Molecular Biology Quiz: DNA and RNA Concepts

Human Genome Organisation

• Human DNA, stretched out, measures approximately 6 feet (1.8 meters)

The Human Genome

• The nuclear genome is 3.2 Gb
• The mitochondrial genome is 16.5 Kb
• 25% of the genome is genes and related DNA
• 75% of the genome is extragenic DNA
• 10% of the genome is coding and regulatory DNA
• 90% of the genome is non-coding DNA
• 60% of the genome is unique low copy number DNA
• 40% of the genome is repetitive DNA
• The exome comprises 2% of the genome
• Functional RNAs present in the genome include rRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and microRNAs

The Mitochondrial Genome

• A single double stranded (ds) circular chromosome
• Contains 2-10 copies per mitochondrion
• Contains 16,569 bp
• Contains 37 genes; 13 code for oxidative phosphorylation enzymes; 2 code for mt rRNAs and 22 code for mt tRNAs

mtDNA vs Nuclear DNA

• mtDNA is circular, nuclear DNA is linear
• mtDNA has no introns, nuclear DNA has introns
• mtDNA has small intergenic spaces (1-2bp), nuclear DNA has large intergenic spaces (Kb)
• mtDNA codon usage differs from nuclear DNA’s
• mtDNA is maternally inherited, nuclear DNA is inherited from both parents
• mtDNA replicates rapidly, nuclear DNA replicates more slowly
• mtDNA has no proof-reading or DNA repair, nuclear DNA does
• mtDNA mutation rate is high (10-100x) compared to nuclear DNA

Chromosomes: Structure

• Chromosomes are composed of DNA, which is organized into nucleosomes
• A chromosome during duplication includes DNA synthesis
• A chromosome has two sister chromatids that are joined at the centromere
• The chromatids separate at the centromere
• A chromosome has telomeres which are located at the chromosomal tips

Chromosomes: Organisation

• Chromosomes have loops of chromatin
• Nucleosomes are 10nm in diameter
• A 30nm chromatin fiber is made from folded nucleosomes.
• DNA is organized into a double helix
• The diameter of a double helix is 2nm

Histones

• Histones are small (10-20 kDa)
• Histones are highly conserved
• Histones are very basic proteins
• Histones are heavily acetylated/methylated
• Eight (8) histones form a core around which DNA is wrapped
• Histones are attached to linker DNA.
• Histones do not dissociate from DNA during DNA replication.

Heterochromatin & Euchromatin

• Euchromatin is the fraction of DNA that is transcriptionally active and adopts a relatively extended conformation.
• Heterochromatin is a chromosomal region that remains condensed throughout the cell cycle and shows litle or no active gene expression
• Heterochromatin is either constitutive (always inactive) e.g., the centromere, or facultative (can be condensed or dispersed) - e.g., the mammalian X-chromosome
• Histone modifications, in chromatin, affect gene expression

The Centromere

• The centromere is the chromosomal constriction where sister chromatids are joined
• The centromere is essential for chromosome attachment to the spindle and segregation
• The centromere contains highly repetitive specific DNA sequences

The Telomere

• Telomeres are the tips of chromosomes
• They are composed of repetitive DNA sequences
• Essential for maintaining the integrity of chromosomes
• Telomeres are linked to ageing
• Telomerase is needed to prevent loss of telomeres during DNA replication

Nucleotides

• There are two purines: Adenine (A) and Guanine (G)
• There are two pyrimidines: Cytosine (C), and Thymine (T)
• Uracil (U) replaces Thymine (T) in RNA

Different Sugars in DNA and RNA

• DNA has 2-deoxyribose, RNA has ribose
• The sugar differs by the presence or absence of a hydroxyl group

DNA – RNA – Protein Synthesis

• Transcription generates RNA from DNA
• RNA splicing removes introns from RNA
• Translation synthesizes proteins from RNA

Genes in the human genome

• The human genome contains approximately 21,306 protein-coding genes
• In addition to protein-coding genes, the human genome codes for functional RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, miRNA)

Gene Structure

• Genes comprise a control region and protein coding regions
• The control region contains binding sites for transcription factors
• Protein coding regions have universal and basal transcription factors , a promoter, and a transcription initiation site, as well as stop signals.

Sense and antisense DNA strands

• The sense strand is the coding strand; its sequence determines the protein sequence
• The antisense strand serves as the template for mRNA production
• The sequence is the same as the mRNA except for T being replaced by U.
• Strands are always read 5'→3'

Non-coding RNA

• Non-coding RNA is RNA that does not encode proteins
• Positional classification of ncRNA includes intergenic, intronic, and exonic ncRNA

Repetitive DNA

• Repetitive DNA sequences exist as tandem repeats or short simple repeats (SSRs).
• Examples of repetitive DNA include satellites, minisatellites, and microsatellites.

How do Tandem Repeats arise?

• Tandem repeats can arise from replication slippage (polymerase stuttering).

Mobile Genetic Elements

• Mobile genetic elements include transposons (jumping genes), which can move around the genome, often flanked by short, inverted repeats sequences.
• Retrotransposons are a type of transposon which move via an RNA intermediate.
• Transposable elements (TEs) can give rise to repetitive genomic DNA, including pseudogenes.

Pseudogenes

• Pseudogenes are non-functional copies of protein-coding genes arising through reverse transcription of mRNAs.
• Pseudogenes may have arisen through gene duplication.
• Pseudogenes can have serious implications for genetic diagnostics.