Understanding DNA: Structure and Location

• DNA, or DeoxyriboNucleic Acid, is the molecule of inheritance, representing an organism's complete set of DNA and genetic instructions which is called the genome.
• Diploid cells contain two genomes, while haploid cells contain only one.

DNA Location

• In bacteria, DNA is located in a circular chromosome and plasmids.
• In animal cells, DNA exists as chromosomes in the nucleus and in small amounts within the mitochondria.
• Plant cells contain DNA as chromosomes in the nucleus, along with smaller quantities in chloroplasts and mitochondria.

DNA Structure

• Nucleotides are the monomers of DNA.
• DNA has a double helix structure, with two strands running in opposite directions in an anti-parallel arrangement.
• Phosphate bonds link the 5' carbon of one sugar to the 3' carbon of the next in the DNA backbone.
• Hydrogen bonds hold the two DNA strands together via complementary base pairs (A with T, and C with G).
• Uracil is a base found in RNA but not DNA.
• DNA's antiparallel structure is important for hydrogen bonding between complementary nitrogenous base pairs.
• A DNA molecule with 20% guanine (G) will contain 30% adenine (A), 30% thymine (T), and 20% cytosine (C).
• During DNA replication, each strand serves as a template for a new strand, resulting in a new strand with half parent template and half new DNA, this is the semi-conservative model.

DNA Replication

• DNA replication involves a coordinated effort of enzymes, including DNA helicase, single-stranded binding proteins (SSBP), DNA gyrase, RNA primase, DNA polymerase, DNA clamp, and DNA ligase.
• DNA helicase unwinds the DNA helix, while single-stranded binding proteins stabilize unwound DNA.
• DNA gyrase prevents tangling above the replication fork.
• RNA primase adds RNA primers to the 3' end of the template DNA.
• DNA polymerase builds new DNA strands by adding nucleotides.
• The leading strand is synthesized continuously in the 5' to 3' direction, while the lagging strand is synthesized discontinuously in Okazaki fragments.
• DNA Polymerase I removes RNA primers and replaces them with DNA nucleotides, and DNA ligase joins the DNA strands together.

Protein Synthesis

• Protein synthesis involves transcribing a gene into messenger RNA and translating mRNA into an amino acid sequence.
• Transcription is the process of copying a gene into messenger RNA (mRNA) in the nucleus.
• Translation is the process of converting messenger RNA into an amino acid sequence at the ribosome.
• Gene expression and regulation are exemplified by the lac-operon in prokaryotic cells.
• Differential gene expression controls cell differentiation during growth.
• Exons are coding components of DNA, while introns are noncoding components.
• Codons are sequences of three nucleotides in mRNA that correspond to specific amino acids, while anticodons are sequences of three nucleotides in tRNA that pair with codons in mRNA.

Amino Acids and Protein Structure

• Amino acids are the building blocks of proteins, containing an amine group (-NH2), a carboxyl group (-COOH), and a variable group.
• Peptide bonds link amino acids together and a long chain of amino acids forms a polypeptide.
• The primary structure of a protein is the sequence of amino acids.
• The secondary structure involves pleating or coiling.
• The tertiary structure involves folding into a three-dimensional shape.
• The quaternary structure is formed when two or more polypeptides combine.

RNA Types

• Messenger RNA (mRNA) carries DNA messages from the nucleus to the ribosome.
• Transfer RNA (tRNA) carries amino acids to the ribosomes for protein synthesis.
• Ribosomal RNA (rRNA) makes up part of the ribosome and helps read mRNA messages to assemble proteins.
• RNA polymerase unwinds DNA and guides mRNA creation.
• A gene segment that codes for a specific protein is called a codon.
• Three bases on tRNA that are complementary to the mRNA codon are called the anticodon.

Genetic Processes

• Transcription is the process of making mRNA from the DNA code in the nucleus.
• Translation is the process of making proteins at the ribosomes.
• Denaturation changes a protein's shape, stopping its function, and can be caused by heat, pH changes, or chemical exposure.
• The Golgi apparatus modifies and ships proteins to their final destination.
• Ribosomes use peptide bonds to bond each amino acid together.
• Each protein functions at a specific pH, and changes can damage it.
• A promoter is the binding site for RNA polymerase that initiates transcription.
• A terminator is the sequence at the end of a gene that signals for transcription to stop.
• Operators are genetic 'off-switches' that interacts with a repressor to regulate transcription.
• A regulatory gene codes for a protein involved in altering the expression of other genes.

Lac Operon

• The lac operon is a set of three genes involved in processing lactose found in E. coli.
• Lactose leads to increased expression of lac genes.
• Lac Z encodes for Beta-galactosidase, Lac Y encodes for Permease, and Lac A encodes for Transacetylase.
• Lacl is a regulatory gene in the lac operon containing an active repressor.
• An inducer initiates gene expression, such as allolactose in the lac operon.
• Allolactose is a metabolite of lactose that binds to the Lacl repressor, inactivating it.

Mutations

• A somatic mutation occurs in a body cell and is not passed on, while a germline mutation occurs in a gamete and is passed onto offspring.