Nucleic Acids

Cheatsheet Content

### Nucleosides & Nucleotides - **Nucleoside:** Base + Sugar (Ribose for RNA, Deoxyribose for DNA) - Bases: - **Purines:** Adenine (A), Guanine (G) (double ring) - **Pyrimidines:** Cytosine (C), Thymine (T) in DNA, Uracil (U) in RNA (single ring) - **Nucleotide:** Nucleoside + Phosphate group(s) - Monophosphate (NMP), Diphosphate (NDP), Triphosphate (NTP) - Building blocks of DNA and RNA. - Examples: ATP (Adenosine Triphosphate), dGTP (deoxyguanosine triphosphate) ### DNA Primary Structure - A linear sequence of deoxyribonucleotides linked by **phosphodiester bonds**. - The 5'-phosphate of one nucleotide links to the 3'-hydroxyl of the next. - This creates a sugar-phosphate backbone with bases projecting from it. - Sequence is read from 5' to 3' end. ### DNA Forms: A, B, and Z - **B-DNA:** - Most common form in physiological conditions. - Right-handed helix. - Major and minor grooves present. - ~10-10.5 base pairs per turn. - **A-DNA:** - Forms under dehydrating conditions (less water). - Shorter, wider, right-handed helix. - Bases tilted relative to helical axis. - Deeper major groove, shallower minor groove. - **Z-DNA:** - Left-handed helix. - Zigzag backbone (hence 'Z'). - Forms in regions with high GC content or specific protein interactions. - Biologically rare but significant for gene regulation. ### RNA Secondary Structure - RNA is typically single-stranded but can fold back on itself to form complex 3D structures. - Common motifs: - **Hairpins/Stem-loops:** Short double-helical regions formed by complementary base pairing within the same strand. - **Bulges:** Unpaired bases within a helical region. - **Internal loops:** Unpaired bases on both sides of a helical region. - **Pseudoknots:** More complex structures involving base pairing between a loop and an external sequence. - These structures are crucial for RNA function (e.g., tRNA, rRNA, ribozymes). ### DNA Secondary Structure (Preliminary) - The most common secondary structure of DNA is the **double helix**. - Two antiparallel polynucleotide strands wound around a central axis. - Stabilized by hydrogen bonds between complementary base pairs: - A-T (2 H-bonds) - G-C (3 H-bonds) - Also stabilized by hydrophobic interactions between stacked bases (base stacking). - The strands are complementary, meaning the sequence of one strand dictates the sequence of the other. ### DNA Melting & Denaturation - **Denaturation (Melting):** The process of separating the two complementary strands of a DNA double helix. - Caused by breaking hydrogen bonds and base-stacking interactions. - Can be induced by heat, extreme pH, or denaturing agents (e.g., urea, formamide). - **Melting Temperature ($T_m$):** The temperature at which half of the DNA strands are denatured (separated). - Higher GC content leads to a higher $T_m$ because G-C pairs have three hydrogen bonds (stronger) compared to A-T pairs (two hydrogen bonds). - Longer DNA molecules also have higher $T_m$. - **Renaturation (Annealing):** The process where denatured complementary DNA strands re-associate to form a double helix when conditions return to normal. - Used in techniques like PCR and hybridization.