Biology Chapter on DNA Structure and Function

Study Notes

DNA is the genetic material, meaning it stores information
DNA is responsible for inheritance, passing genetic traits from generation to generation
DNA contains the code for building all other cellular molecules, including proteins
The code for building proteins is contained in genes
DNA's complementary structure allows it to be replicated, ensuring accurate copies of the code
DNA's structure also allows its code to be read, leading to protein synthesis
Variations in DNA sequence cause phenotypic differences, which are observable characteristics
Variations in DNA sequence can lead to different susceptibilities to diseases
Defects in DNA replication and repair contribute to a multitude of diseases

DNA is a deoxyribonucleic acid
Consists of two strands of repeating units called nucleotides
The two strands are twisted into a double helix
A single nucleotide contains:
- A deoxyribose (a pentose, 5-carbon sugar)
- A nitrogenous (nitrogen-containing) base
- A phosphate group
Polynucleotides are formed by condensation reactions
Nitrogenous bases can be purines (adenine (A), guanine (G)) or pyrimidines (cytosine (C), thymine (T), uracil (U))
Purine bases have a nine-membered, double-ringed structure
Pyrimidine bases have a six-membered, single-ringed structure
DNA molecules exist as a double helix with two antiparallel polynucleotide strands
The two strands are held together by hydrogen bonds between complementary base pairs (A=T, C≡G)
One strand runs 5' to 3', the other runs 3' to 5'

The nucleus of eukaryotic cells contains multiple linear chromosomes
The human nucleus has a diameter of about 15 μm
The total length of the naked DNA in a human cell is about 7.5 feet or 2.3m
DNA is compacted within the nucleus through organization into nucleosomes, chromatin, and chromosomes

DNA polymerase has separate sites for DNA synthesis and editing
DNA polymerase 1 has an error rate of 1 in 100,000 bases
DNA polymerase can proofread and correct mistakes during replication, reducing the error rate to 1 in 100 million bases
DNA synthesis occurs in the 5' to 3' direction

There are two main categories of DNA repair: single strand repairs and double strand repairs
Single-strand defects, if not repaired, can lead to mutations
Double-strand breaks, if not repaired, can lead to genetic instability

This mechanism corrects small lesions that do not significantly distort the DNA helix structure
Uracil DNA glycosylase removes uracil from DNA using "pinch, push and pull" action
Once uracil is removed, the sugar-phosphate backbone is removed
DNA polymerase adds new nucleotides and DNA ligase seals the nick, completing the repair

Repairs larger lesions, such as pyrimidine dimers, that significantly distort the DNA helix structure
Nucleases cut out the damaged region
DNA helicase unwinds the DNA strands, creating a 12 nucleotide gap
DNA polymerase fills in the gap and DNA ligase seals the nick, completing the repair

DNA mismatch repair (MMR) is a highly conserved pathway involved in maintaining genomic stability
MMR repairs base-base mismatches and insertion/deletion mispairs generated during replication and recombination
MMR system identifies the newly synthesized lagging strand by the presence of a nick
Mismatch proofreading proteins like MutS bind to mismatched base pairs
MutL scans nearby DNA for the nick and triggers removal of the strand containing the mismatch
Individuals with one defective copy of a mismatch repair gene are prone to specific cancer types

Quinolones target bacterial type II topoisomerases
Topoisomerase prevents DNA supercoiling, controls under- and over-winding, removes knots and tangles in the bacterial chromosome
Quinolones convert topoisomerases into toxic enzymes that fragment the bacterial chromosome
Quinolones are effective against Gram-negative bacteria, used for urinary and respiratory tract infections