DNA Structure and Genomes Part I-A (Exam 1)

Teaching Misconceptions

• Many people picture teaching as simply giving information, like dropping coins.
• Actual teaching involves more complex interactions, symbolized as a person floating up in a balloon.

DNA Structure and Genomes

• Part I-A: This section focuses on DNA structure and the structure of viral, bacterial, and eukaryotic genomes.

DNA Molecule Structure

• Draw a nucleotide in your notebook and label the phosphate, sugar, and base (adenine).
• Also label the 3' and 5' ends.

Nucleotide Components

• A nucleotide has three parts:
  • Phosphate
  • Sugar
  • Base (e.g., adenine)

Purines and Pyrimidines

• Purines: Adenine and Guanine
• Pyrimidines: Cytosine, Uracil (RNA only), and Thymine (DNA only)

5' and 3' Ends of DNA

• The diagram shows the 5' end of a DNA strand.

DNA Characteristics

• DNA forms a double helix with a major and minor groove.
• B-DNA has 10 base pairs per turn.

Viral Genomes

• Viral genomes are often linear double-stranded DNA, housed within a capsid.

Genome Sizes

• Genome sizes vary significantly among organisms.
  • Viruses have the smallest genomes, measured in kilobases (Kb).
  • Eukaryotes generally have the largest genomes, measured in gigabases (Gb).
  • Protists, insects, and plants typically have genomes measured in gigabases (Gb).
  • Bacteria have genomes in megabases (Mb).
  • Fungi have genomes in megabases (Mb).
  • Mollusks, bony fish, amphibians, reptiles, and birds—genome sizes typically fall within megabases (Mb).
  • Mammals have genomes in gigabases (Gb).

Bacterial Genomes (E. coli)

• E. coli's genome is circular.
• Its genome structure can vary depending on the growth phase (exponential or stationary).
• Genes are organized in operons, typically contiguous stretches of DNA.

Eukaryotic Genomes

• Eukaryotic DNA is housed within the nucleus and mitochondria (chloroplasts).
• Chromatin is composed of DNA and proteins, including histones and non-histone proteins.
• DNA is organized at various levels, from the nucleosome to the chromosome.

Eukaryotic Genome Genes (Introns)

• Prokaryotic genes are organized into operons.
• Eukaryotic genes have introns, which are non-coding regions.
• Eukaryotic genes have regulatory sequences, like promoters, enhancers, and silencers, upstream and downstream.
• Eukaryotic genes consist of exons (coding sequences) and introns.

Repetitive DNA in Eukaryotes

• Eukaryotic genomes contain various repetitive DNA sequences.
  • Non-repetitive DNA constitutes approximately 46.06%.
  • Repetitive sequences make up about 53.94%.
    • Tandem repeats and interspersed repeats are significant classes of repetitive DNA.
    • Some repetitive elements include mini- and microsatellites, tandem repeats, pseudogenes, and others like satellite repeats.

Eukaryotic Genomes - Diploid

• Diploid organisms have two sets of chromosomes.
• A somatic cell has 46 chromosomes.
• Meiosis and fertilization ensure chromosome number consistency.

Chromatin Components and Organization

• Eukaryotic chromatin is composed of DNA and proteins (histones and non-histone proteins).
• Histones are positively charged proteins, key to DNA packaging.
• Non-histone chromosomal proteins include scaffolding, kinetochore, and telosome (or shelterin) proteins.
• Nucleosomes and the various levels of DNA packaging tightly condense the DNA.

Nucleosome and Chromatosome Formation

• Nucleosomes form by DNA wrapping around histone octamer complexes.
• The addition of H1 histone creates a chromatosome.

Heterochromatin Versus Euchromatin

• Heterochromatin: tightly packed, transcriptionally inactive regions.
  • Dark bands and contains gene-poor regions
  • Tight H1 association
• Euchromatin: loosely packed, transcriptionally active regions.
  • Light bans and contains gene-rich regions
  • Loose H1 association

Chromatin Condensation

• DNA, wrapped around histones to form nucleosomes is organized into increasingly tighter structures.
• The degree of chromatin compaction affects gene activity.

Chromosome Territories and TADs

• Chromosomes occupy specific territories within the nucleus.
• TADs (topologically associating domains) are chromosomal regions that interact more frequently with each other.

Chromatin Conformation and Gene Expression

• Epigenetics refers to changes in gene expression, not due to changes in DNA sequence, but to chromatin conformation.
• Epigenetic changes can be triggered by behaviors and environmental factors.

Histone Modifications

• Histone modifications affect chromatin structure and gene expression.
  • Examples include acetylation, phosphorylation, methylation, and ubiquitination
• These modifications often involve the addition or removal of chemical groups to specific amino acids on histone tails. Histones are basic proteins in chromatin, crucial for DNA packaging and gene regulation.

Chromatin Remodeling Complexes

• Chromatin remodeling complexes alter chromatin structure.
  • They move nucleosomes and chemically modify histone tails, impacting gene expression.

Dive into the intricate details of DNA structures, including the compositions of viral, bacterial, and eukaryotic genomes. Learn to identify nucleotide components and the significance of purines and pyrimidines in genetic material. This quiz will enhance your understanding of essential concepts in molecular biology.