Chapter 2: DNA Structure & Synthesis

1. PURPOSE

1. This chapter covers DNA structure, synthesis, and repair

2. There is a lot of information here; consider how much time you can devote to studying the material and prioritize information based on how much you can reasonably cover

3. Some topics are particularly high yield; usually it is because there are diseases or drugs that involve these pathways

   1. Enzymes involved in DNA synthesis

   2. Types of DNA mutations

   3. DNA repair mechanisms and associated diseases

   4. Nucleotide synthesis and diseases

2. NUCLEOTIDE BASES

1. DNA and RNA, which carry the code for making proteins, are made up of individual bases

   1. Adenine (A)

   2. Guanine (G)

   3. Cytosine (C)

   4. Thymine (T)—DNA only

   5. Uracil (U)—RNA only

2. Purine bases (A, G) have 2 rings while pyrimidine bases (C, T, U) have just 1

3. DNA base pairing depends on nucleotide properties

   1. To keep DNA size uniform must have 1 purine + 1 pyrimidine

   2. A and T/U pair together with 2 hydrogen bonds

   3. C and G pair together with 3 hydrogen bonds

   4. This means that C-G rich regions of DNA are highly stable (CpG islands)

3. DNA STRUCTURE

1. DNA strands are composed of bases along a phosphate-sugar backbone

   1. The backbones run in opposite directions, and DNA is read along the backbone (5′ → 3′)

   2. DNA is negatively charged

2. During storage, DNA wraps around histone proteins — positively charged proteins (lysine, arginine)

3. This histone-wrapped DNA is stored in a highly condensed structure called chromatin

   1. Heterochromatin is tightly packed and generally inactive

   2. Euchromatin is unwound and generally active

4. EPIGENETICS

1. The DNA sequence determines a protein's sequence (primary structure), but is just one piece of biological variation: Regulation of expression is also important

2. Epigenetics describes this regulation that goes beyond genetics (DNA sequence)

3. For Step 1, the main players in epigenetics are methylation and acetylation of DNA and histones

4. DNA methylation occurs in 2 situations

   1. General methylation of DNA helps the cell distinguish template vs. new strands during replication

   2. CpG islands are methylated to repress expression

5. Histone modification affects how accessible genes are → alters transcription rates

   1. Methylation usually mutes transcription

   2. Acetylation activates transcription (removes + charge from histones)

6. Methylation of chromosomes underlies imprinting, where paternal or maternal genes are turned off

   1. Patients are heterozygous but the normal copy is silenced

   2. Prader-Willi syndrome (maternal silencing, mutation inherited from father)—excessive eating

   3. Angelman syndrome (paternal silencing, mutation inherited from mother)—excessive laughter, smiling

5. DNA REPLICATION

1. The replication process is important because Step 1 likes to test ways in which errors can lead to DNA mutations, which underlie genetic disease and cancer

2. Less important to describe the ...