BIOB11 - LECTURE 2

  • Identify differences and similarities in the composition and organization of the genomes of prokaryotes, eukaryotes, and viruses:

    • Prokaryotes: Typically have a single, circular chromosome located in the nucleoid region. They may also contain plasmids, which are smaller, circular DNA molecules. Prokaryotic genomes are generally smaller and more compact, with a high gene density and less non-coding DNA.

    • Eukaryotes: Have multiple, linear chromosomes housed within the nucleus. Their genomes are much larger and more complex than prokaryotes, containing a significant amount of non-coding DNA, including introns and repetitive sequences. Eukaryotic DNA is organized into chromatin, which involves histone proteins.

    • Viruses: Possess genomes that can be either DNA or RNA, and single-stranded or double-stranded. Viral genomes are very compact, with a high gene density. They come in various forms, such as linear, circular, or segmented.

  • Explain the relationships between genome size, number of genes, repetitive/non-coding DNA content, and gene density in prokaryotes and across different eukaryotes:

    • Genome Size: Generally, eukaryotes have larger genomes than prokaryotes. However, genome size does not always correlate with organism complexity.

    • Number of Genes: Although larger genomes tend to have more genes, the relationship is not linear due to the presence of non-coding DNA.

    • Repetitive/Non-coding DNA Content: Eukaryotic genomes contain a large proportion of non-coding DNA, including regulatory sequences, introns, and repetitive sequences like transposons. Prokaryotic genomes have much less non-coding DNA.

    • Gene Density: Prokaryotes typically have higher gene density (more genes per base pair) compared to eukaryotes because of the reduced amount of non-coding DNA.

  • Identify the % of human DNA that encodes protein vs other types of sequences:

    • Only about 2% of the human genome encodes proteins.

    • The remaining 98% consists of non-coding DNA, including introns, regulatory sequences, repetitive sequences (e.g., transposons, SINEs, LINEs), and other sequences with unknown functions.

  • Describe mechanisms involved in packaging and organizing DNA:

    • Supercoiling: DNA is supercoiled to condense it and relieve torsional stress.

    • Nucleosomes: In eukaryotes, this is the first level of DNA packaging, where DNA is wrapped around histone proteins to form nucleosomes.

    • 30 nm Fiber: Nucleosomes are further compacted into a 30 nm fiber with the help of histone H1.

    • Looped Domains: The 30 nm fiber forms looped domains attached to a protein scaffold.

    • Chromosomes: During cell division, looped domains are further compacted into highly condensed chromosomes.

  • Explain why DNA packaging is important and the sequential levels of packaging mediated by nucleosomes, the 30 nm fiber, scaffolds, and at mitosis:

    • Importance of DNA Packaging: DNA packaging is crucial because it allows the long DNA molecules to fit within the small space of the nucleus. It also protects DNA from damage and regulates gene expression by controlling access to DNA.

    • Nucleosomes: DNA wraps around histone octamers, reducing its length by about sevenfold.

    • 30 nm Fiber: Further condenses DNA, achieving an additional sixfold compaction.

    • Scaffolds and Looped Domains: Organize the 30 nm fiber into larger loops attached to a protein scaffold, providing another level of compaction and organization.

    • Mitosis: DNA is maximally condensed into chromosomes, ensuring accurate segregation of genetic material during cell division.

  • Identify the structure of a nucleosome and the functions of the globular (histone-fold-containing) and N-terminal tails of histones:

    • Structure of a Nucleosome: A nucleosome consists of approximately 147 base pairs of DNA wrapped around a histone octamer, which contains two molecules each of histones H2A, H2B, H3, and H4.

    • Globular Domain (Histone Fold): The globular domain of histones is responsible for histone-histone interactions within the nucleosome and DNA binding. The histone fold domain facilitates the assembly of the nucleosome core.

    • N-Terminal Tails: These tails extend outward from the nucleosome and are subject to various covalent modifications, such as acetylation, methylation, phosphorylation, and ubiquitination. These modifications influence chromatin structure and gene expression.

  • Predict how recruitment of different histone-modifying enzymes will impact chromatin conformation:

    • Histone Acetyltransferases (HATs): Add acetyl groups to histone tails, leading to a more open chromatin structure (euchromatin) and increased gene expression.

    • Histone Deacetylases (HDACs): Remove acetyl groups, resulting in a more condensed chromatin structure (heterochromatin) and decreased gene expression.

    • Histone Methyltransferases (HMTs): Add methyl groups to histone tails. The effect depends on the specific lysine or arginine residue that is methylated; some methylations lead to heterochromatin and gene repression, while others lead to euchromatin and gene activation.

    • Histone Demethylases: Remove methyl groups, reversing the effects of methylation.

  • Explain how histone H1 contributes to the organization of chromatin:

    • Histone H1 (linker histone) binds to the linker DNA between nucleosomes and helps to further compact chromatin.

    • Histone H1 facilitates the formation of the 30 nm fiber by binding to the nucleosome and helping to align nucleosomes end-to-end.

    • H1’s presence leads to a more condensed and stable chromatin structure, which typically correlates with reduced gene expression.

  • Define euchromatin and heterochromatin and predict which regions/locations will exhibit each:

    • Euchromatin: Less condensed, transcriptionally active regions of chromatin. It is typically found in areas with actively transcribed genes and is more accessible to transcription factors and other regulatory proteins.

    • Heterochromatin: Highly condensed, transcriptionally inactive regions of chromatin. It is often found in regions around telomeres and centromeres, and in areas with repetitive DNA sequences.

