Structural and chemical properties of nucleic acids Flashcards
What are the chemical components that make up a nucleotide?
A nucleotide consists of a nitrogenous base (purine or pyrimidine), a sugar (deoxyribose or ribose), and a phosphate group.
How do the sugar and phosphate groups contribute to the overall charge and structure of nucleic acids?
The phosphate groups give nucleic acids a negative charge and contribute to the backbone structure through phosphodiester bonds.
What is the difference between the structural composition of RNA and DNA?
DNA contains deoxyribose sugar and thymine (T), while RNA contains ribose sugar and uracil (U) instead of thymine.
How does the hydrogen bonding between bases contribute to nucleic acid stability?
Hydrogen bonds between complementary base pairs (A-T/U, G-C) stabilize the double helix structure.
What is the role of the 3’ and 5’ hydroxyl groups in nucleic acid polymerization?
The 3’ hydroxyl group forms a phosphodiester bond with the 5’ phosphate group of the next nucleotide, allowing strand elongation.
Define and differentiate between a base, a nucleoside, and a nucleotide.
Base: Nitrogenous ring structure (A, T, C, G, U)
Nucleoside: Base + sugar
Nucleotide: Base + sugar + phosphate
Which nitrogenous bases are purines and which are pyrimidines?
Purines: Adenine (A), Guanine (G)
Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)
How do modifications in nucleotides, such as methylation, affect gene expression?
Methylation typically silences genes by inhibiting transcription factor binding or recruiting repressive proteins.
What are the consequences of base-pair mismatches on DNA stability?
Base-pair mismatches create structural distortions that can lead to mutations if not repaired.
Explain the significance of phosphodiester bonds in the formation of nucleic acid polymers.
Phosphodiester bonds link nucleotides, forming the sugar-phosphate backbone and giving directionality (5’ → 3’) to nucleic acids.
Describe the Watson-Crick model of DNA structure.
DNA is a right-handed double helix with complementary base pairing (A-T, G-C) held together by hydrogen bonds.
What are the key differences between A-DNA, B-DNA, and Z-DNA?
B-DNA: Right-handed helix, most common under physiological conditions.
A-DNA: Right-handed helix, wider and shorter, forms under dehydrated conditions.
Z-DNA: Left-handed helix, forms in GC-rich regions.
How does base stacking contribute to the helical stability of DNA?
Hydrophobic interactions and Van der Waals forces between stacked bases stabilize the helix.
What is the role of major and minor grooves in DNA-protein interactions?
Proteins, like transcription factors, bind to the major groove because it provides more accessible chemical information.
How does supercoiling influence DNA function and replication?
Supercoiling compacts DNA for storage and regulates access for transcription and replication.
How are nucleosomes formed, and what is their role in DNA packaging?
DNA wraps around histone proteins (H2A, H2B, H3, H4) to form nucleosomes, which condense DNA into chromatin.
Describe the structural organization of chromatin and its functional significance.
Chromatin consists of nucleosomes linked by linker DNA, which can be tightly packed (heterochromatin) or loose (euchromatin) to regulate gene expression.
What is the role of histone modifications in regulating gene expression?
Acetylation (activates) and methylation (represses or activates) of histone tails regulate chromatin accessibility and gene transcription.
How are topoisomerases involved in the maintenance of genome integrity?
Topoisomerases prevent DNA tangling by cutting and rejoining DNA strands to relieve supercoiling.
Explain the concept of euchromatin and heterochromatin and their functional differences.
Euchromatin: Loosely packed, transcriptionally active.
Heterochromatin: Densely packed, transcriptionally inactive.
