DNA Structure and Function Quiz

DNA Structure and Function

• Genes are made of DNA and contain instructions for species characteristics.
• DNA is a double helix with two antiparallel strands.
• Adenine (A) pairs with Thymine (T) with two hydrogen bonds, while Cytosine (C) pairs with Guanine (G) with three hydrogen bonds.
• A and G are purines (two rings), while C and T are pyrimidines (one ring), ensuring each base pair has a similar width.
• Phosphodiester bonds connect sugars in the DNA backbone.
• The linear sequence of nucleotides in DNA encodes proteins.
• The genetic code translates the nucleotide sequence into an amino acid sequence.
• The genome contains all the information for an organism's RNA and proteins.

Chromosomes and Chromatin

• Chromosomes are made of DNA, protein, and some RNA.
• DNA is folded into a compact structure with the help of proteins.
• Chromatin is the complex of DNA and tightly bound proteins.
• Histones and non-histone proteins are involved in chromatin structure.
• Each chromosome has two sister chromatids, except for sex chromosomes which are non-homologous.

Nucleosome Structure

• Histones and DNA form nucleosomes.
• A histone octamer (two dimers of H2A/H2B and two dimers of H3/H4) forms the nucleosome core.
• Linker DNA connects nucleosomes.
• Histone proteins have a histone fold, formed by three alpha helices connected by two loops.
• DNA and histones interact through hydrogen bonds, hydrophobic interactions, and salt linkages.
• Histone tails are sites for covalent modifications.
• Histones are highly conserved proteins, particularly H3 and H4.

Chromatin Remodeling

• ATP-dependent chromatin remodeling complexes alter nucleosome structure by sliding, removing, or exchanging histones.
• Nucleosome positioning is influenced by other tightly bound proteins.
• Nucleosomes form arrays in a zigzag model with attractions between histone tails.
• Histone H1 (linker histone) binds to nucleosomes, alters the path of exiting DNA, and contributes to compaction.

Epigenetic Inheritance

• Epigenetic inheritance is the inheritance of traits not based on DNA sequence changes.
• Euchromatin is less condensed and active, while heterochromatin is highly condensed and inactive.
• Heterochromatin prevents gene expression and is found at centromeres, telomeres, and other regions.
• Position effect occurs when euchromatic genes are translocated into heterochromatin, silencing them.
• Position effect variegation refers to the inheritance of silencing patterns.

Histone Modifications

• Histones are covalently modified by acetylation, methylation, and phosphorylation.
• These modifications are recruited by transcription regulatory proteins and influence gene expression.
• Histone modifications can be inherited.

Histone Variants

• Histone variants replace core histones in a histone exchange process.
• Histone modifications occur in coordinated sets and have specific meanings.

Reader Protein Complexes

• Reader protein complexes bind to specific histone modifications and recognize them.
• These complexes provide information about gene location, proximity, and activity.

Chromatin Organization

• Hi-C revealed that chromosomes are folded into topologically associated domains (TADs).
• SMC (Structural Maintenance of Chromosomes) protein complexes form large rings that bind and encircle DNA, helping to organize chromosome loops.

SMC Protein Complex Roles

• In bacteria, SMC complexes separate daughter chromosomes during replication.
• In eukaryotes, cohesin (an SMC complex) folds chromosomes into loops and is stopped by CTCF protein, forming distinct chromatin domains.

Nuclear Organization

• Heterochromatin is often located at the nuclear periphery.
• Euchromatin is typically found in inner regions of the nucleus.

Chromosome Condensation

• Chromosomes condense during M phase, when gene expression stops and histones are modified.
• SMC condensin and topoisomerase II drive condensation, forming a linear chromosome axis.
• Condensation ensures easy separation of sister chromatids and protects DNA during cell division.

Molecular Clocks

• Mitochondrial DNA clocks run faster than nuclear clocks.
• Molecular clocks aid in understanding evolutionary relationships and divergence times.

Genome Size and Evolution

• The human, chimpanzee, and mouse genomes contain similar genes but differ in chromosome structure.
• Rodent lineages have unusually fast molecular clocks.
• Chromosome rearrangements, including breakage, rejoining, duplications, and transposon multiplication, have contributed to genome size changes.

Fugu Genome

• The small size of the Fugu genome is due to smaller introns and intergenic regions, but gene positions remain similar to other organisms.