Nucleic Acids and Genomes Quiz

Nucleic Acid Structure

• Living cells are complex and organized, possessing a genetic program encoded in genes.
• Genes are blueprints for cellular structures, not just storage lockers for information.
• DNA's information is held in the sequence of genes.

Chromosomes and Genome

• DNA typically occurs as linear chromosomes in eukaryotes and circular chromosomes in prokaryotes.
• Chromosome number varies between species, for example, fruit flies have 8 chromosomes per cell.
• A cell's genome is its complete set of chromosomes.
• The human genome contains roughly 3 billion base pairs arranged in 46 chromosomes.

Comparing Genomes (Model Organisms)

• Model organisms like yeast, Drosophila, C. elegans, Arabidopsis, mouse, and humans show varying numbers of genes (e.g., ~6,250 in yeast to ~35,000 in humans).
• The percentage of disease genes shared varies significantly, e.g., from 20% in yeast to over 75% in humans.

From Genes to Proteins

• Genes contain instructions for making proteins.
• Proteins often act individually or in complexes to carry out cellular functions.
• Proteins are ultimately built from the amino acid sequence defined by the gene.

Gene Structure and Function

• Genes hold the genetic information in a genome.
• Genes are units of heredity determining specific characteristics.
• Genes contain open reading frames that can be transcribed and regulatory sequences (promoters and enhancers) controlling gene expression.
• Eukaryotic and prokaryotic genomic DNA differ.

Eukaryotic vs. Prokaryotic Cells

• Eukaryotes: Contain a nucleus, mitochondria, nucleolus.
• Prokaryotes: Lack a nucleus, contain a nucleoid region, and are generally simpler.
• Prokaryotes use circular DNA.
• Eukaryotes use linear DNA.

Prokaryotic Genome

• In prokaryotes, DNA is within an irregularly shaped region called the nucleoid.
• Prokaryotes have no nucleus or membrane-bound organelles around the DNA
• The single DNA molecule in prokaryotes is typically circular and contains fewer repetitive sequences than in eukaryotes
• The DNA and associated proteins in prokaryotic cells are densely packed together within the nucleoid area.
• Prokaryotes do not contain introns.

Eukaryotic Genome

• Eukaryotic DNA is located inside a membrane-bound nucleus, as well as smaller amounts in other organelles like mitochondria and chloroplasts.
• Eukaryotes' DNA is extremely long, requiring complex organization into chromatin and chromosomes.
• Eukaryotic DNA has significant non-coding repetitive DNA sequences.
• Eukaryotic DNA is packaged in chromosomes.

Eukaryotes Complexities

• The percentage of DNA not coding for protein tends to increase in complexity.

How DNA is Packed

• DNA molecules are incredibly long compared to the size of the cell, requiring packaging mechanisms.
• DNA is wrapped around histone proteins, forming nucleosomes.
• Nucleosomes coil to form chromatin.
• Chromatin further condenses to form chromosomes.

Nucleosome

• Nucleosomes are the fundamental structural units of chromatin and chromosomes.
• Formed when DNA wraps around a core of histone proteins.

Non-coding DNA Sequences

• DNA sequences that do not code for proteins include repetitive sequences.
• These sequences may still encode functional non-coding RNA molecules.
• Introns are non-coding sections of genes, initially transcribed and ultimately removed. In addition, there are other non-coding repeats, including pseudogenes.

Viruses

• Viruses are stable, infectious particles comprising nucleic acid (DNA or RNA) and protein.
• They vary in size, shape, and composition.
• Some viruses have a protein capsid surrounding the nucleic acid.
• Complex viruses also have an envelope of glycoproteins and membrane lipids.
• Viruses rely on host cells for replication and may infect a limited range of host cells.
• Viruses with simple structures can self-assemble into mature virus particles.
• Viruses are parasitic, utilizing host metabolic machinery to make more viruses.

Central Dogma of Biology

• Central Dogma explains how genetic information flows within a biological system.
• It starts with DNA, then transcription to RNA, and then translation to protein.

History of Nucleic Acids

• Nucleic acids were discovered in 1869 by Miescher.
• Early research identified DNA as a molecule containing genetic information.
• Watson and Crick proposed the double helix model of DNA structure in 1953.

Nucleic Acids

• Nucleic acids (DNA or RNA) are polymers of nucleotides.
• They serve as information carriers and catalysts.
• Nucleotides are composed of a nitrogenous base, a 5-carbon sugar (ribose or deoxyribose), and a phosphate group.
• Nucleotides exist in active forms -- diphosphate and triphosphate.
• The orientation of base-pairing in DNA is anti-parallel.

Bases of Nucleotides

• Bases are planar, aromatic, and heterocyclic.
• Purines (Adenine and Guanine) form bonds to a pentose via N9.
• Pyrimidines (Cytosine, Thymine, and Uracil) bond to a pentose via N1

Nucleosides

• A nucleoside is a nitrogenous base linked to a pentose sugar.
• They lack a phosphate component compared to nucleotides.

Pentoses

• Ribose is a 5-carbon sugar present in RNA.
• Deoxyribose is a 5-carbon sugar missing an oxygen atom at position 2, and is present in DNA.

Nucleotides (Phosphate Esters of Nucleosides)

• Nucleotides are formed by adding phosphate groups to nucleosides.
• This modification provides energy stores and other crucial functions.
• The direction of DNA synthesis is 5' to 3'.

Properties of DNA Double Helix

• DNA double helix has stable base-pairs (A-T and G-C), which are held together by hydrogen bonds.
• The shape of the DNA double helix is regularly structured and depends on interactions including stacking of bases in the interior with hydrophobic interactions in addition to hydrogen bonds.

RNA Characteristics

• RNA is typically single-stranded and chemically less stable than DNA.
• The 2'-OH group makes RNA prone to hydrolytic degradation.
• It is known to form secondary structures like stem-loops, and can form intra-chain base-pairing.

RNA Types

• Ribosomal RNA (rRNA) is integral to ribosomes.
• Transfer RNA (tRNA) carries amino acids to ribosomes.
• Messenger RNA (mRNA) encodes amino acid sequences in proteins.
• Catalytic RNA (ribozymes) catalyze RNA cleavage.

RNA 2° Structure

• RNA can fold into complex secondary structures such as stem loop structures.