Biology Chapter: DNA Structure and Function

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Study Notes

DNA is a complex macromolecule which stores the genetic information of all living organisms.
DNA structure resembles a ladder with side chains made of deoxyribose sugar and phosphate.
Nitrogenous bases form the 'rungs' of the ladder, connecting the two strands via hydrogen bonds.
The two strands of DNA wind together to form a double helix, which is 20 angstroms wide.

Each DNA strand is made up of repeating units called nucleotides.
Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base.
These nucleotides are linked by a phosphodiester bond between the 3' carbon of one sugar and the 5' carbon of the next sugar, with the phosphate group in between.
Nitrogenous bases are linked to the 1' carbon of the sugar molecule through glycosidic bonds.

There are two types of nitrogenous bases: purines and pyrimidines.
Purines include guanine (G) and adenine (A), and are composed of a five-membered ring fused to a six-membered ring.
Pyrimidines include cytosine (C) and thymine (T), and are composed of a six-membered ring.
The sugar binds to nitrogen number 9 of the purine base and nitrogen number 3 of the pyrimidine base.

In a DNA molecule, the number of purines equals the number of pyrimidines.
The amount of adenine (A) equals the amount of thymine (T).
The amount of guanine (G) equals the amount of cytosine (C).
This means the ratio of (A+ G) to (T+ C) is always 1.
The base ratio (A+ T) to (C+ G) varies among organisms but is constant for any specific species.

DNA replication is the process by which a parent DNA molecule is copied to produce two identical daughter molecules.
Replication is semi-conservative meaning each daughter molecule contains one old and one new strand.
Replication occurs in small units called replicons which have an origin where replication starts and proceeds.

Initiation:
- Begins at a specific sequence called the origin of replication.
- The DNA double helix is unwound by DNA helicase.
- Single-strand binding proteins (SSBs) bind to the separated strands to prevent rewinding.
- The separated strands form two replication forks.
Primer Synthesis:
- DNA polymerases require a 3' hydroxyl group to start adding nucleotides.
- DNA primase synthesizes a short RNA primer (9-12 nucleotides) onto each strand.
Leading Strand Synthesis:
- DNA polymerase III adds new nucleotides continuously to the 3' end of the primer, following the replication fork.
Lagging Strand Synthesis:
- Synthesized discontinuously in small fragments (Okazaki fragments) in the 5'→3' direction, moving away from the fork.
Primer Removal:
- DNA polymerase I removes the RNA primers and replaces them with DNA nucleotides.
Ligation:
- DNA ligase seals the gaps between Okazaki fragments by forming phosphodiester bonds.
Termination:
- Replication terminates at specific termination sites identified by tus proteins.

DNA helicase: Unwinds and separates the DNA double helix at the origin of replication.
Single-strand binding proteins (SSBs): Prevent the reformation of the double helix by attaching to the separated strands.
DNA polymerase: Adds nucleotides to the 3' end of the existing strand, moving in the 5' → 3' direction at the replication fork.
DNA ligase: Links Okazaki fragments on the lagging strand by forming phosphodiester bonds.
DNA primase: Synthesizes RNA primers for DNA polymerase to initiate replication.