DNA: The Molecule of Heredity

DNA: The Molecule of Heredity

• DNA is a polymer of deoxyribonucleotides linked by 3'-5' phosphodiester bonds.
• It's found in both eukaryotic and prokaryotic cells.
• Eukaryotic cells have DNA in the nucleus, mitochondria, and chloroplasts of plants.
• Prokaryotic cells have a single chromosomal DNA and non-chromosomal DNA called "plasmid."
• DNA can be double-stranded linear (nuclear DNA), double-stranded circular (mtDNA, bacterial chromosomal DNA, plasmids, and some viruses), or single-stranded circular or linear (some small viruses).

Structure of DNA

• Primary structure: the linear sequence of nucleotides.
  • DNA forms a double helix with two strands held together by complementary base pairing (A with T, C with G).
  • The sugar-phosphate backbone is formed by alternating sugar and phosphate units.
• Secondary structure: interactions between bases through hydrogen bonds to form the DNA double helix.
  • The two strands of DNA are antiparallel.
  • Base pairing is held together by hydrogen bonds: two bonds between A & T, three bonds between C & G.
  • Hydrophobic interactions between adjacent base pairs provide stability to the double helix.
  • Each turn of the double helix consists of 10.4 nucleotide pairs, measuring 3.4 nm. The distance between adjacent base pairs is 0.34 nm.
  • The double helix structure creates major and minor grooves.
  • Chargaff's rules: the concentration of adenine (A) equals thymine (T), and the concentration of cytosine (C) equals guanine (G).

Types and Forms of DNA

Conformation of DNA

• The conformation of DNA is influenced by base composition, physical conditions (salt concentration, temperature), and the presence of specific proteins.
• B-form: the dominant DNA conformation under physiological conditions (low salt concentration), described by Watson and Crick.
• Z-DNA: produced experimentally, contains a single groove.
• A-DNA and Z-DNA: present in high salt concentration or in the presence of alcohol.

Denaturation (Melting)

• The separation of the two strands of DNA.
• Can be achieved by enzymes like helicase, increasing temperature, or adding alkalis (decreasing salt concentration).
• Melting temperature (Tm): the temperature required to denature 50% of a DNA molecule.
• Annealing (renaturation): reforming of the DNA double helix by cooling thermally melted DNA.
• Hybridization: rejoining between DNA strands, either with other DNA, RNA, or a probe.

Genes: Arrangement of DNA

• A gene is a functional and physical unit of heredity, passed from parents to offspring.
• A segment of DNA that codes for a single protein.
• Eukaryotic genes consist of:
  • Coding regions (exons): code for protein sequences.
  • Non-coding regions (introns): removed during RNA processing.
  • Regulatory sequences: control when, where, and how much protein is produced.

Genome & Chromosomes

• Genome: the complete DNA content of an organism or cell.
  • Humans have 23 pairs of chromosomes: 22 autosomes and 1 pair of sex chromosomes.
  • Mitochondria contain a small amount of DNA.
• Chromosomes: linear pieces of DNA containing many genes.
  • Chromosomes are too fine and tangled in non-dividing cells, referred to as chromatin.
  • During mitosis, they become more condensed and visible, referred to as chromatids.

Chromatin or Chromatid

• Complex of DNA and protein.
• Contains histones and non-histone proteins.
• Non-histone proteins are involved in transcription, replication, and DNA repair.
• Histones are proteins that bind closely to DNA molecules and are responsible for chromatin structure and gene regulation.
• Histones are rich in positively charged amino acids (lysine) which interact with negatively charged phosphate groups in the DNA helix, forming nucleosomes.

Types of Histones

• Linker histones (H1 or H5): connect nucleosomes.
• Core histones (H2A, H2B, H3, H4): associate with DNA to form nucleosomes, forming a complex with 146 base pairs of DNA.

Nucleosomes: Packing of Chromatin

• Each nucleosome consists of 146 base pairs of DNA wrapped around a histone core (two copies of each core histone).
• The DNA wraps around the histone core twice per nucleosome.
• Linker DNA (50 base pairs) connects two nucleosomes.
• Without histones, human DNA would be 1.8 meters, but when wound on histones, it is only 0.09 mm.
• Histone acetylation can affect gene expression:
  • Neutralizes positively charged lysine R groups, decreasing binding force between histones and DNA.
  • This allows chromatin expansion, permitting transcription (transcriptionally active).

Histone Acetylation: Acetylases vs. Deacetylases

• Histone acetylation is an important mechanism in gene regulation.
• Acetylation neutralizes the positive charges on histones, reducing their binding to DNA.
• Hyperacetylated chromatin is transcriptionally active, increasing gene expression.
• Cancer cells have high levels of histone deacetylases, which increase replication.

RNA: Ribonucleic Acid

• tRNA (transfer RNA): 10-15% of total RNA.
  • There are over 20 different tRNA molecules (75-95 nucleotides).
  • They have a similar structure across all organisms.
  • Functions as a carrier of amino acids to the site of protein synthesis.
  • At least one tRNA molecule exists for each of the 20 amino acids used in protein synthesis.
  • Eukaryotic tRNA is less stable than prokaryotic tRNA.
• mRNA (messenger RNA): 1-5% of total RNA.
  • Single-stranded linear molecules.
  • Eukaryotic mRNA is more stable than prokaryotic mRNA.
  • Eukaryotic mRNA features:
    • 5' cap (methylated GTP) protects it from nuclease attack.
    • 3' poly-A tail protects it from nuclease attack.
    • Prokaryotes have a Shine-Dalgarno sequence at the 5' end of mRNA, which helps in ribosome attachment during protein synthesis.
  • mRNA functions:
    • Carries genetic information from the nucleus to the cytoplasm.
    • Contains genetic information in the form of genetic code.
    • May contain information for forming more than one protein.

Additional Information

• The most stable form of DNA under physiological conditions is the B-form.
• Histones are present in all living organisms, except bacteria and some algae.
• Histone acetylation is a crucial mechanism for regulating gene expression.
• Eukaryotic cells have both coding (exons) and non-coding (introns) regions in their genes.
• The genome contains all the DNA in an organism or cell.
• Chromatin is the less condensed form of DNA found in non-dividing cells, while chromatid is the more condensed form found during mitosis.