Molecular Biology Quiz on DNA Structure

Unit 1 - IMTH-IV Semester Molecular Biology

• This unit covers the fundamental concepts of molecular biology.

Gene Expression at the Molecular Level

• Chromosomes are thread-like structures containing genetic material.
• Genes are segments of DNA that code for proteins.
• DNA molecules carry the genetic information and are transcribed to mRNA.
• mRNA carries the genetic code to ribosomes to synthesize proteins.
• Protein synthesis follows the central dogma: DNA to RNA to protein.
• Proteins influence an organism's traits.

DNA as the Genetic Material

• Genetic material must contain information (coding regions/genes), be transmissible (vertical transmission), replicated (haploid to diploid), and vary (recombination).
• DNA fulfills these criteria, making it the genetic material.
• During reproduction, DNA is passed from parents to offspring.
• DNA must be copied during cell division to ensure offspring receive complete genetic instructions.
• DNA variation allows for phenotypic differences among organisms.

Molecular Basis of Inheritance

• DNA is genetically stable due to thymine methylation (at the 5' position.)
• DNA is the genetic information carrier.
• Genes encode for specific proteins (phenotype.)
• mRNA uses triplet code words for amino acid sequences and translation on ribosomes.
• Phenotype is the end product of RNA processing, which uses codons on RNA to code for specific amino acids.

DNA as the Genetic Material—Experiment

• Griffith's experiment demonstrated transformation in bacteria.
• This suggests a heritable substance (DNA) from dead cells transform living bacteria.
• Avery, MacLeod, and McCarty's experiment identified DNA as the transforming substance.
• DNA is the genetic material responsible for transformation.

Building Blocks of Nucleic Acids

• Nucleic acids are composed of nucleotides.
• Nucleotides consist of a nitrogenous base, a sugar (deoxyribose), and a phosphate group.
• There are four types of nitrogenous bases: adenine, guanine, cytosine, and thymine in DNA.

DNA Is a Double Helix

• Rosalind Franklin and Maurice Wilkins used X-ray diffraction to analyze DNA fibers.
• DNA is a double helix with two periodicities along its axis (one primary of 3.4 Å and a secondary of 34 Å.)
• Chargaff's rules: A=T, and G=C. The amount of purines equals the amount of pyrimidines.
• DNA bases are predominantly in their keto tautomeric forms.

DNA Structure

• Diameter: 20 Å
• One complete turn: 34 Å
• Minor groove: (12 Å)
• Major groove: (22 Å)
• Sugar-phosphate backbone
• Nitrogenous bases form pairs with hydrogen bonds.
• Antiparallel strands run in opposite directions (5' to 3' and 3' to 5')

Chargaff (Late 1940s)

• DNA base composition varies from one species to another.
• DNA specimens from different tissues of the same species have the same base composition.
• Base composition of DNA in a species doesn't change with age, etc.
• A = T and G = C, with purines equal to pyrimidines.

Chargaff Base Pairing Rule

• Applies to dsDNA. Crucial for DNA stability.
• A pairs with T; G pairs with C.

B-DNA

• DNA structure is a right-handed double helix.
• Bases are nearly perpendicular to the helix axis.
• Bases are stacked on each other (Van der Waals forces.)

A-DNA vs. Z-DNA

• A-DNA is shorter and wider compared to B-DNA.
• Z-DNA is a left-handed helix.
• A-DNA is more common in dehydrated conditions and Z-DNA is in high salt conditions.

Components of the Human Genome

• A pie chart showing the distribution of various DNA components.
• DNA transposons (3%).
• Simple sequence repeats (3%).
• Segmental duplications (5%).
• LTR retro-transposons (8%).
• Misc. heterochromatin (8%).
• Misc. unique sequences (12%).
• Introns (26%).
• LINES (20%).
• SINES (13%).
• Protein-coding genes (2%).

Symmetry Elements in DNA

• Palindromes: inverted repeats with twofold symmetry in DNA strands.
• Mirror repeats: inverted repeats within the same DNA strand.
• Direct repeats: repeated sequences in the same direction.

Hairpin or Cruciform Structures

• Palindromes result in hairpin or cruciform loops.
• Hairpin: involves one single strand.
• Cruciform: involves both strands of a DNA duplex.

DNA Can Form a Triple Helix (H-DNA)

• H-DNA forms in polypyrimidine/polypurine tracts with mirror repeats.
• H-DNA forms a triple helix structure.

Denaturation and Renaturation of DNA

• Denaturation: DNA strands unwind and separate when heated or exposed to extreme pH.
• Renaturation: DNA strands reassociate when temperature is lowered or pH conditions are optimized.
• This may follow a one-step or two-step process.

Hybridization

• Ability of single-stranded nucleic acids (DNA or RNA) to form hybrids using hydrogen bonding.

Hyperchromicity

• Increased absorbance of UV light when DNA denatures.

Effect of G-C on Tm

• The stability of DNA double-helices depends on the G-C content. Higher G-C content means higher stability and higher melting temperature (Tm).

Cot Analysis of Eukaryotic Genome

• Analyzing rate of renaturation of various components.

Bacterial Chromosomes

• Usually circular.
• Has multiple copies of genes.
• Have different histone like proteins, like HU, SMC, IFS, etc.

Condensed DNA

• DNA packaging, compaction of DNA is done using various small proteins.

Nucleoid

• Complex, irregular structure in prokaryotes where the entire genome is packaged in the cytoplasm.

The Formation of Chromosomal Loops and DNA Supercoiling

• Positive supercoiling: DNA packaging and coiling.
• Negative supercoiling: DNA unpacking.
• Helps compact bacterial and eukaryotic genomes.

Eukaryotic Chromosome Organization

• Multiple genomes (nuclear, mitochondrial, chloroplast.)
• Linear chromosomes.
• Large amounts of non-coding DNA.
• Monocistronic transcription units.
• Discontinuous coding regions (introns/exons).

Eukaryotic Chromosome Packaging

• Overview of DNA from double helix to the formation of chromosomes.
• Levels of structural organization including nucleosomes, chromatin fiber, chromomeres.
• Roles of histone proteins (core and linker) in DNA packaging.

Prokaryote Genomes

• Example: E. coli.
• 89% coding DNA.
• 4,285 structural genes.
• 122 structural RNA genes.
• Prophage remains.
• Insertion sequences (IS) elements.
• Horizontal transfers.

Prokaryotic Genome Organization

• Haploid circular genomes.
• Operons (polycistronic transcription units.)
• Environment-specific genes.
• Plasmids and other mobile genetic elements.
• Asexual reproduction with recombination mechanisms.
• Transcription and translation in the same compartment.

Viral Genomes

• Chromosomes can be DNA or RNA, but not both.
• Linear or circular.
• Mostly lack introns.
• Much smaller than multicellular genomes.