherit the mutation after the next round of replication.
Genetic Variation: Such mutations can be silent, harmful, or occasionally beneficial, contributing to genetic diversity.

Telomerase is an enzyme that extends the ends of linear chromosomes, solving the end-replication problem in eukaryotes.

Function: Adds repetitive nucleotide sequences to the ends of chromosomes (telomeres), preventing loss of genetic information.
Active In: Germ cells, stem cells, and some cancer cells. Most somatic cells have low or no telomerase activity, leading to gradual telomere shortening with each division.

Example: Telomerase activity allows stem cells to divide many times without losing essential DNA sequences.