Biology Chapter on DNA and Genetics

Molecular Biology Terminology

• DNA strand: A single strand of DNA
• Molecule: A group of atoms bonded together
• Pathogenic, Pathogenous: Causing disease
• Chemical substance: A material with a definite composition
• Transform (transformed, transformed): To change the nature or form of something
• Culture medium: A liquid or gel that supports the growth of cells or microorganisms (plural: media)
• Protein synthesis: The process of creating proteins
• Nucleic acid: A molecule, either DNA or RNA, that carries genetic info
• Double helix: A twisted ladder shape of DNA
• Nucleotide: A monomer of nucleic acids, made of a sugar, a phosphate, and a base
• Base pairing: Specific pairing of nitrogen bases (A with T, G with C)
• Pyrimidine: A nitrogen-containing base in DNA and RNA (Cytosine, Thymine, Uracil)
• Purine: A nitrogen-containing base in DNA and RNA (Adenine, Guanine)
• Adenine: A nitrogenous base, found in DNA and RNA
• Guanine: A nitrogenous base, found in DNA and RNA
• Cytosine: A nitrogenous base, found in DNA and RNA
• Thymine: A nitrogenous base, found only in DNA
• Uracil: A nitrogenous base, found only in RNA
• Pentose: A 5-carbon sugar
• Ribose: A 5-carbon sugar (in RNA)
• Deoxyribose: A 5-carbon sugar (in DNA)
• Phosphoric acid: A chemical compound containing phosphorus
• Nucleoside: A nucleotide without the phosphate group
• Adenosine triphosphate (ATP): A high-energy molecule
• Deoxycytidine: A nucleoside found in DNA
• Coenzyme: A non-protein compound necessary for the function of some enzymes
• Phosphodiester bond: A chemical bond
• 3'-end / 5'-end (“3′ / 5′ prime end"): The end of a strand of nucleic acid
• Genetic information: Information passed from one generation to the next
• RNA: Ribonucleic Acid

Other Molecular Biology Terms

• Gel electrophoresis: A technique to separate charged molecules in an electric field
• Single-stranded: Having only one strand, unlike double-stranded DNA
• Replication fork: The point where DNA strands separate during replication
• Helicase: An enzyme that unzips the DNA double helix
• Single strand binding proteins: Prevent DNA strands from re-annealing
• DNA polymerase (I, III): Enzymes that synthesize DNA strands during replication
• Ligase: An enzyme that joins DNA fragments together
• Leading strand: The strand synthesized continuously during DNA replication
• Lagging strand: The strand synthesized discontinuously during DNA replication
• Okazaki fragments: Short segments of DNA synthesized discontinuously on the lagging strand
• Primer: A short, single-stranded DNA or RNA molecule essential for initiating DNA replication
• Primase: Enzyme that builds primers
• Telomeres: Protective caps at the ends of chromosomes
• Gen, genes: A gene is a segment of DNA that codes for a protein or a functional RNA. Genes contain the instructions for making proteins (and some functional RNA).
• Molecular life / biological clock: Molecular mechanisms controlling cell cycles and potentially life spans
• Germ-line cells: Cells that give rise to gametes (eggs or sperm)
• Telomerase: Enzyme that maintains telomere length
• Amino acid: Building blocks of proteins
• Protein chain: A chain of amino acids
• Mutation: A permanent change in the DNA sequence
• Proofreading: The process of removing errors in DNA replication
• Polymerase chain reaction (PCR): Technique for amplifying DNA
• Amplification: Increasing the number of copies of a DNA sequence
• Denaturation: The process in which the DNA is separated into two strands
• Annealing, hybridisation: Binding of DNA segments with complementary sequences
• Polymerization / elongation/ extending: Adding new bases to a growing DNA chain
• Enzyme:Biological catalyst
• Metabolism: The chemical processes of maintaining life
• Messenger RNA (mRNA): RNA that carries the message from the DNA to the cytoplasm
• Transfer RNA (tRNA): Small RNA molecules that transport amino acids during protein synthesis
• Ribosomal RNA (rRNA): RNA that is part of the structure of ribosomes
• small nuclear RNA (snRNA):involved in RNA processing
• small interfering RNA (siRNA):involved in silencing gene expression
• Copy: Replicating genetic material
• Ribosome:The site for protein synthesis in cells. Composed of RNA and proteins
• Amino acid chain: A chain of amino acids built in a specific order to make up proteins
• Clover-leaf: A simplified diagram of tRNA shape
• Spliceosome: RNA-protein complex that splices RNA
• RNA interference: Mechanism of gene silencing using short RNA molecules to target mRNA
• To silence (silenced, silenced): To reduce or stop the activity of a genetic material
• Promoter: A specific region in DNA that signals the start of transcription
• Terminator: A specific region in DNA that signals the end of transcription
• Initiation: Beginning of DNA replication/transcription/translation
• Elongation: During replication, the addition of nucleotides to the growing DNA chain
• Termination: End of replication/transcription/translation
• Complementary strand: A strand of RNA or DNA that has a sequence that is complementary to that of another strand