  • Explain the distinction between facultative and constitutive heterochromatin:

    • Constitutive Heterochromatin: Regions of the genome that are always heterochromatic in all cell types. These regions contain repetitive sequences and structural elements like centromeres and telomeres. They are generally transcriptionally silent.

    • Facultative Heterochromatin: Regions of the genome that can switch between euchromatin and heterochromatin depending on developmental stage or cell type. An example is X chromosome inactivation in females, where one X chromosome is condensed into a Barr body and silenced.

  • Distinguish between genetics and epigenetics:

    • Genetics: Involves the study of genes, heredity, and the variation of inherited characteristics. Genetic information is encoded in the sequence of DNA nucleotides, and changes to this sequence (mutations) can lead to heritable changes in phenotype.

    • Epigenetics: Involves changes in gene expression that do not involve alterations to the DNA sequence. Epigenetic modifications include DNA methylation and histone modifications, which can alter chromatin structure and gene expression patterns. These changes can be heritable but are also reversible and responsive to environmental factors.

  • Explain what X chromosome inactivation is and how it influences coat pattern in Calico cats:

    • X Chromosome Inactivation: A process in which one of the two X chromosomes in female mammals is silenced to equalize the expression of X-linked genes between males and females. The inactivated X chromosome becomes highly condensed, forming a Barr body.

    • Calico Cats: Female cats that are heterozygous for coat color genes on the X chromosome can exhibit a patchy coat pattern due to random X inactivation. In some cells, the X chromosome carrying one allele is inactivated, while in other cells, the X chromosome carrying the other allele is inactivated. This results in different coat colors being expressed in different patches of cells.

  • Discuss how changes to histones and DNA methylation can influence the likelihood a gene will be expressed (transcribed) and identify which modifications are more likely to be associated with heterochromatin/gene repression:

    • Histone Modifications:

      • Acetylation: Generally associated with increased gene expression. Acetylation of histone tails neutralizes the positive charge, leading to a more open chromatin structure.

      • Methylation: Can either increase or decrease gene expression depending on the specific amino acid residue that is methylated. For example, H3K9me3 and H3K27me3 are associated with gene repression and heterochromatin formation.

    • DNA Methylation:

      • Typically associated with gene repression. Methylation of cytosine bases, particularly in CpG islands, can prevent the binding of transcription factors and recruit proteins that promote chromatin condensation.

    • Modifications Associated with Heterochromatin/Gene Repression:

      • Histone methylation at H3K9me3 and H3K27me3

      • DNA methylation at CpG islands

      • Histone deacetylation

  • Identify which sites in DNA can be methylated:

    • In mammals, DNA methylation primarily occurs at cytosine bases that are followed by a guanine base (CpG sites). These CpG sites are often clustered in regions called CpG islands, which are commonly found in the promoter regions of genes.

  • Identify sequences, enzymes, and mechanisms involved in propagation & maintenance of epigenetic modifications to DNA:

    • Sequences: CpG sites are the primary targets for DNA methylation.

    • Enzymes:

      • DNA Methyltransferases (DNMTs): DNMT1 is a maintenance methyltransferase that copies methylation patterns to newly synthesized DNA strands during replication. DNMT3A and DNMT3B establish de novo methylation patterns.

      • DNA Demethylases: TET enzymes (Ten-eleven translocation enzymes) oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can be further modified and eventually removed by the base excision repair (BER) pathway.

    • Mechanisms: During DNA replication, DNMT1 recognizes hemimethylated DNA (where the parent strand is methylated and the new strand is not) and adds methyl groups to the new strand, ensuring that methylation patterns are faithfully copied.

  • Compare genetic and epigenetic changes with respect to being inherited across reproductive generations (offspring) and being subject to change within an individual’s lifetime:

    • Genetic Changes:

      • Inheritance: Genetic mutations are heritable and can be passed on from parents to offspring according to the laws of Mendelian genetics.

      • Change within an Individual’s Lifetime: Genetic changes are generally stable and not easily reversible within an individual’s lifetime, although somatic mutations can occur.

    • Epigenetic Changes:

      • Inheritance: Epigenetic modifications can be inherited across reproductive generations, but they are often reprogrammed during gametogenesis and early embryonic development. However, some epigenetic marks can escape reprogramming and be transmitted to offspring (transgenerational epigenetic inheritance).

      • Change within an Individual’s Lifetime: Epigenetic changes are dynamic and can be influenced by environmental factors, diet, stress, and other exposures. They can be reversed or modified within an individual’s lifetime.

  • Identify what genomic imprinting is and how common it is in your genome:

    • Genomic Imprinting: A phenomenon in which certain genes are expressed in a parent-of-origin-specific manner. In other words, the expression of an imprinted gene depends on whether it was inherited from the mother or the father.

    • How Common: Genomic imprinting affects a relatively small number of genes in the mammalian genome (approximately 100-200 genes).

  • Describe what types of DNA sequences are likely to be more highly conserved between species, across the genome, between different genes, and within the protein-coding sequences of genes:

    • Highly Conserved Sequences:

      • Between Species: Protein-coding sequences, especially those encoding essential functions, and regulatory sequences that control gene expression are highly conserved.

      • Across the Genome: Certain non-coding sequences with important regulatory roles, such as enhancers, promoters, and insulator elements, are conserved.

      • Between Different Genes: Sequences involved in RNA splicing (splice sites) and ribosome binding (Shine-Dalgarno sequence in prokaryotes, Kozak sequence in eukaryotes) are often conserved.

      • Within Protein-Coding Sequences: Exons, particularly those encoding critical functional domains of proteins, are more conserved than introns or non-coding regions.

I hope this detailed explanation is helpful!