Nucleotides and DNA Structure Quiz

Nucleotides, DNA Structure & Organization

• Nucleic acids include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
• Each nucleic acid is composed of nucleotides.
• A nucleotide consists of:
  • A sugar (deoxyribose or ribose)
  • A phosphate group
  • A nitrogen-containing base
• Purine bases (adenine [A], guanine [G]) have two rings.
• Pyrimidine bases (thymine [T], cytosine [C], uracil [U]) have one ring.
• Linking a base to a sugar creates a nucleoside.
• Linking a nucleoside to a phosphate group forms a nucleotide.
• Nucleotides can be further categorized as:
  • Nucleoside monophosphate
  • Nucleoside diphosphate
  • Nucleoside triphosphate
• Nucleic acids contain nucleoside monophosphates.
• High-energy phosphate compounds can be tri-, di-, or monophosphates of nucleosides.

Importance of Nucleotides & Nucleosides & Nitrogenous Bases

• Nucleotides participate in the synthesis of nucleic acids (DNA and RNA).
• Nucleotides like ATP and GTP serve as high-energy phosphate compounds.
• Nucleotides play roles as coenzymes (e.g., NAD, NADP, FAD, FMN, coenzyme A, deoxyadenosylcobalamine).
• Nucleotides act as donors in various metabolic pathways (e.g., UDP-glucose, UDP-glucuronic acid, S-adenosylmethionine, CDP-choline, CDP-ethanolamine).
• Nitrogenous bases act as secondary messengers for hormones (e.g., cAMP, cGMP).
• Methylated nitrogenous bases are important in regulating gene expression.
• Synthetic purine and pyrimidine analogs have medicinal applications (e.g., allopurinol for gout, 5-fluorouracil for cancer).

DNA

• DNA is the genetic material carrying the individual's genetic information.
• In eukaryotes, DNA is primarily located in the chromosomes of the nucleus and in mitochondria.
• In prokaryotes, DNA is found in the single chromosome and plasmids.
• DNA has the functions of:
  • Storing genetic information
  • Transferring genetic information to daughter cells during replication
• DNA must replicate precisely during cell division to ensure each daughter cell receives the same genetic material.
• Nuclear DNA encodes functional proteins and functional RNA.
• Mitochondrial DNA contains genes for proteins in the electron transport chain and ribosomal and transfer RNAs.

DNA Structure

• DNA consists of two chains (strands) that wind around each other in a double helix. (Watson-Crick model)
• Each strand is formed of deoxyribonucleotides linked by 3'-5' phosphodiester bonds between sugars and phosphates.
• Each deoxyribonucleotide is composed of:
  • A deoxyribose sugar
  • A phosphate group
  • A nitrogenous base (A, T, G, C)
• The 5' end has a free phosphate group, and the 3' end has a free hydroxyl group.
• DNA replication proceeds in a 5' to 3' direction.
• The hydrophilic (polar) deoxyribose-phosphate backbone is on the outside of the DNA molecule.
• Hydrophobic (nonpolar) bases are stacked inside, perpendicular to the helix axis.

DNA Antiparallel Strands

• The two DNA strands run antiparallel to each other.
• One strand is oriented 5' to 3', and the other is 3' to 5'.
• Hydrogen bonds between bases and hydrophobic interactions between stacked bases stabilize the double helix.

Base Pairing Rules

• Thymine pairs with adenine (2 hydrogen bonds).
• Cytosine pairs with guanine (3 hydrogen bonds).
• The base-pairing rules ensure that one strand is complementary to the other.
• G-C base pairs are more stable than A-T base pairs due to the stronger hydrogen bonding.

DNA Major and Minor Grooves

• DNA has two grooves: major and minor grooves, on its exterior surface.
• These grooves result from the unequal size of the grooves due to the asymmetry of deoxyribose rings and structural differences in the upper surface of a base pair.

DNA Organization

• In humans, each cell contains 46 chromosomes whose total length is approximately one meter.
• Chromosomes must condense into chromatin to fit within the nucleus.
• Chromatin comprises:
  • Nuclear DNA
  • Histone proteins
  • Smaller amounts of nonhistone proteins (e.g., enzymes involved in DNA replication and transcription).
  • Small amounts of RNA (e.g., snRNA).

Histones

• Histones are basic proteins with positive charges, enabling ionic bonds with negatively charged DNA.
• Five types of histones exist: H1, H2A, H2B, H3, and H4.
• Histones help condense DNA into compact chromosomes.
• Histones protect DNA from degradation by exonucleases.
• Modified histones (e.g., acetylation of H3 and H4) influence chromatin structure and gene expression (activation/inactivation).

Nucleosome Structure

• A nucleosome is a fundamental unit of chromatin.
• It consists of a DNA core wrapped around a histone octamer (2 each of H2A, H2B, H3, and H4).
• A linker DNA segment joins adjacent nucleosomes.
• Nucleosomes are linked together by histone H1.

Chromatin Compaction

• Chromatin undergoes several levels of compaction.
• Initially, nucleosomes form a 10-nm fiber.
• Further compaction results in a 30-nm fiber.
• The 30-nm fiber forms loops attached to a protein scaffold, creating a rosette structure.
• Coils of rosettes form chromatids.

Chromosomes

• Two identical sister chromatids joined at the centromere constitute a chromosome (during metaphase).
• The centromere is rich in A-T base pairs, around 130 base pairs long.
• It has kinetochores, protein complexes that connect to the mitotic spindle and are essential for chromosomal segregation.