Additional Terms

• Genome mutation: Changes affecting whole sets of genes
• Chromosome mutation: Changes in chromosome structure
• Gene mutation: Changes in single genes
• Point mutation: A change in only one nucleotide pair
• Substitution: Replacing one nucleotide with another
• Silent mutation: No change to the amino acid coded for by a mutated codon
• Missense mutation: A change in a nucleotide that changes the amino acid that is coded for
• Nonsense mutation: A change in a nucleotide that creates a premature stop codon
• Frame-shift mutation: A change that shifts the reading frame, causing a significant change in the amino acid sequence from the change point onwards
• DNA damages: Damage to the DNA
• Lung cells: Cells in the lungs
• UV light: Ultraviolet light
• X-ray radiation: Electromagnetic radiation
• Cigarette: Contains many toxins such as nicotine which can damage DNA
• Skin cell: Cells in the skin
• Repair enzymes: Enzymes that fix DNA damage
• Yeast: Unicellular fungus
• Dimers: Chemical bonds formed when two nucleotide bases are linked together
• Spontaneous mutation: A mutation that arises without any known cause
• Deamination: Chemical modification of a nucleotide
• Mutagens: Agents that cause mutations
• Cross-linking: Chemical bonds forming between different parts of the DNA
• Stretching of the DNA: An actual physical twisting or stressing of the DNA chain
• Intercalating substances: Molecules that intercalate into the DNA helix, causing problems during replication
• Antibiotics: Drugs that kill bacteria
• Cytostatics: Cancer drugs
• Excision repair: A DNA repair process involving the removal and replacement of damaged DNA segments
• Base analogues: Molecules that are structurally similar to DNA bases but have different base-pairing properties
• Single strand breaks: Breaks in one strand of the DNA
• Loss of end piece: Deletion of a section at the end of the chromosome
• Deletion: Removing a segment of DNA
• Insertion: Adding a segment of DNA
• Shift in the reading frame: A change that alters the three-nucleotide groups read during translation
• Reading-frame shift: see "shift in the reading frame"
• Compartmentalisation: Segregation of cellular compartments
• Gene expression: The process of converting genetic information into functional proteins
• Destructive / catabolic processes: Break-down reactions
• Constructive / anabolic processes: Build-up reactions
• Operon: A group of genes that are regulated together
• Substrate induction: When enzyme synthesis is triggered based on the presence of the substrate
• End product repression: When enzyme synthesis is reduced or stopped based on the high concentration of product
• Repressor: A protein that binds to the operator and prevents transcription
• Binding site: Specific locations for binding of other molecules or proteins
• Induction: The switch or process to turn a gene on or off
• Structural genes: Genes that code for proteins
• Constitutive genes: Genes that are expressed continuously
• Lac operon: A group of genes involved in lactose metabolism
• Tryptophan
• Gene / genetic technology / genetic engineering: Molecular techniques involved in manipulation to improve or alter an organism/gene
• Gene therapy: Correction of diseased genes using genetic techniques
• Isolation: The separation of a particular molecule from a mixture

DNA Replication and Transcription

• DNA replication: The process of replicating DNA
• Template: The pattern for creating another strand of DNA or RNA
• Topoisomerase: Enzymes that ease DNA strain during replication
• Helicase: Enzyme that unwinds the DNA double helix
• SSB proteins: SIngle-strand binding proteins, prevent DNA from reforming a double helix
• DNA Polymerase III: Enzyme that synthesizes DNA
• DNA Polymerase I: Enzyme that removes primers and fills gaps in the lagging strand during DNA replication
• Primase: Make the RNA primers that begin the strand building at the start of each replicating segment
• Okazaki fragments: Short segments of DNA synthesized discontinuously on the lagging strand during replication
• RNA primers: Short RNA sequences required for DNA polymerase to initiate new strand synthesis
• DNA ligase: Links the RNA primers and Okazaki fragments together
• Transcription: Converting DNA instructions into mRNA which then codes for proteins
• RNA polymerase: Enzyme that carries out transcription
• Promoter: The starting point of gene transcription
• Terminator: The ending point of transcription

Transcription in Prokaryotes and Eukaryotes

• mRNA: Messenger RNA is RNA that codes for protein synthesis and is transcribed from DNA
• Codogenic/template strand/matrix strand/antisense strand: The strand of DNA used as a template to synthesize mRNA, the complementary strand is non-coding and is also known as the antisense strand
• Introns: Non-coding regions that are spliced out of mRNA
• Exons: Coding regions that are part of the final mRNA
• Splicing: The process of removing introns and joining exons during RNA processing
• 3' & 5' end: The ends of a transcribed sequence.
• RNA polymerase: The enzyme that carries out transcription of DNA to produce mRNA

Gene Regulation

• Operon: A group of genes that are regulated together
• Substrate induction: When enzymatic synthesis is triggered based on the presence of the substrate
• End product repression: When enzymatic synthesis is reduced or stopped based on the high concentration of product
• Repressor: A protein that binds to the operator and prevents transcription from occurring
• Binding site: The specific location of binding for a protein and a gene

General Terms

• Genetic code: The set of rules by which information encoded in genetic material is translated into proteins
• Universal: The same genetic code is used by all living organisms
• Codons: Groups of three nucleotides in the mRNA that code for an amino acid
• Degenerate: When multiple codons code for the same amino acid in the genetic code
• Amino acids: Building blocks of proteins.
• Translation: The synthesis of proteins from an mRNA template
• Ribosomes: The organelle in cells where translation occurs.
• tRNA: Transfer RNA delivers amino acids to the ribosome during translation
• Anticodon: Part of the tRNA molecule that pairs with the mRNA codon
• Antibiotics: Medications that kill or inhibit the growth of living microbes; bacteria, fungi, protists or viruses. These substances are not always universally effective across different species (or strains)