Nucleotides & DNA Structure Quiz

Nucleotides are formed when one or more phosphate groups are attached to the 5' carbon of a nucleoside
Nucleoside di- and triphosphates are high-energy compounds such as ATP and GTP.

The primary structure of DNA is determined by the sequence of bases in the nucleic acid chain.
DNA is a polymer of nucleotides (dNTPs), including dAMP, dGMP, dTMP, and dCMP.
Nucleotides are covalently linked by 3',5'-phosphodiester bonds.
DNA strands have two ends: a 5' end with a free phosphate and a 3' end with a free hydroxyl (OH) group.
The base sequence of a DNA strand is conventionally written in the 5' to 3' direction, for example, 5'-TCAG-3' or TCAG.

Two DNA strands are annealed to each other according to base pairing complementarity.
Base complementary (Chargaff’s rules):
- Adenine (A) always pairs with Thymine (T) via two hydrogen bonds.
- Guanine (G) always pairs with Cytosine (C) via three hydrogen bonds.
The amount of adenine equals the amount of thymine.
The amount of guanine equals the amount of cytosine.
The two DNA strands are antiparallel, meaning they run in opposite directions: one is 5' to 3', and the other is 3' to 5'.

The two DNA strands wind around each other to form a right-handed double helix, known as the B form.
The hydrophilic sugar-phosphate backbone of each strand is on the outside of the helix.
The hydrophobic bases are stacked inside the helix.
Each turn of the helix is 10.5 base pairs long and 2 nm wide.
The double helix has two grooves on its exterior surface:
- The major groove serves as a binding site for regulatory proteins.
- The minor groove is for histone binding.

Eukaryotes:
- In chromosomes: Inside the nucleus
- In chromosomes: Inside mitochondria
Prokaryotes:
- Non-chromosomal (plasmids): Inside the cytoplasm.
- Non-chromosomal DNA: Inside the cytoplasm.

Stores genetic information.
Transmits genetic information to the next generation through replication.
Controls protein synthesis within each cell to perform its physiological functions through transcription and translation.

DNA is a polymer of deoxyribonucleotides linked by phosphodiester bonds.
Each nucleotide consists of three components:
- A nitrogenous base (purine or pyrimidine).
- A 5-carbon sugar (deoxyribose).
- A phosphate group.

Purines: Two-ring heterocyclic structures.
- Adenine (A) and guanine (G) are commonly found in nucleic acids.
- Both are found in DNA and RNA.
- Other purine metabolites not commonly found in nucleic acids include xanthine, hypoxanthine, and uric acid.
Pyrimidines (CUT): One-ring structures.
- Cytosine (C) is present in both DNA and RNA.
- Uracil (U) is found only in RNA.
- Thymine (T) is usually found only in DNA.

If the pentose sugar is deoxyribose, the nucleic acid is DNA (deoxyribonucleic acid).
If the pentose sugar is ribose, the nucleic acid is RNA (ribonucleic acid).

One or more phosphate groups are attached to the 5' carbon of the pentose sugar.

Nucleosides are formed by covalently linking a base to the number 1 carbon of a sugar.

Nucleosome core: Consists of 140-150 base pairs of supercoiled DNA and 8 histones (2 molecules of H2A, H2B, H3, and H4).
Linking region: Consists of 20-200 base pairs of DNA that joins one nucleosome core to the next. Includes one molecule of histone H1, which protects the linker DNA from digestion by nucleases.

A series of nucleosomes is often called "beads on a string" or a 10 nm chromatin fiber.
This fiber is further coiled to form the 30 nm fiber.
The 30 nm fiber is organized into loops to form the 300 nm fiber.
Further condensation occurs to eventually form the 700 nm chromatid.
Finally, the 1400 nm chromosome is formed.
Each eukaryotic chromosome contains one linear molecule of double-stranded DNA.

Heterochromatin:
- More compact, stains densely.
- Gene-poor (AT-rich).
- Transcriptionally less active, with silenced genes due to methylation.
- Seen in interphase and mitotic chromosomes.
- It is not sensitive to digestion by DNAase (nuclease).
Euchromatin:
- Less compact structure, stains lightly.
- Transcriptionally more active, with gene-rich (CG-rich) regions.
- Generally corresponds to nucleosomes (10 nm fibers) loosely associated or looped (300 nm fibers).
- More sensitive to digestion by DNAase (nuclease).

Double-stranded linear: Eukaryotic nuclear chromosomes.
Double-stranded circular: Mitochondrial, bacterial chromosomes, plasmids, viral, and chloroplast DNA.
Single-stranded circular DNA: Small viruses.

Circular double-stranded DNA with a length of about 16 kb.
Codes for enzymes involved in energy production and the electron transport chain.
Has a mutation rate 5-10 times higher than nuclear DNA.
It is maternally inherited because the ovum contains hundreds to thousands of mitochondria compared to the sperm.

Denaturation: Disruption of hydrogen bonds in double-stranded DNA, separating the strands into single strands (melting). Covalent phosphodiester bonds remain intact, preserving the sugar-phosphate backbone.
Factors causing denaturation: Heat, alkaline pH, chemicals like formamide and urea.
Melting Temperature (Tm): The temperature at which 50% of the DNA molecule exists as single strands. The Tm varies based on the base composition of the DNA molecule.
Renaturation (reannealing): Denatured single-stranded DNA can reanneal if the denaturing conditions are slowly removed.

Nucleases: Enzymes that hydrolyze nucleic acids.
Exonucleases: Remove nucleotides from the 5' or 3' end of a nucleic acid.
Endonucleases: Cut within the nucleic acid, releasing nucleic acid fragments.

There are eight histone molecules found in nature, which are essential for packaging DNA into nucleosomes. These include:
- H2A, H2B, H3, and H4 (two molecules of each).
- H1.